Bi5444 Analysis of sequencing data
Whole-genome sequencing
Whole-exome sequencing
Eva Budinska
DNA
sequencing
Whole genome
sequencing (WGS)
• Whole genome - The complete
genomic information within a
sample or individual
• Allows examination of SNVs, indels, SV and CNVs in coding and non-coding
regions of the genome
• More reliable and uniform sequence coverage over any targeted method
• PCR amplification isn’t required during library preparation reducing the potential of GC
bias.
• Unlimited sequencing read length
• A lower average read depth is required to achieve the same breath of coverage as
WES
• WGS doesn’t suffer from reference bias
• WGS is more universal (WES limited for species other than human)
Whole-exome
sequencing (WES)
• Exome - all the genome's
protein-coding regions
(exons)
• WES is a targeted next-generation sequencing method (targeting
exons)
• Advantages of WES over WGS: Exomes compose only about 2% of the
whole genome => exomes can be sequenced at a much greater
depth => more confidence in low frequency alterations.
Whole-exome
sequencing (WES)
• Disadvantages:
• Not able to identify the structural and non-coding variants
• Omits regulatory regions
• Requires PCR amplification
• WES capture probes tend to preferentially enrich reference alleles at heterozygous
sites producing false negative SNV calls
• Issues with non-uniformity of coverage
• Exome - all the genome's
protein-coding regions
(exons)