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ChimerMarker User Manual

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1. Caper Genotyping General Procedure Chapter Genayping General Pree Chapter 3 Genotyping General Procedure Chapter 3 Genotyping General Procedure Data File En aye Arai Parameters Chapter Genotyping General Pure Overview Chapter 3 and 4 provide detal description of imparting dat
2. partly fone and eg 1 there is heterozygous imbalance in single source samples oe a given allele iti amended by rca pictor on citron aras Bul ce ng sc s le pe gra nec she i Caper 2 Chimera Anal 21 peak height in heterazygoun single source samples The heterozygous imbalance in the mixture peak ratio of ster edi Ay eit must made in he main nase window and Svein the chimera pt SCC The maine eg amigas ging Cherian Automated Chimerism Detection and Quantification Sct Application fom the Main Bar Chose Single Docor er Double Donor Chimera Analysis to anche linked chmerum applestion dey fom the There send for copy ele or dat unfer dialog bores or Single Donor imer Sets and Double Donor Chinertm Seti provide ety o Shuai pedi then oi chen Seton Chico Equation 1 Select Chimera Type E ACM Resp 2 Select Quamtiicaon Type aree oF Select Anahi Type Wah Desolation or Unter ta Without Dramen Fa de Statistical Formeln provide cli top Fam ees idee les ham the eel entered by te vr ien
3. aee mU Date min Aap herr rer Soi i ees Panel Table The Tale Marker and in informatie for the dye colo displayed in the Orly Tr frame columna Dye and Maro be edid im the Pu Night click a cell and art Set Vie o Clar to make all tn the column equal he value tn the hid Indian which Marker the Bini Incas the potion f the Bin center in 5 LefVRight Range Inden th cage ofthe Bin en ter side of the Bin cere Fak ha appear within the Let Right Range f the Bin wil abled with the Allele Name pie and wil be wi mm Allee and a dred Sida 0 minor pena and wil ct ect m Alide Label he The designation ol 0 and 1 i the Control enn I ud ta wth pti m he Autonet As sonitum Distance Chapter 6 Pond or Aloe heuer inpol the tance kb that each allele is frm the beginning ol the sequence For example mese thal he all i381 Eb rom Pei sence NOTE This option a TR analy Fred et field tx mona comment wth he Bin Procedure mentioned peevisusly are crested the position in base pui of expected peaks In the Fares lh several paneled human Li ae nce Sampler of tome
4. Delos w manually create es leave Chimera Method beoe seg or data nah Sie Call and Alle Call ar ommended ler daa spy the amie de Fan Man alle snap with expen Spied th svi Ano Select es Ladder and Auto Panel ipo allie ladder sample was desee thee NOTE data has high tonal ration please the Alternative Method prevented die end of ths If Preiransplant CE data files are not available Import Donor and Recipient Genotypes as Text File Caper 2 Chimera Thera wa pce o he pe uin eie ono am pc ine Ciera ore sui gomas pe o The he se et He b in ere amen pr nat Srta e nt epee ihe 1 Creating Excel and Text File pe eal eir diete cub mates does Tee ol ae Chapter 2 Chimera Review Main Analysis Screen Results Deuter mea Went DR DAR er stare peas Rie ames wi a prem dt ave high quality size calls the comple ha yellow nr ral sets the Size nat apa Ali ale dplyn Elo ach pak er ae any red at le ral Piece e Fel dir cap cra on pen gent nd ern Review Results
5. pt he t You may beers mets andr cena opera ea wi te are rogram anyone trage Sonet to pride to moros nine sch deen su aration able Snes hate re Condos aa equam mcns chewing nt ay rin py eat cy sre rt ya e wh coped prae nang eon sama sons numer Fader c bed Vct pe out raced atu ad nl ny denies pa oan pool nar lema get dett anys lc rop piri Saar may beeen perm e however tse aaro ear eso plenty redis t yun ter and ster sate or aware beer pr te o dote dd ps plates nd pr vss an al is fo comerte the ras td person or ey yas ca aap dep redo soca he pr scepter sod Sew ic eat er een in pn regal cd ra S Mele nio Soar Mati Language Saar Dual Me Sofas ule Ces ondes pite 1 Sta eet ie rg a Se oil a out moe ear oman euren Ups toa preva verso Sf Juma pone sees sh Sores arte pt Yu a tn copa seo cnet Uae ss roin te ast tod Us prod ie peur ton sag ote She previous ess par e compet ca ropa e a Eero computer Sr pp rev aah nda up say at pd unre WARRANTY stent LL warns the oso ety that pane cn re er sees ah Soars wil prom satay serene he coments o ay Sta ee
6. Expected Ss Srl and Sonic traces beste This plane na ec by Sc Pera Dat to oct samples v data ILS roves the option to automatically tthe Sample IL yi by the maximum peak height trace 08 by only highest matched peaks Pie and Pint aon ga a py ol sie alba forthe pret Alves he mi ane hs cli ges apg ages Manual Calibration Proves the option of mama sis many perk have ben modified This ondes contain three columns Standard Sie rent sic a andar ud or size cling Peak Poston fime and ie ie ore automaticaly entered but edie Chapters Fragment Sing Standards What to Expect erly dig np le pny Bea Of Laer O panels pe ng en ram a ge ar age Before amp After Editing Size Call Chapter Pond ioe Chapter 6 Pond or Chapter 6 Panel Editor Chapter Panel Editor Over Sed Functions What Expat Chapter Pine or Overview The Fel ca be cce Gom meras in the Min Analyse wind OR via Panel Editor con in the fan Ward Trmpit Seton bon The purpose a Pan o of expected ali Marts give a ange where grt cf alienis i appear md Biu indie i pecie position oe expected allele In Chera Mathers ae ested by a heriontl gray bar sero the Top o
7. Uncertain Ales When selected piss cm de peaks with Quality ranks of Ok ein and Undead red Lom SA When selected the s wi peak san elo Rum Wizard Sine Alis Fock ejes wl te displayal in the table Hide Et Sample When data i diis Velia Drain peste fr ach rw o data t sumple w h 1 Ext Semple Names E inte lira e am wl only appe cca the Bvt el ic roe Ris Caper Reports and Pong Additional Functions Editing Options Theo Report Seer ational options when actin the tae is right liche Inert Peak this Bin Site indicate the presence of a peak at potion when it has bon labeled with Nope Sym igh ick the else et lnc ee Mti Tye Sed wl change ta Pai ar Type depending Quality rank ol the Ht Key INS len of a peak ta pin that ha been labeled with a Pie or Spe Spb ghi ik the peak el and alec Dl The atl wil change o Ner Hol Key DEL indicate the pesk present the poi i tray a peak right click the peak ell and select Cini Only peaks cemere within a Pane Bi wll change om Spec Type Symbol Posts Type Spe when Once peak scone anna only deed Hot Key CTRLAM To completely eliminate an c
8. nein rd im Relative recent Ute RP are pled along el inthe Rar A rien wii fragment moy rom igh tole The large see mens nen aright ol he en Raw Trace Data Select Pre transplant Sample Identifiers secos ums the lee cal of the donot reci samples to delet and nei peak ogni all posttransplant samples dem recipient or aam This information be at when naming systems are wed pec blot by right mouse cick onthe sample ame emplee Chapter 2 Chimera Analysis Preferences Moli Lineage The pea presse clade being peak ation by hg or ams mul foc chimera mages Telly Berl and other cel type Wy dang Socom valuable information about the Sven gral lt o thea an be sen in aden there are function for comparison of samples at diferent time point o longitudinal silica un produce ace pels ug Done nd Recipient alee cal Select Allele and Size Call Parameters in Wid Tepe Set rom prelonded run templates for commerally avaiable human entienien Kis or select cst parameters amd svete Jemplale using te sve om Set frm dps Slat om dro dom Stan Calor Sole been op denn men gt Data Select Auto Create CHM Pane to have automaticaly caters Clmeryying
9. D e Chapters Anse Examples Screens of Tool Selections Sample View display lctrophorgrame of several ample Mayan Chapter Analyse Save he report table in as or tx format Show or Hide toggle this icon to show or hide the Sample view alternativ pth o display elecopheroprams of mall samples 81 Chi A Sis Profle Comparison alternative pst display profile comparison view com Headings select ny all column hang fo the epo ble Printing Options Preview to view comprehensive search sapor or print dicey from S necis Analysis screen I ome A 27 Prieta an Ems re Chapters MOC Arie Comprehensive Reports E LI Fi page repo iude rac and rear Tae he report eade wes information liom ser mapemen signature box and he analysis seins o specify echan roe tme dale parameter for cocto record The eleceupherograns traces sow each with labels for M maternal and Fetus Results displayed include quality ool meines click o variation standar deviation MCC and loti average MCC NI represents uino loci ll peaks are share and are not i
10. 1 o Dersplotd 1 Unie 1 the number of peaks within Marker exces he ein the additional wi be labeled OM Ladder OL amd gen the Undetemied pad Quilt rank and PL Quay Reasoning When the PL ule never fred Select Delle ot Key DEL t delete the Panel from the Lic and ram the SofiCienetics Chimera peus Open the Soe Chose directory oder and dick Save The Pane wil copie sce theory and wl ao remain the Poel and Panel dir The Pane wil respete aan ML file which an be opened with Internet Explore Excl er Notepad Reload Panel le Rad to uno editing changes to the Panel The mos recently saved Pana willbe tore NOTE ifthe ver makes changes 1o the panel and then answers tothe Th Panel has been changed sane changes to fe the changes will remain in the Orly Vice the user lal Patt or progam deal Sample List The Serpe conis ll he sums upcuded to ithe preci Samples ced nae rl be payed othe On e munie Hone OR the sample and Scoto to enable aed im the rely View Rc sample the and Sle Slt Al display sample traces tn the Dri Vie Sorting Option Sample Name Sethe alphanumeric descending order Sample Name fal option Sorts the samples the lane sre sc
11. format All samples peak information or oy the dye lee sled wil in ie tae Adena heer can git ci nthe Pek Tale ad Copy Table at Key CTRL C to place the current abe information onto the Windows clipboard The feet tm er fe prd amen spre or or ping pop Editing Peaks Double lick the vertical grey peak cente select peak Right click anyother in the 1 Pel Tals local nena the pce the electopheropram where yt onl eo add sedet All The bane pic qo rame will apie Al Lab and pak specail calcul and inthe Pt Tale Delet Undelete Allele ight at the grey har indicating the center of the called peak e the nthe Tal and ce Key DEL Toca allele right ic the peak and Unt Key SHIFTRDEL CConfceytnconfrm Allele Wa peak ie given owe quality sore will ee or Util eed Quality ranking the peak a Pi geen Quali ranking rightclick the center bar and est Cora Key Tic peak will be marked Ts pen and revive a Confemed coment inthe Pat Tate To cont alle rom right chick men Hot Key CHRL ALT M Confinp nconirm All Aland Lino options pero the same actions as the Cowan allele excep that the Quay ranking oral palin tht dye lr fort sample wl elected Right an allele tn he lec
12. 1M Proce though Wizard and data analy See Chapter 3 General Procedure and Chapter d Main napa Overview Custom Panel Creation Fellow the blow Iud daa mery uploaded o Chime Mahe Automatic Panel Creation 2 In Pan Er select Fle Cate Now Pal rom he mem bor cick he Create New Pane 1 The Crate Pine ben appears 1 Fonera ame forthe Panel Name wil be the pm that is played Pd Li Chapter 6 Panel Editor The Typ wil by default display the Anais Type chen iili in Rum Wizard Template Sc The nly option in ChirmerNtarker himerten pe Select tly rte c A Spl leet Panel cdo an ney fl pen edet amp mp wi oa P ed ony spor si inte a 2 User o the dono and alle Sali make a Chinesiyping Feel Required check the Ped ar Wi option and enter a value or the et adsl Bin ranges 9 Marks Parameters ipit opc practi or the panel Select this option api value for pata When find ick OK Jb Tienen Fund wil be created and added tothe Panel List NOTE New Panes ar created based on the Mar Ase View Mode Mes eme a ae m per ry orn ree vien SSUES de Mn sd a dc in the preis aim dir Cort Follow MM above Manual Panel Creation 1 re Et select e Cre Nee Pa om the mena bar or tick the Cae Now Panel on
13. dn Inst Set the minimum RFU vale at which the software wil call peaks hen ia ere one a marker numberof peaks in marker determined bythe numberof peaks she ts niu ten ere NOTE the Der gonad wii try vates ar tren fm euh cl a single peak above inch nera but below inten wil be called and iced Cle Quality and LO Quality Reason peak detected shove the Nor Sat Filer vac The second pak wil ot al however cae ht hl the Mar eset tebe Inch Kane e an concave range for homerygous and heteros peak Peaks within the conclusi ange wil be aged with a Check Quality an IHO conce TER beeruspgu Quality Besson Ti sting helpful for perat ame above the minimam deer lvl but are net high tg o dude in stata itn soni rage ines Uns te of the gh pul a marker lo dee mui Deak threshold For example if he hal et 05 the height of all alle peak mt reach east the hg ote gest peak in oc el seach that heh ie logged with a Cet Quay and Quality leon Mar esc Ua a percentage of Highest marker define he minimum peak W s peak does ot each Ih minima lance tel the peak wil ot cal Chapter Pond or nn he een il llowing wert pa ka a gian pn o e ges peak
14. standard dye calor under The wer lo manually enter dye car and meme The dell channel colar setup Set the dye color chanel before clicking OK inthe Oper Det Chapter General Procedure Raw Data Analysis Raw Data Analysis Window Sample Tree Synthetic Gel Image Raw Trace Data Project Summary Main Toolbar Icons DD mnt iri ele e comple sa that tie ani il be Ths is by fal i as Wind gt E Chapter Genotyping General Procedure Derivative Trace This feature reduces high background noise and sharpens peaks Bele lucas irom dye bok or the DNA tempat can ao reduced ih this funcion What to Expect Theat dln eesti be civilly i he Raw Dal Andr wide The images bdo lemons how the data wl look bor image and alter ght image he parameter ppl Range Aula Analyzes rom O to end of tace hor sire call Manual Range user defined range ick in gel image ond select Get Start Point Smooth eure Gere FFT lo dt gm demain Un only op 40 ol wen Smoothing Boden peaks amd erre you can lose rescato Enhanced Smooth Same Snooth but uae only top 20 of lowest frequencies
15. Adjust Analy Parmeter Aer the king OK i he Run Wizard Astin Seog the Dua Pese appen The dat ing and sed ing parameter applied and finaly Pare applied ei Chek te Don tn bon hen analysis comple the rn the Ans window See Chapter 4 Main rere you neice many ke cl you mayne wo aun sc Pate ie pe nig ep withthe Run Wand tnl simply click he Rm Poet cnn the arme wil be deplayed Ads parameter ae crear and ck OK Ran Wird Mna Sting ow The tbe Ca x wl ppt Ns epson to Call Size Agum On at Cal Ses Ap the lun Wand tom Sted econ was change he Ran Wear Dua Pss Raw Anas wer changed Clk the Arp At Te Psy il ope an es canal with Aut Ran Aut un is pti The nti Sting ox ill appr Ti bee come rameters sting ar ac sae the m Wd Un the iw Tepe Sdn De Prosa and Aan Sting Cek OK when rset Next cec ojo data wil be xe ra ih the pam NOT Andie Ale Laon Se parameter can be changed in the rt Opis Stings eile pple tote dats vit tng to any data with Ran Wird Auto Ram an nic sample dye cor or mache ick the Allein main tiu The aw net on pere the dropdown ae wih alta Ck am opt om pda eRe Midst Addi parameter arces ick OK The hoy Au
16. commen Caen ea Quality Reasons Tress te ron why a peak received Quality rane ce Unicon For explanation of the fy and thee eter dec ec below OR sick the Help om above the Reo Tale SF Saturated Pal up peak muy tame php 15 Low Score Sdn peaks oer Qualiy Sore on Sinai e and ak Morphology and the am e ranae min e PL Beyond Ward Adil ei ox When the number e den iiis marker exec the man OL off Ladder umber of satin the Peak owiehe marker range Fon str Et Pu o Ost nin AM Peak is the marker range bat Single pd called teow the Minim ete pie tt rea meen Mare than ne calles peak presen tin pontem HI High tensity Saturated Repaired fen epprschesand oe excede Intern peak with Characteristic he maximum pak ler e ae etd and qu the Ran isan Date Pr bo ferae cli Chapter 4 Genotyping Main Overview doce not exceed he Peak itn the heterozygous matt d Bes pak tong am foe cus or sn Panel Edo Pel Eso Pel bon Tl err Hina Peak amp within homozygous ee ge Soe Cic the Sane Peak Table con inthe main export Tale information caret being in so or tb
17. 2 Registration 2 Install eens Sever Manager Register License Server Manager for ChmerMorkr Usage unstling ChimerMorlerSofaore usos CHAPTER 2 CHIMERISM ANALYSIS Procedure 5 AUTE CERA TETONAS GAME Genotype the single source samples Automated Chimerism Calculations Print nial MERE lorc REPORT MONTON MANT RELA Procedure What 1o Expect CHAPTER GENOTYPING GENERAL PROCEDURE t Dara us Procedure Maia Toolbar ant Wet to pct Rup Wizard Template Selection Run Wizard Additional Settings s mi 7 with Aun Wize E with AutoRun E mum 2 a Reanahze Indvidual Samples nn z Sample File Tree E E Synthetic Gel mage Electropherogram with Peak Table nn 2 Report ei le Mena x x a a S 7 Applications Mea 5 p Tools Mena E a Hep E Browse By Al color S Profle Comparison View mem E Procedure 2 2 E 2 E What 10 Expect nn Procedure x eons ond Function E Wher 1o gt E Project Pan m Panel Templates nun E nm Sample ist gt da very roi 2 5 Panel Table E 2 Predefined Panels 5 Custom Panel Gratin i e ILI Adjusting
18. rages na Mech Eee oe Word Calibration Pot The Calton Pete chat the migration linearly of the 15 or acen Chri pt po bue it pontine on the function of ime rnv fame umber onthe the leary of so ors Maki Se foe he ample Merci denied peaks el elim low Mati Sore Ctra to et he vamplei Sample ist display the sample inthe Sample ILS The curently Sense emane spe ape ce d de Procedure Afer Stee Standard has chosen and the data ces by the Ran Wizard the Sie Clin Charts Sante used iier Cic Size aliam Charts con ihe main ator The Carton window appears Seca sample toi the Sele Li Tre samples ILS appear in Sop 1S fame Chapter Fragment Sting Standard High in the pl ILS frame and chose Delete oe Size ta cote call and select pii Caran vil forthe sample ad Math Sure wil updated ien editing fined cle Mah Sc the Spe rr ofthe Mai Aye window wil be Icons and Functions Toolbar cons O a y la E Found nthe ain ofthe Man Andi window ionge the layout of the Cation frame Adjust the simam numberof rows and colum ill rows cod Chart Syochrunise When
19. raw data and analis ions capillary rw and deti for geepeng For amanlined merlo for chimera dein Spanien and monitoring pleas the Chine Anas Chapter Import Data Files altae you are ready o begin rent Fin aw data es tbe pleaded program Bois he lato Fie per support abi abl Meg hck nd een er 3 Open mate The Open Date Fils ben wil appear amp The Open dag will appear 2 Navigate la dircory coring rw dia len R Rana ls by uae CTRL and or SHIFT aye teak individus sug Open button inthe Cp dialog Thor art will appear Fle List el OK bution inthe Open Dado Fils bow amd the ples wil be uploaded Features Thee ae several features availabe inthe Open D re at ples e o locate and net data e for upland Click the net othe Ad button the four seri wenn dee te remove ele frm the File is Highlight the sample to remove by single flicking iin the Memo sume rom he Dl File List Add Folder Cl Ada Folder o raw data ies from a folder in he file dinctory ine Click the Df perito choo oidor to mit Chimerlarkr sl baya open when the Add or Add Folder bulbs are Open the Set Chats dialog with and Solo tab and allows the une to choose fom and
20. tae cick Export SCF i exporting Export Electropherogram Tools Expor Hectropheragram The Export too allows ner to sport the ind 1 Dern dropdown mens secl he tpt de 1 Spec e pe and be ep fe name The all Ge name wil e names armel rame Select samples Dye an Image Sze era dropdown ema spy expt oma PES and PNG ae both avaiable PNG Chapter 10 User Management Chapter 10 User Management Chapter 10 User Management it History Audit Teal Chapter 10 User Management Overview Ler management may be implemented ter installation of ChimerMarker The administrator activates User Management om the Help dro donen menu User management provides of ner ard Automat generates an aut ofall edn Procedure Select Help Management Ci Rus Uer Proton to activate fer Enter Organization Name an Administrator En Yt ae no ng ie Anne Ck the Add Ute bution t dation sere Cic the Rite bon op ver ype soe Ra Psi and ick OX to ent Lagi required to open alr the User Manager activated User Manager The ler ab displays user information and contains options or and deleting ser play ers y name type and eration date Orga
21. cent of Ms di CDROM ere ch gene rv Inn br uta stent Lor hd par copa gal mages nck orp esau rer ae wer Sts le rd copay ween mr ore Donen y sd at nd esp aim nd ops he any Stents LE acy iors tse eg rane items paty Sanet Computer mena ran dat cps tormes ith ms dr icons Amen te Aree and pay aan or cid in Dect ome pac er nee Stas may o rsd wh Spel tera tci lease er oh mai ou mo tala Us oe Sarat on 10 vod cons de o cs te mad una tore ai a ac che ec rro cmd uctor aro pr ior ml tw fr etr ot an cdi doy ya a aka ns pin un iio tc nad ere tan id wah pe ayaa mary val othe poda nase Std ls may nr nthe producida tty et MR a na CET EE 2 reg se handy Sm ir y a eon a erasing Sousa ended aptos bush nature compen eam nd ation prat mama sap iy or torta ie etae in ls pln ropa fad Sonet Ls sup Terum ze Sawaya ade rt cnet Shen Li Sota ped eg wi Ein y ted ut Cope Law tec syns pple cy nh eng You Sara thin tcn lr cn e ap ream eed alee pata cota se anther open a ore Sue att eae Sr dean demic or tee ep dive
22. hs options a change he Tc View ating Sore Tre View image ara tap lp fle Chapter Fragment Sizing Standands Fragment Sting Standard Chapter 5 Fragment Sizing Standards Chapter Fragment Sizing Standards Sev See Calcio Clare Fragment Sizing Standard Size Template Editor The St Tepe tr too in ChimerMaker or resting and modifying Standards To open Sr Temple i lect Tn Sr it rom the es bar OR ick Size Template in the un Ward Tepe Son to Due en differentia fragment in sg mus be applied ach gh will conil an ial Lane Standard 15 peaks of nn doe and ag with red or orange dye Sic ie ILS dyed apenas trough apy ae ther dye leid sampl geen hey are slc toe sane trent condone and can derer be med an lo determine the sire f the ter fgets sample A Si Standard template appled to cath ILS and ios between Ihe known HS pal ac NOTE ChimerMaker optimized to size fragments with linear mobility Larger fragments those rn Beh ety qd Gane ds ai and mn wi Size Template Editor Expects Sand empero recede ne camper due lii TUI Size Standard List The Sce
23. CD ROM deve om the sample and open the decay the ChimerMarher Setup executable fle EXE The hcm Wiad launch Gtk the Next bution in Won winde end the Ed Lie Agreement cheek the option 1 tems e the Lime Aprende Nen in the amp Select Ina ChimmerMarker Recommended in the Slat Prag in the deful oler the Browse bun Sce different NOTE The default Dedit Loot fo he program ChimerMarkr vorn nur Ned inthe Sc Prorat Mange oop window i acc bal Prem Menge Gra NOTE Changing Prim Group default may lect program operativen deat 10 Cick ia in he Compete window Th The nta znd will cse 12 Bet the Str CD 1 Lunch ChimerMarker by doublecching the ChimerMarker desktop ion open the Start mens and navigate o sare soon tat was fr alld Chere pernil ChimerMarker 14 The wil appear Click Rom Validation to Launch the software 15 Ihe Ran Validation ut grays indicate 5 dy period Local licensing Option ChimerMarer VAT tan nd above support etme train the cab ies option Tebow train dows mt requies USD device dongle or key This tex am registration Din regione ome ect RC Ah cenae ec to ht ane PC te Ieee neck o Pe ordered ina PC stration fr tat ne PC man be ina
24. O Aledo e OL Select he option to babe lee hat are tie of lee ange at OL e Sce Shing r ae Sele hin abel peak in the iesssphesgrame t ita of the ale la To play rounded et the Dena Pr to ae Fan Doles the ont ste of the alil abel charactor Ea renee Gant ie wil ca over t Print Chart Settings Os Carte Seed he maximum number of samples Max 96 Use the Sample right cick option See Mar rater of es pecie Mex Crt Page Select the maximum number ol sample elcropherograma you would like display Be Anan window at one time Mex 8 Use the Smile Fle PageUp Down to teen grep Mar lee tel number o allele be layers view a once 10 Thi determines far you ent sem lay red neighboring ale and pent report wil be Shu i ith Select option to display the names of all markers ave the dectrophergram ien wor Peak Label Choose up to four labels ie height core display a fig net individual peaks im the Pastor Choc to place peak label at ier the top of the peak to the right side of the pak or in the Mee abel inthe Gel Image Chapter Genotyping Main Analyets Overview Gay hir Sige Duc When selected will psy and print the gel image with a black and white iiim ci
25. Shred should check in Ignore aus where peak ment aga any unshared al exceeding the pele indy ther ser allele Set the deed Threshold for Loci fre Chapter 2 Chimera 8 Spey the percent for Limit of Detection Any sensitivity above the bold I will be red the Thor type denar e epee best un he sm se MEH Type Rs Stings Apply Stute e ill subtract spei vales speci i pei the oir see he tier value foreach marke can be displayed Show Stier selec Song with Apply Suter Aduna o the save ican eto lel comer to your selection the defacing An example af SAL for locus DOSE played here Quai b iem PCR rolls im ler agent e mam Mic amplified tan he ange that sted between dane an eet REVIEW RESULTS The sult dimer are displayed in cete tabe To view erem fora given le ck m ie e name in heat the ef Lcid at ceci cesta cher analy sty are oed Sd m aloe i the report ble To manual iore bae a locis ight ck on cell in the ignore clio and gore Te locus ab ol any rate Inc ar md atom Chapter 2 Chimera EESTI NE Nonsnformatve Marker i Nomnformatve bared om peak pute
26. Genotyping of all sample data Folios the tps for imparting and processing data fom Chapter 2 Genera Procedure ei ther the na window ores es WAR Maternal Cell Contamination Analysis Alter genotyping and the denter for the malermal and fetus samples goto Appleton gt analys Auto Identify baton will automaticly group ie cumple and Trader Chen Tab Losd Tat button can group samples by wing a txt rete from Encl eb a i o ther ord cl programe Reler 10 more ical Groping itn tings a iodo at cl to gon opa dd decal groupe as pt pene Chapters Arye Quantification Type ara allele for caleulations 3 Height ue high of allele for SMCC clone Analysis Threshold Stand for any pre Sta any maternal alle detected im the stutter postion of ek sample vl be Loo Grouping Options Match by Section Fixed Position or Order Match by Section rop Lektion sec which column to group each set of patent Caro identification specs which column the identifiers per inte View oerte Chimera aban be iud Cone fo act ax contro sly mateo me Male group samples and corto ascending sce method Losd Fe Load grouping le frm ten Match by Fixed Pos
27. Previa will show a peint preview ofthe settings selected Chapter 2 Chimera What to Expect The Longitudinal Report contis ender with er rum User Management Chapter 9 tuer Management and Analysis Parameter Chimcrem Tred donor oe rip the chime onthe Y ai and sample Oi or the Note Ths graph e wih Propet and is easly appended w h Sen samples printed om the print preview p So nr ual wth vd me gp midi ded This donar monitoring reprt play he trend with an incu in all an Donor sail and a descr Doro 2 cram percentage Ins malo entered rto sime plan then the weeks pen arpa fr seua sep Chapter 2 Chimera Chimerism Calculations for variation i un plain sese of vain foo somes than cines LEN PCR conditions PCI random evens CE conditions ample of vacation PCR bis Allee in hat have smaller sie range ae able be amplified more than alleles in loci of larger size range in the same amount of time One of the causes of heterozygous imbalance is PCR bias the amplification of Ihe smaller fragment more timos than the larger one In the example above there is almost amplification difference between the two closely spaced alleles at 121511 for both Donor and
28. Save Project Alter ae analyzed and edid the poet can be as Senn rop le coram processed daa is Srp file shee the proces parameter and al ke The rj fle Sol contain any or tied Pan Sie Sindarin To export acumen Pane Chapter Panel Editor export a com Sire Standar oc Chapter 3 Fragment ape an Men er Fragm NOTE Previous versions of ChimerMarker saved projets in SEP format This for canbe opere eth cnet vendor To saver projet goto Fi are Project in the Alps odo The Sa Py Selact a directory and ener s projet nome Click Save o reopen the project go to File 4 Open in the window at folder by ChimeeMarer wil appear Navigate tothe directory containing the SER ors le an Open Ani the at prj nn pte tom tot nen io Cea Chapter Anse Chapter 8 Maternal Cell Contamination Analysis Chapter MCC Analyse reni a Shan aj Ree Mey ams Chapter MCC Maternal Cell Contamination MCC Analysis Overview Pease follow sepe from Chapter 3 or importing of aw sample data The initial for Maternal Cell Contamination Sra 6 of al samples imo Aer reviewing and coming cal the Amie anol be sed under Appl ta in the main menu ear Procedure
29. ve m bh nd autologous tem sells transplant SCT ur hematopole stem cela SCT bone marco MT une rro engraltment cord and peripheral Hood stem cell TISCH sample The program provides accurate genotyping and Eimer anal Senin donor and recipient peak in post MT samples percent himen and quality metic single donor or double donor ces hat lineage copa for analysis of Telly fell and other cll type mehr Golo fc compare of samples did ime pots colla pe sted reido coc tried eel pri ampie yer The herr ne calculations ning methods ChimerMarker is compatible wi Beckman and MegaBACED gents analyzes and cudom primer or commercial availabe human chemistries nchding Poeta Power eub analysis completly linked main shan screen removing the err pone of data rom genotyping start chen any soltar Procedure Import Data Files Afer software you are to begin fragment mss Fi raw data les mut pleaded nthe program Blow it ol fle supped Chime Make md ancla ad 5 Ei Open Data 3 The Oper Date File ben will appear 1 Gk Add buen 5 The Oper dag wil appen amp Nave Onin raw dat ler
30. SOFTGENETICS Copyright Licenses and Trademarks 2001 2012 Sof Genetics LLC All rights reserved No of this publication may be reproduced transmitted transcribed or translated into any language in any form by any means without the written permission of SoftGeneties LLC The software is copyrighted and cannot be altered or given toa third party without the writen authorization from SofiGenetics LLC The software may be licensed from Soft Genetics LLC Mutation Explorer Mutation Surveyor NextGENe JelMarker ChimerMarker and GeneMarker are trademarks of Sof Genetics LLC other product names and or logos are trademarks of heir respective owners Limited Liability of Using the Software In no event shall Soft Genetics LLC be liable for direc indirect incidental special exemplary consequential damages including but not limited to procurement of substitute goods or Services loss of use data or profits business interruption however caused and any theory of liability whether in contract strict liability or tort including negligence or otherwise arising in any way out of use of this software even if advised of the possibility of such damag SoftGenetics End User License Agreement OU ON TANGIBLE MEDIA eg D WITHOUT AN OPORTUNA TO REVIEW iS LICENSE AND YOU DO NOT eters an YOU UN A DE UE AMOUNT YOU 4 Do T VS THE
31. UN edt Baseline Subtraction UT ont ni ot o e beginning ote range Chapters Genotyping Procedure Put A ing the major put ee 020 for smal corn When Manual Pulp chen or snes matin fi cam be and ed to dect decine NOTE Decet atomic Pau Corton in the Ram Wizard Dat rs box man matrix comen perisse ip Correction Saturated Peak Correction saturated are 28000 RFU ne topo nature pes looks pl Ama yalkap peak ay be present mat pele he th mall pull pak ade othe spit in the saturated peak Spike Removal Cod y of cher hip voli mil Spike usually only 12 ram we peaks ual 510 amer wide Crests tint derivative cr len dat Spin av I2 DT cutee 55 ipa FD Second Derivative Trace ALAD AZAD er when yea have ft bef your peaks Dye lab under peak ec per Genayping General Procedure NOTE Do une 24 DT wit Spike Remo because el pes lok ke spikes Process Data Mer the eat ies have ben Chine ty ae ready to be proc The proceso Sep nnd ng kad lin e mir pk an copes oc Rr Eier ines d hese Spee stop ale the Ran Wand sms Ran Wicd Simpy ck he Run Projet i the mi or Run Wizard Template
32. and click Rema move coum lo Al Cs fied down CTRL ot SET bey to mulple options then did Remove Click the emere o move al he in the Sled Cun eld the AD Calas OK in the 5 Tale Columbo and Al er Slings when ished The options in the Sici Column will be displayed slong the topo he tbl in cok Show Only Uncen All When select displays e ry the peaks Guay ranks of Cic yellow TEES Sd Unde ed Lom Sore Albe When selected the Pes wih beue the Wate ld Sale Alt Tk Sere ling wil be displayed in he table de Exts Saale Names When data is displayed in etal Orten smple rame ae repeated hor chow of data dat e spe monct i Pie tata Sample Nemes e then the comple mone vll ony appearance nthe nt ol the rows is Allele Count The Al Count Report Stl displays the number of alleles presenti the uel Marker temple ames are lied in soe nt cur and Markers are ted slong the top rw im clum A Toi Number Shun te rr ol fake dort te ame NOTE Alte rues i applied o the daa See Chapter Panel Eaton Features Orientation Sample names pet ds in ond pone top Caper Reports and Pong Maie pe
33. Show Last Event Open at ive Date Pace ation Help Menu p this ant User Management Alas aioe o anio ace dire ues te proto See Chapter 1 User Management About Displays information speci tothe version af ChimerMater running onthe compte Abo clans inka to tl Tecnica Suppor and the Senec sete Main Toolbar Icons 2 Open rats dat input dig box analy Spee ln War for proce the dat Show Hide Toggles Display or Ber the Sample File Ts funes Gel m ami Tale fames Chapter Genoyping Main Overview ay pins tr rt Allows the mrt select all sola to view hide choose a single de yer Choose single ety singlet nue cing on bein ia to inne rti at nr brn eerste cd ee oem KK te zoom on the image old down the elt mouse bat and rae bon rm the testo igh cree ap i Te ting shay mst Yon acing A pe nhl a the BE Two oer opns a rea at be Ys arg pk llo o SS the meg can Howe by All Colom EE Persea comparative vine of ample by dye color Individual samples can be Stet fo ed dw meni Allee Call Leona Thee ions ae ly after coy dta hasbeen preme and Semple Fi Ts Alle folder Si
34. Tete Pane namen the Nae ld Cheon he appropiate Ande sn he p ropa iem Sect Manually Cre When ind ick OX i Semple mena m The Panel name wil appear Lit however no Markers Bins wl be with the Panel lo thet previous section Er Onesie Markers and Bins Create a Marker in Panel Editor Chapter 6 Pond or Adjusting Panels Bein for und age s hed due ka wat analyzer run condoms ch a tempera into He Marks or bins e manually aligned the ade ladder ng th sft ed mouse by Alig all of he bins within a marker 1 Hold down best key A same me place the mouse oes the gray marker name aras the top of the electrogram wi an ed he nt we et 4 Bag the marker o align the bine withthe peaks of the tee adder 5 the pete sinl nen he Sve dan Yo enable the major panel fate o kin tr je ign en indivi tin 1 Sela gay vertical bar of he bin with the mouse the bar al are Hac down the shi key and click an the serial bar for the bin wl be lined in mu and the panel nme wl bein eft Gelbe mouse to drag the gray vertical bor Mm el pad w h Genotyping and Chimertyping Panels tro fee ud As above
35. genotyping panels conim al loc and skr which may amped by given human ehem ch tete or Poner ESI ESK Chimeryping panels contain only also the donor and replies made lo automatici oett chimeetyping panel nthe een the rum ias the propa wil ue alle cala cf e ap lime Chapter Pane or forthe patin these cod in the panel tr ale the genotyping pe has teen applied othe prot File create Panel SS Lior Donor Recipient Select OK to automaticaly ale chmetyping pare it s Serin ve ot tac o doner and ope the may be made here by the wer Right ick he fe name and acta the propa type automaticaly creates chimertyping panel with the Du Mok ced al of the rl recipient When med in the analysis please ae Chapter 7 Chica Analysts the panel calle riy thee peaks that consistent doner alleles In ation o the clare deemed above or the genotyping panel table chimertyping panels have an Origin column This document the Frida ha were the some of alle el and t ae he in he of mite samples in chimera peels esc Chapter 7 Chern Aral Editing a Chimertyping Panel very that some ol th
36. marken Sher Fer Forward and reverse stutter commonly caused by PCH chemica reactions can be moved ung he Stat In man Wonton nass ler tees are NA Nid mit tthe high peaks inthe mater give repent The v nr ie number o multe uat spied ine Meer Ponce Nadal Raps Geld The ar in percentage of prim r ped Peak inthe Ne Ns Nex potions tht ar bel he ter wil ot b called NOTE The iter meant eliminate era steps of analyzing pes caused by instrument anomalie Stall Statler Fl sing to peak must be called SE eA Wen ala ving ee wil pt all Jour ab volition procedi ii Edit Marker Bins Right the Marker and see Up Ales The Update Marker Alli box vil appear At and cic OK cette Repeat du Dust the poet inthe Van dat ero wc i cunt aes apa i at ppp ner sta on he ume ef eee he al nn and Chime lp aw a be peti is pion to ener mabe BE SE and et af the center ofthe 1 03 I el a the Bin i tent angel e When deii ray ad ih ees puri Ri pn ret lb pa Sona number ebene up ce numer vl To associate Bins with a different Marker old down CTRL key and tlic and dig arms peak atthe a Marker gt hashed til appear Kite n bow and elect Maler The Et ron
37. to black nd white when only singe dye when multiple dye alors lets the gren weil appear in ther opere colon Cick the Background in White to Term the Hack and whic expe for single de cor gel Eectropherogram and Peak Table Features The Epis play lacere signal from copiar struments a sng ie race or dye The nein cre recorded Relative Uns REUS whch are lod along the Ang e ar the pores fte agents The uit lied along ben im he cria i te Ana window are converted to hoe pir size unio ss by Sor Standard selected ond Internal Lan Standard LS o the individual Fragment mobility rom Fight tle ih the mallet fragmenta onthe te rae The Pe Tall contr iento about the ald peaks cen inthe cope Eleciropherogram Trace Display ange Th Ee io ange is sein he Ran Wien Pre Ale opto The Juge prre once and ud radial tng ia rec gh tr tee Te mint med yes a dii i might gegen ee call Ia Panels pp othe dt then ge Mar wil pear bie the Belag Bim np nce ene rios ample Eis upper tla ad mc wi te cer c ch sled pk wich i y
38. AL be wil appear Marker nd preted sme wil appen Use the Maker abel new tne and eck OK The Hight Bins sre nove incorporated it the newly Marker Delete Marker Right clik the Marker bor and select Dele Marker OR rightclick the Marker name im the Pun Lit and Dae Mot Key DEL Poet ep pipe rap wn eire mM pem Aide Et ol Alpes dapes win aa display ths value nthe Allele Lapel inthe Mar Arai widow hi ttc oi er mum Erg This fled im automatically donor and tn om car lei neu Bot available the gin Donor Donor may bale Chapter Pane or una Indices the range ot the in om her ie Le nd Rig a he Bin enter Maer See which Marke ho alle the wit The Markers to ight and Iff the Bin psit P E displays a ella the crete anew Maker forie AB most be mec th Select Ci Gene fhe contis ajo peak in the Ladder sample marked a Eri Ge wil Aloe Lab blow the Epa ofthe Ladders im the Alpe wide Hi tard wil ot py on Alle Lb even a prm Edit Bin Right click he vertical grey kar inthe center of the Bin in Orel Trac Select Et and Edit box appear Adi parameters and cick OK Sec Cee Bin secum above for explanation Ale dior poss
39. Ed Comment bx Enter information in Comet kd The stem comments wil stored and subsequenti for fre The Sole Commons wil appear on the rn See Chapter and Printing HotKey Be Disable Samples Opens the Dine on box and mara sample with red through A table sample cannot be nice for play nuts window and wl ot ape Rot Ta Vice Proce open Se Rr idole Seca Cot Toa e meo stent nt Comento eld and did to iei ampie a Koy 2 Add Samples From th at ahr let A Sample Pc The wi pyar Ci th Ada bon ce onal sae to poe sak Te fe aps wi ae eat ending ie premi be a Chapter Genotyping Main Analysis Overview Sample Grouping From the main fons Proje San The El Nane Grup Edo vil appear See Chapter Sec amd Coin entr and did Mate CR apply the groups numbers wil appear next tne Rename Sample Te Ua the Bei rightclick mend option OR pen mies na To atl he Sample gia Dee and check Enable Sample Ci Synthetic Gel Image and Electropherogram with Peak Table The Spiele ge and play use Anas window Both delay played he Spb mage
40. Edits History Window May 2013 Index 2 Jas armen peer puc pe rat n Sos rod Pina Eton Ga 7 7 95 06 97 308 102 305 306 18 215 208 pur 5 xin Soc Serene io Manat me m peu o xus Y
41. Fragment Sizing Standard Maker ll values sql value inthe highligh cell Only avaiable in ice Sample ILS The Sample ILS displays selected sample s ILS race Clck the Show Dye ico tocar to ye dye core 2 pak withnit green bia halo and die er Sin The sir ton will appen Alf a and lick The gen rangle will now appear tp the peak and iis Sie Stn Apres inthe upper right comer of the and comesponds to the degree of patter match been the amples LS andthe Sie Standard Perfect malas were sco of 1 no oration mes a Navigation in the Sample 15 frame i similar o the navigation options in the Anal window See Chapter Main Anlyls Overview Procedure mentioned previously Sie Standards are read to sig bse to fragment peaks in a IUIS The other dye culo peak ae then based om a ners ae fom ae ate fo pou i e RE Se Tepe Er lle acs apply pe delined commercial Size wele new cii Sze Standard ses othe dite Se redefine Sie Sandande include NP per o Pre Defined Size Standards There ar eo way to choose Size Standard for the dataset If the Sie Standard name ke ply sigh lick he Sce Standard rame in Scr Sido Ln chek OK in Template Eto lc Size Stand wil he
42. Once 3 imp i ceci inthe drop you can the Up Down Arrow keys o coll thug samples Icons and Functions 66 Showide Cross Lines When selected x and yai grid ines wi appear atthe ip of the mouse cor ong with the hoe perez val X shown Ranger hen the Bin a the top and oto of the electropherogram race will appear Ato Scale Marker Wren the rt intensities of low peaks ae to match the testy ol the highest peak Fac gate lr We epee ay meii co iei he amp rg Profile Comparison View Applications Profile Comparison View THe nie Compare View developed a an a way compare several ample acs at once Procedure 1 Select eive samples foc by placing ck mack nthe ac the o te fenes 2 3 will appear in the window to he right A Side the 20 bart the gt de coma the taces Chapter Genay pig Main Anal Overview the Line Li tab to ape hein of acs presenti he viewer Sele any tae to ld ine amp Selecta marker rm the drop down to ew ne marker a Hee 2 Select Show BD trac the tac ina tree dimelo Icons and Functions Dye Color Serio to serm through dye colors OT Wwe Al yewing options ate deal
43. Panel gt 3 i Genotyping and Chimeryping Panes chimertyping Panel nun 5 S 2 Mena E Me Toolbar eons 2 Sing pone wth onl formalen nn lle s E a Peok Table 5 Allele Count m Report Content Options an Morem Cri Cosratanarion MCC Ass m Procedure 124 Results 2 E am and ico E am Comprehensive Report 2 m For stone Tua E Chapter ChimerMarker Chapter 1 Installing ChimerMarker Chapter Computer System Requirements has been esed and validated for various computer sates The minimum eur Windows PC CS Wind NT Vata Wind and dink space 2068 GS 104 desktop or MAC or VMware Fusion ar Appl Boot Camp Arab hand dk space trato of ChimerMaker ie nat support on Linus or UNI sed operating ep hierher wil only PC formats convert Mino ile format a PC formats pls the ABL PRISM 2100 Genetic Analyzer Conversion Unite o comer Mac files ts C lies a tfe omnia Validation Version The validation or version cl be em u omy comple you wish The til Pri emplea SE dee alr he ore Installation LO Inert the intn the CD ROM drive your computer automaticly open a CD naviga tothe
44. Samples Uc ee parce seing to all sample ats Sars an Wound and Ato Run Applies the met parameter stings only to samples that are Eine Sa Fe Tre Applies the new parameter stings only to sample inthe Sa Fe Te Call the Dye Alc the new parameter cing othe dye alc in the REI AL Al De Ac he sew parameter stings to the marker selected in the sil Alle Call Alte by Marie Chapter Genotyping Main Analysis Overview Chapter 4 Genotyping Main Analysis Overview Chapter Genotyping Main Analysis Overview Main Analysis Window Menu Main Toba eons Additional Analysis Options Genotyping Main Analysis Overview Main Analysis Window w nde py lace the cur over ain seperate the ng leropiengran Sample Terr sree wl shane oa tered te by to eral ies down the eft mue and drag te ray ver ine direc you with To open and the frames the Show Hide consi he main toolbar Main Analysis Window Sample File Tree Report Table Synthetic Gel Image Electropherogram Sample File Tree uie samples When a sample 1 le proposed bace well inthe Ra Dae Andi ido Boe General Procedure Daci rin Al Clea a cal ie esce See Chapter Fragment Sing Standards Chapter 4 Genotyping Main Anal veri Sorting Options
45. Select Pope Open or the ambe of samples specified in the Vine Penner The Page el Hot Key Page page Dow p descending order coc the ame number of samples previously by Ps grouping options fee Sale pig cin blew or done ick opin pene eigene nif wees sii it War Pence Dile Sens a Open Chart DeselectAll clc al selected samples im the Sample File T Ut and clones the eg Sort Samples pers the Sort Options Select Fire Secon and Order ig the Sample Type File Lane Well 1D and Sie Sere You can specify key word or index hat by symbol example 10 45 67 file nam and you war to group y 5 key wurd index would 2 Each key erdindexie Da U a Hot Key Search Options Search File pena Fe Soc box Enter any nme serch forthe sample im Click the Search Left cick and CTRL or SHIFT key to highlight samples then ct the Open Selected fut Inc the selected samples will open nthe ain Alpe window Hot Key Sample Information Sample Ifo the Sorge Ii A int of Proper appears and includes Information Sample Name Wel ID Lane Number mtrament Name Chemistry The of vars depending E pene
46. Sine Template kr Ifthe ar Lor ws cn va the an Wizard Tere Seo thon the sled Sine Standard wil appear in the Se Shaded the Sce Temple Eller yan scene the mens then ik the Rn Proceso in the Aras The Ran Wizard will appear Seed the Standard from the Ser dropdown in he un Wizard Temple Sac iow Proceed through he ie Ram Wizard boue and when the De Pre window in comple Sec standa wil app The sce of size calling for each sample ict by the gen yellow nd sheet ta the sample lense in the Sl Fle Treo the Man Analyse window The lane izing quality determined y the Mach Sve which how cil the saps LS peak mac ee Sce Sana Searle recive low Sey the il be mark th yellow sect ling led pie IS peaks cud tbe lied witht Size Stand el en the ample wl be marked wilh a Chapiers Fragment Sting Standard red strikethrough When ow sor samples crus select he Sie Cala Chu com i main rare com e iac calling Low Match Score and Failed Samples Size Calibration Charts The Chr tol i designed to sid he une m determining suce or ure o size call alte GhimerMarer sutomac icing ia Click the Sae Chars on main Ana window As mentioned rev once Se Standard hasbeen applied
47. and lower cae and upper eae Ir condon Restart ere Server te apply he ryan information iml Chimes Mackr after and cargar etr cien Offline Registration HD amd the entire Hape ID string from the Register rie dig and pour Accent and forza eom the CD ini te body af an eal Lo Send he email support seltgenelicszom 1 The Regidor ID claros string wil ie wnt fo fou vin eril Plin ene inc day K Copy and grat ID from the email Reiter ID ld af Oi gain ab sure the nie regir D chaser ring 1 leg Restart rer Server to apply the information Intl ChimerMarkar ofre and configure network ct Installing ChimerMarker Software Install ChimerMarker software on client computers 1 Inet the Suit CD into the or CD ROM drive 1 quar compute ie nil e atomica pem a he op ar CD ROM dive an he compte and the 17 Doubleclick the ChimerMarke executable fle EXE JE The nation Wizard launch 19 the button in the lame window Rend End User check etd the eem ofthe Lee and Select Recommended in the Slot and ck Nest Next im the Desi Last window io indal inte deft older Cick the Browne En different nati
48. et ck and dig Bio the The added peak el be im Sor abi The calculation pated when Unda Carton elec NOTE Add Pad when vo other gren tange acid When select the ale Eto box pese Enter a aie of the peak and click NOTE Only Ses ht inthe Standard can entere in e Clint Dir te feld are ped tar e ph of ene pak wl be uae align Sie Sunland The Fe S etre a when the elected Size Stara spaced peak an the sample ILS her ditior de pulp rer peinlich palm pem NOTES Fir not active for manually added peaks peaks utd the Size Standard ang SE clint mn peaks and or en ag indi NOTE Deleted peak wil ot be recalled wien si leid Update Calibration Aer peak in the Sample ILS select pit The Mc Serve for the ample wil be reacted bed onthe edited peak indicator positions When Sse Carat Char i one Sar Nut Sue indicators t he im the Sape le im Cory Cament Calibration Data When and the frame poston and use positon of the geen tangle peak indicators for the selected sample wil he copi to the Windows and pat sno spends or word
49. igh grey sol becerro a Face ne ap In Ale lid poa ion at the tae parol ook Peak Table The Pak Tale cm iiw ip by ching ie Si Char Tate ie molt Rig ci inde Pd Tae Ue Sew Colon The Cane pr vd in Dye nhe decolor the dini a pi in he ps vei pak bright in REUS ai heal when peas ight vied by the height af the highest peak the dye or Chapter Genotyping Main Analysis Overview the sen under curve of peak The calculation and ende along he zi indicted by the Start and Fu columns the Tele respectively The vas attained whom the peak ane is divided by the are of the highest peak in the dye colar or Marker ho Only indicates which Aare Loc the peak is contain in Allele Oni ich the peak contained in Difference vd nis Inne aae in be aie al hot ar the pk center cm the cer Quality onl Only Asse Push quality ranking for each pak with regant odi pak Sea et in the Tuo Wizard Senge See Chapter 3 General Procedure and or zwar ting of the igi dal such sarod peaks Repaid The pe gay corts calla ovine aio ol pk ple Lor dae vary de te Septal on baton ee Indes the beging and end ofthe clio for the Sever c
50. in he Spe File Te and select Se Se Te Aue et Stings ee a pain SEE Rau ii option you wo aimer automatically resort report every ime you sn check ts fee you want De mantel yo cho oa Soul Curt o Alt We Sell in Ret You may che wheter Vo am i ace when slong eidem epar Leave is eurem i call alle im the ace when you double cic on prede Didi Sons Rt ChimerMarer dein sampler Balled dung nra ling The default ein eade abled samples fom te The ops rey tale to lave fad or cumple tb dented Others The Oilers tab has additional selections for he projet me Sample Groupings When Apply Sample venim rong implemented the Sumple Groaping option fimm will be automaticaly selected Deselect Due Sample meet inactivate the Apply Sample Grouping option The Sample Grouping information is saved and can be recalled by selecting Enalle Sample Grouping See Chapter 9 Additional Tools Filename Group Editor Automatica Sene Ran Wizard to INL e Automatically saves the Run Wizard parameters in an Ini ile when the projet ls saved The location isthe same location as the saved project and the name of this fle ls the name given o the SaveProjctName_ RunlWizardParame
51. in the column ace to he In colum a tale are the seri ae ael The column malle Pl Tb eer Sl ae the i He fia appear Sek He See Chapter 4 Mala Analysis Overview for luca pon ei Features Opin ne When selected he wer to deine speci Chapter Reports and Pong te range Only the peaks within the range wil be displays within the aget Tai Ale Pa When eed the table wil show only all allen within Panel ranges This open fri ace wher Panes applied tthe Goud az When etd lee within the Marker will be led ater the other in the columns at Sl tp o the abe When de cach lel will by a row so that he Marr ame Hed severa ties according othe ume flees nth Marke Ths oly active when Pan s plied othe dala Column button to open the Se Pak Tile box clum options ar sed in Al aro 8 the et The curendy being displayed in the ert Tale aed m the Sted Cas Geld om te igi Selecting Columns Single cic options inthe Cours and click the Add bution tod on option to he ced Columns field Hold CTRL SHIFT key tn mile options then cick Add Click the Add Al ton move all the eine d te the Sead Cate Deeley Sing option inthe Sey Calama
52. les and analyzed data swith editore rv projet fle Close seen piat NOTE is nummer Ce A ihre sting program m Cre he Cure pra View Menu Tie ie cols opos data aye the in Show itor Pereira cs Show Naviga Gel Image Report stow tes Sa ee myo Rr ame oem and Sloe inthe Mar ndis Preference Preference Activate ea renes bov Start up Settings p enge at art up allows you each Ran Mel and Gen Settings Chapter Genotyping Main Analyse Overview Rus Method nic Appt erred usi The wil e program data aput seing and display prompting simpy felowing program s rae How Wisi Adivaes the Run Wizard which wil guide the mer Brough the program s operation sein i tet forthe General Settings Sims Mer When selected the Sample Fe Tree will ie displayed in the Anis window alter Shan Gd page When selected the Sole Gel will Sota Fe displayed in the Anis window afer hy Sh epa hen sets prt Tale wil automatically be displayed im An Ana window EE Display Settings Dy Stings tab u to et haw the dala a displayed in the Allele Label Ds Prior See 0 to 2 decimal places for pak bing
53. 7 Randall by CTRL and or SHIFT epe individus supr amp Open buon in he pc dog 2 Tesco selected will appear i the Dat Fle it Jo OK inthe Open Fils box and the samples wil be uploaded ChimerMarker Features late the Open Data ies ox to make data easier m Ud to ect and select ra dat es for upland Ck the are button nex to button ta zee the four nice med dicii ples from the Dus Feit Highlight the sample t remove by ingle all sample rom he Feit Add Folder liking in the Chapter 2 Chimera Folder o upload row data ies from a specie folder in the le directory tree Click the Deal choose older o whieh ChimerMarkr willays open when the Add or Add Folder bulbos n pene Set Chats dig with 4 and Sloe options and allows une ta chose fm and a ande The ar sas aly enter yer and The dell channel color cup Set the dye colar bear OK inthe Opa Date Fic dig be Raw Data Analysis Cree the raw data le are uploaded the Ra Dts Andi window appears he amples in the Spe Te to open vidual Ras Tac The Sprit me play une gel format w h ager fragmento cated on ight The Engler splay natin a snl foreach dye
54. Additional Tools eroe any Hes setos inthe Select elle le to remove holding down the SHIFT key and dcin atonal amples Wl Se te famen of th spn paired in the Match Op il Samples as Cote trl en the fin clu of Ace Gre tabled Tot e Match by Sections Animal reperies ep omnis ed nthe lid Scion Sep aces Henkel Iden ho ta into grape ined onthe section eer ink the imper Sen The section flename spect wil highlighted red ixi Fe None Lid Conil ent which seston ofthe Glee contains the reference vi sample information onthe wein number entered fm the Match by Som Bid The section the sported wl em nthe Fle Non Lid Match by Fixed Postion Allows wer lo manually identify the charactor of the name ar grouping the sample Sch Sats ike recounted india har Eater the number of the beginning and fing charac o identify how to group the zompicr The til Enter the number of the beginning and Ending charter which par of the contis Meier The tection of fts Blame pected wil be highlighted Fie Nine Li Control Identifier Enter the character from the Conil section highlighted green that describes the control or sample Example normal or ference Slt Case Sensitive 4 he Coal enter nos to be i
55. Allee Call le Cl allows the o set allele calling ange detection threshold ers wil deli peaks inthe proessbe data ange for eseh ane Chapter Genotyping General Procedure Manual Range specific analysis region de let Aul ange input the desir hue range Peas ute the Marsal Range vil not bead NOTE The Pa Tid parameters are only applied o praks aside of the Panel Markers To jst singe or peaks within Pane Marker ranges see Chapter 6 Min Intensity Minin RFU thes of pak eight uas or pk Peaks blow tis value ll nt be call Max Intensity Mm RFU of peak eight Peaks sve this value will be flagged with yellow Allele Lab gens Quality Rank ol Chr and marked wih HI Quality Percentage Global Max Tie im peaks oth Sight he de calor pak tion Recalls any previously saved by the user there are saved stings the program loads the ul ang or Un parias aabt pe Sires any stings defined by the mer that different from the default These can be called fr sonore of analysis on ima dala set Run Wizard Additional Settings Procedure 7 The Rum Wizard Adon box pis Sen an Allelic Ladder and adjust the Peak 10 The Date box appear Th The data and 12 GEL whe the Dats Pring bo Functions Allelic Ladder emt i ee
56. Fight pein the dye color When ow peaks ae creased the ness magnifica facie noted in the x Graci lu Das Organize i the Prin pr euch ample ined nor of dye Solo slestd e all sample im Huet hen ples i Mark Desde Prints an x above deli peak and an F above ite pk the Pk Sic this rint he peak lion om electropho the pin report eh Uo thi tre to customize thet othe pint rept Chapter Reports and Pong Icons and Functions felling com re sea inthe Print Pres window poor ta printing the Print ep 8 Open the Print option bos a printer the pint ange the mabe of opi Bl pena the Rar box Save ach page ofthe Pit rper age Por PNG Sr ecos eene res o Named by sample name saves each ING of x e PEC under ample ame E Hr zz mur osi Pap Number ns page aber a pl name Named by page number save ac ley the page number within the report age Setup E Sup tox Chan papers margins ai Serer him ents ton Spr te n Rt pti ie men abe Rt Cont Opin oca view the ene Poi pae RB zoe Prid rico pogo mn wi tent ing norton the LN pe te to esa scm of the Pie Prec pag
57. Recipient genotypes In contrast the alleles at Penta E for both of these individuals have a larger molecular weight difference resulting in the smaller of the two fragments being amplified more than the larger fragment This is a source of variation heterozygous imbalance due to PCR process In this example both 321511 and Penta are acceptable candidate loci to track Chimerism because there are no shared alleles between the donor and the recipient 21511 is preferable over Penta E because there is less imbalance at 02191197 99 in 021511 compared to 76 86 in Penta E in the original individual samples less random variation Equations Quality Metric These equations pertain to the quality control metric calculations in the Chimerism Analysis These metrics include measurement error locus eror and coefficient of variation calculations are multiplied by 100 to convert results to percentage Chapter 2Chimeriem Measurement Error ME Estimate ratio of Allele 1 in donor and recipient to Allele 2 of donor and recipient at a locus At optimal efficiency the measurement should be 1 indicating that there is imbalance between either allele If ME is high the DNA measurement between the sister alleles of donor and recipient is large Similar to heterozygous imbalance but take into account the entire locus ME A B C 100 Az RI DI allele 1 of recipient allele 1 of donor BER D allele 2 of recipient all
58. Right lick on the pane mein the lat and ect Ae Projet Panel The panel ame willbe displayed atthe top ofthe panel ist Chapter Pane or Aer Panel pple othe dataset Markers and Bins appear in the Hepler and Ru Ta In the the Marker ae horizontal grey ary the Bins appear ax backe above and blow the rc and he center of the peaks marked wi a vertical rey fur Peake that fall ade o the Markers ae mad OM Laer OL that ll within the marker but uti of a are mad OB The allele adder that matches a sample fle swe the Auta Selert Ladder im the Run Wizard The of the adder wed sample e played tn the allele report Sce Caper Repost and Ping Caper Reports and Pong Chapter 7 Reports and Printing Chapter Reports and Printing Report Table Pat Report epa Chapter Reports and Pong Report Table Te perl features of he Te were sine In Chapter Main Analysis Overview Here we wil icta and give examples ol each Rp Sie aval Report Tale Allele List The Ale List Raport Style displays the base size oe Allele Label Pane ie applied of the called peak Mo pe vaca i ref enn ead pf Features ey Semple Nao le Name When plays only the peaks with Quali
59. Selection Procedure 5 The Ron Wizard Fela Selection dialog appear X template a saved ae of andar ole snd anal tamed for fur ec OR Select combination ef standard cor peri Chek New whom ined Icons and Functions Template Name L Set fo exiting pea templates or cese your cnn by enering a Talat Nen clicking the bution When a templates saved only the eng inthe Tepe Slt eof Rom Wizard oreste new template click Sc an cy tempt ee ane template abo be ect from the Ha avale templates inthe ft ston of he window and then ave lor future use By cing Save futon 1 yeu do nat want a template sles the appropriate standard colo nd type of analysis Ud tpl wil slot be Panel Chimerarkr comes reloaded wih many common kit Panes including Promepa overex and Additional ane E por sling Fer ion ext to he Pon Bld Acorn Panel canbe ied inte Pand See Chapter Panel dtr Panel Panel can be selected from available rom the drop down menu or can be ewe and lc y cing Pe Eric limpet a Fane Pane cant be foun in ir ft canbe importe by liking the BB il con Size Standard Chapter Genotyping General Procedure Chimera comes precaded th many commen sire standard
60. Simi Lis al predefined and any custom made SireStandarda Singlet Sern nt iie Ene Stn ace nd Sr Tae wl appr on ie du Additional Options Chapter Fragment Sizing Standard To see ational options for Sie Standard right ick the Sire Standard name and the rap h klong on Set Deen delete the Size Standard rom the Si San List and rm he SltGeneticsChimerMarker See Standard kr NOTE Thi acon reverse spot Size Standard pene the Sy Ae windy Choon and click Save The Site Standard will be opie o the directory and wil remain im the Scr Sud Lt and Simao ChimerMarer Sle Standard discos The Ste Standard wil be exported aw an XML which can be opened w h eres Explorer acl oe Not Reload Sire Standard SE rad change be Sire Standard Th met me ed Se wll te NOTE the user scis Save Size Stand and then answers NO to the Sire Standard has bee hanged sve changes the hans il remain in the Epid Ss Stan and Sce Tale unl aer ira Roe or propa chan Sample List The Sample Li cona il the samples inthe datae Doce and the sample ILS pes m the Spi ILS frame Une ough pls In Expected Size Standard and Size Table The Epica Sce Son frame display a tae the oven fragment peaks that are espect tn appear in the Sample JES Single ck a gr
61. Sore and Comments The in thse anno eet This pen ie saab with Allele Lit Marke Tale nd Pe Table Se Save Report Table To all currently displayed inthe Raport lick the Save Report eon in the Rept Tale Hector Choose ditor enter flame Alea the default and save an Excel st ext et ie expt oy ecd cl epar tbe ds he cll by dig cll nage or Il SHIFT key and cct Right ck om the highlighted cl and scat lei Key The indolis ie med to Windows icon ave cr be pud ino asy Somme per tr program ite acl The and ciam header for doe cle wil be copied with the Menu Options The lowing menu options can be Found in the men bar ol the Min Aaa window File Menu ei EEE Open Data tunes the Open Files w nde where the ner select rae data ino ChimerMarke Accepted Hle formats include abl aM ac md Sweet fd md amr See Chapter 3 General Procedure EP Open Project fe fet co we ee dm i oly Bes ah sf Re Open Project Saves the lant our project that were opened by ChinerMlarler and allows the ver o Lunch anyone af thane four prj dint Save Project Ses Someta Chinearer projet af ap ape discory Raw data
62. al samples ie an ending mira Icons and Functions Print Report Print the longitudinal report as zoomed view global view Save Report Save report as a PNG image Display Settings Change the display settings on the Longitudinal Report including how dates statistics and chart layers Add Samples Bring up dialog box with all samples currently in the projet Add samples by checking the specific sample and specifying a dale Remove Samples Bring up a dialog box with all samples that are in current graph Remove samples by selecting desired samples Adi Patient Information Add patient name sex age and date of transplantation Chimeris Display Switch display of double donor chimeism from individual donors total donor or display all Graph Display Switch from bar graph to line graph and vice versa Show 3D Wil display the graph ina 3 D format Show Sample Lisl Display a table that contained all amples and stats of current samples in graph Chapter 2 Chimera Analysis Display Settings Tate tinge Skt he tat that wil be play Pete on top ofthe bar or line graph foreach sample m Date Format Sting Select the dale display that will be on the X axis ofthe graph ema Satis Specify number of layers to display 7 statistics abel Sune Specify patient information and sample ist should be saved with image meer Add Sam Per em Rene Sa
63. and Elenpergrem a once Single tlc the Shaw Cal kon in de run bar ol through he dye color or un he Show Cala drop down meno dae individual ur ers Navigation Zoom int Joves igh ere the ara weidd Ei o sora om droga bar bx the ection foe jn To won the ager inthe one he tp slider kar low the lol to he image im her Amen or holt down the right mouse Baton and drag Marker acus Specific Viewing Focal tough vidal marker select a marker rom the de doren in the rain et marker une the Up Down Aw keys Synthetic Gel Image Features Be Sot elie dlp sample in iain e agent the eeciopherngram tae delay the mense pole over the Sphere Im lo evel see ne erae Image Utili Cic the Image Utilities co in upper ft comer of he Syn following opio Copy to Clipboard the Inge the Windows clipoant for pasting ints other applications such ax peres separe window containing the Stic Gel The separate window can maximized for Chapter Genoyping Main Anal Overview Image Display Move the tesi slide hor n the upper let comer of the Slit el iq p and den oan Se c deagos Goo View Pree Diply Sting Gel Slt for Single Dye to change the single dye Suh age
64. at have hem selected in the Ave vido Sepe Fle Tre Prins pen tace o each decla and sap selected NOTE The soci of i Aras wide wil repented i the Pit Reet Zum ou fll t che al posi e Pit Rr ak Tale in the Tae foc each dye coor belen the decolor NOTE 1 neither riter nor Tele were recto the Prt wil contain to each color sled or each mpl eco ad alle end witha each dpe cer Dyes Dur Cli the checkt inde the dye oli the Print part ESD Prine al ered dye calor om ome ceci erem Pris Pret Commo Includes the Comento at the top of the Print er Select Pas option dipl Pret Comment on page in tenet Lale Dues amp Number Label dye coor With numberof peaks for ech See Y Ass Pins the ung the Yin seins the wer Ana window Set A ic et ei Spey the size of the printed Minimum anl 4 Maree The brs ep above the ist Ales The Allele Labels appear below the lectropheogram Aide hy Prins only alleles within Panel Alleles that are outside the Pone not cd the Nas Page fr Sale Pints new for sch sample ol continuing the same page the diat Marker When the RFU low peak ae to mate the of the
65. ction When selected ChimerMarker wil logout the user aer the tne entered inthe Wal When the um i ut the o the analysis remains changed unl he user kin ith username and Record Data History When select any changes made to the calls of the project wel be saved the Hoty log Pese E Hio seen Thilo mare fai Edit History Audit Trail When Record Data dit History is sce in the Monger Pi section above change to n the analysis wil Change corer in the the Show Char Tale con in Ana window he Pak Tee wil appear bw the sample change as ben made t cal moco the pin This indican change ha tenet at ale ha ick change and ale View or The Sc EI History window appears Selecta change rom the Et Lis to vie change in the Vela tabe Changes wil be highlight in E 9 Toren a change ight the row in the d Hity ist Value A a a he 10 Cink OK and lick Yer when the warning prompts you Make change to cals by rg clicking any clin that allele ow in the Tele or rightclick the grey veri a the conor fhe peak nthe sace o Ei Ate Et A and Conf See Chapter 4 Analysts Overview ding inte clara Toe Chapter D Use Management
66. ctivate fit before the solves can etd Installation 1 inet the Solonis into the optical or CD ROM deve quur computer not set o open a CD navigate to SEE Double ick the Chime athe Setup fle EXE The hcl Wed lane the Next button in the Won windy the Siehe End Lice Agno check the option Tce he Lie Apre ani ck N in amp Select Install ChimeeMarker Recommended the Sch 2 Ned e Dati Leann window to mel GhimerMarker inthe deal folder Cli Brae bun tr Some diferen deny NOTE Tie default Destination forthe ChimerMarker program Chimerarker ver X Gish Ned nthe Sca Manger rides o sop dic ra Meer Grp NOTE Changing the Frum Crap debuit may affect SCRE Nea ia nd tal hiner 10 Fil ne Isaak Compete winde Th The etaim Wan 12 Bette Spel CD Comer by Cinestar Pise T orton dal es jud isl gt Pros The wind will appear Regiater Now doses 15 Select lel ening registration meth rm the Cre Risto bac 2 Clk Register Local Ten based Key u Chapter 1nsalling ChimerMarker Registration The Neier Ter bud og window appear forthe Raider eral Text band Key method 2 d He computer e i being ished on connection sect Register Online Ifthe comp
67. dataset Siar Mat Sor indicators appear next othe eame the Anas window San eT Samples wi ih Mati Sore by a green ah thue wi a low Mach Save have yellow seri Samples obere ie calling filed receive ard ska rough analyze how cach individual cumple wa mates the Ste Standard elected acces he S Caton Che Wain ss Carton the can muy fw ear ample va iz and view the information Sere Standard pene Sample List The pe nis lese Mah Ser ad se ped toman for sack sample ite dt by tng the hend Tio Ea si react i seing weg eder adco Yin he Singh eck a mpl i oet Rami S and olas Pe torte gt pen kee Rp ple and ict Mao Pied dinde Dich comp ipa edi Sei Tin San oben oye vps Mal Sa hich cepa dt eg pir sch nt dle amic and le Send Fals mates roe 1 ro a fre csi era bed Disabled size Column he Sac wen dnd Sie Standard Sis Top Ey seco wil Spit wer ly Du Sag Na Se nk ele ir Seri Lat ee pie pn te aed pel iei frac mop the lel oa das ogni ren Rod n ne pido pon Chapter Fragment Sting Standard Size Calibration Charts Disabled Size Statistics 1 Sizes were diit in he Sie Standard ace previous action Stor Template the Dial Ster Stns wl appea
68. ded the peaks with peak scores below the Ran Wizard Adil Songs Ale Fe Scare Reject ting ville delayed im the tbe ie Er Semple Nemo When data ia displayed in Verl Ott the sample names repent or ach ow s dita Bal the sali wi ide Er Sample Ner re then the ampie ume wil ry appear once hein ol sone mite ri Caper Report and Pong Bin Table 1a peak detected tn at least one sape the in Tal Ste wil report the presence ce absence ol a peak potion or ft datae Features Options Abie Dad When selected the table will show only called lees win Pane Marker ranges This any active when Vane applied tthe data Se Tae Ets luto eiae the presence of pea at ihe pont the absence of peak at the poniom Regine and a Check ur Undetermined Quay rank the peti Sipe s net a the peak inten FL vale for all and Suid peak value E fo aie potions Selecting fus wil show the peak velia ral potion chug Neate polos Bis Pea Ay Displays peak ser le or all Dir and Speci peak ponere Del S separate if mare one option is elect Orientation Het Gasp names mpg the and Markers appear atthe tp i eum Vora Sample sites appear n We fa lei olm rows Marker and Alle in order of tae pat nes pari
69. dent upper or loner letters Control Match Mode should he und fte character entered the Ci enti need mach Ince should be characters inthe Can eld oy ned to be ete n he enam Output Trace Data Tools Ost Trae Data The Out Tice ener aw sie of sample a Text mt or SCF a es Procedure 1 Select wheter to export the ot SCE Re 5 Cicer the dra and foes to exper dat in File Sect the sample to inthe opt il rm the Slt Somer Select which dye color data tn export rom the Slt Die el S Select wheter export raw or ocd dat rm De Tope option apart ert dat the older Chapter Additional Tools Convert TXT to Binary Te Canet ary too allow ser to plod trace data information in Test fe format for a SCF flk or a ccelo SCH fie The SCF and SCH fle can then be ad by and tasted no dummaloprame fr tons developing Vei sen Fragen nas rumen Procedure 1 the Load Text File utin and select Tet Hs to 2 nor les are pled wl appear im the File d The software wil eae Resmi er to condense number of in a XX number in the Cond Ener fs by namie ba the Con 3 Export to SG if exerting
70. der Minimum Heterozygote Intensity Stutter Adjustment Stutter specified in panel A Stutter contribution Caper 2 Chimera Analysis Y DNA of minor allele not affected by stutter Equation Major allele x X A Stutter contribution RFU Minor allele A Y DNA not affected by stutter is used for Chimerism calculations in equation below Decision Pathway for Single Donor Chimerism Calculations Shared Wil deconvolution 3 7 Chapter 2Chimeriem Anl Decision Pathway for Double Donor Chimerism Calculations
71. e ori Bk gend NOTE When all dye colors are selected the bande in the gl image wil be played in color edle it sacle available when for Single Dye i selected Wil iver gel image sa that he cg we whe andthe ond agant wl be lack Chimeras Analysis Preferences Analysis ere arose ingen rar m nc or lune abou coment raft aus o Uhr at canbe seen ion thre ae functa for pn encia iden podes copre rap Can sper parca are siii contrite wing Dar nd Recien alee cl Set the deine Peak Ratio method Peak Height or Enter File by your laboratory The pation 2 between allie Ladder postive and negative contro Done repent and tue pe Tor Sila vong depen e pi om Hood a coed anri the recipient hum Tools 9 did sample fom the pet om IC ome dl us 9 ati my ny sin ie nn REIN Sn Ladder Sel aga alte he samples designe e Laer by the Le appear in Fa Sh Report When selected the samples designated Pont Neato Cot ier el appear n the Rr Tal Mak Deed Paks ite when selected zmple that ae delet are mark with am the aol the pesk Semper al wer did ae marked wil en Ea the op e the ea all ea Seat rm deploying
72. e ie vind dienen lick Next the Destination Loo window LSM in the ia folder Click the Button lo coe ferent etalon decry NOTE The delas Dotto forthe License Server Manager program is Solano TI Chick Next in the Slr Stain window to tall License Sehr 12 Sc Server Manager open and ick OK in the window ar the sten Alan Yard vil me and the syste wil eat Bestie Seine Register License Server Manager for ChimerMarker Usage 1 pen Sr une Steno Tay y cling ES aic arian he Lone Seve wg rope 2 Chek OK in the dialog box to proceed wilh metering License Server rom th License Server Manager como 3 Select Register rum the Help menu o activate the Product do Sete ChimeeMarker rom the Reiter Rare men 5 he computer Lise Severi bing mal om as an internet connection fe Online the Computer does not have an interme Off Online Registration A acie the Account and on the Seis Chapter Intl Fes your Ani Pat and Ewa the appropriates The Rope norton generated by Licor Server Cii Regiae Your sore wil be registred automatic confimation imal wil E en you oc getan occ NOTE Some chara re can commonly be mired If you get an trie tying far number
73. e ame folder the samp were upended fam Export ABI Sie Standard Exports the Sze Standard Sond ist as XML et rectory ve local e peek orp Chapter Fragment Sting Standard Gens St Stan ltr too eure ta ne changes tothe Sie Saar befor tng BestMatch Mach Selected When end the Das Frcs appears Tach sample inthe dataset compared to the currently lg Size Standard inthe Ss Lit Th geen tangle indicators ae add tn ive he gt Mach AL When elected the Doi Praes box appear A samples in the dataset ae compared Sie Standard Teh Sos ch me etn ne These Sonar wh nt orgs Ma Help The menu contains ein Siar Tte Eo Cli Kyo and the Sz ir Aton Hp tox appears Toolbar cona AAA New Standard Opens the Input box witha tener a new Sie Standard ome Allows forthe creation ol a sow bie Stand pe Delete Dele the Sie Standard atis currently highlighted in the Siar Ste Lint NOTE Ths action irreversible Show Dye Allows the user tn select single dye color in the Sani ILS Cycle through the cars Vl 0 mude he stan tothe Chercos Ste Stan x a Size Match What to Expect Once the Sze Standard be applied to the Seve the ite Size Standard in Sie Temple itr thon exit
74. e br ech npn long with Donor Repent mle Fes fie Chien eri pope ner Ih Mier Tene pent doo down ero Spent the Print tings and lik Tren ee the repr Chapter 2 Chimera ach intormative markers wl be groupe with the appropriate marker om Donor and ecient sample or Marke result at average remit ore payed n rigid und cde Tr the sume mall in preview modes Chapter 2 Chimera Longitudinal Report for Engraftment Monitoring Detection of Malignant Relapse Short Tandem Repeat STRs provide a highly sensiive measure of chimerism in monitoring which is essential for long tem tracking of engraltment and carly detection of malignant replapse Each patient project is easily appended see Tools Add Samples Projet with Sequential Samples from a mentoring study The longitudinal graphs are easily appended with results rom sequential samples The report header provides verifcatlon of the user and the analysis parameters Procedure 1 Open a saved projet start new prj flowing he Analy procedure Chapter 2 2 lo me Ai Samples oe poet to add eri pla X sees Applications Select ingle Donar o Donor Chimera Alsi 3 ios e Longitudinal Report ion Use the Add Samples In to begin study or to add seri
75. e pel wl minor peak nly smal percentage ol he RFU high ofthe T sure thee ies timed E md i posing be Aegis era desig c oral Ar pio pack Chapter Pane or mouse dick on one of the Marker Ls label above the ectropherngrum and select Marker Br I appropri val ira Min cer poe bare Sct the Apply Markers tea ono balan ame level in sch marker u Tes har eet eran a erent range em appre vate or 44 Sve the panel with mame hat wil inate the study cane number and emery ping Typical Human Wentieation Cenotyping pande we a 20 minimum inane tr si Deere iube sek 20 mine peaks mus be lez 20 of he eight of the major peak at hal Iran For her detection and monitoring detect avr peaks omm dier Se te Min 1 Spproprie level for your inthis example the fier eet to any Peak tie SV ce mre eight ofthe alt peak a the oc wil Sled Peak that are en than of the taller peak height will not be led ereure that al peaks the ster potion are called et the Options Functions and Icons Tha olin replantea cf mes opi Menu Options The Pa tr contain thre mens options Ti and Help The Fie ment allows the ave amd expe The mona Comte optio
76. e sam stop a peak o le the pesk The green tang Wl lum yellow when the peak Additional Options Goce a peak right anywhere in the Exp Se Senden frame The igh fick mem wil aper wih te flowing poem The Et Sis tn appear parameters and click SE Enter he era be ple Gar Inc ILS gent aate abr im ert Enabled When selected a 1 wil appear m the Face Siar Tale Dec option to date the Sein the Se Standard sie wile und peter recepit nthe ele IE wil ot be und se Dic fi pain vara ample i pis NOTE vale i changed inthe Se you must click anche clin the See before ving the or will atthe potion inthe Expected Sz Standen feo in the Sample LS where Sie shoul be The Edt Rar bot wil ChimerMacher wil auium inthe S eld if there are two more present in the rae Ads a noma and cick OK A prem angle ell appara the rase potion tasting whe the ew war ped NOTE The eight ofthe now Sa in the Exe St Sard acis dependent n the height ofthe Select Sie to remove the Size completely rum the Sie Standard the Size can be ET doc Ene nc Ea NOTE Sing mare sce when ther are Sits in the Sie Star SetValue ta Column Chapter
77. e the Sue vales i ang m Sand die fo Ween sigan paier of ach sample 12 When the Size Standard ta complet ec ie Se Core DR ck Save Changes co ek OK in Sar Tampa Eli M Proceed with Run Ward daz analysis Icons and Functions of ens aid m prr in Tepe aie Menu Options The Size plate or contis three ment options File and The Fie men allows the wer to and export Sie Standards The Best mer contains options for selecting Ste Standard The Ha es ig Hoi fr Bis Tonle Ei File Mena New Size Standard put Dig bo with a eld o enter new Size Standard name Fallow he sepe abo Cut Deletes the Size Standard tht is currently highlighted in the Siar Sand Lint NOTE acom ever Seve Changes Svcs inant change to the Sie Standard in the offene Chirer arker Standard directory Opere opa Dido box wilh a to ete new Sire Standard name The Sze Standard aed o the Se Shand it ndi Solent Cher Marker S tana roy Import Size Standard pere a Windows Explorer window to the Chimer Marke Sir Standard directory Us the Import Sce option to nd exported Ss Esport Size Standard sports the currently selected Sze Standard in the Sie ist as an XML t a specified rectory sve local e hor opte Import ABI Size Standard pere Windows Explorer wind toth
78. ele 2 of donor Cm lngerof Aor Locus Error LE Estimate relative deviation of a locus from the Average LLE Average Locus Average 100 Locus the chimerism level calculated for that individual locus using the alleles only from that locus High LE high variation of locus from the rest of the sample Low LE low variation of locus from the rest of the sample Coefficient of Variance CV Ratio of the standard deviation to the average percent chimerism of the sample It gives measure of variation within the sample relative to the sample s average CV Standard deviation o Average SCHM 100 If the CV is small all data points in the sample varies by only a small fraction is large indicate that the data varies greatly or there is an outlier in the sample Margin of Error MOE Calculated by obtaining value in Table according to degree of freedom and confidence interval multiply by the Standard Error of the Mean MOE SE T score Standard Error of the Mean SE St Dev Square root of N where N informative markers Large MOE indicates sampling variability in the data and results are more open to interpretation Small MOE indicates less sampling variability in the data and results may be less open to interpretation of Detection Homozygous Total DNA in Marker 100 Heterozygous 172 Total DNA in Marker 100 Threshold set in panel un
79. er nk ep Analysis Preferences Moli Linesge Analysis The program preferences include beg peak ratios by height or area w h mi mi anula of and ther cel type population doing mol Genotype the single source samples Follow the sep for importing and processing data rom Chapter 3 and 4 Genotyping General Procedure and Genotyping Main Analy Revie Review the results in mai nay Chapter 2 Chimera Analysis Alter reviewing the result and making any Chapter Genotyping Moi Anas Use Tools gt Panel Editor sd comas the panel a described in Chapter Panc Editor The may be any combination of letus and umber example in place of RECIPIENT labs may wo type in the recipient ID amber or name 1 aueh the dm Wand Prost dropdown or 2 the Chimenyping panel from the dropdown Set Only Call Mele Preset in CHM Pan lo coc erase Ajos lies pure ped lo proven eth genotyping aay 6 Renew in the cstophermprams and ded report able Mayans Chapter 2 Chimera Review Results purl and open 1 there heterozygous imbalance in sing
80. f lowest mente tn he ght the begining ange and looks at the tii SQ 60 Enhanced Basline Subtraction This feature nly cen where the data has excessive baseline tn ne or mere of the es ora an slope scion fon in am made The lc ca ene dea a the awa ale for every 30 aa al ook at he 300 fame cian Chapter Genotyping General Procedure laetutions where lere san ceded on font in the ml STR range sould beamed This renes caused by wavelength to other The funtion shouldbe ae a Maal Pulp Come was u ine fa Data window Spike Removal Removes peaks rom voltage spike caused by or debris im he path Spike are rici hana wide oot see Spe enm hen 2 Deut Trac his eem ppd Size Call Chine Une in mont genotyping software applications and is recommend for mast analyses This method Sen aa angen ir ot ain Fe fime graph ie determine linear Sacs Souther EM Measurement of DNA Length by Cal 197 Anl cong 100 319325 Cubic Spine Method ae an alternative method tha may be moe appropriate or some data This method pote cn se ire rap An empleaba cli equae Aspnes aura December LIH pages 87 79 Local Southern Method Cubic Spline Method
81. fthe eetroperogram Bim are slated by the atthe and boum ofthe NOTE Only in the Panel Lor d vertical gray hrs within the cacropherogram indicate the center of the Fer all her views in the has in ne indicate the center ol Ihe denied Panel Editor Project Panel The Prope Panel tics he template panel forthe project nd al adr sample that the lr recopier tas Tee Hla ames are n bel ord n main naps Tendo when See Bet Laer und for he Rum Ward acies the er om is Ties the rere lider or uch poe ladder fora given samples en the Panel Templates The inches lit of all predefined and castor Ponce saved to the Pace folder i he dior Single fic Ut fm the panel name to display the trae Single rightclick un the Panel eris popup menu of options Doubles te Panel someto expand te feller and view the Marke withthe fand Singe kick the Marker name to play tha Marke the Orel Trace ae Additional Options Zo ee addtional options foreach Panel right cick the Panel name and the right vll appen wih te folowing E Chapter Pane or pene Ei Fone box king the Pe wil change he Pane in Pan El Set be Pid fom
82. i mae ste pce irl acr enn be died i e Ser X ied along wih Apply Sater lick the toe cies io aa yu ieu the deal ting Chapter 2 Chimera Analysis An cumple of SAI for lacus 25139 gt displayed here Quai spec when PCR el in the Sal Capen me Envi Beten donor and epic REVIEW RESULTS The automated calculations ae displayed inthe cete tae To view the rns for a given le cick E NE Nonsnformatve Marker is Nor Inommative bared om peak pate and parameter chen in tings NAN No Available Number No rests am for the following peak pater ME Eee TE Locus Eve Margin af May ams Chapter Analysis Tools and Icons Test Analysis Sting Se Mali Sample View fle Comparison View El Analy Sings Reopens th Cimerem Stings Dilo ax Set Multiple Sample View lo view race ol ceci er Chapter Analysis Comparison View to vin selected rc and level of 20 or 3D lie Save the report ib in orte format Show Hide or hide the El Anti Parameter ion to munch the Chimes Analysis Seti Boe Chapter 2 Chimera Sample ise alternative to display of multiple samples C
83. ition reap lef choca Lean ta ech pain Casi Identification characters Ica that the enters in the View Preference Chime tb cam rand Match by Order reap Seale the rains ee gap Mayans Chapter MCC Anis Grouping by Text File Rules 1 Sample name im et fle mn be identical to ample name lade in pect ann ina ym 3 it column cond ampi A ach amo win aro separate by ab waning ace to create group information ile must be an a tab delimited The following stration show example of prong information essed in De and Notepad Band Ele Aer eating the file goo Files select Save Save se typo select Text Tab Test Fermi ums Chapters Arye Results The automated are displayed in the center table To ve the results or a given ile ik on beide mae nthe ot st the left marke hat ar ignore ar highlighted red in the copra A ey O Fllename list Results Table Tools and Icons a Analysis Setting Reopens Analyse settings dialog bo IT se mar sample view sea lle samples view POTE Brie Compara V 20 HIMMEL st sae ECO Aule i ce Comm
84. ker can installed any computer network configuration Soft sas the Lie Server Manager LSM to control the nurber uf concurrent the ening option ol Cheer 1200 an above LSM wen et entation mo hare Pied component ChinerMarker ad LSM ae ims the sam EXE The ere Liens Server Manager program i valo considered Server computer Computer un the or than the Server are called Cin computer Server Marge vl the apo comple Pee re al ork and dow al applications before installing Install License Server Manager Chapter tl ChimerMarier secte ito the optical CD ROM dive I your computer se o automaticly open a CD navigate the pic or CD ROM deve an the commuter anc epe e d Doubt lk the Chmer larkr Setup executable Se EXE he eii Win wil lunch the Neat bon in the Home window the Sul E e Lice Agreement heck the option 1 ep the tem ofthe Leve Agreement and lick in Teal Me File window Seed Iul Server Manager Sot Pira window and ick Tick Nes in the window Next in the Se Program Manager Crp window and Next inthe Sh window enter he LSM instalation wizard ick the Next buon in the lone nd sd the Sene Ed er Ayement check he option 1 ep the ferme of the License and lick Net h
85. le source sample for given all iti recommended by mca publicat on certo anos ve ze for eri caulina ant og ia Eva The pk ant sechs in evade peak ight in single simple The teres imbalance ithe mitur elite Any must be made inthe main analysis window and saved in the hierin project SCC This sitis inert of e gin ervand int the Chimeram Application and Caper 2 Chimera Analysis Automated Chimerism Calculations ect Applications rom the Main To Bar Choe Single Donor or Double Donor Chimeriem Anais to ael ied timc pat yon Te Boyne di AG or ana options Da oe ete nd oral cast a povided too te per hoe econ on Cherie Eaton Selec Chimera Type coord papers Selec Analysis Type Without Salsa Parcs provide check a options to lacur ifte erg ble ica an the e end by the un fare Shared Allele lances whee I peak arca Sy armband le alll needing he peak ny o re ie share peak containing oer te all Set the desire Error tan and Specify the percent for Limit of Detection Thread Any smitty above the threshold wil be flagged med Threshold type donor recipiente o use ype the KOHN Type selected in the Bai Senge py cient w
86. lves you to and change parameters in the Dejo Option Slings window This test window fontaine tential to the Hum Wind stings the Pret Option Sting box folct Ren See Chapter General rece NOTE Run dom not need to selected ate adjusting the Addin Ail Eastin Pak stings The changes willatomatially be applied when the rit Opt Settings window la Project Comments ean inthe Po ger Applications Menu The Appia oer cita individual modas for speci ae analysis These modules present and sopmling opa for is peter application Ti Spex of Analyt inge onore doe donor may sli om this drop down ent Tools Menu The Te rer contain and Se Ei ation o other miscellaneous meen Panel Editor variety of ola o ads edit nd cate conil Panes See Chapter Size Template Editor Allows e compare of spl le be standar to Tein and nave standard for ute we or resa sive standard apis Fragment Sizing Standards Positive Control Template Editor pc Obi menu the sive coo genotypes making dem Be Zac nthe Mind acrem af Run Wizard for nomad postive Control Soe Chapter 2 General and 9 Additonal Trl File Conversion Ii ol allen ote ad disces fies cinto peel a
87. m and chosen m tings Available Number No see canbe calcu or flowing peak pater ME Messurement MOE Margin of Ene Alternative Method Procedure The leave wirkt i designed for problema dat much as for les hat have p pe ur hia fe migration from capt variation eer fme Optimal Unze emer are roce by intone o CE stor however the atreve work in ChimerMarkr provider Ihe dl i ow scucate detection and monitoring in same seal sei iia analy tara with vive and ll cil of inge denar sd pie ample far enc re Re low the steps in Chapter 3 Genotyping Deal Ate genaty pg single sau sample the cane panel construct described in Chapter 6 Panel Editor ern tthe main srs er and alia the Ron Wizard Use the chimeram panel forthe aee under nase and raya te dta te new formation stilt origin c nth pen donor arc pri rm pal e om radi pe D a done pe Di ro donar arc involved peak ord DIR indicate he peak dom ecu in both the donor and the uen Chapter 2 Chimera Select Pre transplant Sample Identifiers une the calls of the donors and recipient trareplan samples to automatically delet and el peak origin im all post raplat samples donar recipient or shared This can be et Sect when
88. mple Name Select sample to a by checking the box ion ext to each sample name er pan e pum paw Date Specify dates foreach sample Remove Samples Sample Name Select sample to remove by checking the boc next in each sample name May ams Caper 2 Chimera Anais Patient Information Note the following entries ae included in print report headers Number applicable Input he case number for ibis sample oF project Nane Specify Patient Name ID This will appear as header on graph Gender Specify patient sex Age Specify patient age Date of Birth Specify the patein s date of birth or check No Datei date is valle Date of Transplantation Specity date of transplantation using the drop down menu or check Use Current Date or No Date Tees Tue Specify the transplantation to be displayed on report Donor Information Use this section to briefly describe your donors donor sex elation to patent and so ments Add comments to the project f needed Any comments added wil be printed with the Print Settings for Double Donor Tye Select type of donor chimerim to display rnt Settings Select print settings for the graph NOTE Keep Show Setting selected wil print the report as zoomed in the graphical view Chart Tye Selat the typeof chart to print
89. n app in the Sandell of Run Wizard Tempe Sl and wl be pepe Alternatives the Size Standard name now flos the est below In Sie Template Eo select oa Mat Al The Dal be pare top al Sire Standards Tae Sie Standard with bet average Math Sor acon al inthe datas wil highlighted in he Sce Sander Land appear the Exped Sce Simard NOTE Hota will aot vay shone the core Size Standard User E Omer the Sine Standards chose click OK in the Sse Temple 2 Size Standard il then appear In Six Stand of Rus Wizard Temple Solon bw and fll be wed ose te data Custom Size Standard Creation Fellow the below cese new Sire Standart hve on the uploaded to Chimes Marr 1 de Sie Eto select File Se ick the New Chapter Fragment Sting The lapi Dila box appears Enters Sze Standard name and dick OK The Eset See Stn ame wil be blank ata Known peak im the Sample frame The leet Sx box pen Ener bue ak inthe Sis fld dand dick OK 9 A gren vil the inthe a new peak wil appen im parc MM 10 Corte S operation forthe ret ofthe posta the pes will interpolate Sire value afer ae added to the Se Standard recommended ia un
90. n pe ong an aa ft ec oe bt in nervi M EE T Allele Evaluation rer defile confidence evel f lide Peak core is am git taken nto cc iral rato and peak morphology Rejected samples appear in rei amples that ke check yellow and samples that have passed appear gren Auto Selec Best Ladder ladder sample in he defined in the View Pape Chinon ar ek Laer samples ae then compared o de chosen Pane Each Ladder hat within the range of the sec par wil and appear ont in te Sample Te Aut Slo Bes Ladder wil ch ample il wid ein ladder that Pes mache hat prin repart provide the le mb fee der oo ium Auto Panel Adjustment When the Markers and o chosen Panel ell he signed with he ana ofthe Ladder pis it dame win ire he pir ar tid Dy Cline deed Procedure in the Vine Charm Ladder enfer alleles and variant or virtual alleles are Speed i the Conte Colum inthe Panel Sce Chapter Pane fior This information i ed or Prem regulon end NOTI Panels hat do not conan ira als he manly autos in the Pec Et by el He Major of Pal on thon Mir Nori fuel Fo optim Auto pe ft See Chapter
91. nalyser or ue ih by the Convert Texto Binary Flo File Name Group Tool ond specially with the MSI and LOH applications Fe Crop Tou aloes users merece samples and tur samples shoud Tent sported See Chapter Tool Chapter Genotyping Main Analysis Overview Convert Text to Binary Files For customer developing their own instrumentation the Ter lo Bary Fs opin allows sers apad furor vc color Tet es without eade for comverson into SCF iur ole dta or SCH vector i trace ies for analysis wath Chapter Additonal Output Trace Data Provides the option the or tae data TX or SCF fle Select the samples to dye Slo datatype and the dicor the ac See Chapter Additional Tonle Export Elettopherogram Albers the ner expert the tract image topic eer Magic Wizard Cosina ls option bons Start Your Ps Ra and Rap Allows the une to easily ses the Ope Dui or plead windows The can bo the cur pecu pened project by seeing black arrow met o pore Dt Kus Inuches the Kan Wizard Selecting Aulam rove aa um with e pocas opti sted See Chapters General Procedure Report Alles the Se js o Print Raport Selecting Print Report wil uch he Prin Report Stig box Ses Chapter Reports and
92. ncluded the chimeric caleulations or indias parameters could not be calculated based on data ChimerMarker software abo contin the t allow the analyst manually exclude loc om cleans 1f needed The second page Includes the header signature box and the results table that was displayed in the MCC analysts resul window Chapter Additional Tools Chapter 9 Additional Tools Chapter 9 Additional Tools Automated Control Concordance lane Group Edior Caput Dua Ca TT to Binary aperi ero Chapter 9 Additional oats Automated Control Concordance Positive Control Template Editor 1 Tode Positive Conil Template dior AAA 2 ee sing rere on ea rom functions to Add new pese ve 4 Sec the appropriate postive fle from draplow menu inthe run wird Summary rage ae tthe o the main analysis window For example pog has one tive Seil Heat ith paar oral ep the message PC err Example of Positive and Negative samples in concordance with controla S Ifthe positive control samples are not in agreement with the template the message will be PC error and red lines will indicate the peaks in error Example of Positive sample not in concordance with positive control template Chapter Additional Tools Negative Co
93. nh cence sie cu cien do oa usr sgh is CTE or Ar TOUPDATES FONT SOFIA CREATE rto OR rons PR RAE TRYOUT PRODUC SAMPLER OR FOR RESALE CS OF SOFTWARE Y ml amar Jn mesa oro e can repli ch nez Sa ptr try ana with cutn hec ay een Lay due ome lle nied sates LC aan ce Saar hn Stet TED WARS SE TOR m CINES LEAL Yu MAY ta cs NINA Fur fre sra tn Pacem arte eoe trn tthe edo he Arman ano com Ls Come Sage ooo namen QUAUTYORFITNES AN PARTIC ARPURPOSE e psn fn den lo te Sms Aemen came oed sl are ee Seer ST Aon CONSE GOETH INDIRECT INCIDENTAL DAMAS ANY LOST Ok LOST SAVINGS EVEN IE perso the datio dr ining cations nantes iy a prod tac Meme les You agree that repre aay country ar od sy manner pain By Und Ser par dan Ar any nr erento ai Le n Sin te aa en perl ems ander on Ls Ju reper ad amat ua te nemo tos uds ont hnos km Si ut Cth eh Sct yowar eu teri posed der aortas tment tan Al ci ine are ane an na ach igh eot yo a any th tern Ar in nce TABLE OF CONTENTS CHIMERMARKER V 3 0 2 CHAPTER 1 INSTALLING CHIMERMARKER netten 2
94. nization yor planas Run User Protection When elected nee be prompted to lg em with une Wheridesdecil asy poc can lunch wath man and perd the Adi lier where ne d por be input Thine sho where te er pe cante EE e dead by sighing te tectae nd selecting Dae NOTE Only the can add and delete use My re where the thal aged ene a The mus be ened ties ream Access Right Rig f Uber ben where the diferent corp available each wer type can be ented Ching the Set Dealt button wil eam Are Right forthe cr Tape selected back detis NOTE Only the Admit can change Rights for User Tap Change User confirmation of ston then chen th ain iy 1 Chapter 10 User Management di ie er Mistry tb monitors ne acy scit with the ner manager function Date Time Rezo the compute forthe activi the te era hat performed be activi ison the usr manager activity that wa event hat oa For ample if we added hen the of the prem Bat Corea Settings The Le Manager Sting tab containa addtional option foe the User Menge fun
95. ns with alle sumple and exporting Fine The id men costera aviation or Fun Eier File Menu New Panel launcher the Cre Nas log wih the options anew Panel Aamo Maly Delete Current Pane Marker Delete the Panel Marker that highlighted in the Lat Sore Changes Sven and changes to the Panel Sonetos Cher Marker Panel directory Hot Key CTRL Saye as New Fane pene the net Dig box with fied i entra new Panel name The Pane sade othe Lie Chimer Marker Pal etry a Windows Explorer window he sre fer he sample n we spline Use Spt Pai option previa ported Face Fla oh oa nece comps Import PreDefined Panels Opens the MLPA Panel folder Use this option to additional MEC Helland MLPA Pare Import Panels Launches the port rn bon Opens Panels and Bins les and convert them to si Food ein XML format for nein Chapter Pane or pers cure selected Palin the Pe a am XML filet spec on local o tra Perl lone Pan iii Be ret ve changes to ih before ing Tools Menu Match Ladder pene the Sci Lader box Choose an allelic ladder sample fram the drop down ment Click OK and the ne wilt ty li withthe peak in he selec alder sample NGTE Large ferne peak an Bi poston reves wih the Mal Lae
96. ntrol Concordance 1 View Chica bo V Doogie conos tae id red im negative control sample that has Wil sent in negative contd INC emo in the Proc Summary Bar Filename Group Editor jet Apply Sample Grouping OR Tools File Name Group Tol The Fame Grp ir be aed group aly members the usd m ther namen or pled anche Procedure 1 Select Projet Sample Gaping 2 The Fe Nome Grp window appears the Fl and sce d files o pii the daa samples donot morally pede the Fle Nome Lat Bd amp Choose Mah Seti or by Fed Postion 5 totor values the deco and Cantal dentition Tora Cond Knife value and dick Mach 2 fom he Fle Nene Li wil pied ito Maal done When the sample are grouped come dick OK OR Sick the Save Groups to Tle icon to swe Ihe row informate bed fe 5 ic Name Grup wid wil dene and ging information vill appear net othe sample ir gin os 10 navigate by group inthe Sample Fe hold down the CTRL ley and the PageUyDewn keya Supls groups le opened rici Icons and Functions widow where av il can e located and Filme Grp om e window where addtional rane data les can be uploaded into the Flame Lit aper
97. of de ide Fuweler amd Via Chimera alo dh opportunity custom Panel he predefined Panel da not ice ree woking vi low ira decur cf hor ue Fara cn 2 RN Panel with ChimecMaker Pat Eto il The Panels displayed by default morelos Powerex Mop Sy tem D Peer Sym E NY Pre Defined Panels The predefined Panel appear inthe Pie Lit Single any Pan inthe Panel Ld oe In addition to the Panels played by dealt the has the option o import standard Panes and les the sep Blo opor anes and i Text file Panels and Bins Files 1 Pel Er Fe Import ABI Pans om the mem 1 The opos fr Gone Map box appear X Ck the aces baton the Poe Fie id A Windows Explorer sce laa Navigate to the location of the Panel bt ile and dick Open 3 Next clk the acces Baton fo Bs Ld fo eld and ete the Bion amp Chek Open NOTE She in Bol Bin t fle dow not eit 2 Chek OK inthe Inport Panel from ene ape bex the Panes fie il be ito ChimerMarker Selects newly upload ane iom oe Lit Marken and oth they lg ith hepa in the Th Save the edited Panel and owe Panel Ei 12 the Run Project on in the Man As window 13 Select the Pana fom the Pai nthe Run Wind Tell Schon
98. olumn tn the pt Tal Let within te column then ight the ell and Decl Bin Colon When Vra Otto e selected the Tale rans wich tain the information il he deleted not he olmo eich contain the sample tomaten Binning Options To aunt whieh Bins are displayed nd to merge Bin in the Kor Th ick the Bin ica in the tolb o he Rept Tab The Repo stars bos wil appear Display Bins By deat fine wll be selected with checkmark at the Individual delet Bin for Royo Tale By single efec bum Gele al my cell inthe Cm hx Select Unt Al To det only a fov Bi light the sone then hold CTRL ce SHIFT hey and seit dona non Nes and sleet or Unde i Include or exclude the spectively OK inthe Report bor when fined and only Ben wih checo PH be delayed inthe Ta To male to more Bins become one singe efi a sone do highlight tt New hold down SHIFT Bey to select ational rows Right ick the rows and select Hat Key OK inthe pet Cam bon then finshed and the selec Bins wi be averaged together Gal Bire adjacent tr one another may selected for merging Orly the height and area for thee enki new merged Bn il Peak Table TM Rpt e dap nr eid tes ames are
99. ompan lire path ody proie comparison view T Column Hendinge select any or all available coun headings fr the table LB mach report it diy fom Longitudinal Report Actives the Longitudinal Report Options o mento Chimera end Help lon quick ference and description o abbreviations and stitial parametro used im a ka Comprehensive Research Report Single Done Report page La 1 Caper 2 Chimera Anal Single Done Report age 2 Compre reper fr ace suple gn ime pi den ear cpr ce amd ble The port baer os lemon hom rer mangement an he any ste to es he ects Pte me panes a lerne The ans each pe calor pray with nce oc D door nd cipem Reno cae qud conse merce som orm nal pa ese an ae st nd e men alles ur Ieee pmo bene te Checker doo coma act Te compres may be rine ely sve ag or pe imag Chapter 2 Chimera Chapter 2 Chimera Analysis Page Revs Table Print Individual Markers isis mad
100. on Program N inthe Fran Manager Grup window Pagan Monago Grup NOTE Changing the Pnyrm Cri default may ek mesadas ic Fido elit Complete window The nda Wa will ce eee Sofia CD Chapter Intl ChimerMarker 28 Launch Chimerrker by double the ChimerMarker desktop kun OR open the Start nen and to Soft Cera esr sat td Cert pe The Emule window wll appear Configure Network Client to configure the conte Lime 0 Configure Connection to License Server Manager the Neto Confort Box 3L Input Server Name or Serve IP Adres of the Linse Server anager sever Chek Configure and CimerMarker sare wil automatically open if connection ir papery enable and a Questions Al yor have any questions daring installation setup o program operation lese contac s at 04 2378540 GE GS DR ema tech supportatsftgenctics com May 2013 Chapter 2Chimeriem Analysis Chapter 2 Chimera Chapter 2 Chimerism Analysis Chapter Chimeriam Analysis Deme Mors and Functions ne and Esport Reni seien Ener Caper Chimera Analysis Overview Cierro alerted chimes ware ingles The stare can be o monto
101. ond ioe ample vil be highlighted in he Semis Lit e darker ar temas peak height a potion andthe itr calo line i e avra Mele spl tics that pin mg SSeS eher ange in Edt When tare W vam the nerf ef or range an die mi an la ae etg de Bound lo ta iii lee opine sc by de Major Ads Pa Uses eeu defined and hight information in the Panel le Reed hen Tart mus be ad y 1 gt 3 pus e rr alg withthe datum Bot hed or panel wh evenly pa alls Misc of Poel Aigo cee ofthe the ceie ea within ane 52 of rn only ere are ovr ad rn pe Saving a panel with signal information Fr optima atta distet pane hen sve vial ran SS ee pe and Sesh at ero at me to ove veric o ce Se tami tat mt AD pti analysers Vnd 30 2 Ber wou ane ved wi adder gal om ch pri andy vio sgl norman fr he er provides the program with ned o Shut tial e da Arm er ran euren je Panel Ones kas bee and saved wth eral information ican beset arth per pel TH panel har pal ination an no amt sd tulip ae ma projet
102. ore a t appears in the Size Caio Carte See Chapter Fragment Sing Standards Sample with higher scores wil appear t the top of he st Overlay Trace The Tre all samples in the Sample Lit The Marker burs appear above the a Bis appear wii I eectropleragaro the aad bio Tha srr the Hn inte by the vertical rey kar tn the only in The view an e changed by the Hae Made Other pons cade Mar sra Navigation tn the Diei Tra frame i similar to the navigation option the Main Ales window See her Main Analia Overview Marker Option Create Marker Hold down CTRL key and lice and drag peaks the Oros hashed box will appear ha bu amd icd Cae Maior The Crate Maver bo pert Ad parameters and click OK Maer Name Edit Maker to change ow the Marke wil ied i he Panel owen The pale range of the Marke is defined by the range of the hashed and i Vereor native nthe Mara for Nucleotide Repeat Chapter 6 Pond or Aue Dei ned om the peaks present in the ChimerMarker wil attempt to detect the Ranke of nude in eth reprat unito he allen and pace Pine appropiate hr Mena See thn optan names of in alle unt ia ir ad wil lace Beat poled interval Auto Binning Fan Rin Wid Check th
103. peak rom hight or ares in peak ap om the electopberogrm aie Enter commen nomenclature fo Ladder amples he dant mtt e nal Spal ees Upon m anal CniemcrMarker wl automatically cam the dato Henares or he Vio tur values and steely bel he ladder samples wil an and hc ampie leeren Hue ont inthe amp Fe Tr Default ie LADDER NOTE The adt alec the operation of the Salt nd Automat Adjust im e Ram Wizard Seg box Afer modifying he Ladder ente machte Rn Wizard and poced trough Data Pre Laer and Alc Poel tne ke ect Cul Ete commen Glen fo Posie Contemp in datu mat be in ll capa eters Upom Rest ara ChimerMsrker wil automatic the lena forth Partie Con eter ve and labe the Positivo Con samples itt a PC and play the eame tn green font inthe pl Fle Te Deal C estive and Negative Controls by Chapter Genoyping Main Analysts Overview Cm Eres common fr Negative Conta samples datan Upon int wil scan the date leone for the Nagai Conr oir van and neuem label the Negative Ctrl amples with an and display the sample ere sd ot nthe Sample Fle Te NOTE To implement change in the Monter gh click any ample
104. r funtion Virtual Panel Sica Pone from the Panel Lt and click Virtua Peli the Tele mena The Cot Virtual proces bo vel appear Click OK anda wil be adi t the Fe Lit eld VP Aline This newly Treated Panel ie an vercion of he origina panel nected in fe Pe Li Sig the anginal Panel tothe Ladder pea aves o an average Clio NOTE Wie reommended ta we Viral Pt only when mal to the Marker and Bin placement sare required Use Mar Pa on fr larger austen sport the Project Panel Exports the slec Panli the Lit as an XML le pedia dre comple Help Menu The mena contain a link ta Hot ir Click Keye and the Pre Lor to H box appear Toolbar Icons B ees is Aide ann ica ie er Ferment eves arl opened Pel which in Soi l id Save Change with Signal nfo iran which i wih the Pac NOTE A Pane mua be net ligne wth in the before Sao Cams wi Sal dnt ander for the tane Afi Raid and ie Pane Tere o gt Delete Current Delete whichever Panel Marker curry highligh Pe id is ever stow ye IB gt 233 rota ge tern ein th Oe Ve ys hh aby M e o Chapter P
105. r the atem lel he SE Clon Char overage ee pair Prin the standard deviation and he difference beturen the maximum and fase pair sine samples called fr ech LS peak ached a e abled peas poston Do state wl be cl for doable the begining or end fe Sce Standart Size Standard Trace The sc Sidor Trace othe selected Size Standard Enable Sizes are red dii Sy Fach ek nthe Ser ste ra reps noc Rs ur ream be Sample LS eit oh e ly mic gl ne li ee te tc erde let Sr Shaded inc The bse prt ac wah prem trample pot indicar located bee the The peaks nee fr a alin can be edid iie Sle Fame as decried lo Navigation nthe Sample 15 eame sito navigation options inthe Amis window See Chapter 4 Main Analysis Overview Editing Size Call Single eii a gen pen indicator to ale The angle Ua wil be Sele mle gen slo ld dow he CTRL bey and sick and dag irc te sed eniin gel green triangle peck lento ar hc op ofan unmarked peak in an Settee Removes green triangle peak from 15 and the peak will not conser in the Mar or calis ll Se calculation plated when Up Callan cect Chapier Fragment Sting Standard atthe pesk poston and seed Ail A green angle peak cir appear he To the pee tange hold CTRL hey and
106. ro Sapp ence ep e og Law Scr Aliis When the 3 wis acres the Wired Allee Eatin Sing willbe displayed inthe abe Hie Etre Sample Nene Thin fare nat ce Ale Ct Ker Se Print Report The Print gri plays and or Pk information far al or selected ples ina To acer the Pt Rt goto Pit ar OR ii the Fit Report con he Mu Andi window The wi appear Sc desired acing and dick Preview lo ew the Print Ropar ore printing er cic OK lo fei ping previewing report The rere mat uc foreach mpl i td on e ale por NOTE The Vir Pence Sette options wil act how the Print Reet plays ChimerMarker Print Report mom Caper Reports and Pong Report Content Options The tsi printing the une to chose the Samples tn print Doe and Comet pons Exch trrphergra wil eed with respective sample le iie ened Te Adam be provides ore Ses A Rt ane en Nerd Pit Tee har Osea Peine aby Ecler with he report Samples Al Sp Pit all he samples in the peo San ony tone sample es th
107. s including Genen 50 and LIZA iom Size Standard cos by elecing the Se Temple om non Ss dl Ser Chapters Fragment Sing Standard ln ali e ich mei ice be sil Standard Color the dye colar which contain the intemal ane standart Analysis Type The Ana option inactivated ChimerMarkr Run Wizard Data Process Procedure 5 The Dis witdew of Run Wizard appear he afore aee sg la e Dua Prom Icons and Functions Raw Data Analysis Auto Range frame The range in comers fes vil find the data ange I Range te not cece marly ente the and end eae cl the tet or analyte NOTE t automate sire cal fail to high uration dealt Runge and input the ri dits range Ei Cocina manual eet bleed peaks bert und or experiments with on cle analysts Ale for amd cie flow REL by eng an number gere an I bene Soot tine by ring ele ie pk This feature u any in cases where the data i extremely dificult o analyze and cannot erected vith Sos nto The ficare wll may surte dat pins by eig a simat fe peak ape bed Ban at of This function remove bce completely wl be aed ab 0 o
108. s option to enter the number of be pus on the right and et of he cee ol the Fits 105 clc sth Bn Width then the otal Bin ange wl Ene pa When the ar automatically lated with he ose ai ofthe Bin poston to ln uc pi Mico bse pl amis corded up tou who der alm Edit Marker Marker bar OR right ci the Marker br and elec Ei Maker Marler appear parameter and ck NOTE Te Ere bs cam ab be arme by ightlckng Marke name inthe Li nd seen Meier Mame the Maver to change bow the arise Rois Une the vale ito the iae the umber of lae ps re bere ec allein the Marker Bus BA tenen To move Marker leor ight hold down SHIFT key ad lec and dag the Maker ar To act te pair ange over which a Marker oct hold down SHIFT hey and the edge the Marker fr un a ended row then and den the Marte o reae decas ange Marke bot and ei Ei The bon appears Ad the Beulen ld values as rere ia Mater ned nl slight adjustment othe ight felt rg cc the Marker bar and slot Aja Mater Marker il move automaticaly fo align lowest pr Filtering Parameter Mis Hot ud Soe te minim RFU vale at which minare pea 5 the only peak ina mars The IPS dene er treni
109. ters inl Opens the Chanel box and allows the user to choose from ABI and Beckman Couler standard dye colors The user can also manually enter dye color and name The default channel color setup is ABI See Chapter 3 General Procedure Project Menu The Pret men tin options for how the data peces nd print Fan he Wird ud bia the proto eap ther to selec ar program cng mane The proces ion ca ls be acople by king be om i he liu Auto Run pr hierher wil proce data using e let ato ome or ofthe parameters require changing t improve analis Pet ROE pins change the rl scing and pices the sample for arly Chapter Genotyping Main Analysis Overview Add Samples to Project The can ad rl to a project that has already ern sized and analyz When the Ope Dat i b will appear Click Ad ta elec individual le project and lick OK The row data ile will be id and pem ih de tae ung te othr le retard added Pom the Spe Print Report Pint abs tie rin pr Stings x which lls the une ta define dla sting in the rs Report The sltware pert printing of the sample lectropherograms You can Choose all simples selected samples pint sampler along wi he lide i denied Sce Chapter 6 Reports and Pinoy Options A
110. tings cn in he Rpt Take The All Rt Sc t wil appe Sale eri oso ts Defeat ain oem c ee de ARA Sg Your options wil br and and will be recall the nex time sa er Soi Adler ac Sue Ded Sal Roo incide spn t or Sole Fee Sort Options Sot by Maker Si By hy menu ad fom yt mena to ort Ascending or Desig 1 Ascer chosen then Ie quay pea wil be ered to the top of table sending chose Bn the oer quay be plac ft tbe Thi option oy aval wih Marker Tale Count Rp Si Sort by Column et Cl ge menu an ewe fm he ur he tea cd incen Turon navale with Rad Sy Editing Peaks o pels firt lel single or double click the cell n the Tale then right liek see mem options or ich Ari Ta and Key DEL ell pk be flore iom the Ror Tate Ts pes given a quay wore it wil moive a Ci eo Undermine e Qual ranking te Pa gren Quality ranking right check ne peak cll and select Con Key Ernten The peak will be masked Pa geen Peak Information Chapter Genotyping Main Ani Overview doen CTRL key and click the peak cell of interest The Alb Inf box wll appear rona Information such as Sample Dye Sze Marker Allele
111. tora Pak and slot Et Allee The box appears Add ar change the value inthe All and or Slee Ral The Alle will blank Panel has been pple tothe date Check Conor De Alt toma give the peak Quay anco ie gen an allele im the or Pa Table and select Lii Comos The Comente bon Scc a comment fom ets Tone ot enter now comment in the Comes Click coment wi pee Cots eamm fe Tae Only greet Uy cud i emere Added cc 0 irl add nes othe comment Chapter Gentyping Main Analysts Overview pena win Show a record al a edi estore onthe The Se EA wind I any active when Managemen Attn te Ey ion I ec Boe er Management Report Table The nt window Raport Tale contains additional information about sample peaks See Chapter 7 Reports and Printing Navigation The er Tots inka to other frame tn the Mai Ale window Doubleclick on the desi lle ne tt Autom eg o meno tothe cll af and Hit Ener OR fo move i Stern cli zm In en Ih peak the Select by holding dne SHIFT key DR hold et onse button and dag over ese There by wich Report Tolle and ther eames in the Anio window are linked are canta pna tl Vis Presence t play Settings Ci the Report S
112. ty rank of Check yellow and Undermine d Sow Rejected Low Score Alleles When and the peaks with peak cores lo the Run Wizard Senge Alle Este Sor eject sting wil doployed in the ide Sample Names When data in Veta Ono sample same are mesi for sch nw of data the vample sciat wil Hi Sale selected shen the sample name will only a creas vl sd ma Repent hese Allee Lael inthe seco sel poston of maker when only detected nn mathe Oy active when the Peel ly option te sc t So le Names Weg None displayed in the Table by default egere of iate Great Select display Sc Halt and or Aro peak within he same coll Parr eara the stats ren A Name enabled when Verio Crit loco rl Sample names appear onthe lin rne and Markers appear the op tia Sample names appear in the far 68 column in sows with Makes acd wen Ale im ander of op Gems nt a al Allows spot sy word BRE cl af ede opor mon lao pa fap ot not mid hn lw op int dd Sport ltr When selecto displays only the peaks with Quality ranks of Clack ew and deed Los Sore Ades When see
113. uter Eos teme comen or bo a Server slot Register Offline Online Registration AL acie the Mecnun and Password on te Sof Goin CD 3 Ener your Accu anton and aldo tremo tn the The Rent Cole automatically generated by Regter Your software wil be regere automatica A confirmation e mail wil be sent to you once statin copie NOTE Some caracte can be misread 1f you get an errr trying to rst check for number 1 dl lover cae ee armer 4 and upper Lakh Citar and raga Registration Cic the Register The license menage displays the line registration procedure Ema the Uber ID Aroa and o ch ticking the oe er ih the ID this ID io the legten ID Chick to complete quce cick OK 8 Enter your Accu and information rom the Soi Geni CD ard ess Copy O ro norton ab wit die got Cardi and pote into the of an email Send emitted supporte ils ID wi be en o yos i tl within one E Copy and paite Regt frm the eal io iid amp ChimerMarkr and begin nays en Network licensing Option Installing License Server Manager and ChimerMarker Software The pon of Chimerklar
114. ze Cii eli oft ai Show Chan Table Toggles display show only the Toll the Talle and or jst the pud EZ al ir 2 e alle by samples by marker or by dye Term alight modifications to the samples without having acia Kan Ward Sting o change Rak Deen Tat Shi oak Marker Dropdonen Menu Wear den S Allows he selection sa marker o view Thin ix available air the samples have Event Log Displays cach lan sce or allure Magic Wizard SB Aen te Set You Praet Ronan or Ret dialog Report Table leans Thelen are cae die above t Ret at Chapter Genotyping Main Anal Overview Report Settings Report display Save Report hor Toi oa ce Bl tb deleted Text i Cites Cotman Allows unr ai which ko include encode Apr Tale Additional Analysis Options addition to the Main Ana widow there are ober options in which the sample dat can be ewe nae By aad Prol Compara Vine Browse By All Colors ice the Browse by Colors io in the Msi Analia widow tole evi and peak cis op in he Al Cr rer hcg samples i Color ns click topos mare in and Soe fom the

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