LabSolutions' assay for panel and single gene tests includes both full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).
Covers clinically important regions of each gene, including coding exons, +/-10 base pairs of adjacent intronic sequence, and select noncoding variants. Any variants that fall outside these regions are not analyzed. For some genes, analysis may extend to the promoter region, include additional intronic variants, or be limited to targeted variants or exons. To find details, search for a specific gene or test.
Detects intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality.
Provides an average coverage depth of at least 350x.
Using orthogonal technologies, LabSolutions’ confirms clinically all significant findings that do not meet stringent NGS quality metrics.
Direct sequencing of the amplified captured regions was performed using 2X100bp reads on Illumina next-generation sequencing (NGS) systems. A base is considered to have sufficient coverage at 20X and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. Low coverage regions, if any, are limited to ~1% or less of the nucleotides included in this panel. A list of these regions is available upon request.
Alignment to the human reference genome (hg19) is performed and annotated variants are identified in the targeted region. Variants are called at a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Single nucleotide variants (SNVs) meeting internal quality assessment guidelines are confirmed by Sanger sequence analysis for records after results are reported. Indels and SNVs at director discretion are confirmed by Sanger sequence analysis before reporting.