The phylogeny of 48 alleles, experimentally verified at 21 kb, and its application to clinical allele detection.

ABSTRACT:

Background

Sequence information generated from next generation sequencing is often computationally phased using haplotype-phasing algorithms. Utilizing experimentally derived allele or haplotype information improves this prediction, as routinely used in HLA typing. We recently established a large dataset of long ERMAP alleles, which code for protein variants in the Scianna blood group system. We propose the phylogeny of this set of 48 alleles and identify evolutionary steps to derive the observed alleles.

Methods

The nucleotide sequence of > 21 kb each was used for all physically confirmed 48 ERMAP alleles that we previously published. Full-length sequences were aligned and variant sites were extracted manually. The Bayesian coalescent algorithm implemented in BEAST v1.8.3 w

SUBMITTER: Srivastava K 

PROVIDER: S-EPMC6371619 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature