BCR-ABL1 Kinase Domain Mutation Status (including educational clinical scenario)

Transcription

1 BCR-ABL1 Kinase Domain Mutation Status (including educational clinical scenario) Issue date: 23rd February 2018 Closing date: 23rd March 2018 Results for the BCR-ABL1 Kinase Domain Mutation Status trial can only be submitted via the following web entry pages. Please do not start to complete this survey until you have all of your data to enter. Any numerical fields must be completed using only decimal points to separate numbers, and not commas e.g. enter 6.3 not 6,3. Please do not enter symbols e.g. % into numerical fields. For educational purposes this trial includes a supplementary clinical scenario. For your own records you may wish to document your results on the PDF version of the SurveyMonkey hosted data entry pages, which can be found in the BCR-ABL1 Kinase Domain Mutation Status section of our UKNEQAS LI website ( You may also wish to print out or save a Print Screen for each data entry page for your records, as you will not be able to access your results after you have completed your data entry submission. Results for sample(s) KDM 126 and KDM 127 will not be scored as this is not yet an accredited programme. Repeat samples are available for all programmes. In the event that your local quality control criteria are not met please contact UK NEQAS LI as soon as possible. Please do not submit results based on a suboptimal extraction. Requests for repeat samples should be made by (admin@ukneqasli.co.uk). Should this not be possible please telephone our Administration team on the number provided below. Please make a repeat sample request as soon as possible. If following repeat sample(s) processing, results obtained still do not pass local internal QC please contact UK NEQAS LI. Contact details UK NEQAS LI, Pegasus House, 4th Floor, 463A Glossop Road, Sheffield, S10 2QD, UK. Tel: +44 (0) , Fax: +44 (0) admin@ukneqasli.co.uk 1

2 website: Throughout the survey * denotes a mandatory field 2

3 * 1. Participant ID 2. How would you classify your laboratory? Clinical: hospital affiliated Clinical: private Research: translational Research: clinical trials Pharmaceutical Biotechnology Other (please specify) 3. What is the specialty of your laboratory? Molecular Genetics Cytogenetics Haematology Histocompatibility and Immunogenetics Histology Other (please specify) 3

4 Process Infomation * 4. Please give details of the amino acids (aa) analysed within your assay ~ aa (NP_ ) Other (please specify) 5. Please provide the Genbank or Ensembl accession number of your ABL1 reference sequence, including version. 6. Assay journal reference Branford S. et al (2002). Blood 99:9, Hochhaus A. et al (2002). Leukemia, 16:11, Soverini S. et al (2004). Clinical Chemistry, 50:7, Ernst T. et al (2008). Haematologica, 93:2, Alikian M. et al (2012). American Journal of Hematology 87:3, Branford S. and Hughes T. (2006). Myeloid Leukemia Methods and Protocols eisbn , Gruber F. et al (2005). Leukemia, 19:12, Branford S. et al (2006). Leukemia, 20, Polakova K. et al (2008). Leuk Res 32:8, Wang L. et al (2006). Haematologica, 91:2, MODHEM (Network for Molecular Diagnostics of Hematologic Malignancies) In house method (no reference) Other (please specify) 4

5 Method Information * 7. Input (template) material cdna DNA * 8. PCR methodology Single reverse transcriptase PCR Semi-nested reverse transcriptase PCR Nested reverse transcriptase PCR Other (please specify) 9. What is the target(s) of your PCR amplification strategy? BCR-ABL1 fusion (targeting ABL1 on the translocated chromosome 9) ABL1 (targeting ABL1 on the non-translocated chromosome 9) Both * 10. Analysis Method Sanger sequencing Pyrosequencing Allele specific PCR Ion Torrent PGM (NGS) 454/Roche Junior (NGS) Solexa/Illumina MiSeq (NGS) PACBIO RSII (NGS) Ion Torrent S5 (NGS) Other (please specify) 5

6 11. Sequencing approach (if applicable) Forward Reverse Both, forward and reverse 12. If you perform multiple assays, please describe your processes 6

7 Results Sample KDM 126 * 13. Sample KDM 126: Did you detect a DNA sequence change? Yes No 7

8 Results Sample KDM 126 IMPORTANT: Please report sequence changes using the HGVS system ( DNA sequence change e.g. c.944c>t Amino acid change e.g. p.thr315ile * 14. Sample KDM 126: please enter details of the DNA sequence change(s) detected Sequence change 1 Sequence change 2 Sequence change 3 Sequence change 4 Sequence change 5 * 15. Sample KDM 126: please enter details of the resulting amino acid change(s) Amino acid change 1 Amino acid change 2 Amino acid change 3 Amino acid change 4 Amino acid change 5 8

9 Quantification Sample KDM Sample KDM 126: Mutant quantification Sequence change 1 Sequence change 2 Sequence change 3 Sequence change 4 Sequence change Sample KDM 126: Quantification calculation Mut/(Mut+WT) x 100 Mut/WT x 100 Mut/ABL1 x 100 Other (please specify) 9

10 Results Sample KDM 127 * 18. Sample KDM 127: did you detect a DNA sequence change? Yes No 10

11 Results Sample KDM 127 IMPORTANT: Please report sequence chamges using the HGVS system ( DNA sequence change e.g. c.944c>t Amino acid change e.g. p.thr315ile * 19. Sample KDM 127: Please enter details of the DNA sequence change(s) detected Sequence change 1 Sequence change 2 Sequence change 3 Sequence change 4 Sequence change 5 * 20. Sample KDM 127: Please enter details of the resulting amino acid change(s) Amino acid change 1 Amino acid change 2 Amino acid change 3 Amino acid change 4 Amino acid change 5 11

12 Quantification Sample KDM Sample KDM 127: Mutant quantification Sequence change 1 Sequence change 2 Sequence change 3 Sequence change 4 Sequence change Sample KDM 127: Mutant quantification Sequence change 1 Sequence change 2 Sequence change 3 Sequence change 4 Sequence change Sample KDM 127: Quantification calculation Mut/(Mut+WT) x 100 Mut/WT x 100 Mut/ABL1 x 100 Other (please specify) 12

13 Supplementary clinical scenario Please submit your response to the clinical scenario in the spaces provided below. If you have any additional information (e.g. reports) that you would like to submit then please do so by to or by FAX to +44 (0) Please ensure that your participant number is clearly stated on every page of any such additional information. A CML patient expressing e13a2 BCR-ABL1 was treated with imatinib. She achieved 4% BCR-ABL1 IS at 3 months and 0.4% at 6 months, but the level at 9 months rose slightly to 0.5% and rose again to 1.5% at 12 months. Since the 12 month result indicated failure of therapy according to the European LeukemiaNet (ELN) recommendations a Tyrosine Kinase Domain (TKD) mutation test was requested. Sample KDM 126 represents the peripheral blood sample provided. 24. Do you routinely provide clinical interpretation of BCR-ABL1 Kinase Domain Mutation (KDM) results to referring clinicians? Yes No 25. With reference to the AMP (Association for Molecular Pathology) joint consensus recommendations for the interpretation of sequence variants in cancer please select the most appropriate classification for any mutation(s)/variants(s) detected in sample KDM 126. Li, M.M. et al Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. The Journal of Molecular Diagnostics 19(1):4-23 (2017) Variant classification (Li et al, 2017) Sequence change 1 Sequence change 2 Sequence change 3 Sequence change 4 Sequence change 5 13

14 26. Please comment on the clinical significance of any mutation(s)/variant(s) detected in sample KDM 126, including any relevance to patient management in the context of this clinical scenario. 27. Please provide details of any relevant supporting references; this may include but is not limited to guidelines, clinical trial publications etc. Where possible use the following format, for example: Baccarani, M. et al. European LeukemiaNet recommendations for the management of chronic myeloid leukemia. Blood. 22(6): (2013) Reference 1 Reference 2 Reference 3 Reference 4 Reference Any further comments? 14

15 * 29. Participant ID 15

16 Important Information Thank you, you have now completed your results return for BCR-ABL1 Kinase Domain Mutation Status trial (not accredited). PLEASE NOTE: This is your last opportunity to review your data before submitting it. You will not be able to return to this survey after you have selected the DONE button on the next page. If you wish to review the results you have entered please make use of the PREV button to review the information on previous pages. For your own records you may wish to document your results on the PDF version of the SurveyMonkey hosted data entry pages, which can be found in the Pilot BCR-ABL1 Kinase Domain Mutation Status section of our UKNEQAS LI website ( Contact details UK NEQAS LI, Pegasus House, 4th Floor, 463A Glossop Road, Sheffield, S10 2QD, UK. Tel: +44 (0) , Fax: +44 (0) website: Throughout the survey * denotes a mandatory field 16

17 End Please select the DONE button to confirm your results for KDM have now been successfully submitted to UK NEQAS LI. We do not currently have the functionality to provide each participant with an additional results received receipt or directly record successful Survey Monkey data submission on our own UK NEQAS LI website. For Survey Monkey hosted data submission the completed column on the UK NEQAS LI web page will be labelled as 'n/a' not applicable. 17