Journal
GENOME MEDICINE
Volume 7, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13073-015-0145-3
Keywords
-
Categories
Funding
- Research Grant Council of the Hong Kong Government [GRF 17125114, HKU783813M, HKU 784611 M, HKU 770411 M]
- SK Yee Medical Foundation general award
- Center of Excellence in Immunology and Immune Mediated Diseases
- Rachadapiseksompot Fund
- Chulalongkorn University
- Centre for Genomic Sciences of Faculty of Medicine, University of Hong Kong
- Hong Kong RGC AoE program on nasopharyngeal cancer
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Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for widespread applications. Here we introduce a novel tool (HLAreporter) for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads. Accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly developed tools such as HLAminer and PHLAT.
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