Abstract
Conventional Sanger sequencing reliably detects the majority of genetic mutations associated with hereditary cancers, such as single-base changes and small insertions or deletions. However, detection of genomic rearrangements, such as large deletions and duplications, requires special technologies. Microarray analysis has been successfully used to detect large rearrangements (LRs) in genetic disorders. We designed and validated a high-density oligonucleotide microarray for the detection of gene-level genomic rearrangements associated with hereditary breast and ovarian cancer (HBOC), Lynch, and polyposis syndromes. The microarray consisted of probes corresponding to the exons and flanking introns of BRCA1 and BRCA2 (≈1,700) and Lynch syndrome/polyposis genes MLH1, MSH2, MSH6, APC, MUTYH, and EPCAM (≈2,200). We validated the microarray with 990 samples previously tested for LR status in BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, MUTYH, or EPCAM. Microarray results were 100% concordant with previous results in the validation studies. Subsequently, clinical microarray analysis was performed on samples from patients with a high likelihood of HBOC mutations (13,124), Lynch syndrome mutations (18,498), and polyposis syndrome mutations (2,739) to determine the proportion of LRs. Our results demonstrate that LRs constitute a substantial proportion of genetic mutations found in patients referred for hereditary cancer genetic testing. The use of microarray comparative genomic hybridization (CGH) for the detection of LRs is well-suited as an adjunct technology for both single syndrome (by Sanger sequencing analysis) and extended gene panel testing by next generation sequencing analysis. Genetic testing strategies using microarray analysis will help identify additional patients carrying LRs, who are predisposed to various hereditary cancers.
Highlights
Sequencing and large rearrangement (LR) analyses detect DNA changes within hereditary cancer genes and are offered to individuals with a personal and/or family history of cancer to identify pathogenic mutation carriers
Patients with pathogenic mutations in BRCA1 or BRCA2 have a diagnosis of hereditary breast and ovarian cancer syndrome (HBOC), a condition for which there are extensive medical management guidelines aimed at the prevention and early detection of breast and ovarian cancer
We correctly identified all 88 positives among 357 samples that were previously examined for deletions and duplications in MLH1, MSH2, MSH6, and the 3’ terminal region of EPCAM by multiplex quantitative Polymerase chain reaction (PCR) and/or Multiplex ligation-dependent probe (MLPA)
Summary
Sequencing and large rearrangement (LR) analyses detect DNA changes within hereditary cancer genes and are offered to individuals with a personal and/or family history of cancer to identify pathogenic mutation carriers. Patients with pathogenic mutations in BRCA1 or BRCA2 have a diagnosis of hereditary breast and ovarian cancer syndrome (HBOC), a condition for which there are extensive medical management guidelines aimed at the prevention and early detection of breast and ovarian cancer. There is an increased risk for colorectal cancer associated with mutations in the APC (familial adenomatous polyposis [FAP] or attenuated-FAP) and MUTYH (MUTYH-associated polyposis) genes. Conventional Sanger sequencing reliably detects the majority of genetic mutations associated with hereditary cancers, such as single-base changes and small insertions or deletions. Microarray analysis has been successfully used to detect large rearrangements (LRs) in genetic disorders
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