bims-lifras 2024-06-02 papers

Issue of 2024–06–02
six papers selected by
Joanna Zawacka, Karolinska Institutet

JCO Precis Oncol. 2024 May;8 e2300466

Genetic Testing Utilization: Discrepancies Between Somatic and Germline Results in Patients With Cancer Reviewed at the UW Health Precision Medicine Molecular Tumor Board.

Isaac P Horn, Anna L Zakas, Kelcy J Smith-Simmer, Laura E Birkeland, Rachel Sundstrom, Mark E Burkard, Jennifer M Weiss.

PURPOSE: Somatic and germline testing are increasingly used to estimate risks for patients with cancer. Although both germline testing and somatic testing can identify genetic variants that could change a patient's care and eligible treatments, the aims of these tests and their technologies are fundamentally different and cannot be used interchangeably. This study examines the timing and results of somatic and germline genetic testing for patients with cancer at UW Health.
METHODS: Eight hundred and seventy-seven participants underwent somatic genetic testing, which was reviewed by the Precision Medicine Molecular Tumor Board (PMMTB). Patients were diagnosed with cancers, including breast, colorectal, endometrial, pancreatic, or ovarian cancer, and met National Comprehensive Cancer Network criteria for germline genetic testing. Germline testing details were collected by medical record review.
RESULTS: The results of this study found that only 310 patients (35%) had germline evaluation before PMMTB review. The percent of germline pathogenic/likely pathogenic variants identified in actionable genes was 28%. Most germline variants were identified in the BRCA1 (26%) and BRCA2 (28%) genes. In total, 65% (54/83) of germline variants were detected with both germline testing and somatic testing; however, 35% (29/83) of germline variants were not identified on somatic results. These results demonstrate the importance of combination germline and somatic testing.
CONCLUSION: This study highlights the differences in genetic testing types and demonstrates that conducting germline testing at earlier stages of diagnoses is necessary to identify potentially actionable and treatment-specific variants in patients with cancer.

DOI: https://doi.org/10.1200/PO.23.00466

J Med Genet. 2024 May 28. pii: jmg-2023-109772. [Epub ahead of print]

Variant classification changes over time in the clinical molecular diagnostic laboratory setting.

Elan Hahn, Chloe Mighton, Yael Fisher, Andrew Wong, Vanessa Di Gioacchino, Nicholas Watkins, Justin Mayers, Yvonne Bombard, George S Charames, Jordan Lerner-Ellis.

BACKGROUND: Variant classification in the setting of germline genetic testing is necessary for patients and their families to receive proper care. Variants are classified as pathogenic (P), likely pathogenic (LP), uncertain significance (VUS), likely benign (LB) and benign (B) using the standards and guidelines recommended by the American College of Medical Genetics and the Association for Molecular Pathology, with modifications for specific genes. As the literature continues to rapidly expand, and evidence continues to accumulate, prior classifications can be updated accordingly. In this study, we aim to characterise variant reclassifications in Ontario.
METHODS: DNA samples from patients seen at hereditary cancer clinics in Ontario from January 2012 to April 2022 were submitted for testing. Patients met provincial eligibility criteria for testing for hereditary cancer syndromes or polycystic kidney disease. Reclassification events were determined to be within their broader category of significance (B to LB or vice versa, or P to LP or vice versa) or outside of their broader category as significance (ie, significant reclassifications from B/LB or VUS or P/LP, from P/LP to VUS or B/LB, or from VUS to any other category).
RESULTS: Of the 8075 unique variants included in this study, 23.7% (1912) of variants were reassessed, and 7.2% (578) of variants were reclassified. Of these, 351 (60.7%) variants were reclassified outside of their broader category of significance. Overall, the final classification was significantly different for 336 (58.1%) variants. Importantly, most reclassified variants were downgraded to a more benign classification (n=245; 72.9%). Of note, most reclassified VUS was downgraded to B/LB (n=233; 84.7%).
CONCLUSIONS: The likelihood for reclassification of variants on reassessment is high. Most reclassified variants were downgraded to a more benign classification. Our findings highlight the importance of periodic variant reassessment to ensure timely and appropriate care for patients and their families.

Keywords: Clinical Decision-Making; Genetic Counselling; Genetic Predisposition to Disease; Genetic Variation; Germ-Line Mutation

DOI: https://doi.org/10.1136/jmg-2023-109772

Science. 2024 May 31. 384(6699): 961-962

Germline variants alter immune surveillance.

Nicola Waddell, Venkateswar Addala.

Germline-derived epitopes shape tumor development through immunoediting.

DOI: https://doi.org/10.1126/science.adp7370

Cancer. 2024 May 29.

The role of family history in predicting germline pathogenic variant carriers who develop pancreatic cancer: Results of a multicenter collaboration.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) surveillance is recommended for some individuals with a pathogenic or likely pathogenic variant (PV/LPV) in a PDAC susceptibility gene; the recommendation is often dependent on family history of PDAC. This study aimed to describe PDAC family history in individuals with PDAC who underwent genetic testing to determine the appropriateness of including a family history requirement in these recommendations.
METHODS: Individuals with PDAC with a germline heterozygous PV/LPV in ATM, BRCA1, BRCA2, EPCAM, MLH1, MSH2, MSH6, PALB2, or PMS2 (PV/LPV carriers) were assessed for family history of PDAC in first-degree relatives (FDRs) or second-degree relatives (SDRs) from nine institutions. A control group of individuals with PDAC without a germline PV/LPV was also assessed.
RESULTS: The study included 196 PV/LPV carriers and 1184 controls. In the PV/LPV carriers, 25.5% had an affected FDR and/or SDR compared to 16.9% in the control group (p = .004). PV/LPV carriers were more likely to have an affected FDR compared to the controls (p = .003) but there was no statistical difference when assessing only affected SDRs (p = .344).
CONCLUSIONS: Most PV/LPV carriers who developed PDAC did not have a close family history of PDAC and would not have met most current professional societies' recommendations for consideration of PDAC surveillance before diagnosis. However, PV/LPV carriers were significantly more likely to have a family history of PDAC, particularly an affected FDR. These findings support family history as a risk modifier in PV/LPV carriers, and highlight the need to identify other risk factors.

Keywords: genetic testing; germline mutation; pancreatic cancer; risk factors

DOI: https://doi.org/10.1002/cncr.35383

Res Sq. 2024 May 14. pii: rs.3.rs-4351728. [Epub ahead of print]

Newborn Screening for Li-Fraumeni Syndrome: Patient Perspectives.

Makenna Beigh, Jennie Vagher, Rachel Codden, Luke D Maese, Sabina Cook, Amanda Gammon.

Background Li-Fraumeni syndrome (LFS) is an inherited cancer predisposition syndrome with an estimated prevalence of 1 in 3,000-5,000 individuals. LFS poses a significant cancer risk throughout the lifespan, with notable cancer susceptibility in childhood. Despite being predominantly inherited, up to 20% of cases arise de novo . Surveillance protocols facilitate the reduction of mortality and morbidity through early cancer detection. While newborn screening (NBS) has proven effective in identifying newborns with rare genetic conditions, even those occurring as rarely as 1 in 185,000, its potential for detecting inherited cancer predispositions remains largely unexplored. Methods This survey-based study investigates perspectives toward NBS for LFS among individuals with and parents of children with LFS receiving care at single comprehensive cancer center in the U.S. Results All participants unanimously supported NBS for LFS (n = 24). Reasons included empowerment (83.3%), control (66.7%), and peace of mind (54.2%), albeit with concerns about anxiety (62.5%) and devastation (50%) related to receiving positive results. Participants endorsed NBS as beneficial for cancer detection and prevention (91.7%), research efforts (87.5%), and family planning (79.2%) but voiced apprehensions about the financial cost of cancer surveillance (62.5%), emotional burdens (62.5%), and insurance coverage and discrimination (54.2%). Approximately 83% of respondents believed that parental consent should be required to screen newborns for LFS. Conclusion This study revealed strong support for NBS for LFS despite the recognition of various perceived benefits and risks. These findings underscore the complex interplay between clinical, psychosocial, and ethical factors in considering NBS for LFS from the perspective of the LFS community.

DOI: https://doi.org/10.21203/rs.3.rs-4351728/v1

JCO Oncol Pract. 2024 May 30. OP2300817

Downstream Revenue Generated by Patients With Hereditary Cancer in the Multigene Panel Testing Era.

Caitlin B Mauer Hall, Brian D Reys, Amber P Gemmell, Connor L Campbell, Sara M Pirzadeh-Miller.

PURPOSE: Patients with hereditary cancer syndromes face increased medical management recommendations to address their cancer risks. As multigene panels are the standard of testing today, more patients needing clinical intervention are being identified. This study calculates the downstream revenue (DSR) generated by patients ascertained by a genetic counselor (GC) with a hereditary cancer likely pathogenic/pathogenic variant (LPV/PV).
METHODS: Retrospective chart review was performed for patients seen in a high-volume cancer genetics clinic between October 1, 2009, and December 31, 2021, with LPV/PVs in hereditary cancer predisposition genes. DSR and work relative value units (wRVUs) were calculated for each patient before and after they met with a GC. Subgroup analyses calculated DSR/wRVUs from patients affected and unaffected with cancer and those whose genetic counseling visit was the first at the institution (naїve).
RESULTS: A total of 978 patients were available for analysis after exclusions were applied. Patients generated $73.06 million (M) in US dollars (USD) in DSR and 54,814 wRVUs after their initial genetic counseling visit. Unaffected patients (n = 370, 37.8%) generated $11.38M (USD) and 13,879 wRVUs; affected patients (n = 608, 62.2%) generated $61.68M (USD) and 40,935 wRVUs. Naïve patients (n = 367, 37.5%) generated $15.39M (USD) and 11,811 wRVUs; established patients (n = 611, 62.5%) generated $57.67M (USD) and 43,003 wRVUs. Unaffected, naïve patients (n = 204, 20.9%) generated $5.48M (USD) and 5,186 wRVUs.
CONCLUSION: By identifying patients with hereditary cancer, GCs can bring in substantial DSR for their institution. Naïve and unaffected patients provide the greatest GC value-add as these patients represent new business and revenue sources to the institution. As multigene panels continue to expand, the number of patients needing downstream services will increase. Recognizing patients at increased cancer risk will improve patient outcomes while simultaneously providing DSR for institutions.

DOI: https://doi.org/10.1200/OP.23.00817