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Abstract
The use of genetic testing to identify individuals with hereditary cancer syndromes has been widely adopted by clinicians for management of inherited cancer risk. The objective of this study was to develop and validate a 34-gene inherited cancer predisposition panel using targeted capture-based next-generation sequencing (NGS). The panel incorporates genes underlying well-characterized cancer syndromes, such as BRCA1 and BRCA2 (BRCA1/2), along with more recently discovered genes associated with increased cancer risk. We performed a validation study on 133 unique specimens, including 33 with known variant status; known variants included single nucleotide variants (SNVs) and small insertions and deletions (Indels), as well as copy-number variants (CNVs). The analytical validation study achieved 100% sensitivity and specificity for SNVs and small Indels, with 100% sensitivity and 98.0% specificity for CNVs using in-house developed CNV flagging algorithm. We employed a microarray comparative genomic hybridization (aCGH) method for all specimens that the algorithm flags as CNV-positive for confirmation. In combination with aCGH confirmation, CNV detection specificity improved to 100%. We additionally report results of the first 500 consecutive specimens submitted for clinical testing with the 34-gene panel, identifying 53 deleterious variants in 13 genes in 49 individuals. Half of the detected pathogenic/likely pathogenic variants were found in BRCA1 (23%), BRCA2 (23%), or the Lynch syndrome-associated genes PMS2 (4%) and MLH1 (2%). The other half were detected in 9 other genes: MUTYH (17%), CHEK2 (15%), ATM (4%), PALB2 (4%), BARD1 (2%), CDH1 (2%), CDKN2A (2%), RAD51C (2%), and RET (2%). Our validation studies and initial clinical data demonstrate that a 34-gene inherited cancer predisposition panel can provide clinically significant information for cancer risk assessment.
Highlights
It is important to identify individuals with hereditary cancer efficiently and in a cost-effective manner, as they account for 5–10% of all cancers [1]
Gene Selection. e 34-genes selected for this panel are associated with well characterized cancer syndromes, along with more recently discovered genes associated with increased cancer risk (Table 1). e genes selected increase the lifetime risk of cancer of the breast, ovary, colon, rectum, endometrium, pancreas, prostate, neuroendocrine system, and/or other cancer types
Various targeted next-generation sequencing (NGS)-based multigene inherited cancer panels have been developed by clinical diagnostic laboratories [14, 18,19,20,21,22]
Summary
It is important to identify individuals with hereditary cancer efficiently and in a cost-effective manner, as they account for 5–10% of all cancers [1]. NGS technologies perform at higher throughput than Sanger sequencing, since they work in a massively parallel manner [2]. Multigene panel tests utilizing NGS can be a cost-effective and efficient way to detect clinically actionable mutations in appropriately selected patients [3]. Identifying hereditary cancer susceptibility in an individual with a personal and/or family history can be complex. Pathogenic/likely pathogenic variants in multiple genes can be associated with cancer in a specific organ. Ovarian cancer is associated with pathogenic/likely pathogenic variants in multiple genes such as BRCA1, BRCA2, MLH1, BioMed Research International
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