Whole Exome Sequencing

The vast majority of known rare Mendelian disease-causing variants are located in the protein coding regions of genes called exons.

The full complement of exons is called the exome. Next-generation DNA sequencing (NGS) is able to sequence nearly all exons simultaneously in a single test. However, there are still many exons which are difficult to sequence with high confidence.


Most competitor clinical diagnostic exomes utilize a single NGS platform which means that the protein coding regions of many genes are not sequenced to 100%.

The QNA Dx approach utilizes two independent next-generation sequencing platforms which significantly increases the number of exons and genes sequenced completely at >20x coverage so that fewer variants are missed when compared with either single platform alone (Chennagiri et al 2016). Additionally, since both sequencing platforms utilize very different methodologies, variants identified in both platforms and are considered orthogonally confirmed with a positive predictive value (PPV) of nearly 100% eliminating the need for additional confirmation via Sanger DNA sequencing.

Key Features

Innovative Design

Two independent and complementary target capture and sequencing technologies provide:

  • Increased sensitivity and specificity in detecting variants. Use of two unique platforms detect variants that single platforms miss.
  • All reported variants are confirmed with an orthogonal sequencing method.
  • Orthogonally-confirmed variants demonstrate high Positive Predictive Value of ~99.998%.1
  • Sequencing twice significantly increases the number of genes sequenced to 100% (see below).

Additional Service Highlights

Reanalysis offered once within the first 24 months for no charge.

Turn Around Time

• 4-6 weeks standard TAT
• 2-4 weeks rapid TAT


Test Characteristics

  • Orthogonal sequencing is carried out using Illumina NextSeqTM and Thermo Fisher Ion ProtonTM systems to generate a variant list.
  • >100x mean coverage on both platforms; >98% at 20x on at least one platform.
  • This assay will detect SNVs, insertions and deletions
    (delins) less than 8 bp.
  • Sensitivity for SNPs and small delins of 99.65%; Specificity > 99.999%
  • Sanger sequencing follow-up for unconfirmed variants.
  • Protein coding sequences and 8 bp of adjacent intronic sequences are analyzed.
  • Trios are encouraged but not required.


Improvement in gene coverage at >20x using two sequencing platforms. Only approximately half of the coding regions of genes in a traditional single platform Illumina exome (blue columns) are covered at 100% with a coverage of 20x or greater. The addition of Proton (red columns) significantly increases this number leading to fewer chances of missing an important variant.

Comparison of per-exon coverage achieved on Illumina NextSeq and Ion Torrent Proton platforms.  Mean coverage for each exome was normalized to 100x. Coverage for each exon was plotted on a log scale with exons having no reads changed to 1x for plotting.  Dashed lines show 20x coverage for each platform. The upper right quadrant shows exons sequenced well on both platforms. Exons in the upper left quadrant are well sequenced by NextSeq.  Exons in the lower right quadrant are well sequenced by Proton.

How To Order

1More information on methodology is available at Chennagiri et al., Orthogonal NGS for High Throughput Clinical Diagnostics, Sci Rep 6, 24650 (2016).