open access - authors Myriad
Background Germline DNA mutations that increase the susceptibility of a patient to
certain cancers have been identified in various genes, and patients can be screened
for mutations in these genes to assess their level of risk for developing cancer.
Traditional methods using Sanger sequencing focus on small groups of genes and therefore
are unable to screen for numerous genes from several patients simultaneously. The
goal of the present study was to validate a 25-gene panel to assess genetic risk for
cancer in 8 different tissues using next generation sequencing (NGS) techniques.
Methods
Twenty-five genes associated with hereditary cancer syndromes were selected for development
of a panel to screen for risk of these cancers using NGS. In an initial technical
assessment, NGS results for BRCA1 and BRCA2 were
compared with Sanger sequencing in
1864 anonymized DNA samples from patients who had undergone previous clinical testing.
Next, the entire gene panel was validated using parallel NGS and Sanger sequencing
in 100 anonymized DNA samples. Large rearrangement analysis was validated using NGS,
microarray comparative genomic hybridization (CGH), and multiplex ligation-dependent
probe amplification analyses (MLPA).
Results NGS identified 15,877 sequence variants,
while Sanger sequencing identified 15,878 in the BRCA1 and BRCA2 comparison study
of the same regions. Based on these results, the NGS process was refined prior to
the validation of the full gene panel. In the validation study, NGS and Sanger sequencing
were 100% concordant for the 3,923 collective variants across all genes for an analytical
sensitivity of the NGS assay of >99.92% (lower limit of 95% confidence interval).
NGS, microarray CGH and MLPA correctly identified all expected positive and negative
large rearrangement results for the 25-gene panel.
Conclusion This study provides
a thorough validation of the 25-gene NGS panel and indicates that this analysis tool
can be used to collect clinically significant information related to risk of developing
hereditary cancers.
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