PMID- 37714157
OWN - NLM
STAT- MEDLINE
DCOM- 20230928
LR  - 20231005
IS  - 2667-2375 (Electronic)
IS  - 2667-2375 (Linking)
VI  - 3
IP  - 9
DP  - 2023 Sep 25
TI  - SpecHLA enables full-resolution HLA typing from sequencing data.
PG  - 100589
LID - S2667-2375(23)00240-0 [pii]
LID - 10.1016/j.crmeth.2023.100589 [doi]
LID - 100589
AB  - Reconstructing diploid sequences of human leukocyte antigen (HLA) genes, i.e., 
      full-resolution HLA typing, from sequencing data is challenging. The high 
      homogeneity across HLA genes and the high heterogeneity within HLA alleles 
      complicate the identification of genomic source loci for sequencing reads. Here, 
      we present SpecHLA, which utilizes fine-tuned reads binning and local assembly to 
      achieve accurate full-resolution HLA typing. SpecHLA accepts sequencing data from 
      paired-end, 10x-linked-reads, high-throughput chromosome conformation capture 
      (Hi-C), Pacific Biosciences (PacBio), and Oxford Nanopore Technology (ONT). It 
      can also incorporate pedigree data and genotype frequency to refine typing. In 32 
      Human Genome Structural Variation Consortium, Phase 2 (HGSVC2) samples, SpecHLA 
      achieved 98.6% accuracy for G-group-resolution HLA typing, inferring entire HLA 
      alleles with an average of three mismatches fewer, ten gaps fewer, and 590 bp 
      less edit distance than HISAT-genotype per allele. Additionally, SpecHLA 
      exhibited a 2-field typing accuracy of 98.6% in 875 real samples. Finally, 
      SpecHLA detected HLA loss of heterozygosity with 99.7% specificity and 96.8% 
      sensitivity in simulated samples of cancer cell lines.
CI  - Copyright (c) 2023 The Author(s). Published by Elsevier Inc. All rights reserved.
FAU - Wang, Shuai
AU  - Wang S
AD  - City University of Hong Kong, Department of Computer Science, Kowloon, Hong Kong.
FAU - Wang, Mengyao
AU  - Wang M
AD  - City University of Hong Kong, Department of Computer Science, Kowloon, Hong Kong.
FAU - Chen, Lingxi
AU  - Chen L
AD  - City University of Hong Kong, Department of Computer Science, Kowloon, Hong Kong.
FAU - Pan, Guangze
AU  - Pan G
AD  - City University of Hong Kong, Department of Computer Science, Kowloon, Hong Kong.
FAU - Wang, Yanfei
AU  - Wang Y
AD  - City University of Hong Kong, Department of Computer Science, Kowloon, Hong Kong.
FAU - Li, Shuai Cheng
AU  - Li SC
AD  - City University of Hong Kong, Department of Computer Science, Kowloon, Hong Kong. 
      Electronic address: shuaicli@cityu.edu.hk.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20230914
PL  - United States
TA  - Cell Rep Methods
JT  - Cell reports methods
JID - 9918227360606676
SB  - IM
MH  - Humans
MH  - Alleles
MH  - Genotype
MH  - Cell Line
MH  - *Diploidy
MH  - Histocompatibility Testing
PMC - PMC10545945
OTO - NOTNLM
OT  - CP: Genetics
OT  - CP: Immunology
OT  - HLA LOH
OT  - HLA sequence
OT  - HLA typing
OT  - cancer
OT  - haplotype
OT  - phase
COIS- Declaration of interests The authors declare no competing interests.
EDAT- 2023/09/16 05:42
MHDA- 2023/09/28 06:42
PMCR- 2023/09/14
CRDT- 2023/09/15 18:41
PHST- 2023/01/11 00:00 [received]
PHST- 2023/06/20 00:00 [revised]
PHST- 2023/08/21 00:00 [accepted]
PHST- 2023/09/28 06:42 [medline]
PHST- 2023/09/16 05:42 [pubmed]
PHST- 2023/09/15 18:41 [entrez]
PHST- 2023/09/14 00:00 [pmc-release]
AID - S2667-2375(23)00240-0 [pii]
AID - 100589 [pii]
AID - 10.1016/j.crmeth.2023.100589 [doi]
PST - ppublish
SO  - Cell Rep Methods. 2023 Sep 25;3(9):100589. doi: 10.1016/j.crmeth.2023.100589. 
      Epub 2023 Sep 14.