PMID- 20670352
OWN - NLM
STAT- MEDLINE
DCOM- 20110218
LR  - 20101109
IS  - 1399-0039 (Electronic)
IS  - 0001-2815 (Linking)
VI  - 76
IP  - 6
DP  - 2010 Dec
TI  - Evaluation of computational methods for the reconstruction of HLA haplotypes.
PG  - 459-66
LID - 10.1111/j.1399-0039.2010.01539.x [doi]
AB  - Human leukocyte antigen (HLA) haplotypes are frequently evaluated for population 
      history inferences and association studies. However, the available typing 
      techniques for the main HLA loci usually do not allow the determination of the 
      allele phase and the constitution of a haplotype, which may be obtained by a very 
      time-consuming and expensive family-based segregation study. Without the 
      family-based study, computational inference by probabilistic models is necessary 
      to obtain haplotypes. Several authors have used the expectation-maximization (EM) 
      algorithm to determine HLA haplotypes, but high levels of erroneous inferences 
      are expected because of the genetic distance among the main HLA loci and the 
      presence of several recombination hotspots. In order to evaluate the efficiency 
      of computational inference methods, 763 unrelated individuals stratified into 
      three different datasets had their haplotypes manually defined in a family-based 
      study of HLA-A, -B, -DRB1 and -DQB1 segregation, and these haplotypes were 
      compared with the data obtained by the following three methods: the 
      Expectation-Maximization (EM) and Excoffier-Laval-Balding (ELB) algorithms using 
      the arlequin 3.11 software, and the PHASE method. When comparing the methods, we 
      observed that all algorithms showed a poor performance for haplotype 
      reconstruction with distant loci, estimating incorrect haplotypes for 38%-57% of 
      the samples considering all algorithms and datasets. We suggest that 
      computational haplotype inferences involving low-resolution HLA-A, HLA-B, 
      HLA-DRB1 and HLA-DQB1 haplotypes should be considered with caution.
CI  - (c) 2010 John Wiley & Sons A/S.
FAU - Castelli, E C
AU  - Castelli EC
AD  - Departamento de Clinica Medica, Faculdade de Medicina de Ribeirao Preto, 
      Universidade de Sao Paulo, Ribeirao Preto-SP, Brazil.
FAU - Mendes-Junior, C T
AU  - Mendes-Junior CT
FAU - Veiga-Castelli, L C
AU  - Veiga-Castelli LC
FAU - Pereira, N F
AU  - Pereira NF
FAU - Petzl-Erler, M L
AU  - Petzl-Erler ML
FAU - Donadi, E A
AU  - Donadi EA
LA  - eng
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Tissue Antigens
JT  - Tissue antigens
JID - 0331072
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Algorithms
MH  - *Alleles
MH  - Brazil
MH  - Computational Biology/*methods
MH  - Female
MH  - HLA Antigens/*genetics/immunology
MH  - Haplotypes/*genetics/immunology
MH  - Humans
MH  - Male
MH  - Sequence Analysis, DNA/*methods
EDAT- 2010/07/31 06:00
MHDA- 2011/02/22 06:00
CRDT- 2010/07/31 06:00
PHST- 2010/07/31 06:00 [entrez]
PHST- 2010/07/31 06:00 [pubmed]
PHST- 2011/02/22 06:00 [medline]
AID - TAN1539 [pii]
AID - 10.1111/j.1399-0039.2010.01539.x [doi]
PST - ppublish
SO  - Tissue Antigens. 2010 Dec;76(6):459-66. doi: 10.1111/j.1399-0039.2010.01539.x.