期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 114, 期 30, 页码 8059-8064出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1707945114
关键词
MHC; autoimmune diseases; transplantation
资金
- Public Health Service Grant/Cooperative Agreement from the National Cancer Institute (NCI) [5U24-CA076518]
- National Heart, Lung and Blood Institute (NHLBI)
- National Institute of Allergy and Infectious Diseases
- NHLBI
- NCI [5U10HL069294]
- Health Resources and Services Administration (HRSA/DHHS) [HHSH250201200016C]
- Office of Naval Research Grants [N00014-14-1-0028, N00014-15-1-0848]
The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99-100% four-digit typing accuracy for both class I and II HLA genes, taking only similar to 3 min to process a 30 x whole-genome BAM file on a desktop computer.
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