Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Genomic DNA obtained from the submitted sample is prepared for sequencing using a PCR-free method and the entire genome is sequenced. While the underlying technology sequences the whole genome, analyzed targets include exons +/-20bp of flanking region, plus select non-coding variants. The Invitae Exome is designed to be sequenced to sufficient depth to ensure each base pair has a ≥99% probability to be accurately determined. This is achieved by an average coverage above 35x across our reportable range with 99.5% of the reportable range above 20x. The base pairs meeting ≥99% probability of genotypic accuracy are considered covered at high confidence. Reads are aligned to a reference sequence (GRCh37), and sequence changes are identified and interpreted in the context of a single clinically relevant transcript.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than 50 bp but sensitivity for these may be marginally reduced. The Invitae Exome permits reliable detection of deletions and duplications spanning 10,000 bases of genomic sequence (on average 2 exons; Piovesan, et al. 2016, PMID 28025344) with high confidence; smaller events may be detected and will be reported when sufficient resolution exists. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality.

Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications) or regions with high homology or repetitive regions, may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or expansion repeat numbers. Unless indicated, risk association alleles, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay.

Invitae confirms all clinically significant findings (e.g., pathogenic or likely pathogenic variants sufficient to explain the patient 's phenotype) that do not meet stringent quality metrics using orthogonal technologies, except when noted in the website Exome Gene Coverage Search Tool. Genome regions not sequenced to Invitae quality standards using this technology may be excluded from analysis. Since WGS technology has no PCR enrichment of targeted regions, non-human contamination has a higher impact on overall sample quality metrics and can cause higher sample failure rates in Saliva and Buccal specimens. Therefore, blood is the preferred specimen for the Invitae Exome, when available.