What is whole genome sequencing (WGS)?

What is Whole Genome Sequencing (WGS)?

Whole genome sequencing is a comprehensive molecular genetic method that sequences the entire DNA of an organism—approximately 3,200 megabases in humans—capturing nearly all genomic variation including single nucleotide variants, insertions/deletions, copy number variants, and structural variants across both coding and non-coding regions. 1, 2

Technical Definition and Scope

WGS provides the most complete collection of an individual's genetic variation by sequencing all ~3 billion base pairs of the human genome, not just the protein-coding regions (exons) that comprise only about 2% of the genome. 3, 1 This distinguishes it from:

• Gene panels: Target specific genes (typically 0.5 megabases) at very high depth (500-1000×) 1
• Whole exome sequencing (WES): Sequences only 20,000 protein-coding genes (50 megabases) at 100-150× depth 1, 4
• WGS: Covers the entire ~3,200 megabase genome at 30-60× average depth 1

How WGS Works

The process involves shotgun sequencing where DNA is fragmented, sequenced in short reads, and then computationally assembled. 3 There are two primary assembly approaches:

• Reference-based assembly: Each sequence read is mapped to an existing reference genome sequence 3
• De novo assembly: Sequence reads are compared to each other and overlapped to build longer contiguous sequences without a reference 3

WGS requires substantial computational infrastructure and storage capacity to process the approximately 5 million variants generated per individual within clinically relevant timeframes. 2

Clinical Applications

WGS is increasingly used as a first-tier diagnostic test for patients with rare genetic disorders and undiagnosed conditions, particularly in pediatric cases. 1, 2, 5, 6 The technology is now offered in CLIA/CAP-certified laboratory environments by multiple academic centers and commercial laboratories. 1, 4

WGS eliminates the need for sequential genetic testing by capturing most genomic variation in a single comprehensive test, making it more cost-effective when multiple genetic loci could explain a clinical syndrome. 4, 2

Advantages Over Other Methods

• Comprehensive variant detection: Identifies single nucleotide polymorphisms, small insertions/deletions, copy number variants, and structural variants that may be missed by targeted approaches 4, 2, 7
• Non-coding region analysis: Captures mutations in regulatory elements and other non-coding regions that affect gene expression 7
• Superior for structural variants: Better detection of large genomic rearrangements compared to exome sequencing 1, 4
• Eliminates testing cascade: Avoids the time and cost of sequential single-gene or panel testing 4, 2

Important Limitations

WGS generates massive amounts of data requiring specialized bioinformatics expertise and multidisciplinary collaboration between laboratory scientists and clinical specialists to interpret the ~5 million variants per genome. 2 Key challenges include:

• Variants of uncertain significance (VUS): Many identified variants lack established clinical significance, complicating interpretation 4
• Resource intensive: Requires comprehensive computational infrastructure, substantial storage capacity, and expert interpretation time 2
• Depth trade-offs: The 30-60× coverage may be insufficient for detecting low-frequency mosaic variants compared to the higher depth achieved with panels (500-1000×) 1
• Chromosomal abnormalities: Large chromosomal rearrangements may still require array comparative genomic hybridization for optimal detection 8

Quality Standards

All clinical WGS must be performed in CLIA/CAP-certified laboratories with review and sign-out by board-certified clinical molecular geneticists to ensure accurate variant interpretation and reporting. 1, 4, 8 Validation of clinically relevant variants should be confirmed by independent methods such as Sanger sequencing before making clinical decisions. 4

Current Clinical Context

The era of genomic medicine has arrived, with WGS transitioning from research to routine clinical practice. 1 Multiple institutions now offer clinical WGS that can be used in regular patient care, though the technology continues to evolve rapidly. 1 The Medical Genome Initiative consortium has published best practice recommendations to standardize WGS implementation and expand access to high-quality testing. 5, 6

Members of the Medical Genome Initiative strongly believe that clinical WGS is appropriate as a first-tier test for patients with rare genetic disorders and should at minimum replace chromosomal microarray analysis and whole-exome sequencing. 6