As the SARS-CoV-2 virus that causes COVID-19 has mutated, there has been a growing need to sequence the viral genome from many more COVID-19-positive samples to better understand the virus and its transmission.

The human genome contains ~3 billion base pairs, approximately 1-5% of which are translated into functional proteins. Mutations in these proteins are the most likely to result in a direct phenotypic consequence. Although whole-genome sequencing (WGS) provides rich information about single nucleotide, structural, or copy number variants, whole-exome sequencing (WES) often makes more sense when time or resources are limited.

As genomic DNA samples can often be collected only once, researchers cannot afford to repeat sequencing time and time again to achieve good coverage. For example, formalin-fixed, paraffin-embedded (FFPE) tissues— generally collected from cancer patients for histopathological diagnosis—are difficult to extract good quality DNA from due to specimen processing protocols.

Researchers who once relied on WGS for reliable variant information are now turning to WES for its faster turnaround time and cost-effectiveness. Considerable evidence is emerging that applying WES in clinical research settings will lead to improved diagnosis and, in some cases, treatment of genetic disease.

Sequencing metrics such as depth of coverage, on-target rate, GC-bias, Fold-80 base penalty, and duplication rates provide important information about the efficiency and specificity of hybridization-based NGS target enrichment experiments.