Recommendations from HL7 Clinical Genomics & Anatomic Pathology Workgroups, NCBI, and LOINC/Lister Hill Center at NLM To the College of American Pathologists Cancer Biomarker Reporting Template Committee September 25, 2013 Updated for sharing re: IOM initiative Feb 17, 2015

Clinical Workflow for NGS of Cancer

Confidential Dana-Farber / Partners HealthCare – Copyright 2011 – All Rights Reserved LOINC Panels/Codes Already Serve as a Template for DNA Variant Details Extension of LOINC codes for coding of somatic biomarkers is a natural evolution. LOINC Code NameExample valuesource Transcript Reference Sequence Identifier NM_ NCBI RefSeq Gene identifierEGFRHGNC Nomenclature DNA Sequence Variationc.2573T>GHGVS Nomenclature DNA Sequence Variation identifier rs NCBI dbSNP (in combination with nucleotide change and somatic/germline indicator) Genomic source class Somatic, Likely Somatic, Unknown Origin, Likely Germline, Germline LOINC Answer List Drug efficacy sequence variation interpretation Resistant, Responsive, Presumed Resistant, Presumed Responsive, Unknown Significance, Benign, Presumed Benign, Presumed Non- Responsive LOINC Answer List

Goal: Cross Devise Compatibility  Platform Agnostic Source:

CAP Cancer BioMarker Reporting Committee Biomarker - Problem, ROI and Scope College of American Pathologists’ Biomarker Reporting Committee Problem 1.Clinicians think of biomarkers (e.g. : EGFR Exon 19 deletions) and need to understand non- standardized results (e.g. biomarker, HGVS nucleotide change, COSMIC representation or HGVS amino acid change) 2.Bioinformaticists think of specific nucleotide changes 3.Cancer Registrars also need to understand non-standardized results (as listed above), largely dependant on testing platform 4.From Report: How can clinicians connect nucleotide change with clinical guidelines, which are often expressed in terms of biomarkers? 5.From Lab: How can a molecular pathologist map from the nucleotide change to the biomarker? ROI Eliminate bottleneck in reporting, by enabling algorithms to map from identified mutations to biomarkers. Increase efficiency of Molecular Pathologists (a very limited resource). Scope College of American Pathologists – Cancer BioMarker Reporting Templates – somatic, nucleotide biomarkers for clinical reporting

Mapping from Machine Generated Sequence Variation to Cancer BioMarker Reporting Template Lung Cancer BioMarker Reporting Template + EGFR Mutational Analysis (Note B) + ___ No mutation detected (wild-type EGFR allele) + ___ Mutation identified (select all that apply) + ___ Exon 18 Gly719# + ___ Exon 19 deletion# + ___ Exon 20 insertion## + ___ Exon 20 Thr790Met### + ___ Exon 21 Leu858Arg# + ___ Other (specify)####: ______________________ + ___ Cannot be determined (explain): __________ # This EGFR activation mutation is associated with response to EGFR tyrosine kinase inhibitors. ## This form of EGFR activating mutation is generally associated with resistance to EGFR tyrosine kinase inhibitors although insertions at or before position 768 can be associated with sensitivity. ### This mutation is typically secondary to other EGFR activating mutations and is associated with acquired resistance to tyrosine kinase inhibitor therapy. If seen in untreated/pretreated patients, may be present in the germline and indicate a hereditary cancer syndrome, in which case genetic counseling is suggested. #### There is limited data on response to EGFR tyrosine kinase inhibitors for many of the uncommon EGFR activating mutations. Machine Readable to BioMarker Mapping Machine readable version from NGS: Chr: 7 Seq: NC_ genomic start: Ref: C Allele: T HGVS Clinical Genetics Representation: NM_ : c.2369C>T NP_ :p.Thr790Met Human Understandable Biomarker: EGFR Exon 20 Thr790Met Machine (platform NGS) Molecular Pathologist (platform ABI Seq) Oncologist (platform kit)

Source: Is it these specific EGFR Exon 19 deletions or ALL EGFR Exon 19 deletions?

Multiple Transcript Reference Sequences Which is the canonical Transcript Reference Sequence & associated Exon placement???

Recommendations from HL7 Clinical Genomics & Anatomic Pathology Workgroups, NCBI, and LOINC/Lister Hill Center at NLM For each Gene: provide a canonical reference sequence For each Exon: derived from the canonical reference sequence For each term ‘deletion’, ‘insertion’, ‘mutation’: define what is meant (e.g. mutation = DNA change type is ‘missense’, etc… OR if ‘Exon 20 deletion’ is it all deletions in Exon 20 or a specific list of Exon 20 deletions)? Cancer biomarkers will be encoded in LOINC and provided to NCBI for inclusion in the MedGen (medical concept terminology) and mapped to variants in ClinVar and if available tests within Genetic Test Registry. In this way, biomarkers will be mapped to specific changes at the cDNA, protein and genomic coordinate levels, as well as be maintained over time as genome builds change and available for inclusion in bioinformatic pipelines. In addition, laboratories can report actionable biomarkers in a platform independent manner, while providing additional information on evidence (e.g. genomic coordinates or results from test kit or PCR & gel).