Mapping by admixture linkage disequilibrium in human populations: limits and guidelines.

PubWeight™: 7.16‹?› | Rank: Top 1%

🔗 View Article (PMC 1918304)

Published in Am J Hum Genet on October 01, 1994

Authors

J C Stephens1, D Briscoe, S J O'Brien

Author Affiliations

1: Laboratory of Viral Carcinogenesis, National Cancer Institute, National Institutes of Health, Frederick Cancer Research and Development Center, MD 21702-1201.

Associated clinical trials:

Genetic Markers for Focal Segmental Glomerulosclerosis | NCT00001393

Articles citing this

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics (2003) 53.11

Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet (1998) 22.90

Methods for high-density admixture mapping of disease genes. Am J Hum Genet (2004) 12.02

A high-density admixture map for disease gene discovery in african americans. Am J Hum Genet (2004) 10.87

MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nat Genet (2008) 9.50

Design and analysis of admixture mapping studies. Am J Hum Genet (2004) 7.20

Transmission-disequilibrium tests for quantitative traits. Am J Hum Genet (1997) 7.10

Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet (1997) 6.72

Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations. Am J Hum Genet (1997) 6.35

Mapping disease genes: family-based association studies. Am J Hum Genet (1995) 5.82

Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Genet (2001) 5.66

Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. Am J Hum Genet (2000) 4.74

Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet (2003) 4.67

Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet (2004) 4.52

Incorporating genotypes of relatives into a test of linkage disequilibrium. Am J Hum Genet (1998) 3.83

A genomewide single-nucleotide-polymorphism panel with high ancestry information for African American admixture mapping. Am J Hum Genet (2006) 3.77

Population stratification confounds genetic association studies among Latinos. Hum Genet (2005) 3.19

Admixture mapping of white cell count: genetic locus responsible for lower white blood cell count in the Health ABC and Jackson Heart studies. Am J Hum Genet (2008) 3.06

Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet (2001) 3.04

Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels. Am J Hum Genet (2007) 2.91

A scan for linkage disequilibrium across the human genome. Genetics (1999) 2.79

Prospects for admixture mapping of complex traits. Am J Hum Genet (2004) 2.73

Polymorphic admixture typing in human ethnic populations. Am J Hum Genet (1994) 2.37

Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am J Hum Genet (2000) 2.32

Measuring and using admixture to study the genetics of complex diseases. Hum Genomics (2003) 2.31

Analysis of genomic admixture in Uyghur and its implication in mapping strategy. Am J Hum Genet (2008) 2.30

Population genetic inference from genomic sequence variation. Genome Res (2010) 2.29

Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. Am J Hum Genet (2002) 2.29

Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians. Hum Genet (2003) 2.27

Linkage analysis of a complex disease through use of admixed populations. Am J Hum Genet (2004) 2.21

Genomewide linkage scan for opioid dependence and related traits. Am J Hum Genet (2006) 2.15

Racial admixture and its impact on BMI and blood pressure in African and Mexican Americans. Hum Genet (2006) 1.98

Elevated male European and female African contributions to the genomes of African American individuals. Hum Genet (2006) 1.97

A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery. Am J Hum Genet (2008) 1.92

Review and evaluation of methods correcting for population stratification with a focus on underlying statistical principles. Hum Hered (2008) 1.92

"Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits. Am J Hum Genet (2003) 1.82

Genome-wide screen for asthma in Puerto Ricans: evidence for association with 5q23 region. Hum Genet (2008) 1.81

Marker selection for the transmission/disequilibrium test, in recently admixed populations. Am J Hum Genet (1998) 1.66

Consistent long-range linkage disequilibrium generated by admixture in a Bantu-Semitic hybrid population. Am J Hum Genet (2000) 1.65

Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population. Proc Natl Acad Sci U S A (2010) 1.64

Regional admixture mapping and structured association testing: conceptual unification and an extensible general linear model. PLoS Genet (2006) 1.44

A classical likelihood based approach for admixture mapping using EM algorithm. Hum Genet (2006) 1.43

Genome-wide association identifies candidate genes that influence the human electroencephalogram. Proc Natl Acad Sci U S A (2010) 1.38

Admixture mapping as a tool in gene discovery. Curr Opin Genet Dev (2007) 1.23

Hybrid zones as a tool for identifying adaptive genetic variation in outbreeding forest trees: lessons from wild annual sunflowers (Helianthus spp.). For Ecol Manage (2004) 1.22

Dissecting complex diseases in complex populations: asthma in latino americans. Proc Am Thorac Soc (2007) 1.21

Putative ancestral origins of chromosomal segments in individual african americans: implications for admixture mapping. Genome Res (2004) 1.18

A general mechanistic model for admixture histories of hybrid populations. Genetics (2011) 1.17

Admixture mapping of quantitative trait loci for BMI in African Americans: evidence for loci on chromosomes 3q, 5q, and 15q. Obesity (Silver Spring) (2009) 1.12

Genetic isolates: separate but equal? Proc Natl Acad Sci U S A (1999) 1.10

Exploring population admixture dynamics via empirical and simulated genome-wide distribution of ancestral chromosomal segments. Am J Hum Genet (2012) 1.07

Comparison of measures of marker informativeness for ancestry and admixture mapping. BMC Genomics (2011) 1.07

Mapping genes that predict treatment outcome in admixed populations. Pharmacogenomics J (2010) 1.05

Softwares and methods for estimating genetic ancestry in human populations. Hum Genomics (2013) 1.00

A Method for Inferring an Individual's Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations. Front Genet (2013) 0.99

Genome-wide distribution of ancestry in Mexican Americans. Hum Genet (2008) 0.96

Admixture mapping of lung cancer in 1812 African-Americans. Carcinogenesis (2010) 0.95

Mexican-American admixture mapping analyses for diabetic nephropathy in type 2 diabetes mellitus. Semin Nephrol (2010) 0.92

Database mining for selection of SNP markers useful in admixture mapping. BioData Min (2009) 0.91

Characterization and correction of error in genome-wide IBD estimation for samples with population structure. Genet Epidemiol (2013) 0.91

Spectrum of nonrandom associations between microsatellite loci on human chromosome 11p15. Genetics (2001) 0.90

Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping. Eur J Hum Genet (2013) 0.86

Recent admixture in an Indian population of African ancestry. Am J Hum Genet (2011) 0.85

Admixture mapping of ankle-arm index: identification of a candidate locus associated with peripheral arterial disease. J Med Genet (2009) 0.84

Power comparison of admixture mapping and direct association analysis in genome-wide association studies. Genet Epidemiol (2012) 0.83

Disruptions in energy balance: does nature overcome nurture? Physiol Behav (2007) 0.83

The role of local ancestry adjustment in association studies using admixed populations. Genet Epidemiol (2014) 0.80

Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure. Proc Natl Acad Sci U S A (2015) 0.79

Population genetic structure and origins of Native Hawaiians in the multiethnic cohort study. PLoS One (2012) 0.79

Somatic mutations in cancer development. Environ Health (2011) 0.77

Admixture mapping: from paradigms of race and ethnicity to population history. Hugo J (2010) 0.76

Cohort profile: the Baependi Heart Study-a family-based, highly admixed cohort study in a rural Brazilian town. BMJ Open (2016) 0.76

Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture. Genet Sel Evol (2017) 0.76

Human population admixture in Asia. Genomics Inform (2012) 0.76

Impaired collagen chaperone results in preterm PROM. Proc Natl Acad Sci U S A (2006) 0.75

Articles cited by this

Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet (1989) 62.23

Identification of the cystic fibrosis gene: genetic analysis. Science (1989) 33.61

Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland. Nat Genet (1992) 15.62

Mutation of human short tandem repeats. Hum Mol Genet (1993) 14.03

Hepatocellular carcinoma and hepatitis B virus. A prospective study of 22 707 men in Taiwan. Lancet (1981) 13.54

A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet (1989) 12.57

Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci U S A (1988) 8.22

Mapping complex genetic traits in humans: new methods using a complete RFLP linkage map. Cold Spring Harb Symp Quant Biol (1986) 8.22

Linkage disequilibrium in subdivided populations. Genetics (1973) 5.22

Sample sizes required to detect linkage disequilibrium between two or three loci. Theor Popul Biol (1975) 4.15

Linkage disequilibrium in admixed populations: applications in gene mapping. J Hered (1994) 3.46

Human genetics: the molecular challenge. Cold Spring Harb Symp Quant Biol (1986) 2.54

Polymorphic admixture typing in human ethnic populations. Am J Hum Genet (1994) 2.37

Recombination of haplotypes leads to biased estimates of admixture proportions in human populations. Proc Natl Acad Sci U S A (1988) 2.16

Mapping the human genome: current status. Science (1990) 1.79

Application of DNA fingerprints for cell-line individualization. Am J Hum Genet (1990) 1.62

Transient linkage disequilibrium in Drosophila. Nature (1971) 1.58

Detecting high-resolution polymorphisms in human coding loci by combining PCR and single-strand conformation polymorphism (SSCP) analysis. Am J Hum Genet (1991) 1.35

HLA antigens and insulin-dependent diabetes. Nature (1988) 1.13

Articles by these authors

(truncated to the top 100)

Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science (1996) 15.63

Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat Med (1996) 10.49

Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science (2001) 8.68

Molecular phylogenetics and the origins of placental mammals. Nature (2001) 8.42

HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science (1999) 8.11

Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort (SFCC), ALIVE Study. Science (1997) 5.91

Tempting fate: control of communicable disease in England. BMJ (1993) 5.62

Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes. Am J Hum Genet (1998) 5.24

A canine distemper virus epidemic in Serengeti lions (Panthera leo). Nature (1996) 5.07

Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS. N Engl J Med (2001) 4.98

Identification of an amplified, highly expressed gene in a human glioma. Science (1987) 4.21

Mechanism of met oncogene activation. Cell (1986) 4.20

Human endothelial cell growth factor: cloning, nucleotide sequence, and chromosome localization. Science (1986) 4.17

Genetic evidence for two species of elephant in Africa. Science (2001) 4.13

Genetic restriction of AIDS pathogenesis by an SDF-1 chemokine gene variant. ALIVE Study, Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort (SFCC) Science (1998) 3.86

Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol (1994) 3.71

Genetic acceleration of AIDS progression by a promoter variant of CCR5. Science (1998) 3.60

HLA and AIDS: a cautionary tale. Trends Mol Med (2001) 3.51

Trends in indigenous foodborne disease and deaths, England and Wales: 1992 to 2000. Gut (2002) 3.48

Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nat Genet (1997) 3.47

Linkage disequilibrium in admixed populations: applications in gene mapping. J Hered (1994) 3.46

Genetic basis for species vulnerability in the cheetah. Science (1985) 3.16

Transactivation induced by human T-lymphotropic virus type III (HTLV III) maps to a viral sequence encoding 58 amino acids and lacks tissue specificity. Virology (1986) 3.15

Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet (2001) 3.04

Chromosomal organization of the human dihydrofolate reductase genes: dispersion, selective amplification, and a novel form of polymorphism. Proc Natl Acad Sci U S A (1984) 2.99

A genetic linkage map of microsatellites in the domestic cat (Felis catus). Genomics (1999) 2.99

The ets sequence from the transforming gene of avian erythroblastosis virus, E26, has unique domains on human chromosomes 11 and 21: both loci are transcriptionally active. Proc Natl Acad Sci U S A (1985) 2.80

A scan for linkage disequilibrium across the human genome. Genetics (1999) 2.79

East African cheetahs: evidence for two population bottlenecks? Proc Natl Acad Sci U S A (1987) 2.73

Segmental aneuploidy as a probe for structural genes in Drosophila: mitochondrial membrane enzymes. Genetics (1973) 2.62

The GLI-Kruppel family of human genes. Mol Cell Biol (1988) 2.52

Molecular distance and divergence time in carnivores and primates. Mol Biol Evol (1991) 2.50

Racial differences in HLA class II associations with hepatitis C virus outcomes. J Infect Dis (2001) 2.47

General outbreaks of infectious intestinal disease in England and Wales: 1995 and 1996. Commun Dis Public Health (1998) 2.35

Genomic ancestry of the American puma (Puma concolor). J Hered (2000) 2.34

Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am J Hum Genet (2000) 2.32

Expression of the human c-fms proto-oncogene in hematopoietic cells and its deletion in the 5q- syndrome. Cell (1985) 2.28

Detecting single base substitutions as heteroduplex polymorphisms. Genomics (1992) 2.26

Genetic restriction of HIV-1 pathogenesis to AIDS by promoter alleles of IL10. Proc Natl Acad Sci U S A (2000) 2.24

The t(11;14)(p15;q11) in a T-cell acute lymphoblastic leukemia cell line activates multiple transcripts, including Ttg-1, a gene encoding a potential zinc finger protein. Mol Cell Biol (1989) 2.24

Estimation of heterozygosity for single-probe multilocus DNA fingerprints. Mol Biol Evol (1992) 2.23

A radiation hybrid map of the cat genome: implications for comparative mapping. Genome Res (2000) 2.22

Molecular dating and biogeography of the early placental mammal radiation. J Hered (2001) 2.13

Canine and feline parvoviruses can use human or feline transferrin receptors to bind, enter, and infect cells. J Virol (2001) 2.08

The -glycerophosphate in Drosophila melanogaster. II. Genetic aspects. Genetics (1972) 2.05

Unusual polymorphisms in human immunodeficiency virus type 1 associated with nonprogressive infection. J Virol (2000) 2.04

Establishment and characterization of three new continuous cell lines derived from human breast carcinomas. Cancer Res (1978) 1.97

Molecular cloning and chromosomal localization of the human T-cell receptor zeta chain: distinction from the molecular CD3 complex. Proc Natl Acad Sci U S A (1988) 1.95

Risk factors for sporadic cases of Escherichia coli O157 infection: the importance of contact with animal excreta. Epidemiol Infect (2001) 1.94

What can analysis of calls to NHS direct tell us about the epidemiology of gastrointestinal infections in the community? J Infect (2003) 1.89

Reliability, validity, and responsiveness of four knee outcome scales for athletic patients. J Bone Joint Surg Am (2001) 1.85

Influence of seasonal migration on geographic distribution of mitochondrial DNA haplotypes in humpback whales. Nature (1990) 1.83

Dispersion of the ras family of transforming genes to four different chromosomes in man. Nature (1983) 1.82

Immunologic and virologic response to highly active antiretroviral therapy in the Multicenter AIDS Cohort Study. AIDS (2001) 1.79

The consequences of demographic reduction and genetic depletion in the endangered Florida panther. Curr Biol (1993) 1.79

Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biol (2001) 1.78

Genetic variance of laboratory outbred Swiss mice. Nature (1980) 1.77

Exclusive and persistent use of the entry coreceptor CXCR4 by human immunodeficiency virus type 1 from a subject homozygous for CCR5 delta32. J Virol (1998) 1.69

Public health implications of campylobacter outbreaks in England and Wales, 1995-9: epidemiological and microbiological investigations. Epidemiol Infect (2002) 1.67

The human homologs of the raf (mil) oncogene are located on human chromosomes 3 and 4. Science (1984) 1.66

Genetic mapping in mammals: chromosome map of domestic cat. Science (1982) 1.65

Genetics of HIV-1 infection: chemokine receptor CCR5 polymorphism and its consequences. Hum Mol Genet (1999) 1.65

The interleukin 3 gene is located on human chromosome 5 and is deleted in myeloid leukemias with a deletion of 5q. Proc Natl Acad Sci U S A (1987) 1.64

Mapping of an endogenous retroviral sequence to human chromosome 18. Nature (1983) 1.64

Extensive conservation of sex chromosome organization between cat and human revealed by parallel radiation hybrid mapping. Genome Res (1999) 1.64

Shoulder arthroscopy with the patient in the beach-chair position. Arthroscopy (1988) 1.62

Application of DNA fingerprints for cell-line individualization. Am J Hum Genet (1990) 1.62

Isolation of HTLV-transformed B-lymphocyte clone from a patient with HTLV-associated adult T-cell leukaemia. Nature (1984) 1.58

Transient linkage disequilibrium in Drosophila. Nature (1971) 1.58

Phylogenetics, genome diversity and origin of modern leopard, Panthera pardus. Mol Ecol (2001) 1.58

C-C chemokines, pivotal in protection against HIV type 1 infection. Proc Natl Acad Sci U S A (1998) 1.57

Molecular genetic characterization of the RD-114 gene family of endogenous feline retroviral sequences. J Virol (1984) 1.57

Molecular analysis of integrated human papillomavirus 16 sequences in the cervical cancer cell line SiHa. Virology (1987) 1.57

A lion lentivirus related to feline immunodeficiency virus: epidemiologic and phylogenetic aspects. J Virol (1994) 1.56

On estimating functional gene number in eukaryotes. Nat New Biol (1973) 1.55

Comparative genomics: tracking chromosome evolution in the family ursidae using reciprocal chromosome painting. Cytogenet Cell Genet (1998) 1.54

Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus). J Hered (2003) 1.53

Diurnal intraocular pressure variations: an analysis of 690 diurnal curves. Br J Ophthalmol (1992) 1.50

Class II HLA alleles and hepatitis B virus persistence in African Americans. J Infect Dis (1999) 1.48

Anatomy, histology, and vascularity of the glenoid labrum. An anatomical study. J Bone Joint Surg Am (1992) 1.48

Widespread retinal degenerative disease mutation (rdAc) discovered among a large number of popular cat breeds. Vet J (2009) 1.48

Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics (1996) 1.46

The Lake Casitas wild mouse: evolving genetic resistance to retroviral disease. Trends Genet (1991) 1.46

A gene (Bevi) on human chromosome 6 is an integration site for baboon type C DNA provirus in human cells. Cell (1978) 1.45

Origin of the HIV-susceptible human CD4+ cell line H9. AIDS Res Hum Retroviruses (1989) 1.45

A molecular solution to the riddle of the giant panda's phylogeny. Nature (1985) 1.43

Campylobacter coli - an important foodborne pathogen. J Infect (2003) 1.42

Novel alleles of the chemokine-receptor gene CCR5. Am J Hum Genet (1997) 1.39

Genetic fingerprinting reflects population differentiation in the California Channel Island fox. Nature (1990) 1.38

Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Mol Biol Evol (1997) 1.38

Interacting gene-enzyme systems in Drosophila. Annu Rev Genet (1976) 1.37

Comparative analysis of malate dehydrogenases of Drosophila melanogaster. Biochem Genet (1973) 1.37

Verocytotoxin-producing Escherichia coli (VTEC) O157 and other VTEC from human infections in England and Wales: 1995-1998. J Med Microbiol (2001) 1.36

Genetic and phylogenetic divergence of feline immunodeficiency virus in the puma (Puma concolor). J Virol (1996) 1.36

Phylogenetic reconstruction of the Felidae using 16S rRNA and NADH-5 mitochondrial genes. J Mol Evol (1997) 1.35

Detecting high-resolution polymorphisms in human coding loci by combining PCR and single-strand conformation polymorphism (SSCP) analysis. Am J Hum Genet (1991) 1.35

CCR2 chemokine receptor and AIDS progression. Nat Med (1997) 1.34

Evolutionary conservation of ten microsatellite loci in four species of Felidae. J Hered (1995) 1.33

Prevalence of antibodies to feline parvovirus, calicivirus, herpesvirus, coronavirus, and immunodeficiency virus and of feline leukemia virus antigen and the interrelationship of these viral infections in free-ranging lions in east Africa. Clin Diagn Lab Immunol (1996) 1.32

Analysis of multiple isoenzyme expression among twenty-two species of Mycoplasma and Acholeplasma. J Bacteriol (1981) 1.32