Abstract 4685: Characterization of variants of uncertain significance (VUS) in breast and ovarian cancer predisposition genes

PURPOSE Genetic testing has clinical utility in the management of patients with hereditary cancer syndromes. However, the increased likelihood of encountering a variant of uncertain significance in individuals of non-European descent such as Asians may be challenging to both clinicians and patients. This study aims to evaluate the impact of variant reclassification in an Asian country with variants of uncertain significance reported in cancer predisposition genes. METHODS A retrospective analysis of patients seen at the Cancer Genetics Service at the National Cancer Centre Singapore between February 2014 and March 2020 was conducted. The frequency, direction, and time to variant reclassification were evaluated by comparing the reclassified report against the original report. RESULTS A total of 1,412 variants of uncertain significance were reported in 49.9% (845 of 1,695) of patients. Over 6 years, 6.7% (94 of 1,412) of variants were reclassified. Most variants of uncertain significance (94.1%, 80 of 85) were downgraded to benign or likely benign variant, with a smaller proportion of variants of uncertain significance (5.9%, 5 of 85) upgraded to pathogenic or likely pathogenic variant. Actionable variants of uncertain significance upgrades and pathogenic or likely pathogenic variant downgrades, which resulted in management changes, happened in 31.0% (39 of 126) of patients. The median and mean time taken for reclassification were 1 and 1.62 year(s), respectively. CONCLUSION We propose a clinical guideline to standardize management of patients reported to have variants of uncertain significance. Management should be based on the patient’s personal history, family history, and variant interpretation. For clinically relevant or suspicious variants of uncertain significance, follow-up is recommended every 2 years, as actionable reclassifications may happen during this period.

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Initial Results of Multigene Panel Testing for Hereditary Breast and Ovarian Cancer and Lynch Syndrome

The American Surgeon ◽

10.1177/000313481508101006 ◽

2015 ◽

Vol 81 (10) ◽

pp. 941-944 ◽

Cited By ~ 8

Author(s):

Dt R. Howarth ◽

Sharon S. Lum ◽

Pamela Esquivel ◽

Carlos A. Garberoglio ◽

Maheswari Senthil ◽

...

Keyword(s):

Ovarian Cancer ◽

Genetic Testing ◽

Breast And Ovarian Cancer ◽

Variants Of Uncertain Significance ◽

Panel Testing ◽

Pathogenic Mutations ◽

Uncertain Significance ◽

Multigene Panel Testing ◽

The Impact ◽

Multigene Panel

Multigene panel testing for hereditary cancer risk has recently become commercially available; however, the impact of its use on patient care is undefined. We sought to evaluate results from implementation of panel testing in a multidisciplinary cancer center. We performed a retrospective review of consecutive patients undergoing genetic testing after initiating use of multigene panel testing at Loma Linda University Medical Center. From February 13 to August 25, 2014, 92 patients were referred for genetic testing based on National Comprehensive Cancer Network guidelines. Testing was completed in 90 patients. Overall, nine (10%) pathogenic mutations were identified: five BRCA1/2, and four in non-BRCA loci. Single-site testing identified one BRCA1 and one BRCA2 mutation. The remaining mutations were identified by use of panel testing for hereditary breast and ovarian cancer. There were 40 variants of uncertain significance identified in 34 patients. The use of panel testing more than doubled the identification rate of clinically significant pathogenic mutations that would have been missed with BRCA testing alone. The large number of variants of uncertain significance identified will require long-term follow-up for potential reclassification. Multigene panel testing provides additional information that may improve patient outcomes.

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A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer

10.1101/031419 ◽

2015 ◽

Author(s):

Eliseos J Mucaki ◽

Natasha G Caminsky ◽

Ami M Perri ◽

Ruipeng Lu ◽

Alain Laederach ◽

...

Keyword(s):

Ovarian Cancer ◽

Sequence Analysis ◽

Repetitive Sequences ◽

Low Frequency ◽

Unified Framework ◽

Breast And Ovarian Cancer ◽

Protein Coding ◽

Variants Of Uncertain Significance ◽

Uncertain Significance ◽

Coding Variants

Background: Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT). Methods: We captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream of ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, and TP53 were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk patients without identified mutations in BRCA1/2. Aside from protein coding changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented by in silico and laboratory analysis of UTR structure. Results: 15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels). Conclusions: We have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.

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Performance of In Silico Prediction Tools for the Detection of Germline Copy Number Variations in Cancer Predisposition Genes in 4208 Female Index Patients with Familial Breast and Ovarian Cancer

Cancers ◽

10.3390/cancers13010118 ◽

2021 ◽

Vol 13 (1) ◽

pp. 118

Author(s):

Louisa Lepkes ◽

Mohamad Kayali ◽

Britta Blümcke ◽

Jonas Weber ◽

Malwina Suszynska ◽

...

Keyword(s):

Ovarian Cancer ◽

In Silico ◽

Copy Number ◽

Gc Content ◽

Copy Number Variations ◽

Cancer Predisposition ◽

Predictive Values ◽

Prediction Tools ◽

Predisposition Genes ◽

Female Index

The identification of germline copy number variants (CNVs) by targeted next-generation sequencing (NGS) frequently relies on in silico CNV prediction tools with unknown sensitivities. We investigated the performances of four in silico CNV prediction tools, including one commercial (Sophia Genetics DDM) and three non-commercial tools (ExomeDepth, GATK gCNV, panelcn.MOPS) in 17 cancer predisposition genes in 4208 female index patients with familial breast and/or ovarian cancer (BC/OC). CNV predictions were verified via multiplex ligation-dependent probe amplification. We identified 77 CNVs in 76 out of 4208 patients (1.81%); 33 CNVs were identified in genes other than BRCA1/2, mostly in ATM, CHEK2, and RAD51C and less frequently in BARD1, MLH1, MSH2, PALB2, PMS2, RAD51D, and TP53. The Sophia Genetics DDM software showed the highest sensitivity; six CNVs were missed by at least one of the non-commercial tools. The positive predictive values ranged from 5.9% (74/1249) for panelcn.MOPS to 79.1% (72/91) for ExomeDepth. Verification of in silico predicted CNVs is required due to high frequencies of false positive predictions, particularly affecting target regions at the extremes of the GC content or target length distributions. CNV detection should not be restricted to BRCA1/2 due to the relevant proportion of CNVs in further BC/OC predisposition genes.

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Psychological and Behavioral Implications of Screening for Breast or Ovarian Cancer Predisposition Genes BRCA1 and BRCA2

Baylor University Medical Center Proceedings ◽

10.1080/08998280.1999.11930150 ◽

1999 ◽

Vol 12 (2) ◽

pp. 87-92

Author(s):

Karen T. Lesniak ◽

Tonya G. Callaway ◽

Becky Althaus ◽

Charles A. Guarnaccia ◽

Joanne L. Blum

Keyword(s):

Ovarian Cancer ◽

Cancer Predisposition ◽

Brca1 And Brca2 ◽

Predisposition Genes

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Prevalence of hereditary breast and ovarian cancer predisposition gene mutations among 882 HBOC high-risk Chinese individuals

Gynecologic Oncology ◽

10.1016/j.ygyno.2020.05.457 ◽

2020 ◽

Vol 159 ◽

pp. 264

Author(s):

D. Shao ◽

C. Zhu ◽

F. Guo

Keyword(s):

Ovarian Cancer ◽

High Risk ◽

Gene Mutations ◽

Cancer Predisposition ◽

Breast And Ovarian Cancer ◽

Cancer Predisposition Gene

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Functional CDKN2A assay identifies frequent deleterious alleles misclassified as variants of uncertain significance

eLife ◽

10.7554/elife.71137 ◽

2022 ◽

Vol 11 ◽

Author(s):

Hirokazu Kimura ◽

Raymond M Paranal ◽

Neha Nanda ◽

Laura D Wood ◽

James R Eshleman ◽

...

Keyword(s):

Functional Characterization ◽

Ductal Adenocarcinoma ◽

Proliferation Assay ◽

Variants Of Uncertain Significance ◽

Pathogenic Variants ◽

Deleterious Alleles ◽

Increased Risk ◽

Uncertain Significance

Pathogenic germline CDKN2A variants are associated with an increased risk of pancreatic ductal adenocarcinoma (PDAC). CDKN2A variants of uncertain significance (VUSs) are reported in up to 4.3% of patients with PDAC and result in significant uncertainty for patients and their family members as an unknown fraction are functionally deleterious, and therefore, likely pathogenic. Functional characterization of CDKN2A VUSs is needed to reclassify variants and inform clinical management. 29 germline CDKN2A VUSs previously reported in patients with PDAC or in ClinVar were evaluated using a validated in vitro cell proliferation assay. 12 of the 29 CDKN2A VUSs were functionally deleterious (11 VUSs) or potentially functionally deleterious (1 VUS) and were reclassified as likely pathogenic variants. Thus, over 40% of CDKN2A VUSs identified in patients with PDAC are functionally deleterious and likely pathogenic. When incorporating VUSs found to be functionally deleterious, and reclassified as likely pathogenic, the prevalence of pathogenic/likely pathogenic CDKN2A in patients with PDAC reported in the published literature is increased to up to 4.1% of patients, depending on family history. Therefore, CDKN2A VUSs may play a significant, unappreciated role in risk of pancreatic cancer. These findings have significant implications for the counselling and care of patients and their relatives.

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BRCA1 and BRCA2 mutations in breast and ovarian cancer families from south west Colombia

Colombia Medica ◽

10.25100/cm.v50i3.2385 ◽

2020 ◽

pp. 163-175

Author(s):

Laura Cifuentes-C ◽

Ana Lucia Rivera-Herrera ◽

Guillermo Barreto

Keyword(s):

Breast Cancer ◽

Ovarian Cancer ◽

In Silico ◽

Novel Mutation ◽

In Silico Analysis ◽

Moderate Increase ◽

Brca1 And Brca2 ◽

Variants Of Uncertain Significance ◽

Uncertain Significance ◽

Colombian Pacific

Introduction: Breast cancer is the most common neoplasia of women from all over the world especially women from Colombia. 5%10% of all cases are caused by hereditary factors, 25% of those cases have mutations in the BRCA1/BRCA2 genes. Objective: The purpose of this study was to identify the mutations associated with the risk of familial breast and/or ovarian cancer in a population of Colombian pacific. Methods: 58 high-risk breast and/or ovarian cancer families and 20 controls were screened for germline mutations in BRCA1 and BRCA2, by Single Strand Conformation Polymorphism (SSCP) and sequencing. Results: Four families (6.9%) were found to carry BRCA1 mutations and eight families (13.8%) had mutations in BRCA2. In BRCA1, we found three Variants of Uncertain Significance (VUS), of which we concluded, using in silico tools, that c.8112C>G and c.3119G>A (p.Ser1040Asn) are probably deleterious, and c.3083G>A (p.Arg1028His) is probably neutral. In BRCA2, we found three variants of uncertain significance: two were previously described and one novel mutation. Using in silico analysis, we concluded that c.865A>G (p.Asn289Asp) and c.6427T>C (p.Ser2143Pro) are probably deleterious and c.125A>G (p.Tyr42Cys) is probably neutral. Only one of them has previously been reported in Colombia. We also identified 13 polymorphisms (4 in BRCA1 and 9 in BRCA2), two of them are associated with a moderate increase in breast cancer risk (BRCA2 c.1114A>C and c.875566T>C). Conclusion: According to our results, the Colombian pacific population presents diverse mutational spectrum for BRCA genes that differs from the findings in other regions in the country.

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