TY - JOUR
T1 - Ethnic divergence and linkage disequilibrium of novel SNPs in the human NLI-IF gene
T2 - Evidence of human origin and lack of association with tuberculosis susceptibility
AU - Ma, X.
AU - Wright, J.
AU - Dou, S.
AU - Olsen, P.
AU - Teeter, L.
AU - Adams, G.
AU - Graviss, E.
N1 - Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2002
Y1 - 2002
N2 - Sequence variation in the human genome has been used as a tool in studying human diseases and the evolutionary history of man. A human inherited predisposition to tuberculosis has been suggested and studied; however, genetic mechanisms are still ambiguous. In the present study, we scanned the regulatory and coding region of Nuclear LIM Interactor-Interacting Factor gene (NLI-IF), which is physically close to the tuberculosis-associated gene NRAMP1. Thirteen biallelic single-nucleotide polymorphisms (SNPs) were identified from four ethnic populations (African-American, Caucasian, Hispanic, and Asian) with population-specific distribution of alleles. The extent of linkage disequilibrium (LD) between 402T>C, and 472-42G>A varied distinctly from complete LD in the non-African-American groups to strong but incomplete LD in African-Americans. Both SNPs were in significant LD with the polymorphism 3′ UTR in NRAMP1 among these ethnic groups (P < 0.02), except 402T>C in African-Americans. In a case-control study with a Caucasian population, three cosmopolitan SNPs (204C>A, 402T>C and 472-42G>A) in NLI-IF showed no significant association with human susceptibility to tuberculosis. Our results support the "out-of-Africa" model of human origin, and suggest the time for the common ancestor dispersing from Africa could not have been more than approximately 385,620 years ago.
AB - Sequence variation in the human genome has been used as a tool in studying human diseases and the evolutionary history of man. A human inherited predisposition to tuberculosis has been suggested and studied; however, genetic mechanisms are still ambiguous. In the present study, we scanned the regulatory and coding region of Nuclear LIM Interactor-Interacting Factor gene (NLI-IF), which is physically close to the tuberculosis-associated gene NRAMP1. Thirteen biallelic single-nucleotide polymorphisms (SNPs) were identified from four ethnic populations (African-American, Caucasian, Hispanic, and Asian) with population-specific distribution of alleles. The extent of linkage disequilibrium (LD) between 402T>C, and 472-42G>A varied distinctly from complete LD in the non-African-American groups to strong but incomplete LD in African-Americans. Both SNPs were in significant LD with the polymorphism 3′ UTR in NRAMP1 among these ethnic groups (P < 0.02), except 402T>C in African-Americans. In a case-control study with a Caucasian population, three cosmopolitan SNPs (204C>A, 402T>C and 472-42G>A) in NLI-IF showed no significant association with human susceptibility to tuberculosis. Our results support the "out-of-Africa" model of human origin, and suggest the time for the common ancestor dispersing from Africa could not have been more than approximately 385,620 years ago.
KW - Human origin
KW - Linkage disequilibrium
KW - NLI-IF
KW - NRAMP1
KW - Single-nucleotide polymorphism
KW - Tuberculosis
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U2 - 10.1007/s100380200016
DO - 10.1007/s100380200016
M3 - Article
C2 - 11950066
AN - SCOPUS:0036221007
SN - 1434-5161
VL - 47
SP - 140
EP - 145
JO - Journal of Human Genetics
JF - Journal of Human Genetics
IS - 3
ER -