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As precision oncology research evolves, next-generation sequencing (NGS) technologies are expected to detect a broad spectrum of genomic alterations across increasingly diverse sample types and sequence contexts.
Ion Torrent technology and Oncomine NGS solutions enable robust detection of BRCA1 and BRCA2 variants, including variants occurring within homopolymer regions. Published studies, analytical validation data, and independent laboratory evaluations demonstrate accurate BRCA1/2 variant detection performance across Oncomine workflows [1−12].
Continuous advances in instrumentation, chemistry, bioinformatics, and workflow design have further strengthened performance in genomic regions that can be technically challenging for NGS technologies.
Homopolymer regions are stretches of identical nucleotides, such as AAAAAA or TTTTTT, that naturally occur throughout the genome. Homopolymer regions are subject to single base insertions and deletions that create frame-shift mutations. These regions can present analytical challenges for NGS technologies by generating characteristic low-level sequencing artifacts that can affect variant calling.
For BRCA testing, however, understanding the prevalence and context of variants occurring in longer homopolymer regions is important. To understand the prevalence of somatic variants in primary, untreated tumors, data from The Cancer Genome Atlas (TCGA) was interrogated using the cBioPortal [13–15]. From breast, ovarian, pancreatic, and prostate cancers, 112 somatic BRCA1/2 variants (4.8%) were identified among 2,347 samples. Of these variants, 67% were SNVs, 25% were deletions, and 8% were insertions, demonstrating that SNVs comprise the majority of somatic BRCA alterations.
Among the 32 frameshift indels identified in the TCGA cohort, only 3 were associated with homopolymer regions longer than 5 bp, corresponding to an incidence of ~0.13% across all tumors analyzed. These findings indicate that longer homopolymer-associated BRCA variants represent a very small subset of all BRCA alterations.
In contrast, studies of advanced-stage, high-grade ovarian carcinomas report a higher prevalence of BRCA1/2 mutations. For example, the PAOLA-1 clinical study reported a BRCA1/2 mutation prevalence of ~29%, reflecting the prevalence of HRD-positive tumors in this population [16]. In our re-analysis of the PAOLA-1 variant data, homopolymer regions longer than 5 bp accounted for approximately 1% of all samples. Together, these studies demonstrate that while BRCA1/2 mutation prevalence varies considerably across tumor types and disease stage, homopolymer-associated variants consistently represent only a small fraction of all relevant BRCA alterations, with an observed prevalence ranging from approximately 0.1% to 1%.
Yes, Ion Torrent-based Oncomine NGS solutions can detect BRCA variants occurring within homopolymer regions. The performance of Oncomine solutions has been evaluated through analytical validation studies, multicenter investigations, independent laboratory evaluations, and internal performance analyses [1−12]. These studies demonstrate strong overall BRCA1/2 variant detection performance, including detection of indels and variants occurring within challenging sequence contexts.
As with any NGS workflow, performance depends on multiple factors, including sequence context, variant characteristics, sample quality, assay design, sequencing depth, and bioinformatics analysis. Accordingly, homopolymer length should not be interpreted as a binary threshold at which variants suddenly become undetectable. Rare variants within extended homopolymer regions may warrant additional review based on the laboratory’s specific performance evaluation, sample quality review procedures, and appropriate orthogonal confirmation strategies.
The Oncomine Comprehensive Assay Plus, available on the Ion Torrent Genexus System and Ion GeneStudio S5 Systems, enables accurate detection of BRCA1/2 variants within its comprehensive genomic profiling (CGP) offering for solid tumor research. The assay also supports homologous recombination deficiency (HRD) research by detecting mutations in 47 homologous recombination repair (HRR) genes, including large genomic rearrangements (LGRs) in BRCA1/2, and assesses the hallmarks of genomic scarring with the genomic instability metric (GIM).
The Oncomine Comprehensive Assay Plus has demonstrated consistently high analytical performance for BRCA1/2 variant detection across multiple independent ovarian and breast cancer research studies [1–4]. From the cited studies, the assay achieved a high overall concordance ranging from approximately 95.6% to 100% for BRCA1/2 mutational status with orthogonal reference methods. These studies also reported high sequencing success rates, strong reproducibility across testing sites, and robust performance with low DNA input, highlighting the assay’s suitability for broad molecular profiling in cancer research.
BRCA testing performance of the Oncomine BRCA Assay
For laboratories requiring a more targeted approach, the Oncomine BRCA Assay, available on the Genexus System and Ion GeneStudio S5 systems, enables accurate and sensitive detection of BRCA somatic and germline mutations from FFPE tissue or whole blood. The Oncomine BRCA Assay has been widely adopted in molecular pathology laboratories across the world and referenced in several publications [6–12].
The assay has also demonstrated robust analytical performance through verification studies using clinical research samples. The assay enables comprehensive assessment of relevant variants, while its coverage uniformity and sequencing depth support the accurate detection of both somatic and germline variants across diverse sample types. Across manual and automated workflows, the assay demonstrated SNV and indel sensitivities of 94–100% with positive predictive values (PPV) of 92–100% at both somatic (5% allele frequency) and germline (50% and 100% allele frequency) variant levels [5].
While Ion Torrent technology demonstrates high overall sensitivity for BRCA variant detection, certain long homopolymer-associated indels may warrant additional review. In one example, scientists evaluated 157 high-grade ovarian cancer research samples negative at tumor testing by Ion Torrent sequencing and found that the prevalence of homopolymer indels overlooked by ion semiconductor techniques was low, with only one confirmed variant identified among a small number of candidates [6].
The study concluded that careful evaluation of background information for context helps minimize this technique-bound limitation, highlighting situations where deeper investigation of homopolymer regions would be recommended [6].
The combination of Ion Torrent sequencing technology and Ion AmpliSeq chemistry provides a targeted NGS approach that supports comprehensive BRCA analysis with low input requirements, streamlined workflows, and high sequencing success rates.
Continuous improvements in sequencing chemistry, instrumentation, bioinformatics, and workflow design have further strengthened the analytical performance of Oncomine assays, enabling robust detection of relevant BRCA variants while expanding performance in technically challenging genomic regions.
Through ongoing innovation, analytical validation support, scientific collaboration, and customer-driven workflow optimization, Thermo Fisher Scientific continues to partner with laboratories to support accurate, reliable, and scalable variant detection using Ion Torrent technology and Oncomine NGS solutions.
For Research Use Only. Not for use in diagnostic procedures.
References
5. Internal R&D data.
PMR-009352