PMID- 30735756
OWN - NLM
STAT- MEDLINE
DCOM- 20200226
LR  - 20200901
IS  - 1879-1166 (Electronic)
IS  - 0198-8859 (Print)
IS  - 0198-8859 (Linking)
VI  - 80
IP  - 9
DP  - 2019 Sep
TI  - Tools for building, analyzing and evaluating HLA haplotypes from families.
PG  - 633-643
LID - S0198-8859(19)30133-8 [pii]
LID - 10.1016/j.humimm.2019.01.010 [doi]
AB  - The highly polymorphic classical human leukocyte antigen (HLA) genes display 
      strong linkage disequilibrium (LD) that results in conserved multi-locus 
      haplotypes. For unrelated individuals in defined populations, HLA haplotype 
      frequencies can be estimated using the expectation-maximization (EM) method. 
      Haplotypes can also be constructed using HLA allele segregation from nuclear 
      families. It is straightforward to identify many HLA genotyping inconsistencies 
      by visually reviewing HLA allele segregation in family members. It is also 
      possible to identify potential crossover events when two or more children are 
      available in a nuclear family. This process of visual inspection can be unwieldy, 
      and we developed the "HaplObserve" program to standardize the process and 
      automatically build haplotypes using family-based HLA allele segregation. 
      HaplObserve facilitates systematically building haplotypes, and reporting 
      potential crossover events. HLA Haplotype Validator (HLAHapV) is a program 
      originally developed to impute chromosomal phase from genotype data using 
      reference haplotype data. We updated and adapted HLAHapV to systematically 
      compare observed and estimated haplotypes. We also used HLAHapV to identify 
      haplotypes when uninformative HLA genotypes are present in families. Finally, we 
      developed "pould", an R package that calculates haplotype frequencies, and 
      estimates standard measures of global (locus-level) LD from both observed and 
      estimated haplotypes.
CI  - Copyright (c) 2019 American Society for Histocompatibility and Immunogenetics. 
      Published by Elsevier Inc. All rights reserved.
FAU - Osoegawa, Kazutoyo
AU  - Osoegawa K
AD  - Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood 
      Center, Palo Alto, CA, USA. Electronic address: kazutoyo@stanford.edu.
FAU - Mack, Steven J
AU  - Mack SJ
AD  - Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, 
      USA.
FAU - Prestegaard, Matthew
AU  - Prestegaard M
AD  - National Marrow Donor Program, Minneapolis, MN, USA.
FAU - Fernandez-Vina, Marcelo A
AU  - Fernandez-Vina MA
AD  - Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood 
      Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School 
      of Medicine, Stanford, CA, USA.
LA  - eng
GR  - R01 AI128775/AI/NIAID NIH HHS/United States
GR  - R01 GM109030/GM/NIGMS NIH HHS/United States
GR  - U19 NS095774/NS/NINDS NIH HHS/United States
PT  - Journal Article
PT  - Review
DEP - 20190205
PL  - United States
TA  - Hum Immunol
JT  - Human immunology
JID - 8010936
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - Child
MH  - Gene Frequency/genetics
MH  - Genetic Loci
MH  - HLA Antigens/*genetics
MH  - Haplotypes/*genetics
MH  - Heterozygote
MH  - Humans
MH  - Linkage Disequilibrium/genetics
MH  - Nuclear Family
MH  - Pedigree
MH  - *Software
PMC - PMC6682467
MID - NIHMS1525565
OTO - NOTNLM
OT  - 17th International HLA and Immunogenetics Workshop
OT  - HLA
OT  - Haplotype
OT  - Linkage disequilibrium
OT  - Next generation sequencing
COIS- Conflicts of Interests The authors declared no conflicting interests.
EDAT- 2019/02/09 06:00
MHDA- 2020/02/27 06:00
PMCR- 2020/09/01
CRDT- 2019/02/09 06:00
PHST- 2018/08/07 00:00 [received]
PHST- 2019/01/30 00:00 [revised]
PHST- 2019/01/30 00:00 [accepted]
PHST- 2019/02/09 06:00 [pubmed]
PHST- 2020/02/27 06:00 [medline]
PHST- 2019/02/09 06:00 [entrez]
PHST- 2020/09/01 00:00 [pmc-release]
AID - S0198-8859(19)30133-8 [pii]
AID - 10.1016/j.humimm.2019.01.010 [doi]
PST - ppublish
SO  - Hum Immunol. 2019 Sep;80(9):633-643. doi: 10.1016/j.humimm.2019.01.010. Epub 2019 
      Feb 5.