Next-generation sequencing (NGS) technology has led to the ability to test for multiple cancer susceptibility genes simultaneously without significantly increasing cost or turnaround time. With growing usage of multigene testing for inherited cancer, ongoing education for nurses and other health-care providers about hereditary cancer screening is imperative to ensure appropriate testing candidate identification, test selection, and posttest management. The purpose of this review article is to (1) provide an overview of how NGS works to detect germline mutations, (2) summarize the benefits and limitations of multigene panel testing, (3) describe risk categories of cancer susceptibility genes, and (4) highlight the counseling considerations for patients pursuing multigene testing.
ABSTRACT Purpose Efficient and scalable solutions are needed to identify patients who qualify for germline cancer genetic testing. We evaluated the clinical validity of a brief, patient-administered hereditary cancer risk assessment digital tool programmed to assess if patients meet criteria for germline genetic testing, based on personal and family history, and in line with national guidelines. Methods We applied the tool to cases seen in a nationwide telehealth genetic counseling practice. Validity of the tool was evaluated by comparing the tool’s assessment to that of the genetic counselor who saw the patient. Patients’ histories were extracted from genetic counselor-collected pedigrees and input into the tool by the research team to model how a patient would complete the tool. We also validated the tool’s assessment of which specific aspects of the personal and family history met criteria for genetic testing. Results Of the 152 cases (80% ((121/152)) female, mean age 52.3), 56% (85/152) had a personal history of cancer and 66% (99/152) met genetic testing criteria. The tool and genetic counselor agreed in 96% (146/152) of cases. Most disagreements (4/6; 67%) occurred because the GC’s assessment relied on details the tool was not programmed to collect since patients typically don’t have access to the relevant information (pathology details, risk models). We also found complete agreement between the tool and research team on which specific aspects of the patient’s history met criteria for genetic testing. Conclusion We observed a high level of agreement with genetic counselor assessments, affirming the tool’s clinical validity in identifying individuals for hereditary cancer predisposition testing and its potential for increasing access to hereditary cancer risk assessment.
Several genes are associated with hereditary susceptibility to breast cancer. Most notably these include BRCA1 and BRCA2; however, other less common gene mutations which confer elevated breast cancer risk are associated with Cowden syndrome, Li-Fraumeni syndrome, Peutz-Jeghers syndrome, ataxia-telangiectasia heterozygosity and hereditary diffuse gastric cancer. In this article we highlight the genetic epidemiology, gene function, genotype-phenotype correlations, cancer risks and clinicopathologic findings for the cancer susceptibility genes related to these syndromes. We also examine genes, such as CHEK2, which confer a lower penetrance for breast cancer in comparison to these highly penetrant genes.
Clinical genomic tests increasingly use a next-generation sequencing (NGS) platform due in part to the high fidelity of variant calls, yet rare errors are still possible. In germline DNA screening, failure to correct such errors could have serious consequences for patients, who may follow an unwarranted screening or surgical management path. It has been suggested that routine orthogonal confirmation by Sanger sequencing is required to verify NGS results, especially low-confidence positives with depressed allele fraction (<30% of alternate allele). We evaluated whether an alternative method of confirmation—software-assisted manual call review—performed comparably with Sanger confirmation in >15,000 samples. Licensed reviewers manually inspected both raw and processed data at the batch, sample, and variant levels, including raw NGS read pileups. Of ambiguous variant calls with <30% allele fraction (1707 total calls at 38 unique sites), manual call review classified >99% (n = 1701) as true positives (enriched for long insertions or deletions and homopolymers) or true negatives (often conspicuous NGS artifacts), with the remaining <1% (n = 6) being mosaic. Critically, results from software-assisted manual review and retrospective Sanger sequencing were concordant for samples selected from all ambiguous sites. We conclude that the confirmation required for high confidence in NGS-based germline testing can manifest in different ways; a trained NGS expert operating platform-tailored review software achieves quality comparable with routine Sanger confirmation.
ABSTRACT Clinical genomic tests increasingly utilize a next generation sequencing (NGS) platform due in part to the high fidelity of variant calls, yet rare errors are still possible. In hereditary cancer screening, failure to correct such errors could have serious consequences for patients, who may follow an unwarranted screening or surgical-management path. It has been suggested that routine orthogonal confirmation via Sanger sequencing is required to verify NGS results, especially low-confidence positives with depressed allele fraction (<30% of alternate allele). We evaluated whether an alternative method of confirmation—software-assisted manual call review—performed comparably to Sanger confirmation in >15,000 samples. Licensed reviewers manually inspected both raw and processed data at the batch-, sample-, and variant-level, including raw NGS read pileups. Of ambiguous variant calls with <30% allele fraction (1,707 total calls at 38 unique sites), manual call review classified >99% (1,701) as true positives (enriched for long insertions or deletions (“indels”) and homopolymers) or true negatives (often conspicuous NGS artifacts), with the remaining <1% (6) being mosaic. Critically, results from software-assisted manual review and retrospective Sanger sequencing were concordant for samples selected from all ambiguous sites. We conclude that the confirmation required for high confidence in NGS-based germline testing can manifest in different ways: a trained NGS expert operating platform-tailored review software achieves quality comparable to routine Sanger confirmation.
6542 Background: Patients often use both positive and negative BRCA1/BRCA2 genetic test results to aid in surgical management decisions, but little is known about the existence of racial/ethnic differences in the use of genetic test results. The objective of this study was to evaluate differences in rates of contralateral prophylactic mastectomy (CPM) by race. Methods: A retrospective chart review was performed. Women with a personal history of breast cancer who underwent genetic testing for the BRCA1 and BRCA2 genes at our institution between 1996 and 2008 and were eligible for CPM were included in the study. Genetic test result, race/ethnicity as reported by the patient, years of follow-up since receipt of test result, and decision regarding CPM were recorded. Pearson chi square analyses and Fisher's exact tests were performed to test for significance. Results: 881 women were included in the study. Twenty percent (n = 180) were found to have a BRCA1 or BRCA2 mutation, while 80% (n = 701) were found to have an uninformative negative result. The study population was 87% (n = 771) Caucasian; 7% (n = 58) African American; and 6% (n = 52) Hispanic. Median follow up time was 3 years. There were no significant differences in either follow up time or percentages of BRCA positivity, based on race/ethnicity. Among those with a positive result, 45% (67/149) of Caucasians, 33% (5/15) of African Americans, and 50% (8/16) of Hispanics underwent CPM, but this was not statistically significant. Caucasians and Hispanics with positive results were significantly more likely than their counterparts with negative results to undergo CPM (Caucasians, 45%; 67/149 vs. 16%; 101/622; p<.001; Hispanics, 50%; 8/16 vs. 11%; 4/36; p = 0.004), but this same trend was not observed among African Americans (positive results, 33%; 5/15 vs. negative results, 14%; 6/43; p = 0.10). Conclusions: Among those with a BRCA1/BRCA2 mutation, there does not appear to be any significant difference in the use of CPM based on race/ethnicity. However, Caucasians and Hispanics appear to be more likely than African Americans to use the results of genetic testing to make surgical management decisions. No significant financial relationships to disclose.
Hereditary breast and ovarian cancer syndrome, caused by a germline pathogenic variant in the BRCA1 or BRCA2 (BRCA1/2) genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers.Identification of those who have a BRCA1/2 mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies.We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a next-generation-sequencing-based test to detect pathogenic variation in the BRCA1 and BRCA2 genes.We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy-number variants (CNVs, also known as large rearrangements) with zero errors over a 114-sample validation set consisting of samples from cell lines and deidentified patient samples, including 36 samples with BRCA1/2 pathogenic germline mutations.
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