PMID- 18473345
OWN - NLM
STAT- MEDLINE
DCOM- 20081212
LR  - 20091119
IS  - 1098-1004 (Electronic)
IS  - 1059-7794 (Linking)
VI  - 29
IP  - 10
DP  - 2008 Oct
TI  - An unusual haplotype structure on human chromosome 8p23 derived from the 
      inversion polymorphism.
PG  - 1209-16
LID - 10.1002/humu.20775 [doi]
AB  - Chromosomal inversion is an important type of genomic variations involved in both 
      evolution and disease pathogenesis. Here, we describe the refined genetic 
      structure of a 3.8-Mb inversion polymorphism at chromosome 8p23. Using HapMap 
      data of 1,073 SNPs generated from 209 unrelated samples from CEPH-Utah residents 
      with ancestry from northern and western Europe (CEU); Yoruba in Ibadan, Nigeria 
      (YRI); and Asian (ASN) samples, which were comprised of Han Chinese from Beijing, 
      China (CHB) and Japanese from Tokyo, Japan (JPT)-we successfully deduced the 
      inversion orientations of all their 418 haplotypes. In particular, distinct 
      haplotype subgroups were identified based on principal component analysis (PCA). 
      Such genetic substructures were consistent with clustering patterns based on 
      neighbor-joining tree reconstruction, which revealed a total of four haplotype 
      clades across all samples. Metaphase fluorescence in situ hybridization (FISH) in 
      a subset of 10 HapMap samples verified their inversion orientations predicted by 
      PCA or phylogenetic tree reconstruction. Positioning of the outgroup haplotype 
      within one of YRI clades suggested that Human NCBI Build 36-inverted order is 
      most likely the ancestral orientation. Furthermore, the population 
      differentiation test and the relative extended haplotype homozygosity (REHH) 
      analysis in this region discovered multiple selection signals, also in a 
      population-specific manner. A positive selection signal was detected at XKR6 in 
      the ASN population. These results revealed the correlation of inversion 
      polymorphisms to population-specific genetic structures, and various selection 
      patterns as possible mechanisms for the maintenance of a large chromosomal 
      rearrangement at 8p23 region during evolution. In addition, our study also showed 
      that haplotype-based clustering methods, such as PCA, can be applied in scanning 
      for cryptic inversion polymorphisms at a genome-wide scale.
FAU - Deng, Libin
AU  - Deng L
AD  - Beijing Institute of Genomics, Chinese Academy of Sciences, P.R. China.
FAU - Zhang, Yuezheng
AU  - Zhang Y
FAU - Kang, Jian
AU  - Kang J
FAU - Liu, Tao
AU  - Liu T
FAU - Zhao, Hongbin
AU  - Zhao H
FAU - Gao, Yang
AU  - Gao Y
FAU - Li, Chaohua
AU  - Li C
FAU - Pan, Hao
AU  - Pan H
FAU - Tang, Xiaoli
AU  - Tang X
FAU - Wang, Dunmei
AU  - Wang D
FAU - Niu, Tianhua
AU  - Niu T
FAU - Yang, Huanming
AU  - Yang H
FAU - Zeng, Changqing
AU  - Zeng C
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Hum Mutat
JT  - Human mutation
JID - 9215429
SB  - IM
MH  - Chromosome Inversion/*genetics
MH  - Chromosome Mapping
MH  - Chromosomes, Human, Pair 8/*genetics
MH  - Genetic Variation
MH  - Genetics, Population
MH  - Genome, Human
MH  - *Haplotypes
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
MH  - Phylogeny
MH  - *Polymorphism, Single Nucleotide
EDAT- 2008/05/14 09:00
MHDA- 2008/12/17 09:00
CRDT- 2008/05/14 09:00
PHST- 2008/05/14 09:00 [pubmed]
PHST- 2008/12/17 09:00 [medline]
PHST- 2008/05/14 09:00 [entrez]
AID - 10.1002/humu.20775 [doi]
PST - ppublish
SO  - Hum Mutat. 2008 Oct;29(10):1209-16. doi: 10.1002/humu.20775.