Confirmatory Germline Testing

Jessica Stoll, MS, CGC

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Senior Director, Genetic Counseling

Tempus AI

NYSGTF Upstate NY Genetics Conference

October 9, 2024

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Disclosures

Jessica Stoll is an employee and stockholder of Tempus AI

Outline

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Q&A

Tumor/Normal Matched Testing

Tumor/normal matched design provides more accurate insights through true somatic identification

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Differentiates germline vs somatic variants, �improving accuracy of somatic tumor NGS calls, including Tumor mutational burden assessments

TMB evaluations based only on somatic variants

Identifies potential germline findings that �may have hereditary cancer risk implications

Beaubier N, Bontrager M, Huether R, et al. Integrated genomic profiling expands clinical options for patients with cancer. Nat Biotechnol. 2019;37(11):1351-1360.�Vega DM, Yee LM, McShane LM, et al. Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project. Ann Oncol. 2021;32(12):1626-1636.�Liu YL, Stadler ZK. The Future of Parallel Tumor and Germline Genetic Testing: Is There a Role for All Patients With Cancer?. J Natl Compr Canc Netw. 2021;19(7):871-878.

Image adapted from: Mandelker D, Ceyhan-Birsoy O. Evolving Significance of Tumor-Normal Sequencing in Cancer Care. Trends Cancer. 2020;6(1):31-39.

Potential Germline Findings

Solid Tumor/Normal Testing Can Help You Identify More Patients Who May Benefit From Hereditary Cancer Testing

Findings Published in the Journal of the American Medical Association Network Open

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KEY TAKEAWAYS

• Solid Tumor/Normal testing may identify incidental germline findings in cancers that may not be indicated for hereditary testing*
• The study identified incidental germline findings in 5.4% of patients with cancers lacking hereditary testing guidelines*, compared to a rate of 8.6% for patients with cancers that have hereditary testing guidelines**
• This may increase detection of P/LP germline variants over a guideline-based testing approach

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READ THE FULL PUBLICATION

Yap TA, Ashok A, Stoll J, et al. Prevalence of germline findings among tumors from cancer types lacking hereditary testing guidelines. JAMA Network Open. 2022;5(5). doi:10.1001/jamanetworkopen.2022.13070

* (bladder, brain, lung, esophagus, cholangiocarcinoma and head and neck cancers); ** (breast, ovarian, pancreatic, prostate, endometrial, and colorectal cancers)

Potential Germline Findings Detected in Tumor Types Lacking �Hereditary Cancer Testing Guidelines

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Findings published in the Journal of the American Medical Association Network Open

KEY TAKEAWAYS

• Solid Tumor/Normal testing may identify potential germline findings in cancers that may not be indicated for hereditary testing*
• This may increase detection of P/LP germline variants over a guideline-based testing approach

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* bladder, brain, lung, esophagus, cholangiocarcinoma and head and neck cancers ;

Yap TA, Ashok A, Stoll J, et al. Prevalence of germline findings among tumors from cancer types lacking hereditary testing guidelines. JAMA Netw Open. 2022;5(5):e2213070.

READ THE FULL PUBLICATION

FOR INTERNAL USE ONLY

Germline Testing Based on Somatic Results

FOR INTERNAL USE ONLY

Factors to Assess for Follow-up Germline Testing

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Factors to consider when assessing the need for follow-up germline testing vary between publications

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¹Mandelker D, et al. Germline-focused analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group. Ann Oncol. 2019 Aug 1;30(8):1221-1231. doi: 10.1093/annonc/mdz136.

Existing guidelines are not designed to catch every LP/P germline variant

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ESMO guidelines are based on a “germline conversion rate” of >10%¹

Important considerations

• Germline testing may be necessary despite paired tumor-normal report
• Paired testing may not be validated for germline analysis
• Ensure your gene/variant of interest is covered in the follow-up germline test being considered
• Consider multigene panel testing rather than targeted variant testing
• Tumor testing done on patients with certain hematologic malignancies may require using cultured fibroblasts for germline testing
• Genes that warrant follow-up germline analysis may differ in pediatric versus adult populations
• Genetic counseling if a patient is found to carry a germline variant

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Takeaways

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• VAF can be a helpful metric, but some leniency is needed
• VAF of ~50% is what is expected for heterozygous germline variants
• For some genes such as TP53, APC, RB1, and NF1 younger ages of diagnosis is associated with a higher likelihood of germline conversion
• Not all genes are equally likely to be converted to a germline variant.
• A lower conversion rate to germline is expected for APC, MEN1, PTEN, TP53, and VHL¹
• Founder mutations are more likely to be germline variants
• BRCA1/2
• CHEK2
• MUTYH

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¹Lincoln SE, Nussbaum RL, Kurian AW, et al. Yield and Utility of Germline Testing Following Tumor Sequencing in Patients With Cancer. JAMA Netw Open. 2020;3(10):e2019452. doi:10.1001/jamanetworkopen.2020.19452

50%

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>50 to 80%

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20 to <50%

<20%

>80%

Suspicion for Germline Variant

Germline Conversion Rate

APC

MEN1

PTEN

TP53

VHL

Founder Variants

Microsatellite Instability (MSI)

MSI-High Tumors and Lynch Syndrome

• High prevalence of MMR germline mutations in MSI-High tumors, regardless of primary cancer site
• Highest proportions of Lynch syndrome among patients w/ MSI-H/I tumors were in urothelial (37.5%), colorectal (19%), and gastric (15.4%)

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• Guidelines recommend considering germline testing for any MSI-High or MMR deficient tumor

Latham et al J Clin Oncol 2018

NCCN Genetic/Familial High-Risk Assessment: Colorectal v1.2022

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Confirmation of Variants Suspicious for Germline Presence

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Case Examples

Case Study: Concurrent Testing

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55yo M w/ mCRPC prostate adeno

Clinical history:�Diagnosed age 54�Gleason 8�Fhx: mother w/ breast cancer

Germline Common Hereditary Cancers Panel

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Case Study: Concurrent Testing

KEY TAKEAWAYS

• Somatic testing is not designed to capture all germline mutations
• Additional germline testing may be warranted even in the absence of germline mutations from tumor/normal matched sequencing
• PMS2 germline deletion missed by tumor/normal matched sequencing
• Patient’s personal & family history warranted additional germline work-up
• Germline testing and somatic testing may be complementary in evaluating treatment options
• Patient matched to PARP inhibitor based on somatic BRCA2 mutation
• MSI-High tumor matched to immunotherapy due to the underlying PMS2 germline mutation

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Case Study: Tumor Only vs. Tumor/Normal Matched Testing

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76yo female w/ lung adenocarcinoma

Clinical history:�Family history of lung cancer in a sister

Case Study: Tumor Only vs. Tumor/Normal Matched Testing

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74yo sister diagnosed with lung adenocarcinoma

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Case Study: Tumor Only vs. Tumor/Normal Matched Testing

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Sister #1: Tumor Only Sequencing

Sister #2: Tumor/Normal Matched Sequencing

Case Study: Tumor Only vs. Tumor/Normal Matched Testing

KEY TAKEAWAYS

• Variant allele fraction may be a helpful tool in determining when to consider follow up germline testing
• VAF is affected by multiple factors however and shouldn’t be used as the only determining factor
• Germline mutation in this family appeared on tumor only sequencing at <20% VAF in Sister #1
• Patient clinical and family history should be taken into consideration when considering follow up germline testing
• Sister #2’s tumor/normal matched testing prompted additional evaluation for Sister #1
• Tumor/normal matched sequencing further increases the accuracy of germline vs. somatic variant calling
• May help identify patients that would not have been referred for germline testing and genetic counseling

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Summary

• A tumor/normal matched approach can help improve the accuracy of somatic testing
• This approach may also aid in the identification of germline variants
• There are multiple factors to consider in follow up germline assessment based on somatic results
• Existing recommendations are not designed to capture every germline variant
• Somatic tests have limitations when it comes to germline variant detection
• Patients meeting germline testing criteria may still need additional germline testing in the absence of an obvious germline variant on a somatic test report

Questions?