Whole Genome Sequencing

UNDERSTANDING WGS

What is WGS?

WGS involves sequencing all 6 billion base pairs of an individual's DNA, providing a complete picture of their genetic makeup. This technique captures information from both exons (coding regions) and introns (non-coding regions) of the genome.

Benefits of WGS

Comprehensive coverage: WGS analyzes the entire genome, including regulatory and non-coding regions, providing a more complete genetic profile.
Detection of various variant types: WGS excels at identifying single nucleotide variants (SNVs), structural variants, copy number variations (CNVs) and balanced translocations.
Higher sensitivity: WGS has a significantly lower false-negative rate compared to other sequencing methods, potentially missing only 2 out of every 10,000 variants at 75x coverage.
Uniform depth of coverage: WGS provides more consistent coverage across the genome, making it easier to detect CNVs.
Potential for future reanalysis: As new genetic associations are discovered, WGS data can be reanalyzed without additional sequencing.

Accuracy of WGS

30x Coverage:

Single Nucleotide Variants (SNVs):
- Accuracy rates are typically above 99%. Most sequencing platforms can reliably call SNVs with this coverage level.
Small Insertions and Deletions (Indels):
- Accuracy rates range from 90-95%, depending on the size and location of the indel. Small indels (1-5 base pairs) are generally well detected, but larger indels and those in repetitive regions may be missed or inaccurately called.
Structural Variants (SVs) and Copy Number Variants (CNVs):
- Detection rates are lower, often around 70-80%, especially for complex or small variants. Sensitivity drops significantly for variants less than 50 base pairs or in highly repetitive regions.
Overall Sensitivity and Specificity:
- Sensitivity for variant detection can be around 95-99%, and specificity (true negative rate) is also generally high, but may drop in low-complexity or high-GC regions.

100x Coverage:

Single Nucleotide Variants (SNVs):
- Accuracy rates increase to over 99.9%. The higher coverage allows for better differentiation between true variants and sequencing errors.
Small Insertions and Deletions (Indels):
- Accuracy rates are typically above 97%. Higher coverage significantly improves the detection of both small and large indels.
Structural Variants (SVs) and Copy Number Variants (CNVs):
- Detection accuracy improves, with sensitivity around 85-90%, and the ability to detect smaller variants (below 50 base pairs) and complex structural rearrangements increases.
Overall Sensitivity and Specificity:
- Sensitivity for variant detection is generally above 99%, and specificity remains very high, allowing for better distinction of true positives from false positives, even in challenging genomic regions.