Residency · Residency · Medical Genetics Genomics
Whole Exome vs. Whole Genome Sequencing: Clinical Applications
Introduction
Whole exome sequencing (WES) and whole genome sequencing (WGS) represent broad genomic interrogation strategies that have become central to clinical genetics practice. While WES targets the approximately 1-2% of the genome encoding proteins, WGS captures both coding and noncoding regions. Understanding the strengths, limitations, and appropriate clinical applications of each is essential for optimal test selection.
Whole Exome Sequencing
Technical Overview
WES targets approximately 22,000 genes comprising roughly 30-45 Mb of coding sequence (exons) plus flanking intronic regions. It uses hybridization capture with probe sets designed against exonic regions, achieves typical sequencing depth of 100-150x mean coverage, and detects SNVs and small indels in coding regions with high sensitivity. Commercially available capture kits include those from Agilent SureSelect, Roche SeqCap, IDT xGen, and Twist Bioscience.
Clinical Diagnostic Yield
The overall diagnostic yield for suspected genetic disorders is 25-40% depending on phenotype and patient selection. The highest yield is achieved in neurodevelopmental disorders (30-40%), multiple congenital anomalies (35-45%), and suspected inborn errors of metabolism (30-50%). Trio analysis (proband plus both parents) increases yield by approximately 10-15% over proband-only testing through de novo variant identification and phasing.
Limitations
WES has incomplete coverage of some exons, particularly in GC-rich regions. It has poor detection of structural variants, copy number variants (though improving with algorithmic advances), and repeat expansions. Deep intronic variants, regulatory elements, and intergenic regions are not captured. Capture bias introduces uneven coverage across the exome. The mitochondrial genome is incompletely captured unless specifically supplemented.
Whole Genome Sequencing
Technical Overview
WGS sequences the entire 3.2 billion base pair human genome without a capture step, using PCR-free library preparation for uniform coverage. Typical sequencing depth is 30-40x for constitutional analysis and 60-90x for higher sensitivity. WGS achieves more uniform coverage than WES, including over coding regions, and detects SNVs, indels, structural variants, copy number variants, repeat expansions, and mitochondrial variants.
Advantages Over WES
WGS provides superior uniformity of coverage across coding regions (paradoxically achieving better exome coverage than WES itself). It detects structural variants including balanced translocations, inversions, and complex rearrangements. Noncoding variant detection encompasses deep intronic splice-altering variants and regulatory variants. Short tandem repeat (STR) expansions critical for diseases like fragile X, Friedreich ataxia, and myotonic dystrophy are identified. Comprehensive coverage of pharmacogenomic variants including CYP450 and HLA loci is achieved. The mitochondrial genome receives complete coverage at high depth due to high copy number. Copy number detection is more accurate than WES-based CNV calling.
Clinical Diagnostic Yield
Recent studies demonstrate a diagnostic yield of 30-50% in pediatric rare disease. The incremental yield over WES is approximately 5-10% additional diagnoses, primarily from structural variants, noncoding variants, and repeat expansions. The 100,000 Genomes Project (Genomics England) demonstrated WGS feasibility at scale with diagnostic rates of approximately 25% across diverse rare diseases.
| Feature | Whole Exome Sequencing (WES) | Whole Genome Sequencing (WGS) |
|---|---|---|
| Target region | ~1–2% of genome (exons) | Entire genome (3.2 Gb) |
| Capture step required | Yes (hybridization) | No (PCR-free) |
| Typical depth | 100–150x | 30–40x |
| SNV/indel detection (coding) | Excellent | Excellent (more uniform) |
| Structural variant detection | Limited | Superior |
| Repeat expansion detection | Poor | Good (with specialized tools) |
| Noncoding variant detection | Minimal (flanking intronic only) | Yes |
| Mitochondrial genome | Incomplete | Complete (high depth) |
| Diagnostic yield (rare disease) | 25–40% | 30–50% |
| Incremental yield of WGS over WES | — | ~5–10% additional diagnoses |
| Cost | Lower | Higher (decreasing) |
| Data storage/interpretation | Smaller dataset | Large dataset; noncoding interpretation challenging |
Clinical Decision-Making: WES vs. WGS
Factors Favoring WES
WES has lower cost (though the gap is narrowing rapidly), faster turnaround in many laboratories, smaller data storage and analysis burden, and is well-established in clinical laboratory practice with extensive validation. It is sufficient when the suspected condition likely involves coding variants in known disease genes.
Factors Favoring WGS
WGS is preferred when a structural variant or balanced rearrangement is suspected (such as in recurrent miscarriage or intellectual disability with normal microarray), when a repeat expansion disorder is suspected, after negative WES with strong clinical suspicion of a genetic etiology, when comprehensive pharmacogenomic data are needed, in research settings aiming for maximum variant detection, for suspected mitochondrial disorders (complete mtDNA coverage), and for conditions known to involve noncoding regulatory variants.
Practical Considerations
WGS generates approximately 100 GB per sample versus approximately 10 GB for WES. WGS identifies 4-5 million variants per genome versus approximately 80,000-100,000 for WES. The vast majority of noncoding variants lack established clinical significance, creating interpretation challenges. However, WGS data can be reanalyzed as new gene-disease associations are discovered without need for re-sequencing.
The Trio Approach
Sequencing the proband with both biological parents dramatically improves interpretation by enabling identification of de novo variants (present in proband but absent in parents) and facilitating compound heterozygosity phasing for recessive conditions. The candidate variant list is reduced from thousands to tens. Diagnostic yield increases by approximately 10-15% over proband-only analysis. Cost-effectiveness analyses generally support trio over singleton despite higher upfront cost.
Emerging Trends
Rapid WGS (rWGS) achieves turnaround times of 24-48 hours for critically ill neonates and has demonstrated improved outcomes and cost savings in NICU settings. Ultra-rapid WGS achieves sub-24-hour results in select centers. Multiple health systems and countries are moving toward WGS as a first-tier test replacing sequential testing algorithms. Long-read WGS is emerging as a technology that can resolve complex structural variants, repeat expansions, and methylation in a single assay.
Clinical Pearls
WGS provides more uniform coverage of coding regions than WES, making it technically superior even for exome-level analysis. Trio analysis is strongly recommended for both WES and WGS in pediatric presentations to maximize diagnostic yield through de novo variant detection. A negative WES does not exclude a genetic diagnosis, as structural variants, repeat expansions, and noncoding variants may be missed. Rapid WGS in critically ill neonates has demonstrated clinical utility, with studies showing changed management in 30-70% of diagnosed cases.
References
- Clark MM, Stark Z, Farnaes L, et al. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. NPJ Genomic Medicine. 2018;3:16.
- Turro E, Asber HN, Caulfield MJ. Whole-genome sequencing in diagnostics. Lancet. 2020;396(10266):1903-1905.
- Petrikin JE, Cakici JA, Clark MM, et al. The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants. NPJ Genomic Medicine. 2018;3:6.
- Smedley D, Smith KR, Martin A, et al. 100,000 Genomes Pilot on rare-disease diagnosis in health care: preliminary report. New England Journal of Medicine. 2021;385(20):1868-1880.