1. Navigating from Somatic Tumor Testing to Germline Genetic Testing
45 minutes x 2 presentations

2. Somatic Testing vs. Germline Testing
Identifies mutations in the tumor (ie. acquired changes)
Performed on tumor tissue
Patient has cancer
Purpose is to identify treatment options, determine prognosis
Ordered by oncologist
Patient not often consented
Germline
Identifies mutations in the germline (ie. mutations you are born with)
Performed on blood/saliva
Patient may be unaffected
Purpose is to identify patients with inherited cancer predisposition syndromes
Often ordered by GC, sometimes by oncologist, surgeon, PCP, etc.
Patient often receives counseling
So all of this is GENETIC testing…but what are the differences?

3. What genes are analyzed?
198 gene panel offered here at Markey

4. What genes are they analyzing?
Panel sizes vary…
FoundationOne analyzes 315 genes.
Many of these are genes that are clinically actionable and known to cause hereditary cancer if they are identified in the germline.
Caris analyzes 617 biomarkers, >500 of these biomarkers are genes (point mutations, sequencing, etc.)
Guardant analyzes 73 genes (also now doing tumor free testing, analyzing blood and looking at cell free tumor DNA)
Many other labs out there offering testing—many now doing liquid biopsies which do not require tumor

5. ASCO Policy Statement
ASCO supports the communication to patients of medically relevant incidental germline findings from somatic mutation profiling conducted in the clinical setting. Oncology providers should communicate the potential for incidental and secondary germline information to patients before conducting somatic mutation profiling and should review the potential benefits, limitations, and risks before testing.
So what do organizations think of this tumor testing and what we do with this information?? Well, ASCO has a policy statement that they updated in Nov
ASCO Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility – from November 2015
Addresses concerns regarding multigene panel testing for germline testing, quality assurance in genetic testing, education of oncology professionals, access to cancer genetic services, and also what we’re here to discuss…germline implications of somatic mutation profiling.

6. Ready for Surprises?
NGS offers promise, but poses significant challenges for oncologists who are ill prepared to handle incidental findings that have clinical implications for at- risk family members. This report underscores the need for oncologists to develop a framework for pre- and post- communication of risks to patients undergoing routine tumor-only sequencing
Goal of this paper was to describe the spectrum of potential and germline genomic events incidentally identified during routine somatic tumor sequencing and to provide a framework for pre- and post-test consent and counseling for patients and families. A panel of med oncs, cancer geneticists, and genetic counselors retrospectiely grouped 111 patients based on probability of possessing a potentially inherited mutation in a cancer susceptibility gene both prior to and after incorporating tumor-only results. These were GI malignancies. Identified 3 BRCA2 germline mutations. Underscores need for oncologists to develop a framework for pre- and post-test communication to patients undergoing testing.

7. Discussion Prior to Testing
Catennaci et al.
In this paper, they identified mutations in EACH of these groups.
Catenacci et al. 2015

8. How often are germline findings identified in tumor?
Meric-Bernstam et al. (2016)
1000 advanced cancer patients offered tumor-normal sequencing with 202-gene panel (19 clinically actionable in germline) at MD Anderson
422/100 (42%) had pathogenic somatic variant in one of 19 genes
43/1000 (4.3%) had a likely pathogenic germline variant identified
Tumor types included breast, colon, brain, melanoma, sarcoma, ovary, head and neck
Schrader et al. (2016)
1566 advanced cancer patients offered tumor-normal sequencing with MSK-IMPACT panel (341-gene panel)
198/1566 (12.6%) had pathogenic germline variant in cancer susceptibility gene
Germline findings concordant with cancer type in only 81/198 (40.9%) cases
Seifert et al. (2016)
439 unselected cancer patients offered tumor-normal sequencing of 247 genes (36 genes strongly associated with hereditary cancer) at UNC
19/439 (4.3%) had pathogenic germline variant
12/19 (63%) were concordant with cancer type
These studies were all tumor-normal paired so they could identify germline variants in these patients.
Differences in numbers may be due to number of genes on panel..Seifert panel did not include PALB2, PMS2, BRIP1, etc.
4-12% of mutations may be germline. Fits with 5-10% of cancers being hereditary, so makes sense.
Few things to note: these were done in all tumor types, not just breast, colon, etc. Germline findings were only concordant with the type of cancer in 41% or 63% of cases.

9. Percentage of Somatic vs. Germline Variants
From MD Anderson study. Which genes did they identify pathogenic variants in?
B) The percentage of somatic vs. germline variants.
TP53 somatic variants were much more common. 337 patients had somatic mutation, 10 had germline mutations
Compare to BRCA1 where there were 3 patients with somatic and 11 with germline and 3 with somatic BRCA2 mutations and 10 with germline BRCA2 mutations
Okay…so it’s gonna happen. WHEN do you refer for germline testing? WHO do you refer?
Meric-Bernstam et al.

10. Suggestive of Germline Finding
All BRCA1 and BRCA2 pathogenic variants regardless of tumor type (NCCN guideline)
Founder mutations (ie. MSH2 exon 1-6 deletion, TP53 R337H)
Uncommonly somatically mutated genes (ie. CHEK2, PALB2)
Gene consistent with phenotype
Same mutation detected in multiple primary tumors
Underlying mutation pattern (ie. hypermutated tumor)
High mutant allele frequency (MAF)
Uncommonly somatically mutated genes – if mutation is in a gene that isn’t often mutated or not often mutated in that specific tumor, may be suspicious for germline mutation. If mutation in gene is common in that tumor type, unlikely to be germline.
Gene consistent with phenotype—high penetrant genes with clear phenotype—triage based on phenotype…RB1 with no retinoblastoma? Unlikely. NF1 mutation with no neurofibromas? Unlikely.
--moderate risk genes – depend on tumor type, family history, mutant allele frequency
Hypermutated tumor – MMR genes, POLE, POLED1

11. Mutant Allele Frequency
Mutant allele frequency (MAF) can be suggestive of a germline mutation
MAF >50% suggest loss of heterozygosity (LOH)
Germline mutations in tumor suppressor genes often undergo LOH events
High MAF also seen in normal course of tumor development without a germline mutation

12. Mutant Allele Frequencies
Do not use MAF to rule OUT a germline mutation!
Incidental Germline Variants…
Black line shows median mutant allele frequency (46% in germline, range %) (33.4% in somatic, range 1.2%-96.5%)
Meric-Bernstam et al.

13. Refer If Tumor Testing Is Normal?
Regardless of tumor results, if the patient meets criteria for germline testing (NCCN guidelines), REFER!
Large deletion in somatic can mask germline point mutation
Somatic vs. germline labs cover different areas of the genes
Pathogenic variant in germline may not be considered pathogenic in somatic, therefore not reported
Not all hereditary cancer genes are on tumor panels
Yes!
These tests are not the same. Somatic testing is not a substitute for germline testing and vice-versa. If the patient meets criteria for germline testing, still refer them even if tumor testing is normal.

14. Considerations for incidental findings
Insurance coverage
Single-site vs. full panel
Patients confused about germline vs. somatic testing
Patient previously declined counseling/testing
Sick patients
Need to be seen relatively quickly
May not directly impact patient
Who do we disclose results to?

15. Markey Cancer Center Genetic Counseling
Questions or want to refer a patient? Justine M. Cooper, MS, CGC