Whole-genome sequencing

Whole-genome sequencing (WGS) determines the order of nucleotides across almost the entire genome of a person or other organism: the protein-coding exons, but also introns, regulatory regions and other noncoding DNA. For a human, that is about 3 billion base pairs. The Human Genome Project produced the first reference sequence in the early 2000s after more than a decade of work with Sanger sequencing; next-generation sequencing machines now read a human genome in days by sequencing millions of short DNA fragments in parallel.

In a typical workflow, DNA is broken into fragments that are each read many times, and software either lines the reads up against a reference genome or assembles them from scratch by finding overlaps, as in early shotgun sequencing. Comparison with the reference then reveals single-nucleotide variants, small insertions and deletions, copy number changes and larger rearrangements. Because it covers noncoding DNA, WGS can find disease-causing changes that exome sequencing misses, although such changes are harder to interpret.

WGS is used to diagnose rare genetic diseases, notably in critically ill newborns, to profile tumors, to trace outbreaks by comparing pathogen genomes and to study evolution and population history. Every genome carries millions of variants, most of them harmless, so results can include findings of uncertain meaning or ones unrelated to the reason for testing.