UNC Health Registry Data Source Documentation
Contents
1. iD Name MRNQ Blood Work Alt Contact Ref Phys 1c0 9 Ancillary Studies Patient Listing Identification Informed Consent HIPAA Interview Appointments i z S Patient Name CASPER GHOST Filename 210048827 pdf EE Filename 1626058547_pdf ES Backlog MRN 41742446 Timestamp 7 24 2012 8 50 49 AM Timestamp 7 24 2012 8 51 29 AM Calendar CDART ID 00000245874260 ss ee racking Sata Status ID 6692 First Name CASPER Ethnicity No Events Definition Tracking Consented esi Middle Initial Hispanic Latino Ancillary Studies Return New NEW Last Name GHOST Marital Status Single never married Consent Obtained Suffi Education Level Postgraduate or Release Notes e if professional degree Video Paper Form Only Maiden i Port Status N Date of Birth 07 16 1964 E Race 1 Oth Blood Draw Check Back Gender Female ans Baseline Interview Scheduled Primary English Race Other Thank You Letter Language ae First Contact 07 23 2012 Work for pay Yes Es Last MiForms 07 23 2012 Hours of work 40 or more per week Consenter Andrew Hjelt Date of Consent 07 23 2012 Contact Info Figure 3 Patient Summary Page Contains contact and demographic information and links to Informed Consent an HIPAA Documents Note Log Address1 000 NOWHERE WAY Home 000 000 0000 Timestamp 7 24 2012 8 48 07 AM Address2 Phone City HAUNT Work Phone State North Carolina Cell Phone 111 111 1111 Zip 00000 Email Best HomePhone Contact Edit Demographics Date of Contact 07 08 20 at Le Hea2. programming framework specifically designed to meet the needs of health research projects at the Cecil G Sheps Center at UNC Chapel Hill Sheps SIRS provides reusable modules for data collection management and tracking for a diverse set of studies registries and research coordinating units SIRS is specifically designed to provide a framework for programming that simplifies common programming tasks and allows customization while meeting applicable security requirements The SIRS framework is completely web based and open source utilizing MySQL Apache JavaScript and PHP The Sheps Integrated Research System offers many advantages to investigators e Security Data management expertise e Input and feedback from experienced SIRS programmers e Ability to incorporate designs from previous studies Continuity within projects but across projects over time e Faster into the field capability Lower cost e Availability of common components with tested and verified code e Thorough data auditing All system login procedures and data submissions e g from study staff or survey respondents through the Internet are encrypted via the Secure Sockets Layer SSL protocol to a secure central database at the Sheps Center User level permissions are based on user roles and are defined within the project system to limit each user s access to only those records they are authorized to see The central database for projects runs on a
3. schema modifications This database provides a data environment for major code changes which sometimes continue over a period of months Application code running against the development database will always be found in the HEAD branch of the code versioning system LIMS code development is done using the Eclipse software development tool With few exceptions aspects of the LIMS application Java source code SQL scripts database packages help documentation etc are maintained within Eclipse and all of these files are backed up in a code versioning system on bioinfostore unc edu There are two branches of code development HEAD and Branch_X where X represents the base version number of the latest or highest release At the time of writing this document the latest release is 11 e g Branch_11 is the current branch Before releasing a new version of the LIMS we conduct unit and integration testing During unit tests developers verify that the newly added code functions properly and solves reported bugs Integration testing is used to make sure the changes don t break existing functionality We have a series of general test cases that we run before releasing a new version The steps for deploying a new version are documented and stored in our group s internal directory We are implementing code reviews as a part of the deployment process Each release is tagged with a version number The code versioning system CVS maintains a history of
4. data from the Carolina Data Warehouse for Health CDW H is used at the beginning of enrollment to assign cancer specific questionnaires based on subject specific ICD 9 billing codes At approximately the same time that an individual visits the clinic the hospital tumor registrar begins to record information from a subject s medical records in order to fulfill state cancer reporting requirements This data is electronically stored using a software product called ERS Electronic Registry Systems Cincinnati OH As diagnostic tumor staging and course of treatment information become available this information is abstracted into software that can format state compliant reports The UNC Health Registry Study purchased an instance of the ERS medical record abstraction software in order to enable staff to view abstracted information on the subset of UNC Hospital patients who have consented to the Health Registry study and enter additional information on treatments received See Hand Abstraction for more information Finally the SAS UNC partnership is working to developing a health outcomes analysis tool based using a secure medical workspace concept This tool will link to UNC Healthcare data and enable researchers to discover analytic cohorts and run analyses in a secured environment CDW H Billing Codes Cancer Specific Questionnaire Assignment Cancer specific questionnaire assignment is driven by ICD 9 billing codes from UNC Hospitals b
5. not given the individual s final status will be set as Refused If the individual is interested but has not provided consent the status is set to Check Back which can be set to A brief intake questionnaire is completed during the consenting visit Basic demographic and contact information is obtained including name address date of birth gender and race Additionally marital status employment status and information about the referring physician are recorded To obtain the most up to date contact information for each subject this information is confirmed during telephone interviews Health Registry recruiters utilize computer tablets running MiForms software Mi Co Durham NC to record notes conduct the intake questionnaire and to process consent document signatures The tablets are connected to a secure wireless network and data is sent to a database and fileserver over an encrypted network connection Paper copies of all consent documents are used filed and back entered in the event of connectivity issues Section 3 Biospecimens Upon enrollment into the Health Registry a subject may provide biospecimens such as blood or tumor tissue On or after the participant s date of consent blood samples are drawn by a phlebotomist logged and collected by health registry staff and transported to the UNC Biospecimen Process Facility Blood samples are not collected for partipants who have a portacath installed Subjec
6. study requesting tissue for research After surgery is performed TPF staff then take custody of tissue and send it on to pathology for tissue analysis After the pathology lab has sampled the tissue any remainder is sent to the TPF for processing and banking The process of transporting a sample from the surgical suite to the sample s final banking normally takes an hour or less The TPF uses two interfaces to perform their work Scheduled surgical procedures are cross referenced with a list of consented subjects from the Health Registry study Matching surgery events are examined by study staff and placed on a target list Surgical appointment target lists are printed for TPF staff each morning The TPF LIMS system is used to record information on any samples collected Information included in the LIMS system includes specimen ID banking status and notes from the pathology report Section 4 Questionnaires Interview based data is collected during the enrollment process and subsequent baseline and follow up interviews Limited demographic data is collected at the time of enrollment onto tablet computers The tablets include data pre populated from the CDW H schedule The enrollment questionnaire provides an opportunity to collect and confirm basic data including name date of birth referring physician and contact information Once an individual is consented and enrolled into the UNC Health Registry subsequent questionnaire data is s
7. surgery Treating hospital code Treatment Treatment date Regional treatment modality Boost treatment modality Chemotherapy Hormone steroid therapy Immunotherapy Hematologic transplant endocrine procedure Other treatment Palliative procedure First or subsequent treatment Treating hospital code Recurrence Recurrence date Recurrence type Recurrence metastasis site Cancer status Patient status Date of last contact Follow up method Other Cancer status Patient status Date of last contact Follow up method Medical Record Hand Abstraction A set of fields is created in the ERS system to detail information on first course of treatment for a study subject These fields are entered by UNC HR CSC staff and appended to the ERS record Hand abstracted fields include a variable to signify whether first course of treatment was performed outside of the UNC cancer hospital In a portion of those cases documentation from outside clinics are scanned and received by the hospital tumor registrar and are available for enumeration of treatments Because first course of treatment will vary by cancer site and other individual factors the detail of each record will vary The availability of information for an individual s treatment will influence the completeness of these hand abstracted fields In many cases this additional abstraction will serve as a basis to validate treatment information fou
8. the code versions and a change history for each file in the repository From Eclipse you can view the change history for a given file and compare it to another version We document the changes in each release on our group wiki When new studies are added to LIMS the BSP lab managers meet with the principal investigator to discuss the sample processing workflow Then the BSP lab managers create protocols within the LIMS to standardize the procedures in each step of the workflow Additionally each lab technician receives periodic training to learn the lab s standard operating procedures as well as to maintain certifications pertinent to the work in the lab ie blood borne pathogen HIPAA and CITI training The LIMS has the functionality to maintain a listing of the certifications and validity dates for each user The LIMS also has the functionality to track project specific IRB certifications On a monthly basis the BSP lab managers generate check in reports from LIMS to verify the validity of sample collection and drop off dates In the LIMS project setup there is an option to send check in reports to study staff and lab managers on a weekly or daily basis There is a scheduled task that runs daily and emails the report to registered users This helps the study staff and lab validate what samples were sent and received each week The LIMS maintains an audit trail for each sample processed in the system Each audit record contains the technician
9. UNC Health Registry Data Source Documentation Table of Contents i Health Registry Data Collection Overview ssssssssssussususnnnununnunnnnnnnnnunnnnnnunnnnnnnnnnnnnnunnnnnnnnnnnn nnaman 2 Section 1 Tracking Study Events ss sssssssssususnnsununsunnnnnnunnunnnnnnunnnnunnnnnnnnnunnennnnnnnnnnnanannnnnnannnnnnnnn nnan an 3 S ction 2 Enrollment egeegenegeeeengeesgeeeetergerre eetrrerregeEue degen 7 Section 3 Biospecimens ssssssssssususnsnununnnununununnnnnnnnanununununnnnununnnnnanannnnnnnnnnnnananunnnnnn nnan nnannnanananannnn nannan nna 8 Biospecimen Process Facility Blood Samples ssssssusssssususnunnunnnnuunnununnunnnnunnunnunnunnnnunnunnnnnunnnnnnnunnnnnnnnnna 8 Tissue Procurement Facility TiSSte csssssssssssssessssssesesesesessneeessesesneeneesceseessesenauaeanseaeeeseeseesnaneneeseeeees 9 Section AITTelt ENT 10 Enrollment Questionnaire sicsicncsicascccacscscssescsecicsescescensccncsavev cccteestendveisecactnucscnds scecedccesckcescseresacvenavandescruesstests 10 Baseline Questionnaire CDART ssssssssssssssssssesssssssseseeeeeeeeeesesseseeeseeneneneaesenesesesenenauanavaeeeseneeeeeanseseeees 10 Cancer Specific Questionnaires CDART sssssssssssssssssssesesessssseseeseseeneenscesesseesesananansnaeeeeeeeeeenenaneneess 10 Annual Follow up GDART st siicisisccncsseesecsiiccecasssceseseescesecesectsetecectecescedacsusesceacestsoeasde svc ateczegecntenctestrazacusceess 11 Section 5 Medical Records Abstraction
10. compare treatment analysis survival incidence by site stage race etc Any data item in the software can be selected and used for reporting purposes The software contains a follow up module that allows the user to automatically schedule follow up lists and letters with patients ERS provides three days of initial on site training for new users as well as unlimited on line training A complete user manual is provided as well as a Video Library of training tutorials see online Resource list below The software is updated quarterly ERS notifies ISD or user via email that the software update and document detailing update changes is available and quarterly training webinars are provided that are awarded continuing education credits from the National Cancer Registrars Association NCRA ERS provides unlimited support to users for all registry and technical issues To be a CTR Certified Tumor Registrar one is required to have a minimum of a 2 year degree in a health related field and pass the national CTR test As of 2012 each registrar must be certified to perform abstraction There are internal edit checks within the software that come up if illogical information is entered such as female for prostate cancer zip code and county code matching errors as well as procedure and staging conflicts such as entering pathologic staging when the patient has had neoadjuvant therapy Required fields cannot be left blank Additionally about 10 of the case
11. demographic data tumor staging information treatment information and follow up information The following table contains the patient and cancer specific information for research purposes UNC Cancer Registry abstracted medical record variables Demographics Patient UNCHR ID First name Middle name Maiden name Last name Name prefix Name suffix Date of birth Current county Ethnicity Sex Race Tobacco history Family cancer history Alcohol history Diagnosis and Staging Sequence of the primary Site code Topography code Grade Histology Date of diagnosis Diagnosis zip code Comorbidities Site description Tumor size Tumor extension involvement Lymph node involvement Number of positive nodes Number of nodes examined Prostate tumor extension involvement Pathology report number Primary payer insurance Survival months since diagnosis Tumor record number General stage AJCC stage basis Pathologic T Pathologic N Pathologic M Pathology AJCC stage group Clinical T stage Clinical N stage Clinical AJCC stage group Clinical staged by TNM edition number Justification for clinical staging elements Justification for pathologic staging elements General stage text Type of source documents Diagnosis comments Operative findings Comments Surgery Surgery date Surgery type Scope of lymph node surgery Lymph node removed Surgery of regional sites First or subsequent
12. duce little or no tissue COLLECTED Tissue are not banked by TPF Sample sent to Surg Path Too Small Cases in which the PA can TISSUE NOT Not Enough see tumor but there is not COLLECTED Tissue enough tissue to be given to TPF Sample sent to Surg Path No Tumor Seen Cases in which there is TISSUE NOT No Tissue either no cancer diagnosis COLLECTED or the tumor cannot be No Sample Sent seen or palpated examples to Surg Path include abnormal mammograms benign disease cases and cases with only normal tissue are not banked by TPF Not Targetable Procedure Cases that will not produce TISSUE NOT tissue COLLECTED No Consent Cases that blank consent TISSUE NOT form is found in the chart COLLECTED recently updated Withdraw Cases that subject revoked TISSUE NOT the consent signed prior COLLECTED the surgery recently updated
13. ed date 20576377 STEPHEN WOOD 1010912012 10 05 2012 pmi Baseline QuestionnaireNeeddate 41764259 NEW STEVE WONDER 101812012 07 30 2012 gene Figure 7 Interviewer Appointment Queue The Hot List indicates interviews scheduled for the current day while the Queue lists individuals with an outstanding interview status Section 2 Enrollment Enrollment into the Health Registry occurs when an individual is deemed to be eligible based on clinic schedule data is approached by a health registry recruiter and informed consent is provided by the patient after learning about the risks and benefits of participation The enrollment process begins with a list of eligible individuals visiting cancer clinics at the NC Cancer Hospital each day Clinic schedule data is obtained from UNC Healthcare appointment scheduling systems through the Carolina Data Warehouse for Health CDW H and is prepared on a daily basis The clinic schedule report is populated with a list of individuals who screen to be eligible based on date of birth and residence which are available from the hospital appointment scheduling system Schedule reports are generated daily for Health Registry recruiters who use this information to approach patients around the time of their appointment Once approached an individual is informed about the purpose of the study shown a brief video summarizing the purpose and scope of the Health Registry and made aware of potential risks If consent is
14. es contain skip patterns that enable or disable further questions in a sequence depending on outcome Examples include information on rate of alcohol consumption dependent on answering a lifetime alcohol consumption in the alcohol information form as well as age based skips that are utilized in the historic height and weight form questions refer to height and weight at ages 40 50 and 60 Cancer Specific Questionnaires CDART A series of cancer specific questionnaires were developed to capture data on specific disease related points of interest and are included in baseline and follow up questionnaires administered to study participants Example areas include Breast Prostate Colorectal and Hepatobiliary cancers Assignment of cancer specific questionnaires occurs through an ICD 9 billing code based classification The results of this classification appear to interviewers in the Patient Tracking System A manual method of assignment is also specified in the event that the billing code feed fails to correctly classify an individual s disease Annual Follow up CDART After completion of the baseline questionnaire and applicable cancer specific questionnaire forms an annual follow up interview serves to capture changes in this information as well as any subsequent cancer specific information as the result of new diagnoses Section 5 Medical Records Abstraction Medical records information comes from multiple source systems Billing code
15. gistry s Certified Tumor Registrars use ERS as a data collection tool for manual electronic medical records abstraction required by state law Approximately 80 of the hospitals in North Carolina use ERS The ERS software tool for the UNC Cancer Registry is maintained and hosted by ERS and delivered as a virtualized desktop It is accessed via website and requires entry of credentials The UNC Health Registry Cancer Survivorship Cohort HR CRC purchased the ERS software tool to facilitate transfer of UNC Cancer Registry data directly to HR CRC via an ERS developed software patch The UNC HR CRC ERS will be managed by the Lineberger Data Warehouse and HR CSC IT team and ERS programming support group in conjunction with ISD to assure versioning comparability In addition to the required CoC data sets see Table 1 ERS makes available to the UNC HR CSC other data fields including those that can be customized to fit our specific needs The additional fields include expanded research and diagnostic fields clinical trial fields as well as user defined fields that can be created and maintained by the user The HR CRC staff will manually abstract these additional data fields see Table 2 from the electronic medical record to complement the data that is provided directly in ERS from the UNC Cancer Registry Coding manuals are online and maintained by the ERS software company ERS provides users with a very extensive reporting module for data analysis to
16. ility but may also result in long term storage within the facility Through a query interface sets of containers may be identified pulled and be further processed within the facility or be shipped to other facilities An audit trail is maintained on containers and content This trail records such things as when and who drops off containers to the BSP when the container was created as it moves through processing in the BSP as directed by the studies protocols which technician created it when and where it was stored when and where it was pulled from etc The system will track materials that are transferred to other facilities or PI collaborators as well The LIMS has the capability of accepting processing logs generated bythe Autopure LS DNA extracton robot and the Multiprobe II aliquoting robot These logs can be transferred to the LIMS at the completion of each run These logs are linked to the individual samples histories and can be referred to in the future for a variety of reasons The results from analysis done within the facility are recorded in the LIMS database This includes agarose gel analysis with image optical density with wave graph real time PCR and bioanalyzer results Analysis reports are available to both the facility staff and project staff through the Web interface The current inventory of a given project is also available as a report This shows the entire project history in terms of material that was checked i
17. illing systems and serves as an initial diagnosis until more specific information is acquired through pathologic data A rule based algorithm has been implemented to assign questionnaires based on ICD 9 billing codes Source data originates from CDW H billing code reports These reports contain medical record number MRN corresponding to each subject the patient s date of visit and ICD 9 code CDW H Data Sources Used by the Billing Code Questionnaire Assignment Algorithm Hospital Past Diagnosis Report All hospital side billing diagnoses since 4 2009 for patients who were seen at a UNC cancer clinic in the last 14 days P amp A Past Diagnosis Report All Physician Associates billing diagnoses since 4 2009 for patients who were seen at a UNC Cancer clinic in the last 14 days This data is used in conjunction with individual date of consent to select the billing records corresponding to the visit closest to the date of consent this is often but not always a visit on the subject s date of consent Billing codes from the selected date for each patient are matched against a questionnaire mapping table The mapping table identifies 220 specific ICD 9 codes Questionnaire assignments are displayed to interviewers in the Patient Tracking System so that the appropriate forms are selected during the time of interview Abstracted Medical Record Data Elements Medical Record information on consented patients consists of
18. lth Registry Time of Contact 06 29 PM Contact Reason Select phone call reason ng Sahel aposten J M status Definitions Edit Appointment Time 60 Baseline Questionnaire Scheduled Kathryn Allman 09 09 2012 202 GI Gastric Scheduled Kathryn Allman 08 09 2012 ethod of Contact Select Method of Contact el Sticky Note fist Show Final Tasks Call Comments Figure 4 Patient Contact Information and Call Log ee a Interview Appointments Status ID 6692 202 GIGastric Scheduled Backlog Tracking Consented Calendar Consent Obtained Task Explorer Informed Consent Saved HIPAA Saved Demographics Saved Video Paper Form Only Ancillary Studies Parking Voucher Saved Release Notes Consent Checkback Blood Draw Needed Checkback ICD 9 Completed Port Status N Blood Draw Check Back Barcode Link Blood Draw Red Tube Blood Draw Lavender Tube Baseline Interview Scheduled Thank You Letter First Contact Date 2012 07 23 00 00 00 Last Contact 2012 07 23 00 00 00 Date of Consent 2012 07 23 00 00 00 Note Log Timestamp 7 24 2012 8 48 07 AM Tracking Status Events Definition Figure 5 Participant Event Status Page Specific Information on Events and Cancer Specific Interview Home 41742446 GHOST CASPER Select Site Filter Version 1 1 17 fix3 Summary Scheduling Events Blood Work Alt Contact Ref Phys Ancillary Studies Patient Listing ICD 9 Codes Service Date Entry Ty
19. mirrored server system with automatic fail over features daily backups and transaction logs This system is physically located in a Tier II Data Center providing backup power sources climate control fire protection and 24x7 surveillance Audit logs are reviewed routinely to verify security measures are operational The servers are scanned weekly for vulnerabilities and are currently maintained at the highest level of vendor and CERT security recommendations Data are never shared outside the project unless authorized by the project leader User authentication is based on user passwords Password creation requirements are in place to guarantee strong passwords as defined by the CERT security recommendations The lead systems administrator is GIAC Security Essentials certified through May 2014 The UNC Sheps Center endeavors to preserve the privacy confidentiality and security of protected health information that may be part of health records or research datasets Protected Health Information PHI is handled according to appropriate Health Insurance Portability and Accountability Act of 1996 HIPAA Privacy and Security Regulations Sheps Center programmers and research staff who work with sensitive data are required to complete appropriate HIPAA training with periodic updates complete Sheps Center internal training comply with the UNC IT Security Policies and agree to the provisions of the Sheps Center s Rules of Behavior and Sanction P
20. nd in other sections of the ERS record Hormone immunotherapy and chemotherapy agents involved in the first course of therapy are noted in appropriate sections of the free fields A best estimate of treatment start date is recorded based on records This estimate is based on record of dispensing administration within visit notes Each agent s NSC NCI National Service Center number is recorded Often courses of treatment consist of regimens For a particular drug regimen multiple drugs may be administered each with it s own NSC number Each drug in the regimen is recorded Treatment completion status is recorded and corresponds to reasons for interruption or suspension of treatment Successful completion and unknown completion status are also recorded in this field UNC HR CRC abstracted medical records variables Chemo Agent 1 6 Chemo Agent NSC Start Date End date Number of Cycles Cycle duration Completion status Hormone Agent 1 Start date Hormone Agent NSC Immunotherapy Agent 1 Start date Immunotherapy Agent NSC Other Treatments Outside of UNC Binary Date of HR abstraction ERS free data fields modified to include those listed in this table Data will be abstracted for multiple treatments when necessary 1 2 etc Appendix 1 System Specific Information Patient Tracking System The Sheps Integrated Research System SIRS is a secure enterprise database and
21. nto the facility created by the facility and shipped from the facility No Personal Health Information PHI is maintained anywhere in the BSP systems When donor samples are checked into the facility the system allows for limiting the use of the samples based upon donor preferences i e allow genetic research destroy at project completion or restrict research to original project On a daily basis the Lineberger Data warehouse and Biospecimens Repository LDBR loads LIMS production data for reporting The data warehouse uses a read only account to connect to the LIMS database Storing LIMS data in the data warehouse allows the Health Registry staff to create reports for their samples These reports include information about the samples that have been checked in the sample inventory and nucleic acid analysis data Future TPF LIMS System Development of the future TPF LIMS System will be based on the BSP LIMS system and will be similar in scope development and implementation The Future TPF LIMS system will store information on collected tissue pathology status sample processing protocols and methods and banking and inventory information Electronic Registry System ERS Electronic Registry System ERS is a Cancer Registry software tool that includes the standard data set required by the Commission on Cancer CoC and meets the requirements of the North American Association of Central Cancer Registries NAACCR The UNC Cancer Re
22. ocol to measure aliquot and store child samples the sequence of which has been pre programmed into the LIMS All protocol steps are proscribed by the BSP LIMS system which provides an interface to input measurements record notes and to assign child sample container identification numbers Child samples are banked in freezers in two separate locations to provide a fail safe against equipment failure or physical breach allowing samples to be securely stored Requests to pull samples to perform additional protocols to mail to destroy are handled by communication between Health Registry staff and BSP technicians Once a technician is requested to handle a sample the detail of the request is logged Sample s are identified in the LIMS system pulled from storage and prepared according to the request A confirmation is sent back to Health Registry staff to notify that the request has been completed Tissue Procurement Facility Tissue The Tissue Procurement Facility is a group sponsored by UNC Lineberger Comprehensive Cancer Center and partner of the UNC Health Registry study A staff member from the Tissue Procurement Facility identifies targetable surgical procedures scheduled among consented patients that involve tumor tissue In the event that a research specimen can be saved the TPF banks the sample for future use TPF staff are present each morning and include documentation for surgical staff indicating patient consent in a
23. ogy hours Final status if collected on a Friday Surgery Stopped updated from Aborted Surgery was stopped this generally occurs when frozen sections from complex surgery cases show metastatic disease and the surgeon decides that the patient is better off without continuation of surgery NO TISSUE COLLECTED Completely Submitted to Path Cases in which tissue procurement is not allowed to take any tissue because all of the tissue is needed by pathology examples include lymphoma workups spleens submitted to hemepath medical kidneys uterus cases with complex atypical hyperplasia BRCA ovaries NO TISSUE COLLECTED Not Enough Tissue Sample sent to Surg Path Canceled Cases that were on the schedule but were either cancelled or moved to another date NO TISSUE COLLECTED Improper Consent Cases in which HIPAA was not signed the consent form was not signed dates were invalid or surgeon did not consent patient prior to surgery TISSUE NOT COLLECTED Infectious Case that are known tobe TISSUE NOT infected with HIV HBV COLLECTED HCV or TB are not banked by TPF Margins Wide local excision TISSUE NOT Not Enough WLE melanomas or COLLECTED Tissue breast re operative cases in which margins were Sample sent to previously positive are not Surg Path banked by TPF Biopsies Scope cases which TISSUE NOT Not Enough pro
24. olicy The Sheps Center strives to implement reasonable security controls guided by FISMA HIPAA and OMB Circular A 130 Appendix III Overview of BSP LIMS Quality Assurance Quality Control The Biospecimen Process Facility BSP Laboratory Information Management System LIMS uses Oracle as a data repository There are three databases hosted on two servers supported by Instructional amp Information Systems UNC School of Public Health Backups occur on both servers on a daily basis As the need arises snapshots of the production database are copied to the two additional databases staging and development In the unlikely event of data corruption on the production server the School of Public Health will be able to restore the system from the latest backup The purpose of the staging database is to provide a test environment for application code prior to its release into the laboratory environment With the use of custom SQL scripts it is possible to rapidly setup a mirror image of the production database This is useful for rapid response to LIMS maintenance issues Users can report bugs by sending an email to informaticshelp unc edu This will create a help request in the Lineberger Bioinformatics group ticket system Application code running against the staging database is always found in the highest numbered branch within the code versioning system The development database is also periodically mirrored from production but with possible
25. patient lookup scheduling of interviews and cancer specific questionnaire are key features of the system interface Additionally the system is used for generation of patient contact materials and is a key administrative interface and is a method for loading subject specific study consent and HIPAA documents The interface also provides staff with a way to record and verify a subject s vital death status Details on the specific use of the study tracking system are detailed in the Interviewer Protocol Document Screenshots Home Select Site Filter x z Scheduling Summary ist Mailing Summary ist Q Label Number Found Event Status n REcords Last Processed Patient Listing Backlog 821 Thank You Ready fur mail merge 8 7 5 2013 4 11 PM Interview Appointments ICD 9 Needed 733 Thank You Ready for labels 0 7 5 2013 4 15 PM Interview Scheduled Today il Backlog Interview Scheduled Today 2 Thank You Ready to mark as mailed 0 7 5 2013 4 54 PM Need Interview Scheduled 527 Calendar Ready to abstract 0 Task Explorer Tracking Status Search Events Definition A First Name Ancillary Studies Year of Birth a Release Notes Ancillary Study Summary List No records found Figure 2 PaTSy Home Screen This dashboard provides summary information on Interview Status Thank You letters and Ancillary Study Tasks Home 41742446 GHOST CASPER Select Site Filter e Version 1 1
26. pe z i 151 05 05 2012 Manual by Andrew Hjelt Interview Appointments 123 12 123 123 1 Kathryn Allman Baddog 12312 123 1231 Katyn Aliman e Calendar LCE Katyn Aliman jl Task Explorer 123 12 123 123 1 Kathryn Allman Une Sets 128 12 123 1231 Kathryn Allman Events Definition 123 12 123 123 1 Kathryn Allman el Ancillary Studies 123 12 123 123 1 Kathryn Allman Release Notes H a Figure 6 ICD 9 Entry Screen Cancer specific ICD 9 Codes trigger specific questionnaires Patient Listing Hot List Interview Appointments count 7 Calendar Baseline Questionnaire Scheduled GE SE 8912012 712372012 Za Kathyn Alin Baseline Questionnaire Scheduled wt 41847322 MANMOHAN LAKHANI Tracking Status ee ea a LAKHANI 40812012 912412012 Andrew Hie Events Definition GU Prostate Ancillary Studies Questionnaire Deel 19924188 RETURN ANDREW HJELT 1072972012 712312012 Andrew Hie Release Notes alee Baseline Questionnaire Scheduled Zen ouestonnaleSchediled 41876681 RETURN JANE DOE mom 111812012 Luis Serpa Baseline Questionnaire Scheduled Bee EE RETURN JOHN DOE mmm 111872012 Luis Serpa Baseline Questionnaire Scheduled 102712012 at 10 30 AM Nora 9242157 RETURN FRED ASTARE 3126 2013 111872012 Nora Christ Christopher Baseline Questionnaire Scheduled 01 10 2013 3 00 PM Caroline 41915752 NEW PENELOPE CRUZ mm 111512012 Caroline He Hempel Queue lt lt first lt prev next gt last gt gt Baseline QuestionnaireNe
27. read only WEB access provided to principle investigators and their staff The thick client tracks creation storage movement and discarding of containers vials and plates and the specifics of container contents material type volume concentration technician comments etc and is accessed only by BSP Facility staff All containers have a study context BSP staff has access to all studies but only specific PI staff as setup within the system can access information associated with their project via the WEB client LIMS users are required to login using their user id and password The passwords must be atleast 8 characters and must contain a number and a special character etc The LIMS will not allow users to re use their last two passwords Each user is assigned a role which defines what features are available to them In addition to roles PI staff members are associated with projects Staff members can log into the WEB client to view reports for samples in their projects Each container created by the system is assigned a BSP identifier that is unique in effect this is the facility asset identifier for that container sample Each container is labeled with the BSP identifier project donor identifiers type of contained material volume concentration if applicable date of creation and current storage location Containers may be pre assigned to a protocol path which eventually leads to the departure of the containers from the fac
28. s are identified by the UNC Cancer Registrar and are reabstracted to check for accuracy A quality control protocol involving reabstraction of a proportion of records to monitor data quality of additional HR CSC abstracted data elements will be implemented Additionally both UNC Cancer Registry and UNC HR CSC manually abstracted medical records data elements will be compared with planned EMR extractions for additionally quality assessment Resources 1 ERS Website http www ers can com 2 FORDS manual for 2013 http www facs org cancer coc fords fords manual 2013 pdf 3 7th edition AJCC staging manual http www cancerstaging org products ajccproducts html ISBN 978 0 387 88440 0 must purchase for 65 see website Appendix 2 System Specific Data Mappings CPR OR Tissue Collection Tracking The UNC Health Registry TPF Report contains tissue banking status information that is reported in coarser granularity based on several specific banking status categories This table explains the scenarios where tissues are not collected Status Explanation Tissue Status On TPF Report Banked Tissue was received and processed TISSUE COLLECTED After Hours Cases that run past 5 30pm Monday through Friday Cases are then targeted the next morning before they are put on formalin by pathology with the exception Friday cases after hours cases will be updated the next day Temporary status due to pathol
29. s name and a date and timestamp The audit trail tracks everything that is done to the sample from the time it was checked into the system to when it was discarded or shipped to another facility There are audits for sample check in storage assignment extractions open and closing of protocols discards plan changes etc The LIMS uses several different types of input fields on the interface depending on the type of data being entered For numeric values such as volume and concentration the LIMS displays an input field that allows the user to select a number from an ordered list There are up and down arrows next to the data field for stepping through the values in the sequence The LIMS uses checkboxes for yes and no fields For example to mark a sample as discarded the user can check the discard box Dropdown boxes are used to select values like units container types and project names Input fields for comments participant ids drop off courier etc are free text The LIMS provides data quality assurance and quality control by validating data entered into the system For example Optical Density measurements are taken on the Nanodrop and the DropSense The equipment saves the optical density measurements and concentrations to a file When that file is loaded into the LIMS the system will verify that the data is numeric If it s not the LIMS will display an error message to the user Ifa donor code format is defined in a project check in pro
30. s s ssssusesssununnusnnnnnunnunnennnunnnnnnnnnunnnnunnnnnnnnnunnennnnnnnnnnn annn 12 CDW H Billing Codes Cancer Specific Questionnaire Assignment csssssssseeeseeeeeeeeeeeeees 12 Abstracted Medical Record Data Elements cssssssssseceenenssssseessssssssnaensneneeseeeeeeseeseeeseseseeneaeneseseseees 13 Medical Record Hand ADstraction ssssssssssssssssssssssseeeseseeeeeeeeeeneeseseseseeneneasesesesesenenananauaeeeeeneneananansneess 15 Appendix 1 System Spe cific Information sssssssssussssusuusununnununnnnunnnnunnnnunnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnna 17 Patient Tracking Syste nis suerge 17 Overview of BSP LIMS Quality Assurance Quality Control ssssssssssuususnsnsunnnnunnunnnnunnnnnunnunnnnunnnnnnnne 18 BioSpecimen Facility Information Technologies LIMS ssssssssseessssssssesssseseeeseseeeeeeseeeneeeeseeees 20 Future TPF LIMS System vsiecciciciiasececettasciscacaccucstcas cdacnctadsascc cccancssasdsanscdacisatsdnusseeceasaauccdesscandsacsusecantdediucsieace 21 Electronic Registry System ERS s ssssssssssssssssssssssssseseseeeeeeeeseseeceseseeeeneneassenesesesenenauavavaeneeeeeeeanenaeeeeess 21 Appendix 2 System Specific Data Mappings s ssssssssssussneunuusunnnnunnnnunnnnunnnnunnnnnnnnnunnnnnnunnnnnnnnnnnnnna 23 CPR OR Tissue Collection Trackin gisius 23 Health Registry Data Collection Overview Clinic Appointment coe nformed Health Registry Rec nent HR introduced to patient Ee ae re Ss de
31. tails are entered into clinic scheduling system Baseline Tumor Tissue Medical Record Questionnaires Specimen Abstraction MRA Administered Collection Includes data from UNC Hospital 5 Tissue sample snap frozen Cancer Registry and manual General amp Cancer specific anapara embedded bstracti Annual Follow Up Questionnaires amp MRA Tracking System Flags patient Des after Pe record with study Initial Appointment R Status Figure 1 Stages of Data Collection Section 1 Tracking Study Events With a large and complex study ensuring a proscribed sequence of events requires operational systems that accurately and regularly record subject status so that the next event can be ascertained and future workloads be determined Subjects enrolled in the UNC Health Registry can take a variety of trajectories through study events depending on date of enrollment specific cancer type and length of follow up Tracking progress through study participation events requires a system for logging the sequence of events for each individual Upon a subject s enrollment into the study in the hospital Recruitment Schedule gt Successful Consent gt Enrollment they become eligible to receive the telephone based baseline questionnaire As cancer specific billing codes are generated during visits to UNC Hospitals the tracking system automatically matches codes that trigger cancer specific questionnaires Interviewer dashboard
32. tocol the LIMS will check to see that the entered text fits the desired format The user will not be able to check in the sample until he she enters a participant id in the correct format Each protocol can define certain fields as required When processing samples through a protocol technicians aren t able to complete a work set until they have entered data into all required fields These are justa couple examples of cases where the LIMS validates user input BioSpecimen Facility Information Technologies LIMS The BSP utilizes a state of the art specimen tracking system designed specifically to meet the immediate inventory style tracking needs of multiple health research projects It is referred to as the LIMS Laboratory Information Management System The LIMS has been designed to be flexible and extendible for future needs All samples entering the lab receive 2D bar code labels that allow us to follow any sample s progress through the specific procedures indicated by the appropriate study protocol Samples that enter the lab are given a BSP ID number further protecting a study subject s rights These labels also contain a human readable portion and additional study encoded ID information The BioSpecimen Processing Facility LIMS is Oracle based and maintained by the School of Public Health with security and backup The user interface developed and maintained by the School of Medicine is implemented as a Java thick client with limited
33. tored in CDART Carolina Data Acquisition and Reporting Tool a web based application that is well suited for computer assisted telephone interviewing CATI The baseline questionnaire consists of a common set of interview elements collected of all subjects shortly after consent Questionnaire elements cover a wide selection of topics including historic height and weight exposure to alcohol quality of life and access to healthcare Annual follow up consists of questionnaire forms administered on an annual basis Enrollment Questionnaire At the time of consent a brief enrollment questionnaire is administered to record basic demographic details including name date of birth gender race ethnicity language education status marital status referring physician information and contact details This questionnaire is administered by consenting staff in the clinic Questionnaire data is recorded on computer tablets with a secure wireless connection and is stored in a study maintained database Baseline Questionnaire CDART After enrollment into the study subjects complete a baseline questionnaire consisting of more than 20 constituent questionnaires measuring health symptoms quality of life and related variables These questionnaires have been validated in the literature and underwent testing and IRB approval The baseline interview lasts between 45 minutes to an hour and can be completed over multiple calls A few of the questionnair
34. ts may choose delay or refuse the blood draw procedure As a result the final blood draw status and number of approaches are recorded in the study database All blood draw events are logged by Health Registry recruitment staff using computer tablets running MiForms software Participants are assigned a unique barcode number used to track blood samples A recruitment staff member brings the patient to a phlebotomy suite for the blood draw and gives the phlebotomist barcoded red and lavender tube vials The time of blood collection is logged in MiForms and samples are temporarily refrigerated on site Within two hours of collection batches of refrigerated participant blood samples are transported and logged into the BSP for further processing aliquoting and banking Biospecimen Process Facility Blood Samples Once participant blood samples are taken following consent into the study they are sent to the UNC Biospecimen Process Facility BSP Each sample taken is collected in a tube with a serial number linked to the individual Samples are batched packed in a cooler and walked to the BSP laboratory by a Health Registry staff member a trip that lasting 5 to 10 minutes Once the samples are delivered to the BSP they are entered into the BSP laboratory information management system LIMS by the laboratory technician and Health Registry staff member Once blood samples are signed into the LIMS BSP staff are assigned new work and apply a prot
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