Renewed Interest in Haplotype: From Genetic Marker to Gene Prediction

Abstract

A haplotype refers to a set of multiple SNP alleles from one parental genome and has a clear genetic interpretation, often as a biologically meaningful quantity. With the current biotechnologies for genotyping diploidic human genomes (a pair of haplotypes), however, genotype data include only partial haplotype information and, in general, are insufficient to directly infer a pair of haplotypes (with more than two SNP loci) since SNP genotypes are typed locus-by-locus. Using genotype data, haplotype analysis methods refer to a class of statistical genetic analysis methods, for inferring haplotypes, or estimating haplotype frequencies (and related statistics), or assessing haplotypic associations with a phenotype. These methods are an important set of statistical tools for genetic analyses. With advent of both genotyping/sequencing technologies, we anticipate an increasing interest in haplotype-based association analysis. In this chapter, we have introduced the concept of haplotype and its roles in genetic studies, have also documented the aspects of earlier method developments, have described some key methods and related software, and have discussed the renewed interest in recent years. While exhaustively reviewing literature on haplotype analysis is not of primary interest, this chapter serves an introduction to the haplotype analysis, opening a door to a rich and dynamic set of literature accumulated in the past decades.