PMID- 32940337
OWN - NLM
STAT- MEDLINE
DCOM- 20211115
LR  - 20221207
IS  - 1477-4054 (Electronic)
IS  - 1467-5463 (Print)
IS  - 1467-5463 (Linking)
VI  - 22
IP  - 3
DP  - 2021 May 20
TI  - In silico tools for accurate HLA and KIR inference from clinical sequencing data 
      empower immunogenetics on individual-patient and population scales.
LID - 10.1093/bib/bbaa223 [doi]
LID - bbaa223
AB  - Immunogenetic variation in humans is important in research, clinical diagnosis 
      and increasingly a target for therapeutic intervention. Two highly polymorphic 
      loci play critical roles, namely the human leukocyte antigen (HLA) system, which 
      is the human version of the major histocompatibility complex (MHC), and the 
      Killer-cell immunoglobulin-like receptors (KIR) that are relevant for responses 
      of natural killer (NK) and some subsets of T cells. Their accurate classification 
      has typically required the use of dedicated biological specimens and a 
      combination of in vitro and in silico efforts. Increased availability of next 
      generation sequencing data has led to the development of ancillary computational 
      solutions. Here, we report an evaluation of recently published algorithms to 
      computationally infer complex immunogenetic variation in the form of HLA alleles 
      and KIR haplotypes from whole-genome or whole-exome sequencing data. For both HLA 
      allele and KIR gene typing, we identified tools that yielded >97% overall 
      accuracy for four-digit HLA types, and >99% overall accuracy for KIR gene 
      presence, suggesting the readiness of in silico solutions for use in clinical and 
      high-throughput research settings.
CI  - (c) The Author(s) 2020. Published by Oxford University Press.
FAU - Chen, Jieming
AU  - Chen J
AD  - Department of Bioinformatics and Computational Biology.
FAU - Madireddi, Shravan
AU  - Madireddi S
AD  - Department of Cancer Immunology.
FAU - Nagarkar, Deepti
AU  - Nagarkar D
AD  - Department of Cancer Immunology.
FAU - Migdal, Maciej
AU  - Migdal M
AD  - Roche's Global IT Solution Centre.
FAU - Vander Heiden, Jason
AU  - Vander Heiden J
AUID- ORCID: 0000-0002-1474-310X
AD  - Department of Bioinformatics and Computational Biology.
FAU - Chang, Diana
AU  - Chang D
AD  - Department of Human Genetics.
FAU - Mukhyala, Kiran
AU  - Mukhyala K
AD  - Department of Bioinformatics and Computational Biology.
FAU - Selvaraj, Suresh
AU  - Selvaraj S
AD  - Roche/Genentech's Biosample & Repository Management.
FAU - Kadel, Edward E
AU  - Kadel EE
AD  - Department of Oncology Biomarker Development.
FAU - Brauer, Matthew J
AU  - Brauer MJ
AD  - Data Science at Maze Therapeutics.
FAU - Mariathasan, Sanjeev
AU  - Mariathasan S
AD  - Department of Oncology Biomarker Development.
FAU - Hunkapiller, Julie
AU  - Hunkapiller J
AD  - Department of Human Genetics.
FAU - Jhunjhunwala, Suchit
AU  - Jhunjhunwala S
AD  - Department of Bioinformatics and Computational Biology.
FAU - Albert, Matthew L
AU  - Albert ML
AD  - Immunology & Infectious Diseases.
FAU - Hammer, Christian
AU  - Hammer C
AUID- ORCID: 0000-0003-4548-7548
AD  - Departments of Cancer Immunology and Human Genetics.
LA  - eng
PT  - Journal Article
PL  - England
TA  - Brief Bioinform
JT  - Briefings in bioinformatics
JID - 100912837
RN  - 0 (HLA Antigens)
RN  - 0 (Receptors, KIR)
SB  - IM
MH  - Alleles
MH  - *Computer Simulation
MH  - Gene Frequency
MH  - Genotype
MH  - Genotyping Techniques/methods
MH  - HLA Antigens/*genetics
MH  - Haplotypes
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Humans
MH  - Immunogenetics/*methods
MH  - Phenotype
MH  - *Polymorphism, Single Nucleotide
MH  - Receptors, KIR/*genetics
MH  - Exome Sequencing/methods
MH  - Whole Genome Sequencing/methods
PMC - PMC8138874
OTO - NOTNLM
OT  - HLA
OT  - KIR
OT  - clinical sequencing
OT  - immunogenetics
OT  - imputation
OT  - whole-genome sequencing
EDAT- 2020/09/18 06:00
MHDA- 2021/11/16 06:00
PMCR- 2020/09/17
CRDT- 2020/09/17 08:48
PHST- 2020/04/27 00:00 [received]
PHST- 2020/07/30 00:00 [revised]
PHST- 2020/08/19 00:00 [accepted]
PHST- 2020/09/18 06:00 [pubmed]
PHST- 2021/11/16 06:00 [medline]
PHST- 2020/09/17 08:48 [entrez]
PHST- 2020/09/17 00:00 [pmc-release]
AID - 5906908 [pii]
AID - bbaa223 [pii]
AID - 10.1093/bib/bbaa223 [doi]
PST - ppublish
SO  - Brief Bioinform. 2021 May 20;22(3):bbaa223. doi: 10.1093/bib/bbaa223.