PMID- 31741008
OWN - NLM
STAT- MEDLINE
DCOM- 20191230
LR  - 20211204
IS  - 1432-1211 (Electronic)
IS  - 0093-7711 (Linking)
VI  - 71
IP  - 10
DP  - 2019 Nov
TI  - Single haplotype admixture models using large scale HLA genotype frequencies to 
      reproduce human admixture.
PG  - 589-604
LID - 10.1007/s00251-019-01144-7 [doi]
AB  - The human leukocyte antigen (HLA) is the most polymorphic region in humans. 
      Anthropologists use HLA to trace populations' migration and evolution. However, 
      recent admixture between populations can mask the ancestral haplotype frequency 
      distribution. We present a statistical method based on high-resolution HLA 
      haplotype frequencies to resolve population admixture using a non-negative matrix 
      factorization formalism and validated using haplotype frequencies from 56 world 
      populations. The result is a minimal set of source components (SCs) decoding 
      roughly 90% of the total variance in the studied admixtures. These SCs agree with 
      the geographical distribution, phylogenies, and recent admixture events of the 
      studied groups. With the growing population of multi-ethnic individuals, or 
      individuals that do not report race/ethnic information, the HLA matching process 
      for stem-cell and solid organ transplants is becoming more challenging. The 
      presented algorithm provides a framework that facilitates the breakdown of highly 
      admixed populations into SCs, which can be used to better match the rapidly 
      growing population of multi-ethnic individuals worldwide.
FAU - Simanovsky, Alexandra Litinsky
AU  - Simanovsky AL
AD  - Department of Mathematics and Gonda brain research institute, Bar-Ilan 
      University, 52900, Ramat-Gan, Israel.
FAU - Madbouly, Abeer
AU  - Madbouly A
AD  - Bioinformatics Research, Center for International Blood and Marrow Transplant 
      Research, Minneapolis, MN, USA.
FAU - Halagan, Michael
AU  - Halagan M
AD  - Bioinformatics Research, Center for International Blood and Marrow Transplant 
      Research, Minneapolis, MN, USA.
FAU - Maiers, Martin
AU  - Maiers M
AD  - Bioinformatics Research, Center for International Blood and Marrow Transplant 
      Research, Minneapolis, MN, USA.
FAU - Louzoun, Yoram
AU  - Louzoun Y
AUID- ORCID: 0000-0003-1714-6148
AD  - Department of Mathematics and Gonda brain research institute, Bar-Ilan 
      University, 52900, Ramat-Gan, Israel. louzouy@math.biu.ac.il.
LA  - eng
PT  - Journal Article
DEP - 20191118
PL  - United States
TA  - Immunogenetics
JT  - Immunogenetics
JID - 0420404
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Ethnicity/*genetics
MH  - Gene Frequency
MH  - Genotype
MH  - HLA Antigens/*classification/*genetics
MH  - *Haplotypes
MH  - Histocompatibility Testing/*methods/statistics & numerical data
MH  - Humans
MH  - Linkage Disequilibrium
MH  - *Models, Genetic
OTO - NOTNLM
OT  - Genetic admixture
OT  - HLA
OT  - Non-negative matrix factorization
OT  - Stem-cell donor registry
OT  - Unsupervised learning
EDAT- 2019/11/20 06:00
MHDA- 2019/12/31 06:00
CRDT- 2019/11/20 06:00
PHST- 2019/04/17 00:00 [received]
PHST- 2019/10/19 00:00 [accepted]
PHST- 2019/11/20 06:00 [pubmed]
PHST- 2019/12/31 06:00 [medline]
PHST- 2019/11/20 06:00 [entrez]
AID - 10.1007/s00251-019-01144-7 [pii]
AID - 10.1007/s00251-019-01144-7 [doi]
PST - ppublish
SO  - Immunogenetics. 2019 Nov;71(10):589-604. doi: 10.1007/s00251-019-01144-7. Epub 
      2019 Nov 18.