从下一代测序数据中进行 HLA-DRB3、-DRB4 和 -DRB5 的分型和拷贝数确定。

Typing and copy number determination for HLA-DRB3, -DRB4 and -DRB5 from next-generation sequencing data.

机构信息

State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.

Shenzen Key Laboratory of Neurogenomics, BGI-Shenzhen, Shenzhen, China.

出版信息

HLA. 2017 Mar;89(3):150-157. doi: 10.1111/tan.12966. Epub 2017 Feb 1.

DOI:10.1111/tan.12966

PMID:28145101

Abstract

BACKGROUND

HLA-DRB3, DRB4 and DRB5 (DRB3/4/5) are paralogues of HLA-DRB1. They have important roles in transplantation and have been reported to be related to many diseases. HLA typing methods for DRB3/4/5 based on NGS data have many limitations now, such as need of polymerase chain reaction (PCR) or low accuracy.

MATERIALS AND METHODS

We present a HLA typing method for DRB3/4/5 based on read mapping and haplotype assembly from NGS data. Also, copy number of DRB3/4/5 is determined by a k-means clustering method according to ratio of sequencing depth between DRB3/4/5 and DRB1.

RESULTS

We achieved 100%, 100%, 100% accuracy on simulated data and 95.88%, 98.89%, 99.34% accuracy on MHC capture Illumina sequencing data at 4-digit resolution with 30-fold coverage for DRB3/4/5 separately. We also explored the DRB3/4/5 profiles in five continental populations through low coverage WGS data generated by the 1000 Genome Project. We found that frequency of DRB4 in African were significantly lower than that in all other populations.

CONCLUSION

Our method for DRB3/4/5 typing has high accuracy. It is a good supplement to regular HLA typing and could help in disease studies, medical applications and human population diversity studies.

摘要

背景

HLA-DRB3、DRB4 和 DRB5（DRB3/4/5）是 HLA-DRB1 的旁系同源物。它们在移植中具有重要作用，并且已被报道与许多疾病有关。目前基于 NGS 数据的 DRB3/4/5 HLA 分型方法存在许多局限性，例如需要聚合酶链反应（PCR）或准确性低。

材料和方法

我们提出了一种基于 NGS 数据的读映射和单倍型组装的 DRB3/4/5 HLA 分型方法。此外，根据 DRB3/4/5 与 DRB1 测序深度比，通过 k-均值聚类方法确定 DRB3/4/5 的拷贝数。

结果

我们在模拟数据上实现了 100%、100%、100%的准确性，在 MHC 捕获 Illumina 测序数据上实现了 95.88%、98.89%、99.34%的准确性，在单独的 30 倍覆盖的 4 位数分辨率下，对于 DRB3/4/5。我们还通过 1000 基因组计划生成的低覆盖 WGS 数据探索了五个大陆人群中的 DRB3/4/5 谱。我们发现非洲 DRB4 的频率明显低于其他所有人群。