Home

User Guide 5.1 2013 Final

Contents

1. Accredited Medical Laborator Reference No 2034 Q The Christie MVEK NHS Foundation Trust Summary of Services Offered for Routine Cytogenetics and FISH Disease group Cytogenetics FISH Chronic Myeloid leukaemia v x BCR ABL1 at diagnosis Chronic myeloid leukaemia y v follow up Screen for Ph plus additional abnormalities including for Ph ve clones Acute myeloid leukaemia y To confirm specific abnormality at diagnosis found by cytogenetics or as indicated by morphology such as CBFB or RUNX1 RUNX1T1 del 5q del 7q and del 17p TP53 on failed specimens APL v at diagnosis Rapid FISH for PML RARA MDS y del 5q and del 7q on failed specimens ET v on request Vv BCR ABL1 PRV s XxX Myelofibrosis v X CMML v X Hypereosinophilia v FIP1L1 PDGFRA PDGFRB FGFR1 if indicated ITP X X Aplastic anaemia v X BMT patients sex mismatched Only if recipient cells is x X Y significant by FISH BMT patients sex matched v if abnormal at diagnosis v if abnormal at diagnosis All follow ups except CML v if abnormal at diagnosis v if abnormal at diagnosis Acute lymphoblastic leukaemia ALL panel BCR ABL1 MLL ETV6 RUNX1 paediatric TCF3 Hypodiploid and hyperdiploid panels if indicated CLL SLL X v TP53 and ATM only Lymphoma on staging bone marrow aspirate X on request if lymphocytosis X
2. 9 Oncology Cytogenetics at The Christie MVEK NHS Foundation Trust USER GUIDE v5 1 Amendments highlighted NHS Foundation Trust The Christie MUO Contents TMT IN eis cniesssctaiatan i anata stirs asic Seas A E A EEEa 3 Contact Details Main Departmental Contacts ccccccsseeeseeesseeeesneeeseseeeesseeeeseeea 4 Hours of Operation sassisk eiras erse e n aS ANE EEE EEE EEREN 4 Samples Sample types Specimen CONTAINETS ccccececeeesseeeeseeeeseeeeeeseeeeesseeeseeaees 5 Dispatch of SAMOS sci cei vsesesentsurenmduntetzaass REE E EEEE EEE E EENE 6 Request cards Specimen Acceptance POliCy ccccccccsseecessseesseeeessneeeeseeeesseeeeeeees 7 Req est card 8 ees es ca iiinn anne nas e a EEEa EEEa i iaia Ea 8 Policy for High Risk SAMPIES sciiiceccctacarsapssadaakeendeadaudersucalishsnndessseraalananianeetendecemsineds 9 Policy of Consent for WSSU Geis eicicasnenasiadadivenesnwinaatxan Screened riesnnedaetotntaciacageaheiuesiiondtse 10 Sample Prioritisation and Reporting TiMES cccssccssssceseeeessseeessneeeesseessseeeeeees 11 About Cytogenetics Techiiques ssssscccsssecsssecsessseccesscsecssecserssseesssetectsssressonesene 12 Telephone Enguiri S neisirsiire nii arte nr ier ire ae mer cnart ts a erern ten tne Meet at mee ar 13 Reporting Hard copy Reports Faxing Reports E mailing Reports ccccccee 13 Summary Of Services OMS i cciccicsicansacenccascinscrscduissresovenias
3. Chromosome analysis is used to monitor the initial response to treatment However more sensitive methods would be required such as RT PCR to monitor patients after cytogenetic remission is achieved Post treatment patients will be monitored for Ph positivity by conventional cytogenetics and the common abnormalities seen at transformation see below Ph negative cells are screened for common abnormalities found in Ph negative clones e Conventional cytogenetic analysis on peripheral blood to monitor remission is unlikely to be successful However peripheral blood neutrophils screened in post treatment samples by FISH is a suitable surrogate marker of bone marrow cytogenetic status e Full karyotype at possible relapse or transformation for t 9 22 and additional abnormalities e Bone marrow samples should be sent for cytogenetic studies if disease acceleration is suspected or if there is a rising level of BCR ABL1 transcripts by RT PCR Technical Cytogenetic analysis is performed on cultured cells from fresh bone marrow 20 cells will be fully analysed according to standard procedures and best practice guidelines Cells may contain cryptic abnormalities and minor clones not represented in the cultured cells which microscopic analysis may not detect Page 17 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 o The Christie VEK NHS Fo
4. analysis of cytogenetic data from patients treated on the Medical Research Council MRC UKALLII Eastern Cooperative Oncology Group ECOG 2993 trial Blood 2007 109 3189 3197 3 Moorman A V Ensor H M Richards S M et al 2010 The prognostic impact of chromosomal abnormalities in childhood B cell precursor acute lymphoblastic leukaemia Lancet Oncology 11 429 38 4 Fielding A et al UKALL14 trial protocol 5 Moorman AV et al Prognosis of children with acute lymphoblastic leukemia ALL and intrachromosomal amplification of chromosome 21 iamp21 Blood 2007 109 2327 2330 Page 28 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 NHS Foundation Trust Q The Christie MUO LYMPHOMA Chromosome translocations help to define disease subtypes the most common are the t 11 14 associated with mantle cell lymphoma t 14 18 with follicular lymphoma and t 8 14 with Burkitt lymphoma However these rearrangements are not specific to one disease and the profile of chromosome translocations needs to be interpreted alongside morphology and immunophenotype for accurate diagnosis Other translocations such as t 11 18 in MALT lymphoma and those involving the ALK gene at 2p23 in Anaplastic Large Cell Lymphoma can be useful diagnostically Furthermore t 14 18 IGH BCL2 t 8 14 IGH MYC 3q27 BCL6 17p TP53 deletion are informativ
5. monosomy 5 deletion of 5q 10 deletion of 20q 5 8 Y 5 and deletions of 17p 3 5 Some cytogenetic abnormalities in the context of cytopaenias of undetermined origin can be considered presumptive evidence of MDS in the absence of definitive morphologic features However none are specific to MDS and are found in AML and other myeloid neoplasms There are also no specific markers for MDS subgroups although isolated deletion of 5q with typical morphology defines a WHO subtype There are no specific abnormalities which would confirm transformation to acute leukaemia but a complex or evolving karyotype might be suggestive Some chromosome abnormalities indicate more aggressive disease and therefore have major prognostic value Karyotype is therefore included as a criterion in prognostic schemes together with blast cell proportion and number of cytopaenias e g International Prognostic Scoring System see Table below Cytogenetics is recommended in all cases where bone marrow examination is indicated Table Cytogenetic risk groups in IPSS for MDS Greenberg et al 2012 Very good prognosis Y del 11q Good prognosis Normal karyotype del 5q del 12p del 20q double including del 5q Intermediate prognosis del 7q 8 19 i 17q any other single or double independent clones Poor prognosis 7 inv 3 t 3q del 3q double including 7 del 7q Complex karyotype 3 abnormalities Very poor prognosis Complex
6. on request if lymphocytosis or if FISH abnormal on other tissue Lymphoma on lymph node y vY if indicated biopsy Lymphoma on paraffin N A vY if indicated embedded tissue Multiple Myeloma confirmed not MGUS vY on request IGH FGFR3 IGH MAF TP53 on CD138 selected cells Other genes on request Fanconi Anaemia v MECOM EVI1 FISH BM MECOM 7q FISH PB Page 14 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Accredited Medical Laboratory Reference No 2034 Version 5 1 Issued August 2013 NHS Foundation Trust Q The Christie LUO Summary of Services Offered for Routine Cytogenetics and FISH cont Disease group Cytogenetics FISH Breast carcinoma N A HER2 amplification status on paraffin embedded tissue Oesophagogastric carcinoma N A HER2 amplification status on paraffin embedded tissue Oligodendroglioma and other N A 1p amp 19q deletion status brain gliomas on paraffin embedded tissue Sarcoma N A Rearrangements of EWSR1 SS18 DDIT3 FUS FOXO1 COL1A1 PDGFB as indicated MDM2 amplification on paraffin embedded tissue Non Small Cell Lung Cancer N A ALK on paraffin embedded tissue Mesothelioma N A Homozygous deletion of CDKN2A p16 Melanoma N A In development please enquire Page 15 45 CPA eM EA Gre Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q
7. Accredited Medical Laboratory Reference No 2034 The Christie MVEK NHS Foundation Trust Summary of services and reporting times Test Target Reporting Time Calendar days FISH for 17p TP53 and 11q ATM deletions on 7 peripheral blood or bone marrow on all cases referred Cell culture and storage of bone marrow cells in case conventional cytogenetic analysis indicated at a later date FISH for t 11 14 IGH CCND1 in atypical cases by 7 days if indicated request indication Full FISH panel including 13q deletion and trisomy 12 Not routine By special request only as well as ATM and TP53 Conventional cytogenetic analysis Not routine Please enquire Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details References 1 Dohner H et al Genomic aberrations and survival in chronic lymphocytic leukemia N Engl J Med 2000 Dec 28 343 26 1910 6 2 Bloor A 2011 Guidelines for the management of CLL and PLL lt http www gmccn nhs uk hp Groups ClinicalSubGroups Haemato Oncology DocumentsInformation GMCCNClinicalGuidelines gt accessed
8. Duty Scientist may advise sending the sample the following day SAMPLES DETERIORATE RAPIDLY IN HOT WEATHER IF SAMPLES MUST TRAVEL A LONG DISTANCE IN HOT TEMPERATURES PLEASE CONSIDER SENDING THE SAMPLE IN A REFRIGERATED BOX Page 6 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide aii aea Version 5 1 Issued August 2013 ratory Reference No 2034 NHS Foundation Trust Q The Christie LUO Request Cards Please fill in all the patient demographics on the request card The reason for referral is important to determine which culture types need to be set up which tests to perform numbers of cells to analyse and sample prioritisation All relevant clinical and haematological information and likely diagnosis can be included If the patient is a participant of a research trial it is important to give details as certain trials can have specific requirements such as levels of analysis by cytogenetics and or FISH The department operates a Specimen Acceptance Policy LP PathGen Christie SpecAccept The following details are essential requirements for request cards and specimens Request Card Specimen bottle 1 Patients full name and date of 1 Patients full name with hospital birth number or NHS number and or 2 Hospital number and or NHS date of birth number 2 Specimen type and site of 3 NHS number for external specimen to distinguish multiple referrals specimens 4 Reason for referral clinical 3 High r
9. The Christie WEG NHS Foundation Trust SERVICE SPECIFICATIONS AND INDICATIONS 1 CONVENTIONAL CYTOGENETIC TESTING AND FISH FOR HAEMATOLOGICAL MALIGNANCIES 2 FISH ON PARAFFIN EMBEDDED TISSUE FOR SOLID TUMOURS Page 16 45 Oncology Cytogenetics User Guide MI CG Christie User Guide Version 5 1 Issued August 2013 a a ae ae oo Sz N d 33 i Z tw gu Pome 3b ee 3 o lt The Christie LVE NHS Foundation Trust CHRONIC MYELOID LEUKAEMIA CML CYTOGENETICS Introduction The characteristic genetic abnormality associated with CML is the translocation t 9 22 which gives rise to the Philadelphia Ph chromosome This distinguishes typical CML from Ph negative MPN and reactive marrows Additional clonal chromosome abnormalities may be present that could change prognosis Confirmation of Ph positivity is an absolute requirement for treatment with tyrosine kinase inhibitors TKIs such as imatinib A small number of cases have normal cytogenetics with a cryptic BCR ABL1 gene rearrangement or variant translocations involving other chromosomes Early cytogenetic response is the most important prognostic factor in CML Consensus strategies for monitoring CML recommend that cytogenetic studies should be part of the periodic review such as performing bone marrow cytogenetics every 3 months until complete cytogenetic remission is achieved Reviewing cytogenetics every 12 months to establish Ph status and to detect Ph negativ
10. This is to avoid unnecessary and labour intensive analytical work and helps the laboratory to process its large workload PET FISH Reporting time targets for paraffin embedded tissue sections referred for FISH have been agreed with local service users as follows HER2 on breast tumours 7 days for FISH total turnaround including IHC 10 days Lymphoma 7 days Sarcoma 7 days Brain tumours 14 days Certain diagnoses and special requests can be turned around more rapidly see above In the majority of cases PET FISH referrals are reported in a significantly shorter time Page 11 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laborator Reference No 2034 NHS Foundation Trust Q The Christie MUO Conventional Cytogenetic Analysis About Cytogenetics Cytogenetics is the microscopic study of chromosomes which can show abnormalities that represent genetic defects in the DNA that they contain These abnormalities can be numerical loss or gains of chromosomes or structural e g translocations inversions deletions Chromosome abnormalities can confirm a clonal disease and can often suggest a more specific diagnosis or a prognosis The abnormalities can be used to monitor remission and diagnose relapse transformation or secondary disease Increasingly cytogenetic abnormalities indicate specific and targeted treatment regimes Cytogenetic Techniques Conv
11. are used to guide treatment decisions in individual patients These are therefore recommended in clinical guidelines 17p TP53 deletions occur in less than 5 of newly diagnosed patients but increase in frequency with advancing disease TP53 gene deletion by FISH predicts a very poor prognosis and resistance to conventional chemotherapy but alternative treatments such as alemtuzumab may be effective Deletion of 11q ATM also show a poor prognosis in some studies and resistance to chemotherapy but there are some reports that the inclusion of rituximab in combination with FC chemotherapy may be beneficial FISH for TP53 and ATM deletions is valid in SLL although the test tissue must be involved FISH for deletion is possible on paraffin embedded tissue sections but the tissue must be heavily infiltrated with disease cells due to the high false positive background see below FISH studies are useful in differentiating mantle cell lymphoma from CLL However blanket FISH testing for IGH CCND1 for the exclusion of mantle cell lymphoma is not performed Please request IGH CCND1 FISH for t 11 14 in all cases of CLL with atypical morphology or a CLL immunophenotype score of 3 or less Referrals There is no evidence that treatment of early CLL improves overall outcome and so FISH testing is recommended only prior to first treatment Chromosomal abnormalities may develop during disease course and FISH analysis should also be consid
12. area marked e Archival material is accepted e Send all slides in a protective container together with the referral card and preferably your own Histopathology report All required fields on the Oncology Cytogenetics laboratory referral card are coloured in blue see page 5 e Please address all samples to Oncology Cytogenetics see page 2 Referral Minimum number of slides required plus one spare Burkitt lymphoma 4 1 Mantle cell lymphoma 1 1 Follicular lymphoma 1 1 MALT 1 1 Brain tumour glioma 2 1 HER2 5 1 ALK 1 1 Mesothelioma 1 1 Page 34 45 CPA Sa E Ba Version 5 1 Issued August 2013 Accredited Medical Laborator Reference No 2034 Q The Christie MUO NHS Foundation Trust HER2 in Breast Cancer HER2 FISH The laboratory provides an accurate and timely HER2 FISH service to determine HER2 status for the use of adjuvant trastuzumab Herceptin therapy in support of NICE guidance in early breast cancer In conjunction with the Breast Tumour Receptor section of the Histopathology department 496 HER2 FISH were performed in 2011 We follow current HER2 testing guidelines which recommend a two tier service utilising immunohistochemistry to detect HER2 protein expression with analysis of equivocal HER2 2 cases by FISH to detect gene amplification However there is provision in the current guidelines for the use of FISH as a stand alone frontline test Other probes such as TOP2A a
13. behalf of the European LeukemiaNet Blood 2010 Jan 21 115 3 453 74 4 Harrison CJ et al Cytogenetics of childhood acute myeloid leukaemia United Kingdom Medical Research Council treatment trials AML 10 and 12 JCO 2010 Jun 28 16 2674 2681 5 Breems DA et al Monosomal karyotype in acute myeloid leukemia a better indicator of poor prognosis than a complex karyotype J Clin Oncol 2008 26 29 4791 4797 6 British Committee for Standards in Haematology Guidelines on the management of acute myeloid leukaemia in adults Br J Haematol 2006 Nov 135 4 450 74 7 Dennis M et al Jan 2011 Greater Manchester and Cheshire Cancer Network Guidelines for the management of Acute Myeloid Leukaemia lt http www gmccn nhs uk hp Groups ClinicalsubGroups Haemato Oncology DocumentsInformation GMCCNClinicalGuidelines gt accessed July 2012 Page 20 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 The Christie MVEK NHS Foundation Trust MYELODYSPLASTIC SYNDROMES MDS CYTOGENETICS Introduction Approximately 50 of confirmed de novo MDS cases have cytogenetic abnormalities at diagnosis which helps to confirm the presence of a clonal disorder and aids the distinction between MDS and reactive causes of dysplasia Numerous abnormalities have been described the most common of which are trisomy 8 10 monosomy 7 deletion of 7q 10
14. is essential for optimal prognosis and most appropriate management Service offered e Rapid FISH diagnosis of MYC gene rearrangements IGH MYC dual fusion to detect the t 8 14 translocation MYC breakapart to detect variant MYC translocations IGK and IGL detect t 2 8 and t 8 22 immunoglobulin gene variants IGH BCL2 to detect the t 14 18 BCL6 to detect rearrangements of 3q27 Follicular lymphoma 70 80 of follicular lymphoma cases show the t 14 18 translocation or the rarer IGK and IGL variants t 2 18 and t 18 22 all involving rearrangement of BCL2 on 18q21 A small proportion of transforming follicular lymphomas will also have a BCL6 or MYC rearrangement Service offered e IGH BCL2 to detect the t 14 18 translocation e BCL2 breakapart BCL6 and MYC breakapart upon request only Page 38 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laborator Reference No 2034 The Christie MUO NHS Foundation Trust Mantle cell lymphoma 70 75 of mantle cell lymphomas have the t 11 14 translocation involving the CCND1 locus A MYC or BCL2 rearrangement is typically absent Service offered e IGH CCND1 dual fusion to detect the 11 14 translocation Other services offered e MALT1 breakapart to detect rearrangements of 18q21 seen in extranodal marginal zone B cell lymphoma of mucosa associated lymphoid tissue MALT lymphoma e ALK breakapart to detect r
15. solid tumour karyotyping service Paraffin Embedded Tissue for FISH on solid tissue such as lymphoma breast sarcoma or brain tumour patients Please send 3ym tissue sections see pg 34 Specimen Containers The laboratory will provide containers to regular referrers for bone marrow and blood collection These bottles contain heparinised tissue culture medium with antibiotics to facilitate the transport of the small amount of bone marrow and avoid desiccation An allocation of specimen bottles will be issued at the beginning of each week month based on the number of samples usually received More bottles can be sent upon request at any time by hospital transport or by post In emergency a blood tube containing lithium heparin can be used Use only heparinised containers Please DO NOT use other anticoagulants such as EDTA which is toxic to cells Fresh solid tissues should be placed in one of our Transport Bottles or other a sterile liquid such as culture medium Hank s balanced salt solution or saline The department is pleased to advise on the use of alternative specimen containers Page 5 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 The Christie MUO NHS Foundation Trust Dispatch of Samples All sample bottles should be fully labelled and placed in a plastic specimen bag with request card in separate pocket Sampl
16. than 2 00 Borderline cases with HER2 Ch 17 ratios between 1 80 and 2 20 will undergo appropriate additional work up Cases achieving a ratio of between 1 80 and 1 99 will be reported as Borderline not amplified and considered HER2 negative those with a ratio 2 00 to 2 20 will be reported Borderline amplified and considered HER2 positive to aid clinical management Breast Tumour Receptors The Breast Tumour Receptor laboratory is an expert specialised service which has been performing HER2 IHC and other breast receptors including ER PgR Ki67 EGFR and Androgen Receptor in paraffin embedded tissues since 1996 The HER2 FISH service was launched in 2001 to complement the HER2 IHC service Using validated and standardised methods the laboratory performed 1900 routine HER2 IHC tests and 496 HER2 FISH tests in 2011 These numbers are significantly in excess of the minimum requirement 250 IHC amp 100 FISH to support quality assured testing Page 35 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laborator Reference No 2034 The Christie MVEK NHS Foundation Trust HER2 IHC interpretation Any given case showing 30 of invasive cancer cells expressing complete strong membrane staining is regarded as HER2 positive Cases expressing moderate membrane staining in greater than 10 of invasive cells or cases with less than 30 invasive cells expressing strong co
17. July 2012 3 British Committee for Standards in Haematology 2012 Guidelines on the investigation and management of Chronic Lymphocytic Leukaemia lt http www bcshquidelines com 4_HAEMATOLOGY_GUIDELINES html gt accessed July 2012 4 Hallek M et al International Workshop on Chronic Lymphocytic Leukemia Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute Working Group 1996 guidelines Blood 2008 Jun 15 111 12 5446 56 5 Pettitt AR et al 2012 Alemtuzumab in combination with methylprednisolone is a highly effective induction regimen for patients with chronic lymphocytic leukemia and deletion of TP53 final results of the national cancer research institute CLL206 trial J Clin Oncol 2012 May 10 30 14 1647 55 6 Tsimberidou AM et al 2009 Chemoimmunotherapy may overcome the adverse prognostic significance of 11q deletion in previously untreated patients with chronic lymphocytic leukemia Cancer 2009 115 373 80 7 Hallek M 2010 International Group of Investigators German Chronic Lymphocytic Leukaemia Study Group Addition of rituximab to fludarabine and cyclophosphamide in patients with chronic lymphocytic leukaemia a randomised open label phase 3 trial Lancet 2010 Oct 2 376 9747 1164 74 8 British Committee for Standards in Haematology 2010 Best Practice in Lymphoma Diagnosis and Reporting l
18. KNEQAS The comprehensive cytogenetics service is provided by a highly skilled team of dedicated scientists and technologists who offer a timely efficient and cost effective analytical and genetic advisory service to clinicians to aid the diagnosis and monitoring of leukaemia and solid tumours All relevant staff are state registered and clinical scientists are formally trained in Clinical Cytogenetics and Molecular Cytogenetics We are a founder member of the UK Cancer Cytogenetics Group UKCCG Page 3 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laborator Reference No 2034 Q Contact Details Address General Enquiries FAX The Christie VEK NHS Foundation Trust Oncology Cytogenetics Pathology Department The Christie NHS Foundation Trust Wilmslow Road Withington Manchester M20 4BX 0161 446 3165 0161 446 3051 Main Departmental Contacts Consultant Clinical Cytogeneticist Principal Cytogeneticists Principal Clinical Scientist in Breast Tumour Receptors Clinical Cytogeneticists Lead Cytogenetic Technologist Secretary Hours of Operation Monday to Friday Weekends Bank Holidays Page 4 45 Nicholas Telford Tel 0161 446 3163 nick telford christie nhs uk Mike Green Tel 0161 446 8608 mike green christie nhs uk Clare Hodgson Tel 0161 446 8607 clare hodgson christie nhs uk Angela Cramer Tel 0161 446 3211 angela cra
19. Tumours HER2 Status Overall Frequency Negative 27 4 1 27 2 19 3 3 5 2 Page 36 45 CPA A P bein e Accredited Medical Laboratory Reference No 2034 Version 5 1 Issued August 2013 o The Christie MVEK NHS Foundation Trust For the period Jan 2011 Jun 2012 Total samples 2 or 2 3 demonstrating HER2 FISH Amplification 27 Total samples HER2 Positive i e HER2 3 amp HER2 FISH Positive 12 Please note that this figure is a reflection of all samples received by The Christie laboratory as well as those from external HER2 testing centres It is not therefore a reflection of the current rate of HER2 2 equivocal cases in the region Turnaround Times Turnaround times for HER2 IHC and FISH are good the limiting factor in producing optimal turnaround efficiency from biopsy to authorised report is dependent on the time taken for the sample to reach the laboratory from the requestor Turnaround times are assessed as time of receipt in the laboratory to release of report for HER2 IHC amp HER2 FISH During 2011 the average monthly turnaround time for HER2 by IHC was 3 3 days Average turnaround time for HER2 FISH was 5 3 days Providing the sample is received by the laboratory in a timely manner service users can expect to receive their results from biopsy within one week for IHC and two weeks for FISH ensuring results are available for MDT meetings References 1 National Institute f
20. WHO Classification of tumours of haematopoietic and lymphoid tissues World Health Organization Classification of Tumours Lyon IARC 2 Greenberg PL et al Revised international prognostic scoring system for myelodysplastic syndromes Blood 2012 Sep 20 120 12 2454 65 3 Bowen D Culligan D Jowitt S Kelsey S Mufti G Oscier D Parker J UK MDS Guidelines Group Guidelines for the diagnosis and therapy of adult myelodysplastic syndromes Br J Haematol 2003 Jan 120 2 187 200 4 Dennis M 2010 Greater Manchester and Cheshire Cancer Network Guidelines for the diagnosis and treatment of Myelodysplastic Syndromes lt http www gmccn nhs uk hp Groups ClinicalsubGroups Haemato Oncology DocumentsInformation GMCCNClinicalGuidelines gt accessed July 2012 5 Ades L et al 2009 Efficacy and safety of lenalidomide in intermediate 2 or high risk myelodysplastic syndromes with 5q deletion results of a phase 2 study Blood 113 17 3947 3952 6 Fenaux P et al 2009 Efficacy of azacitidine compared with that of conventional care regimens in the treatment of higher risk myelodysplastic syndromes a randomised open label phase III study Lancet Oncol 10 3 223 232 Page 22 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 o The Christie LVE NHS Foundation Trust APLASTIC ANAEMIA AA CYTOGENETICS Up to 15 of cases of aplas
21. al service which provides genetic testing to aid diagnosis of leukaemia and other tumours mainly to hospitals in Greater Manchester and the North West of England Malignant diseases are often classified by their genetic abnormalities and certain cytogenetic tests are essential for the optimal diagnosis and treatment stratification of cancer patients Increasingly cancer drugs are being developed that target specific genetic lesions which therefore require a predictive molecular test Handling approximately 5 000 referrals per year we are one of the largest specialist cancer genetics units in the UK The department is the nominated service for leukaemia cytogenetics testing for two local Cancer Networks and is part of the GMC Haematological Malignancy Diagnostics service Working closely with the specialist Histopathology and Breast Tumour Receptor sections of Pathology we provide FISH testing for the diagnosis of various solid tumours and are continually developing assays to expand the diagnostic FISH service The laboratory supports The Christie and other local multidisciplinary team meetings and provides specialised testing for clinical trials The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 whose standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes U
22. and tissue biopsies appear acceptable For this test it is important that we are provided with information regarding the tumour type an H amp E slide marked with the area of interest for analysis and if possible with an informative IHC slide e g calretinin to help guide our analysis to the relevant areas The proportion of cells considered positive by the laboratory for reporting a homozygous deletion is 220 Hemizygous deletion loss of single copy of CDKN2A or apparent monosomy for chromosome 9 loss of CDKN2A and one control signal are not sufficiently sensitive to distinguish malignant tumours and will not be reported References Takeda et al Pathology International 2010 60 395 399 Chung CT et al J Clin Pathol 2010 63 7 630 4 Page 43 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 NHS Foundation Trust Q The Christie LUO Appendix The Christie The Christie NHS Foundation Trust is the largest single site cancer treatment centre of its kind in Europe and is an international leader in cancer research and development The hospital is based in Manchester and as it is a specialist centre patients are referred to The Christie from all over the North West and beyond The Christie covers a population of 3 5 million Over its hundred year history The Christie has pioneered numerous developments in cancer diagnosis and th
23. ay not detect Sample requirements Bone marrow aspirate specimens should be collected fresh into the supplied transport bottles or alternatively into other lithium heparin containing tubes Samples should be sent to the laboratory as soon as possible preferably on the day of collection Peripheral blood specimens from typical MPN cases may be useful if immature cells are present A fresh bone marrow trephine specimen is an option if the marrow is fibrotic or otherwise difficult to aspirate Page 25 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 The Christie A F NHS Foundation Trust Summary of services and reporting times Test Target Reporting Time Calendar days Cytogenetic analysis karyotype 21 FISH 21 Cytogenetic analysis of MPN 14 transforming to AML Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details References 1 Gangat N et al Cytogenetic studies at diagnosis in polycythemia vera clinical and JAK2V617F allele burden correla
24. between aplastic anemia and hypocellular myelodysplastic syndromes Blood 2011 Jun 23 117 25 6876 84 Page 23 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 The Christie MVEK NHS Foundation Trust MYELOPROLIFERATIVE NEOPLASMS MPN are a heterogeneous group of disorders including classical MPN PRV ET and IMF and a number of other entities characterised by proliferation of mature cells of myeloid lineage By definition the distinction of MPN from CML requires exclusion of t 9 22 BCR ABL1 Ideally MPN patient pathways should include molecular exclusion of JAK2 V617F for PV ET and PMF before referral for cytogenetic analysis Polycythaemia Rubra Vera PRV Cytogenetic abnormalities are found in 10 20 of patients overall with PRV infrequently at diagnosis but increasing in frequency with disease course The abnormalities are general myeloid markers including trisomy for chromosomes 8 and 9 del 20q del 13q and 1q gain Generally the abnormalities have no apparent adverse affect and trisomy 8 and 9 are known to persist in PRV for many years without disease progression However an abnormal karyotype as a marker of clonality is a major diagnostic criterion and cytogenetics should be performed where absolute erythropoiesis is confirmed in the absence of JAK2 V617F mutation Patients who progress to myelofibrosis o
25. c disease entity including eosinophilia see below Distinction between CMML and atypical chronic myeloid leukaemia may be difficult and BCR ABL1 FISH will be performed on request A new CMML specific prognostic scoring system CPSS includes cytogenetic risk for stratification and identifies trisomy 8 abnormalities of chromosome 7 and complex karyotype gt 3 chromosomal abnormalities as high risk Hypereosinophilia Rare chromosomal translocations have been described in eosinophilic MPD that define a WHO class Myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA PDGFRB and FGFR1 that are important because of their apparent clinical utility diseases with PDGFRA or PDGFRB rearrangements are reported to respond to imatinib The rare FIP1L1 PDGFRA gene fusion results from an interstitial deletion at chromosome band 4q12 and cannot be detected by routine cytogenetics and must be tested by FISH The related t 5 12 translocation or variants involving the PDGFRB gene may be detected by routine cytogenetics but would also require confirmation by FISH before treatment Other rearrangements associated with eosinophilia are detected such as FGFR1 at 8p11 Diagnosis of HES requires absence of BCR ABL1 this is also examined by cytogenetics but can be requested by FISH in cases of high eosinophilia Cytogenetics should be performed to support diagnosis of this disease only after reactive cases and a number of other diseases associa
26. complexity Summary of services and reporting times Test Target Reporting Time Calendar days Rapid MYC FISH at diagnosis of Burkitt 3 working days Cytogenetic analysis karyotype and 7 subsequent FISH in Burkitt Cytogenetic analysis and or FISH for other 21 lymphoma subtypes Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details Page 29 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 o The Christie MVEK NHS Foundation Trust CHRONIC LYMPHOCYTIC LEUKAEMIA CLL SMALL LYMPHOCYTIC LYMPHOMA Introduction Cytogenetic abnormalities can be found in the majority of patients with CLL although at this time most do not provide useful diagnostic information FISH identifies genomic abnormalities in approximately 80 of newly diagnosed cases including trisomy 12 and deletions of 11q 13q and 17p which have been shown to have prognostic significance However only 11q ATM gene and 17p TP53 gene deletions are associated with shortened survival and
27. d be collected fresh into the supplied transport bottles or alternatively into other lithium heparin containing tubes Samples should be sent to the laboratory as soon as possible preferably on the day of collection Peripheral blood specimens with disease cell involvement are suitable specimens for diagnosis Summary of services and reporting times Test Target Reporting Time Calendar days Rapid FISH at diagnosis 3 working days Cytogenetic analysis karyotype 7 Subsequent FISH prognostic markers 14 Cytogenetic analysis and or FISH post 21 treatment Cytogenetic analysis and or FISH at relapse 14 or transformation Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details References 1 Swerdlow S H E Campo N L Harris E S Jaffe S A Pilieri H Stein J Thiele W Vardiman Eds 2008 WHO Classification of tumours of haematopoietic and lymphoid tissues World Health Organization Classification of Tumours Lyon IARC 2 Moorman AV et al Karyotype is an independent prognostic factor in adult acute lymphoblastic leukemia ALL
28. e clones is also an option Additional clonal chromosome abnormalities in the Ph negative cell line are a recognised phenomenon in a significant proportion of CML patients treated with TKI The majority of these patients are asymptomatic but a small number develop MDS with monosomy 7 and trisomy 8 appearing to confer a higher risk 80 of cases at transformation to acute leukaemia show clonal evolution with recognised additional chromosomal changes Full cytogenetic analysis should always be performed if there is a change in clinical or morphological status there is a rise in BCR ABL1 transcripts or MDS is suspected 14 Referrals e A full karyotype at diagnosis to detect t 9 22 and any additional cytogenetic abnormalities Bone marrow cytogenetics is essential at diagnosis on a pre treatment specimen to demonstrate the translocation t 9 22 Diagnostic samples will be treated urgently and a result will be available within 7 days e FISH at diagnosis to detect BCR ABL1 gene rearrangement FISH is performed on all cases at diagnosis for rapid confirmation of BCR ABL1 status and to establish a signal pattern for future monitoring FISH is also used to detect the BCR ABL1 gene rearrangement in cases with normal cytogenetics and cryptic BCR ABL1 in cases with variant translocations involving other chromosomes and in the small number of cases that fail to grow in culture e Post treatment bone marrows screened for Ph by cytogenetics and FISH
29. e pg 27 and is accessed by referral of cases for specialist review or opinion by the Histopathology department at the Christie Cases referred directly for FISH are accepted Please also see Oncology Cytogenetics User Guide pg 29 for referrals of fresh samples for lymphoma diagnosis Burkitt lymphoma The t 8 14 translocation involving rearrangement of the MYC gene with IGH is observed in 90 of Burkitt lymphoma with the IGK and IGL variants t 2 8 and t 8 22 accounting for the remainder Confirmation of one of these translocations such as by FISH with IGH MYC and MYC gene probes is considered essential for an accurate diagnosis Morphologically atypical Burkitt lymphoma cases are generally also associated with a rearrangement of the MYC gene as are a small proportion of high grade follicular lymphomas and diffuse large B cell lymphoma However the distinction between Burkitt and DLBCL is critical because these two types of lymphoma require different treatments relatively low dose chemotherapy regimens are typically used to treat DLBCL but they are inadequate for Burkitt lymphoma which is highly sensitive to intensive chemotherapy regimens All Burkitt referrals will also be tested with IGH BCL2 and BCL6 probes to aid this distinction Burkitt is associated with simple karyotypes if a full cytogenetic result is available and absence of t 14 18 and BCL6 gene rearrangements Further rapid diagnosis of this highly proliferative tumour
30. e prognostic markers in certain situations and predict progression to high grade disease FISH is available for all of the above abnormalities and is the test of choice as mature lymphocytic cells can be difficult to grow in culture FISH on paraffin embedded tissue sections is usually the most practical as fresh tissue is not usually available see FISH ON PARAFFIN EMBEDDED TISSUE FOR SOLID TUMOURS LYMPHOMA page 44 Cytogenetics can be performed on lymph nodes providing fresh material is sent in tissue culture medium to the Cytogenetics Laboratory as soon as possible Alternatively peripheral blood or bone marrow can be used as test material if these are involved However the limited number of cells which can be fully analysed by routine cytogenetic analysis makes this test of little value in staging Bone marrow infiltration should be confirmed by other methods and significant involvement should be confirmed before cytogenetic analysis is performed Services Offered e FISH on paraffin embedded tissue sections see page 44 e FISH or full karyotype on fresh primary tissue e FISH or full karyotype on bone marrow or blood only if involved lymphocytosis present or if FISH abnormal on other tissue e In Burkitt Lymphoma rapid FISH for MYC and IGH MYC followed by FISH for BCL6 and IGH BCL2 to aid the differential diagnosis of BL from DLBCL Full karyotype on bone marrow or blood if involved to examine additional abnormality and karyotype
31. earrangements of 2p23 including the t 2 5 translocation associated with anaplastic large cell lymphoma Page 39 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 o The Christie MVEK NHS Foundation Trust Brain tumour gliomas Co deletion of 1p and 19q has been shown to be a statistically significant predictor of improved overall survival and chemosensitivity in patients with oligodendroglioma and anaplastic oligodendroglioma Furthermore there is a strong association between 1p 19q co deletion and the pure oligodendroglial phenotype although this genetic alteration can be seen more rarely in other glioma types We offer a FISH screen to establish 1p 19q deletion status on patients with oligodendroglioma and oligoastrocytic tumours EGFR amplification in higher grade tumours can be provided upon request Oncology Cytogenetics were one of the first participants in the pilot EQA for these tests in neurological tumours in 2012 References 1 Fallon KB Palmer CA Roth KA Nabors LB Wang W Carpenter M Banerjee R Forsyth P Rich K Perry A Prognostic value of 1p 19q 9p 10q and EGFR FISH analyses in recurrent oligodendrogliomas J Neuropathol Exp Neurol 2004 Apr 63 4 314 22 2 Smith JS Perry A Borell TJ Lee HK O Fallon J Hosek SM Kimmel D Yates A Burger PC Scheithauer BW Jenkins RB Alterations of chromosome arms ip a
32. entional cytogenetic analysis relies on the culture of cells to produce metaphase chromosomes where individual chromosomes can be visualised Tissue therefore needs to be as fresh as possible with viable disease cells Cells are processed and stained using banding techniques to produce a karyotype Fluorescence in situ hybridisation FISH uses fluorescently labelled gene probes to detect specific gene sequences on the microscope slide This can be used to confirm specific genetic abnormalities at the molecular level FISH can be used with metaphase chromosomes but is also applicable to interphase cells and so cell culture is not always necessary Different strategies are possible with multiple fluorochromes which can be used in conjunction with other fluorescent labelling techniques Page 12 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q The Christie LUO NHS Foundation Trust Telephone Enquiries Telephone enquiries are welcome Cytogenetics staff will be pleased to accept requests to process samples if required urgently to determine treatment or by specific appointments and will make every effort to make results available Reporting Hard copy Reports Signed hard copy reports will be sent to the referring consultant by first class mail Reports can be addressed to other designated persons if requested to do so in writi
33. erapy It works in close partnership with many organisations such as other NHS Trusts Manchester Universities Cancer Research UK and the Paterson Institute for Cancer Research Greater Manchester and Cheshire Haematology Malignancy Diagnostics Greater Manchester and Cheshire Haematology Malignancy Diagnostics GMC HMD service formally opened in December 2007 This will be a comprehensive and coordinated service jointly provided by The Christie and Manchester Royal Infirmary MRI and will include an integrated molecular diagnostic service for leukaemia and lymphoma Routine cytogenetics and FISH based molecular cytogenetic tests will be provided by the Oncology Cytogenetics service and will be further developed as required The GMC HMD service development will allow compliance with national strategy as expressed in the National Institute for Clinical Excellence NICE Jmproving Outcomes Guidance for Haematological Cancers and has been designed to meet the needs in this regard of the Greater Manchester and Cheshire Cancer Network and has been planned with the Greater Manchester Pathology Network Phase 1 of HMD provides enhanced lymphoma diagnosis on paraffin embedded tissue including central lymphoma morphology review and fluorescence in situ hybridisation FISH for diagnostic translocations at The Christie and B and T cell clonality studies by RT PCR at MRI The lead Histopathologist for the service collates an integrated report with overall interp
34. ered prior to subsequent treatments FISH tests are not suitable for monitoring remission Referred samples must be from involved tissue with significant lymphocytosis Peripheral blood is suitable test material in most cases CLL patients suspected of secondary myeloid disease need to be highlighted as they will be handled differently Technical FISH for TP53 and ATM deletions is a standardised procedure and the test of choice FISH for trisomy 12 and 6q and 13q deletions are available on request Cell culture of mature lymphocytes in CLL is unreliable and karyotyping is therefore difficult Full karyotyping is not routinely performed but is available by special advance request FISH for deletion has a high false positive background and levels of less than 10 for TP53 deletion and less than 5 for ATM deletion are not considered significant and will not be reported Levels within 5 above these cut offs will be considered borderline and reported suggesting a need to confirm the result in a later sample e g ATM 5 10 and TP53 10 15 Sample requirements Bone marrow aspirate or peripheral blood specimens should be collected fresh into the supplied transport bottles or alternatively into other lithium heparin containing tubes Samples should be sent to the laboratory as soon as possible preferably on the day of collection MI CG Christie User Guide Version 5 1 Issued August 2013 Page 30 45 CPA Oncology Cytogenetics User Guide P
35. es should be packed in sufficient absorbent packing material to soak up the entire contents in the event of leakage and placed in a cardboard sample box or other recommended receptacle Samples sent through the post taxi or other courier service should comply with Packaging Instruction 650 and regulation UN3373 Any packaging should bear the UN3373 diamond mark and labelled Biological Substance Category B in letters at least 6mm high see below BIOLOGICAL SUBSTANCE CATEGORY B For more information go to www hse gov uk aboutus meetings committees acdp 050208 acdp88p6 pdf Fresh samples should be sent to the laboratory as soon as possible preferably on the day of collection Samples not being sent immediately should be refrigerated overnight at 4 C and sent at the earliest opportunity the following day First class post is usually acceptable At times it may be necessary to send specimens to the laboratory by taxi to avoid delays especially approaching weekends and bank holidays It is advisable that all Friday samples arrive on the day of collection to ensure that the samples are set up in culture before the weekend Myeloma samples need to arrive before 2pm to allow time for cell separation We cannot receive High Risk samples on a Friday see page 9 Please send samples at the earliest opportunity It is advisable to telephone about any samples that could arrive at the laboratory late in the day or out of hours The
36. genetics should be carried out at diagnosis in all cases Cytogenetic abnormalities can be used to monitor response to therapy and confirm relapse e Full karyotype at diagnosis e Rapid FISH for BCR ABL1i and MLL gene rearrangements and ETV6 RUNX1 in children e Subsequent sequential FISH at diagnosis for TCF3 PBX1 specific MLL translocations Hyperdiploidy and Hypodiploidy as required Page 27 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 o The Christie MVEK NHS Foundation Trust e Post treatment bone marrows screened for previous abnormality by routine cytogenetics or FISH as appropriate e Full karyotype and relevant FISH at possible relapse Technical Cytogenetic analysis is performed on cultured cells from fresh bone marrow 20 cells will be fully analysed according to standard procedures and best practice Cells may contain cryptic abnormalities and minor clones not represented in the cultured cells which microscopic analysis may not detect ALL disease cells are notorious for their poor survival in vitro and rapid transport to the laboratory is critical for successful chromosome analysis and FISH ALL disease cells also often have poor chromosome morphology The sensitivity of monitoring follow up cases in remission is therefore likely to be severely limited Sample requirements Bone marrow aspirate specimens shoul
37. gnosis and imatinib is incorporated into intensive treatment regimes Translocations involving the MLL gene such as t 4 11 are common especially in infants and are associated with an unfavourable prognosis The t 12 21 is the most common translocation in paediatric cases and is only detectable by FISH for the ETV6 RUNX1 gene fusion and is associated with good overall survival FISH for this translocation also detects amplification of RUNX1 gene iAMP21 which is incorporated into trial protocols as a high risk abnormality The department provides cytogenetic and FISH investigations to support UKALL14 and UKALL2011 trials Childhood ALL Adult ALL Good prognosis t 12 21 ETV6 RUNX1 high hyperdiploidy high hyperdiploidy del 9p Intermediate Other abnormalities including Other abnormalities including prognosis t 1 19 q23 p13 t 1 19 q23 p13 dup 1q del 6q del 6q 7 7 8 Abnormal 9p 11q23 MLL translocations other than dic 9 20 p13 q11 t 4 11 dic 9 12 p11 21 p11 13 Abnormal 11g Abnormal 11iq del 12p Loss of 13q Abnormal 17p Poor prognosis t 9 22 t 9 22 11q23 MLL translocations t 4 11 iAMP21 RUNX1 amplification Low hypodiploidy 30 39 Near haploidy lt 30 chromosomes chromosomes near triploidy Low hypodiploidy 30 39 Complex karyotype 25 abnormalities chromosomes t 17 19 q23 p13 Abnormal 17p Loss of 13q Adapted from Moorman et al 2010 Moorman et al 2007 Services Offered Cyto
38. gust 2013 Reference No 2034 NHS Foundation Trust Q The Christie MUO Policy for High Risk Samples All samples from patients exposed to a dangerous infectious pathogen ACDP category 3 or higher will be considered a high infection risk This includes known carriers people with prior contact to infected individuals and other risk groups such as IV drug users All samples from patients at High Risk of infection referred for cytogenetic analysis should be identified to the laboratory The sample and request card must be clearly labelled as High Risk HIV Hepatitis B or Hepatitis C samples can be processed by prior arrangement if cytogenetic analysis is critical to patient management All other samples at High Risk of infection with ACDP category 23 pathogen cannot be processed by the laboratory Samples at risk of infection with HIV Hepatitis B or Hepatitis C may be processed by the laboratory However as the samples require special attention we request that these are arranged in advance between the Oncology Cytogenetics laboratory and the referring clinician In particular High Risk samples cannot be processed over a weekend and samples can only be accepted on a Friday in exceptional circumstances Special arrangements must be made for Friday samples Full cytogenetic analysis will only be considered in circumstances where a result will directly influence patient management The culture of cells from HIV Hepatitis B
39. ia 2011 Jan 25 1 82 8 10 Panani A D et al Cytogenetic and molecular aspects of Philadelphia negative chronic myeloproliferative disorders Clinical implications Cancer Letters 2007 255 12 25 11 Tefferi A et al Classification and diagnosis of myeloproliferative neoplasms The 2008 World health organisation criteria and point of care algorithms Leukemia 2007 1 9 12 Such E et al Development and validation of a prognostic scoring system for patients with chronic myelomonocytic leukemia Blood 2013 Apr 11 121 15 3005 15 Page 26 45 oon Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 NHS Foundation Trust Q The Christie MUO LYMPHOBLASTIC LEUKAEMIA LYMPHOMA Cytogenetic abnormalities are found in the majority of B lymphoblastic leukaemia lymphoma by conventional cytogenetic analysis supplemented by FISH WHO recognises a number of subtypes with recurrent genetic abnormalities which define specific entities with distinct phenotypic and prognostic features including t 9 22 BCR ABL1 11q23 MLL t 12 21 ETV6 RUNX1 Hyperdiploidy Hypodiploidy Haploidy and t 1 19 TCF3 PBX1 The frequency and significance of abnormalities differs between adult and paediatric patients see table below The translocation t 9 22 giving rise to the Ph chromosome is more common in adults than children is associated with a poor pro
40. isk label if appropriate information 5 Specimen type 6 Consultant name or initials and hospital 7 Requestor s name and signature 8 Date specimen was taken 9 High risk status if appropriate 10 Private patient if appropriate Please use the current version of the request card Please see following image of version 3 0 Page 7 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 o The Christie NHS NHS Foundation Trust Request Form v3 0 Lab No T Oek enara ae The Christie ONCOLOGY CYTOGENETICS PATHOLOGY DEPARTMENT NHS Foundation Trust THE CHRISTIE MANCHESTER M20 4BX STICK PATIENTS IDENTITY LABEL HERE OR GIVE THE FOLLOWING DETAILS TIME TAKEN POSTCODE DIAGNOSIS PRESENTATION _ REMISSION FOLLOW UP _ RELAPSE PROGRESSION E STAGING B TRIAL HIGH INFECTION RISK YES NO please circle DETAILS If YES please attach sticker amp give details OTHER REFERENCE No e g Path No MANDATORY INFORMATION LF CG Christie Request Form v3 0 In submitting this sample the clinician confirms that consent has been obtained for testing and storage of the patient material All blue shaded areas are considered mandatory and should be completed before sending the form Page 8 45 Oncology Cytogenetics User Guide MI CG Christie User Guide Accredited Medical Laboratory Version 5 1 Issued Au
41. karyotype gt 3 abnormalities Recently developed new therapeutic agents such as 5 azacytidine and lenalidomide have been used for the treatment of MDS and have been reported to be effective in specific cytogenetic subgroups Referrals Samples are accepted on all cases of suspected MDS where bone marrow examination is indicated Full cytogenetic analysis will be performed to test for clonal abnormalities of prognostic significance Samples that fail to grow in culture will have FISH for 5q and 7q deletions Patients with macrocytic anaemia and other cytopaenias are often referred for investigation of possible MDS It would be helpful if cytogenetics requests were called off to avoid unnecessary analyses if the diagnosis of MDS is excluded or cytogenetics is no longer required after the examination of bone marrow morphology Periodic re investigation of bone marrows from untreated MDS patients may be warranted particularly if there is change in clinical or laboratory findings After treatment a screen for previous cytogenetic abnormalities can be performed to monitor remission if a cytogenetic marker was present at diagnosis MI CG Christie User Guide Version 5 1 Issued August 2013 Page 21 45 Oncology Cytogenetics User Guide CPA Accredited Medical Laboratory Reference No 2034 o The Christie MVEK NHS Foundation Trust Technical Cytogenetic analysis is performed on cultured cells from fresh bone marrow The ka
42. mer christie nhs uk hpc heck org Be sure we re registered Shayne Atkinson Elizabeth Elliott Lucy Hammond Kim Hardern Amy McAlpine Fran O Neill Pragnya Patel Samantha Staddon Tel 0161 446 3165 8 30am to 5pm There is no routine service at weekends Samples requiring special attention should be arranged in advance The department is not routinely staffed on Bank Holidays For urgent attention contact The Christie switchboard 0161 446 3000 A letter is sent in advance detailing arrangements at Christmas and Easter Oncology Cytogenetics User Guide MI CG Christie User Guide Version 5 1 Issued August 2013 CPA Accredited Medical Laboratory Reference No 2034 NHS Foundation Trust Q The Christie MUO Samples Sample Types Bone Marrow is the tissue of choice to investigate patients suspected of having leukaemia or related haematological neoplasms Bone marrow aspirate specimens are routinely received although a bone marrow trephine specimen is an option if the marrow is fibrotic or otherwise difficult to aspirate Peripheral Blood can be sent if disease cells are present in sufficient numbers to allow cell culture This is satisfactory for FISH studies in CLL if there is peripheral blood lymphocytosis Other fresh tissues can be analysed and lymph nodes spleen ascitic fluid CSF and solid tumours are occasionally received We do not currently have facilities for long term culture for a comprehensive
43. mplete membrane staining are considered HER2 2 or 2 3 and forwarded for assessment by FISH Assay validation The laboratory conducts a continuous audit evaluating concordance levels between HER2 IHC and FISH During the three years 2009 2011 1586 cases have been tested in parallel for HER2 protein expression by IHC and HER2 gene amplification by FISH with the following results HER2 FISH result 96 FISH Negative 1 FISH Borderline 3 FISH Amplified 11 FISH Amplified 5 5 FISH Borderline 83 FISH Negative 66 FISH Amplified 11 FISH Borderline 23 FISH HER 2 protein IHC Negative or 1 n 238 2 n 1072 2 3 n 229 Negative 3 n 101 94 FISH Amplified 4 FISH Borderline 2 FISH Negative Summary of HER2 status The sample population received at The Christie between 2009 and 2011 were primarily new breast cancers including screen detected lesions In our hands 80 of routinely received breast cancers are ER positive There is a strong relationship between ER negativity and HER2 positivity Up to a third of tumours determined ER negative are HER2 positive whereas only approximately 5 of ER positive tumours are also HER2 positive Our combined ER HER2 positivity rates for all tumours received for dual testing between 2009 and 2011 are as follows ER Negative Tumours HER2 status Overall Frequency Negative 7 5 1 3 1 2 3 8 3 6 5 ER Positive
44. n be used to monitor response to treatment and can confirm relapse or indicate disease progression Referrals e Full karyotype at diagnosis e Rapid FISH for t 15 17 at diagnosis usually lt 24 hours in APL e FISH at diagnosis to detect t 8 21 RUNX1 RUNX1T1 inv i6 CBFB 11q23 rearrangements MLL depending on morphology or as requested e FISH for 5q 7q and 17p TP53 deletions and monosomy 5 and 7 on failed samples e Post treatment bone marrows screened for previous abnormality by routine cytogenetics or FISH as appropriate e Full karyotype at possible relapse for recurrence of previous abnormality clonal evolution or new disease Technical Cytogenetic analysis is performed on cultured cells from fresh bone marrow 20 cells will be fully analysed according to standard procedures and best practice Cells may contain cryptic abnormalities and minor clones not represented in the cultured cells which microscopic analysis may not detect Page 19 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 The Christie MVEK NHS Foundation Trust Sample requirements Bone marrow aspirate or peripheral blood specimens should be collected fresh into the supplied transport bottles or alternatively into other lithium heparin containing tubes Samples should be sent to the laboratory as soon as possible preferably on the day of collecti
45. n the day of collection Low cellularity of the aspirates in AA often leads to small numbers of mitotic cells to analyse and therefore unsuccessful cytogenetic testing Peripheral blood specimens from typical AA cases are unlikely to be useful Summary of services and reporting times Test Target Reporting Time Calendar days Cytogenetic analysis karyotype of AA 21 FISH on the above 21 Cytogenetic analysis of AA transforming 14 to MDS Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details References 1 Marsh JC et al British Committee for Standards in Haematology Guidelines for the diagnosis and management of aplastic anaemia Br J Haematol 2009 Oct 147 1 43 70 2 Maciejewski JP et al Evolution of clonal cytogenetic abnormalities in aplastic anemia Leuk Lymphoma 2004 Mar 45 3 433 40 3 Kim SY et al The characteristics and clinical outcome of adult patients with aplastic anemia and abnormal cytogenetics at diagnosis Genes Chromosomes Cancer 2010 Sep 49 9 844 50 4 Afable MG 2 et al SNP array based karyotyping differences and similarities
46. nd 19q as predictors of survival in oligodendrogliomas astrocytomas and mixed oligoastrocytomas J Clin Oncol 2000 Feb 18 3 636 45 Page 40 45 oon Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q The Christie LUO NHS Foundation Trust Sarcoma We currently provide a service for soft tissue sarcomas on PETs using commercially available FISH probes Probes available EWSR1 to detect rearrangements of 22q12 including the t 11 22 translocation and variants seen in Ewing s sarcoma PNET t 11 22 in desmoplastic small round cell tumour t 10 22 clear cell sarcoma t 9 22 in chondrosarcoma and other tumour types to aid classification SS18 formerly SYT to detect rearrangements of 18q11 2 found in the t X 18 translocation in synovial sarcoma DDIT3 formerly CHOP breakapart probe to detect rearrangements of 12q13 including t 12 16 seen in myxoid round cell liposarcomas MDM2 with control for evaluation of MDM2 amplification status to distinguish atypical lipomatous tumour well differentiated liposarcoma or dedifferentiated liposarcoma from benign lesions MDM2 amplification status has been defined in some studies as MDM2 to control probe ratio of greater than 2 Weaver et al 2008 although no standardised scoring criteria currently exist FOXO1 to detect t 2 13 and t 1 13 in Alveolar Rhabdomyosarcoma COL1A1 PDGFB fu
47. ndled differently Technical Where myeloma is indicated on the referral card and sufficient cells are available FISH is performed on CD138 separated cells and so disease plasma cells should be enriched in the sample Rare CD138 negative cases will not be enhanced To allow time for cell separation and sample processing all samples should be received before 2pm on Friday MI CG Christie User Guide Version 5 1 Issued August 2013 Page 32 45 Oncology Cytogenetics User Guide CPA Accredited Medical Laboratory Reference No 2034 The Christie MVEK NHS Foundation Trust Sample requirements Bone marrow aspirate specimens should be collected fresh into the supplied transport bottles or alternatively into other lithium heparin containing tubes Samples should be sent to the laboratory as soon as possible preferably on the day of collection Summary of services and reporting times Test Target Reporting Time Calendar days Basic 3 FISH panel for IGH FGRF3 IGH MAF 21 TP53 deletion Cell culture and storage of bone marrow cells in case conventional cytogenetic analysis indicated 5 FISH panel including 1q21 and IGH MAFB Not routine Please enquire Conventional cytogenetic analysis Not routine Please enquire Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies wi
48. ng by the consultant Policy for Faxing Reports Oncology Cytogenetics is obliged to follow the Fax policy of The Christie NHS Foundation Trust For security reasons and because it is time consuming the procedure can only be used occasionally and therefore only when urgent reports are required immediately All other reports will be sent by post hospital transport and will usually be received within a day of despatch Faxing will entail Ring the recipient before we send the Fax Check with the recipient that the Fax number and the Fax are available Ask the recipient to stand by the Fax machine Fax the header sheet only first The recipient must phone when the header sheet is received When we receive confirmation by phone the rest of the Fax with the report will be sent E mailing Reports The department has developed protocols for the e mailing of encrypted reports to workplace NHS addresses of referring consultants and other designated staff in the care team Reports which are e mailed directly from the laboratory database will be a copy of the final signed paper report which will also be despatched Reports are encrypted by the Trust s secure e mail portal Ironport and will require entry of a password for access Please enquire if this service may be of use and you are able to supply an appropriate e mail address Page 13 45 Oncology Cytogenetics User Guide MI CG Christie User Guide Version 5 1 Issued August 2013 i
49. ng in Oncology and disease specific Guidelines for CML MPN AML MDS and ALL Urgent referrals Acute leukaemia and CML at diagnosis or possible relapse All acute leukaemia and chronic myeloid leukaemia cases at diagnosis will be treated as urgent and 95 of cases will be reported within 14 calendar days In practice the majority of diagnostic cases are reported within the internal reporting time target of 7 days Rapid FISH tests e g APL Burkitt lymphoma 95 will be reported in 3 working days In practice the majority of cases will have a verbal report available within 24 hours or in 2 3 working days if paraffin embedded Routine referrals for routine cytogenetic analysis 95 of all other referrals will be reported within 21 calendar days The laboratory operates a priority system whereby cases requiring quick attention or by special telephone request but which are not urgent can be analysed out of turn In Abeyance All samples that are not urgent and have an uncertain diagnosis will be held in abeyance pending further information Further details are requested on an interim report by e mail where available which also permits you to suggest a priority level for the referral This is necessary because at the time of biopsy the diagnosis may not be known and chromosome analysis may not be required after bone marrow morphology is examined Consultants are requested to cooperate as fully as possible with this policy
50. on Summary of services and reporting times Test Target Reporting Time Calendar days Rapid FISH at diagnosis 3 working days Cytogenetic analysis karyotype 7 Cytogenetic analysis and or FISH post 21 treatment Cytogenetic analysis and or FISH at relapse 14 or transformation Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details References 1 Swerdlow S H E Campo N L Harris E S Jaffe S A Pilieri H Stein J Thiele W Vardiman Eds 2008 WHO Classification of tumours of haematopoietic and lymphoid tissues World Health Organization Classification of Tumours Lyon IARC 2 Grimwade D et al 2010 Refinement of cytogenetic classification in acute myeloid leukemia determination of prognostic significance of rare recurring chromosomal abnormalities among 5876 younger adult patients treated in the United Kingdom Medical Research Council trials Blood 116 3 354 365 3 D hner H et al European LeukemiaNet Diagnosis and management of acute myeloid leukemia in adults recommendations from an international expert panel on
51. or Clinical Excellence Technology appraisal no 107 Trastuzumab for the adjuvant treatment of early stage HER2 positive breast cancer 2006 http guidance nice org uk TA107 2 Walker RA et al HER2 testing in the UK further update to recommendations J Clin Pathol 2008 Jul 61 7 818 24 Bang Y J et al Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2 positive advanced gastric or gastro oesophageal junction cancer ToGA a phase 3 open label randomised controlled trial The Lancet 2010 376 9742 687 697 4 National Institute for Clinical Excellence Technology appraisal no 208 Trastuzumab for the treatment of HER2 positive metastatic gastric cancer 2010 www nice org uk guidance TA208 5 Ruschoff J Dietal M Baretton G et al HER2 diagnostics in gastric cancer guideline validation and development of sz EEA SA HER 2 Positive Gastric Carcinoma IHC amp FISH showing the heterogeneous nature of the disease images from The Christie Histopathology Oncology Cytogenetics Departments Page 37 45 Oncology Cytogenetics User Guide MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q The Christie MUO NHS Foundation Trust Lymphoma Diagnosis FISH on paraffin embedded tissue PET for lymphoma diagnosis is offered as part of Greater Manchester amp Cheshire Cancer Network Haematology Malignancy Diagnostics se
52. or Hepatitis C samples requires special attention in isolation conditions Processing of these samples will therefore incur an additional charge to the referring department Alternatively uncultured specimens can be fixed for FISH only but a full cytogenetic result will not be possible Any samples at risk of infection with any other ACDP category 3 pathogen or higher will not routinely be processed by the laboratory Any sample of uncertain risk status of infection with ACDP category 3 pathogen or if satisfactory arrangements cannot be made will be disposed of by incineration HIV Hepatitis B and Hepatitis C samples received where no arrangements can be made or without strong indication for cytogenetic analysis will be fixed uncultured for possible FISH only Consequently a conventional cytogenetics result will not be possible In all instances a record of the actions taken will be made and a report issued to the referring consultant Revised Advice on Laboratory Containment Measures for work with Tissue Samples in Clinical Cytogenetics Laboratories 2001 Page 9 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 NHS Foundation Trust Q The Christie MUO Policy of Consent for Testing and Retention of Samples In submitting a sample to Oncology Cytogenetics the clinician confirms that consent has been obtained for testing and
53. py for chronic myeloid leukemia Blood 2006 Oct 15 108 8 2811 3 3 Jabbour E et al Chromosomal abnormalities in Philadelphia chromosome negative metaphases appearing during imatinib mesylate therapy in patients with newly diagnosed chronic myeloid leukemia in chronic phase Blood 2007 Oct 15 110 8 2991 5 4 Hughes T et al Monitoring CML patients responding to treatment with tyrosine kinase inhibitors review and recommendations for harmonizing current methodology for detecting BCR ABL transcripts and kinase domain mutations and for expressing results Blood 2006 Jul 1 108 1 28 37 5 British Committee for Standards in Haematology Goldman J Recommendations for the management of BCR ABL positive Chronic Myeloid Leukaemia URL http www bcshquidelines com pdf CML_quidelines_270707 pdf accessed October 2012 Page 18 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q The Christie LUO NHS Foundation Trust ACUTE MYELOID LEUKAEMIA AML CYTOGENETICS Introduction An abnormal karyotype is found in approximately 55 of AML cases at presentation A large number of chromosome abnormalities have been identified that can aid the diagnosis of AML and identify subtypes the WHO classification now defines certain groups by their cytogenetic abnormalities such as t 8 21 inv 16 t 15 17 t 9 11 t 6 9 inv 3 and t 1 22 Cy
54. r MDS AML almost always have karyotypic abnormalities and there is an increase in frequency of chromosome aberrations and increasing karyotype complexity in disease progression While there is no specific abnormality that will confirm transformation abnormalities such as del 5q monosomy 7 del 17p or complex changes are suggestive Essential Thrombocythaemia ET An abnormal karyotype is unusual in ET 5 of cases and the abnormalities when present are general myeloid markers del 20q 8 9 del 13q gain of 1q del 5q JAK2 mutation is present in 50 of patients but the predictive value is poor and there is lack of diagnostic specificity Given the low abnormality rate the main utility of cytogenetics is the exclusion of CML by the absence of the t 9 22 or BCR ABL1 BCR ABL1 testing should be considered to exclude CML especially for cases with high risk features e g basophilia left shifted WBC granulocyte count gt 16x10 I small megakaryocytes difficult to control thrombocytosis A bone marrow biopsy is recommended in a diagnostic algorithm for the differential diagnosis of ET from other myeloid neoplasms cytogenetics is advised but not mandatory but may be helpful to exclude other abnormalities associated with platelet gain including 3q26 abnormalities and del 5q Again there are no specific chromosome rearrangements that will confirm transformation but abnormalities of chromosomes 7 and 17 7q der 1 7 17p i 17q are sugge
55. re available by special request The laboratory is the largest and most experienced HER2 FISH service for the Greater Manchester and Cheshire Cancer Network and receives specimens from several HER2 immunochemistry testing centres for FISH HER2 testing for gastric cancer Herceptin therapy has also been shown to be effective in HER2 positive patients with advanced gastric or gastroesophageal cancer TOGA study In November 2010 NICE approved the use of Herceptin for patients with HER2 positive HER2 3 by immunohistochemistry gastric or gastroesophageal cancer Following successful validation of HER2 in gastric specimens in 2010 the laboratory now routinely performs HER2 testing in gastric specimens in accordance with Ruschoff s recommendations It is recommended that all cases of gastric tumours are tested and referred directly from the pathologist to avoid delay and avoid possible problems of storage Further information on arrangements for HER2 testing can be obtained from Dr Mansoor at was mansoor christie nhs uk HER2 FISH is performed using approved dual colour assays comprising two fluorescent labelled probes for the HER2 gene and an internal control of chromosome 17 centromere The system detects variation in chromosome copy number polysomy and monosomy Results are expressed as a ratio of HER2 copy number relative to Chromosome 17 copy number HER2 amplification of invasive cancer is confirmed with a HER2 Chi7 ratio of greater
56. retative comments Further development of HMD is expected and will include coordination of leukaemia and myeloma diagnosis in later phases Page 44 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q The Christie MUO NHS Foundation Trust Review History Document Title Oncology Cytogenetics User Guide Document Ref No MI CG Christie User Guide Edition No Version 5 1 Date of Issue August 2013 Review Interval Biennial Author N Telford amp Oncology Cytogenetics Authorised By N Telford Approved by M Green amp C Hodgson Review History Version 1 0 Issued May 2005 Jan 2007 Reviewed and updated Jan 2008 Reviewed and updated Oct 2008 Reviewed and updated Mar 2009 Issued as version 4 1 Additions pg4 new HER2 section pg 23 24 and minor changes Oct 2012 Reviewed and updated Aug 2013 Addition of mesothelioma FISH and minor amendments to ALL CMML and myeloma sections Page 45 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034
57. rvice for the detection of ALK gene rearrangement using a commercially available breakapart probe We require an H amp E slide with the relevant area marked to be sent along with the slides for testing in order to focus our analysis appropriately The optimal thickness of sections for FISH testing is 3 5yum References Camidge DR Doebele RC Treating ALK positive lung cancer early successes and future challenges Nat Rev Clin Oncol 2012 May 9 268 277 Page 42 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 NHS Foundation Trust Q The Christie LUO Malignant Mesothelioma New section Malignant mesothelioma is an aggressive tumour associated with previous exposure to asbestos and with an increasing incidence Homozygous deletion of 9p21 including CDKN2A although not specific to this particular tumour type has been reported in up to 74 of cases of mesothelioma but is not found in benign or reactive proliferations Therefore the detection of homozygous deletion of CDKN2A by fluorescence in situ hybridization FISH can be a useful diagnostic test to distinguish malignant mesothelioma from benign mesothelial proliferations The laboratory has validated a FISH assay for detection of homozygous deletion of CDKN2A in paraffin embedded tissue sections from suspected cases of malignant mesothelioma Both cellular pleural effusions
58. ryotype from a minimum of 20 cells will be fully analysed according to standard procedures and best practice guidelines Cells may contain cryptic abnormalities and minor clones may be present that are not represented in the cultured cells which microscopic analysis may not detect Sample requirements Bone marrow aspirate specimens should be collected fresh into the supplied transport bottles or alternatively into other lithium heparin containing tubes Samples should be sent to the laboratory as soon as possible preferably on the day of collection Peripheral blood specimens from typical MDS cases are unlikely to be useful Summary of services and reporting times Test Target Reporting Time Calendar days Cytogenetic analysis karyotype of new 21 MDS FISH on the above 21 Cytogenetic analysis of MDS 7 transforming to AML Cytogenetic analysis of secondary MDS 14 Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details References 1 Swerdlow S H E Campo N L Harris E S Jaffe S A Pilieri H Stein J ThieleJ W Vardiman Eds 2008
59. sion in Dermatofibrosarcoma protuberans FISH for some of the less common tumours can be undertaken with prior agreement with the laboratory Please contact the Head of Department to discuss the details of specific cases Weaver J Downs Kelly E Goldblum JR Turner S Kulkarni S R Tubbs RR Rubin BP Skacel M Fluorescence in situ hybridization for MDM2 gene amplification as a diagnostic tool in lipomatous neoplasms Modern Pathology 2008 21 943 949 Page 41 45 CPA Oncology Cytogenetics User Guide P MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q The Christie MUO NHS Foundation Trust ALK rearrangement in non small cell lung cancer Approximately 3 7 of cases of non small cell lung cancer NSCLC harbour an ALK anaplastic lymphoma kinase gene rearrangement The most common rearrangement is a paracentric inversion in the short arm of chromosome 2 resulting in the ALK EML4 fusion gene although other fusion partners have been identified Crizotinib Xalkori is a small molecule tyrosine kinase inhibitor of ALK Those cases of NSCLC which are positive for ALK rearrangement show significant benefit from treatment with crizotinib in terms of both tumour shrinkage and progression free survival compared to conventional chemotherapy In 2011 crizotinib was FDA approved for clinical use in the USA for this molecularly defined sub group of lung cancer We offer a FISH se
60. ssuetvaisciausiasacsceaasnes 14 Service Specifications and MGICAIONS w2ic0iccsrensneavsvrsaaciuncuncisedoasvanvastesasacanncanedavesscenncas 16 Conventional Cytogenetic Testing and FISH for Haematological Malignancies T ssa eee E E E E E E 17 AME i sscrceassearssatie scien pension E E EE EA EEEE EE AE 19 MDS rere E EE E E 21 Aplastic A aeMiasse seein eani aa 23 MPN PRV ET PMF CMML Hypereosinophilia Systemic Mastocytosis 25 Lymphoblastic Leukaemia Lymphoma ALL ccscecsssteeesseeseeees 27 Lymph Ma ri aa etre de Ea Men ere merry rie rm rere 29 OT ae ean aeauieades eas mesnta ta nuaeaceceeated N O 30 DOGMA eesin duende ean E EE En Ea eara eaea a aaraa 32 FISH on Paraffin Embedded Tissue for Solid TUMOUIG csecsesssecessorersesreress 34 HER2 in Breast and Gastroesophageal 35 CaNCEN seenen nna Lymphoma serisine ae a a A 38 Brain Tumour COM Asis Se sieutatantcrvcreusncgecainseesdesuuvcenatettnatietuatedlapedcigedviens 40 AIAG INGA acest ee a tatnceace dice aN Ea a E AEE AE ESE 41 ALK testing WANS CIs sa psaccreeetenasnahea a 42 Appendix The Christie Hospital GMC HMD ServiCe ccccccecseseeseseesssneeesssreeesnees 43 Review RTI SU IY icpn E E E e EE O E 44 ayers PA rea OG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laborator Reference No 2034 Q The Christie MUO NHS Foundation Trust Introduction Oncology Cytogenetics at The Christie is a specialist region
61. stive Primary Myelofibrosis Chromosome abnormalities are found in 60 of cases but again are not specific and include del 20q and del 13q Cytogenetic analysis is included in a diagnostic algorithm for myelofibrosis Cytogenetics is incorporated into the updated prognostic scoring system for Primary Myelofibrosis DIPSS Plus and also predicts leukaemia free survival but should be considered alongside other risk factors of the scheme There is no specific marker for transformation but a complex karyotype and abnormalities of chromosomes 5 7 and 17 are again strongly suggestive Risk Cytogenetic Abnormality Favourable Normal karyotype or sole abnormalities of 20q 13q or 9 and all other cytogenetic findings Unfavourable Complex karyotype 3 abnormalities or sole or two 8 7 7q i 17q 5 5q 12p inv 3 or 11q23 rearrangement From Caramazza et al 2011 used in DIPSS for myelofibrosis MI CG Christie User Guide Version 5 1 Issued August 2013 Page 24 45 CPA Oncology Cytogenetics User Guide P Accredited Medical Laboratory Reference No 2034 o The Christie MVEK NHS Foundation Trust Chronic Myelomonocytic Leukaemia CMML Cytogenetic abnormalities are found in up to 40 of cases but are rarely specific the commonest being trisomy 8 monosomy 7 or deletion of 7q and rearrangements of 12p The rare translocations t 5 12 and t 8 13 appear to define a subset of patients with a specifi
62. storage of the patient material This material is tested and surplus retained for possible Oncology Cytogenetics use and only in connection with the original reason for referral It will not be passed on to other parties or used for research or purposes other than the reason that they were originally referred The Oncology Cytogenetics department currently retains fixed cell suspensions from samples for 10 years This allows for further testing of samples and is particularly useful for additional FISH tests or when testing a diagnostic sample is required to establish a FISH signal pattern to enable testing of subsequent post treatment samples Used microscope slides from routine cytogenetic analysis are retained for 10 years A sample not analysed at the time of referral can be reactivated at any time if required A full year of samples and slides are disposed of in the January following the completion of a full ten years of age Page 10 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q The Christie LUO NHS Foundation Trust Sample Prioritisation and Reporting Times Sample prioritisation and reporting performance targets of the professional standards of the Association of Clinical Cytogenetics are used as minimum standards including General Best Practice Guidelines Haemato Oncology Best Practice Guidelines Guidelines for FISH Scori
63. t http www bcshguidelines com documents Lymphoma_disease_app_bcsh_042010 pdf gt accessed October 2012 9 Oscier D et al Chronic Lymphocytic Leukaemia Working Group UK National Cancer Research Institute Prognostic factors identified three risk groups in the LRF CLL4 trial independent of treatment allocation Haematologica 2010 Oct 95 10 1705 12 Page 31 45 Oncology Cytogenetics User Guide p MI CG Christie User Guide CPA Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 o The Christie MVEK NHS Foundation Trust MYELOMA CYTOGENETICS Introduction Myeloma shows a range of recognised cytogenetic abnormalities which can aid subclassification of the disease and are strong prognostic factors The IMWG recommends a basic strategy for FISH testing for t 4 14 t 14 16 and TP53 deletion due to their strong negative impact on prognosis which is also recommended in BCSH Guidelines The combination of FISH testing and ISS International Staging System has been shown to improve risk assessment in myeloma An extended FISH panel also including tests for 1q21 gain and t 14 20 showed a cumulative effect on prognosis and defined a high risk group with 2 or more abnormalities There is emerging evidence of the role of cytogenetic abnormalities defined by FISH studies in directing specific therapies but this is under evaluation Conventional cytogenetic analysis is hampered by
64. ted with eosinophilia have been excluded However persistent unexplained eosinophilia whether formally diagnosed as HES or not will receive a full conventional cytogenetic analysis and will be screened for the FIP1L1 PDGFRA fusion by FISH Systemic Mastocytosis A full cytogenetic analysis is performed although specific chromosome abnormalities are not recognised Screening for KIT D816V mutation is not available in this laboratory but advice will be provided on where to forward the sample for molecular testing which will require separate sample bottles Only cases reported to have eosinophilia will be screened for FIP1L1 PDGFRA fusion by FISH see CEL HES above Referrals 1 Full karyotype when reactive causes of myeloproliferation is excluded 2 FISH for BCR ABL1 performed on all cases of ET Full karyotype of confirmed cases of ET by special request BCR ABL1 FISH on other cases of MPN by request 3 FISH for FIP1L1 PDGFRA in cases of persistent eosinophilia FISH to confirm PDGRFB 5q and FGFR1 8p11 if indicated 4 JAK2 V617F mutation screening is NOT available in this department Technical Cytogenetic analysis is performed on cultured cells from fresh bone marrow The karyotype from a minimum of 20 cells will be fully analysed according to standard procedures and best practice guidelines Cells may contain cryptic abnormalities and minor clones may be present that are not represented in the cultured cells which microscopic analysis m
65. tes Eur J Haematol 2008 Mar 80 3 197 200 2 Haferlach T et al The diagnosis of BCR ABL negative chronic Myeloproliferative diseases CMPD a comprehensive approach based on morphology cytogenetics and molecular markers Ann Haematol 2008 87 1 10 3 Bench A J et al Chromosomal abnormalities amp molecular markers in MPD disorders Semin Heamatol 2005 42 196 205 4 Tefferi A et al Classification and diagnosis of myeloproliferative neoplasms The 2008 World health organisation criteria and point of care algorithms Leukemia 2007 1 9 5 McMullin et al Guidelines for the diagnosis investigation and management of polycythaemia erythrocytosis British Journal of Haematology 2005 130 2 174 6 McMullin M et al Amendment to the guidelines for the diagnosis investigation and management of polycythaemia erythrocytosis British Journal of Haematology 2007 138 821 822 7 Tefferi A et al Cytogenetic findings and their clinical relevance in myelofibrosis with myeloid metaplasia Br J Haematology 2001 113 763 771 8 Gangat N et al DIPSS plus a refined Dynamic International Prognostic Scoring System for primary myelofibrosis that incorporates prognostic information from karyotype platelet count and transfusion status J Clin Oncol 2011 Feb 1 29 4 392 7 9 Caramazza D et al Refined cytogenetic risk categorization for overall and leukemia free survival in primary myelofibrosis a single center study of 433 patients Leukem
66. th professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details References 1 Fonseca R et al International Myeloma Working Group International Myeloma Working Group molecular classification of multiple myeloma spotlight review Leukemia 2009 Dec 23 12 2210 21 2 Munshi NC et al International Myeloma Workshop Consensus Panel 2 Consensus recommendations for risk stratification in multiple myeloma report of the International Myeloma Workshop Consensus Panel 2 Blood 2011 May 5 117 18 4696 700 3 British Committee for Standards in Haematology in conjunction with the UK Myeloma Forum UKMF Guidelines on the diagnosis and management of multiple myeloma 2010 http www bcshguidelines com 4 HAEMATOLOGY _GUIDELINES html 4 Boyd KD et al NCRI Haematology Oncology Studies Group A novel prognostic model in myeloma based on co segregating adverse FISH lesions and the ISS analysis of patients treated in the MRC Myeloma IX trial Leukemia 2012 Feb 26 2 349 55 5 Avet Loiseau H et al Combining Fluorescent In Situ Hybridization iFISH data with ISS staging improves risk assessment in myeloma an International Myeloma Working Group IMWG collaborative project Leukemia 2012 Oct 3 6 Guti rrez NC et al GEM PETHEMA Spanish Group Prognostic and biological implications of gene
67. the low proliferation rate of disease cells in culture and a number of the abnormalities being cryptic Monosomy 13 as detected by conventional karyotyping has been reported not to be an independent prognostic marker which largely negates the value of routine conventional karyotyping However this may still have some prognostic relevance Neutral prognosis t 11 14 t 6 14 Hyperdiploidy Poor prognosis t 4 14 IGH FGFR3 t 14 16 IGH MAF t 14 20 IGH MAFB TP53 deletion Gain of 1q21 If a patient already has an identified high risk feature at diagnosis then there is no need to perform repeat investigations at relapse However if a patient is in a low risk group a full panel of FISH tests will be performed at relapse for risk re stratification to look for new emerging clones that were not detected at diagnosis Referrals The FISH service tests for prognostic markers at diagnosis or relapse Analysis is applicable for symptomatic cases of confirmed myeloma only Cases with an uncertain diagnosis will be stored until a diagnosis of myeloma is confirmed so that unnecessary tests are not performed on MGUS in which the abnormalities do not have the same significance Please contact the laboratory to activate a case following diagnosis FISH testing is not suitable to monitor disease course and remission samples cannot be tested Myeloma patients suspected of secondary disease need to be highlighted as they will be ha
68. tic abnormalities in multiple myeloma undergoing autologous stem cell transplantation t 4 14 is the most relevant adverse prognostic factor whereas RB deletion as a unique abnormality is not associated with adverse prognosis Leukemia 2007 Jan 21 1 143 50 Page 33 45 Oncology Cytogenetics User Guide CPA MI CG Christie User Guide Version 5 1 Issued August 2013 Accredited Medical Laboratory Reference No 2034 Q The Christie MUO NHS Foundation Trust FISH ON PARAFFIN EMBEDDED TISSUE PET FOR SOLID TUMOURS The following FISH services are offered on PETs HER2 in breast carcinoma Lymphoma diagnosis Brain tumour gliomas Sarcoma diagnosis ALK gene rearrangement in non small cell lung carcinoma Malignant mesothelioma Sample requirements e The laboratory only accepts tissue sections The optimal thickness for all sections is 3um The laboratory currently does not accept uncut blocks of tissue and these will be returned to the sender e Sections should be mounted on APES coated or equivalent slides Please label all slides clearly with AT LEAST TWO unique patient identifiers e g name and pathology no e Send one slide per FISH test requested plus a spare slide Please refer to the table below with regards to number of slides for a specific referral reason e In cases where only part of the tissue is infiltrated or only part of the tissue is appropriate for screening please provide an H amp E with the relevant
69. tic anaemia exhibit clonal chromosomal abnormalities which may aid the distinction of AA from hypoplastic MDS although there is no consensus that the presence of chromosomal abnormalities is incompatible with a diagnosis of AA and therefore confirms MDS The finding of a cytogenetic abnormality in AA can be a strong indication of clonal evolution to MDS which is important to characterise as the prognosis of these patients is less favourable and treatment choices differ in particular when high risk chromosomal abnormalities are involved The most common cytogenetics abnormalities in AA are trisomy 8 and aberrations of chromosome 7 Cases with abnormal cytogenetics particularly monosomy 7 and complex karyotypes have been reported to show an increased rate of transformation to AML and a poor response to immunosuppressive therapy Technical Cytogenetic analysis is performed on cultured cells from fresh bone marrow The karyotype from a minimum of 20 cells will be fully analysed according to standard procedures and best practice guidelines Cells may contain cryptic abnormalities and minor clones may be present that are not represented in the cultured cells which microscopic analysis may not detect Sample requirements Bone marrow aspirate specimens should be collected fresh into the supplied transport bottles or alternatively into other lithium heparin containing tubes Samples should be sent to the laboratory as soon as possible preferably o
70. togenetics can also help to define AML with myelodysplasia related changes and therapy related myeloid neoplasms Importantly many cytogenetic abnormalities have prognostic implications and are therefore used in risk stratified treatment regimes Good prognosis t 15 17 t 8 21 and invi6 t 16 16 Intermediate Entities not classified as favourable or adverse including 8 and others t 9 11 prognosis and t 11 19 MLL translocations Poor prognosis Complex karyotype 24 abnormalities abn 3q including inv 3 t 3 3 5 del 5q or add 5q 7 add 7q del 7q 11q23 MLL translocations t 6 11 or t 10 11 t 9 22 17 or abn 17p Adapted from Grimwade et al 20107 Different prognostic scoring systems may vary e g European LeukemiaNet and the significance of cytogenetics will also depend on the demographics of the study population such as paediatric and elderly cases A newly defined entity monosomal karyotype 2 or more autosomal monosomies or 1 monosomy with structural abnormalities is common in elderly patients and although not distinguished in UK data has been reported to confer a dismal prognosis Such prognostic classifications are used to assign risk group in UK MRC AML trials prospectively in AML17 All patients should have conventional cytogenetics performed at diagnosis supplemented by FISH tests as appropriate to identify favourable and unfavourable prognostic abnormalities Cytogenetics ca
71. undation Trust Sample requirements Bone marrow aspirate specimens should be collected fresh into the supplied transport bottles or alternatively into other lithium heparin containing tubes Samples should be sent to the laboratory as soon as possible preferably on the day of collection Peripheral blood specimens from typical CML cases are useful for FISH testing but may not yield sufficient cells for full cytogenetic analysis Summary of services and reporting times Test Target Reporting Time Calendar days Rapid FISH at diagnosis 3 working days Cytogenetic analysis karyotype 7 Cytogenetic analysis and or FISH post 21 treatment Cytogenetic analysis and or FISH at 7 relapse or transformation Further Information The Oncology Cytogenetics laboratory is accredited by Clinical Pathology UK Ltd ref no 2034 CPA standards are compliant with ISO 15189 The laboratory also complies with professional standards issued by the Association for Clinical Cytogenetics ACC and participates in all appropriate EQA schemes UKNEQAS Please see relevant sections of the Oncology Cytogenetics User Guide for full details References 1 Baccarani M et al European LeukemiaNet Chronic myeloid leukemia an update of concepts and management recommendations of European LeukemiaNet J Clin Oncol 2009 Dec 10 27 35 6041 51 2 Kovitz C et al Myelodysplastic syndromes and acute leukemia developing after imatinib mesylate thera

Download Pdf Manuals

Related Search

Related Contents

Toshiba CN32V71 32" TV  Ksix B8542SC01 screen protector    EK20-IDPAYFT USER MANUAL  Explosionszeichnung und Teileliste    MANUEL D`INSTALLATION ET DE CONNEXION  Untitled - Faculty Home - Universiti Teknologi Malaysia  KIVA SYSTEM KIVA KILO  Annexe 4.1 - Transmission DES par e-mail Mode d`emploi  

Copyright © All rights reserved. Failed to retrieve file