Haplotype-resolved genome sequencing: experimental methods and applications

Key Points Haplotypes link together (that is, 'phase') groups of genetic variants that co-occur on single chromosomes. Although haplotypes have an important role in clinical genetics and association studies, they are not typically obtained by contemporary genotyping or sequencing technologies and must be determined separately. Inferential methods for haplotype determination perform fairly poorly for the rare and private variants implicated in many genetic diseases. To phase this class of variants accurately and comprehensively, direct experimental methods are needed. Dense haplotyping methods comprehensively phase variants into haplotype blocks at the scale of a single gene or a small number of genes and corresponding regulatory regions. Contiguity is defined within each block but not between adjacent or distant haplotype blocks. Sparse haplotyping methods phase a more modest number of distant variants distributed along an entire chromosome or a chromosome arm. Resulting haplotypes are not comprehensive but have long-range contiguity that is currently unattainable using dense methods. Reference panels of previously ascertained haplotypes can be used to correct errors in, or increase the density or contiguity of, directly obtained haplotypes. Such hybrid approaches yield improved haplotypes at low costs. Although contiguity metrics are typically used to compare haplotype assemblies, comprehensive comparisons should also include measures of the accuracy, density and allele frequency spectrum of the phased variants. High-throughput DNA sequencing technologies are providing an ever-expanding wealth of genome sequence data, including detailed information on human genetic variation. However, such data typically lack haplotype information (that is, the cis -connectivity of variants along individual chromosomes). This Review describes diverse recent experimental methods by which genetic variants can be resolved into haplotypes, accompanying computational methods and important applications of these methods in genomics and biomedical science. Human genomes are diploid and, for their complete description and interpretation, it is necessary not only to discover the variation they contain but also to arrange it onto chromosomal haplotypes. Although whole-genome sequencing is becoming increasingly routine, nearly all such individual genomes are mostly unresolved with respect to haplotype, particularly for rare alleles, which remain poorly resolved by inferential methods