Case-control association tests correcting for population stratification.

Abstract:

:In case-control association studies unobserved population stratification may act as a confounder, leading to an increased number of false positive results. Methods accounting for population structure by using additional genetic markers broadly follow one of two concepts: Genomic Control (GC) and Structured Association (SA). While extending existing methods of Structured Association we show that it is necessary to incorporate phenotypic information when inferring population structure, otherwise a systematic bias is introduced. Moreover, for moderate population stratification a Wald test statistic should be preferred as a Structured Association test statistic in comparison to a likelihood ratio test. The introduced extensions are compared to existing methods of Structured Association, as well as to Genomic Control, in a simulation study which is based on realistic situations of large case-control studies with moderate population stratification. A disadvantage of Genomic Control turns out to be the large variation in estimating the variance inflation factor, as well as the power loss if population structure increases. We come to the overall conclusion that Structured Association, if applied correctly, is superior to Genomic Control, at least in the case of simple population structure as simulated here.

journal_name

Ann Hum Genet

journal_title

Annals of human genetics

authors

Köhler K,Bickeböller H

doi

10.1111/j.1529-8817.2005.00214.x

subject

Has Abstract

pub_date

2006-01-01 00:00:00

pages

98-115

issue

Pt 1

eissn

0003-4800

issn

1469-1809

pii

AHG214

journal_volume

70

pub_type

杂志文章
  • Determining approximate estimates of inheritance parameters from sib-pair IBD proportions.

    abstract::The use of IBD proportions from a large set of affected sib-pair data to estimate some or all of the main parameters describing the inheritance of a disease susceptibility gene is here considered. We assume there is no recombination present and neglect ascertainment bias, and assume that there are four distinct parent...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1996.tb01186.x

    authors: Green JR,Shah S

    更新日期:1996-03-01 00:00:00

  • Evaluating linkage and linkage disequilibrium: use of excess sharing and transmission disequilibrium methods in affected sib pairs.

    abstract::Two popular and robust approaches to analysing affected sib pair (ASP) data for linkage are the traditional excess sharing methods and the transmission/disequilibrium test (TDT). Here we derive an overall test of linkage for multi-allelic ASP marker data which comprises two component tests: one for excess sharing and ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.2000.6450419.x

    authors: Wicks J,Wilson SR

    更新日期:2000-09-01 00:00:00

  • A note on allelic tests in case-control association studies.

    abstract::This paper reconsiders the relevant contribution of Sasieni in the validity of allele-based tests in case-control genetic association studies. In particular, the author clearly demonstrates that the classical chi-square test applied to allelic contingency tables is biased when the combined case-control population is n...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2008.00438.x

    authors: Guedj M,Nuel G,Prum B

    更新日期:2008-05-01 00:00:00

  • Single-center experience of N-linked Congenital Disorders of Glycosylation with a Summary of Molecularly Characterized Cases in Arabs.

    abstract::Congenital disorders of glycosylation (CDG) represent an expanding group of conditions that result from defects in protein and lipid glycosylation. Different subgroups of CDG display considerable clinical and genetic heterogeneity due to the highly complex nature of cellular glycosylation. This is further complicated ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12220

    authors: Bastaki F,Bizzari S,Hamici S,Nair P,Mohamed M,Saif F,Malik EM,Al-Ali MT,Hamzeh AR

    更新日期:2018-01-01 00:00:00

  • Inheritance and linkage data for an unusual combination of genes (at the LKE, PI and C6 loci) in a single large sibship.

    abstract::Analysis of the groups of a large sibship showed that the locus for the blood group LKE is not closely linked to the loci for MNS, Rh, HLA, Pi, Gm and C6 and is genetically independent of the loci for P1, K, Xg, Au, secretor, and C3. The locus for the Auberger (Au) blood group was shown to be genetically independent o...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1988.tb01097.x

    authors: Whitehouse DB,Attwood J,Green C,Bruce M,McQuade M,Tippett P

    更新日期:1988-07-01 00:00:00

  • Molecular scanning for mutations in the melanocortin-4 receptor gene in obese/diabetic Japanese.

    abstract::Decreased function of the melanocortin-4 receptor (MC4R) was reported to cause late-onset obesity and insulin resistance in rodents. Thus mutations in the MC4R gene drew strong attention as a possible cause of obesity and diabetes. We screened for mutations in the MC4R gene in extremely obese [body mass index (BMI) > ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1017/S0003480099007782

    authors: Ohshiro Y,Sanke T,Ueda K,Shimajiri Y,Nakagawa T,Tsunoda K,Nishi M,Sasaki H,Takasu N,Nanjo K

    更新日期:1999-11-01 00:00:00

  • On measuring genetic distance by selection intensity.

    abstract::A simple selection model (fitness 1, w, w2 for AA, Aa, aa) is employed to change the gene frequency of one population to another. The genetic distance is then defined as d = -log w between the two populations. The distance is symmetrical with respect to the two populations. It is additive: d13 = d12 + d23. The samplin...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1978.tb00922.x

    authors: Li CC

    更新日期:1978-05-01 00:00:00

  • Simultaneous selection of the wild-type genotypes of the G894T and 4B/ 4A polymorphisms of NOS3 associate with high-altitude adaptation.

    abstract::The routine performance of high-altitude (HA) natives in the hypoxic environment of HA exemplifies the process of adaptation mainly through natural selection. The recent therapeutic application of nitric oxide (NO) in HA disorders, for the improvement of oxygenation and vasodilation, ushered us to investigate the endo...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1529-8817.2005.00158.x

    authors: Ahsan A,Norboo T,Baig MA,Qadar Pasha MA

    更新日期:2005-05-01 00:00:00

  • Localization of the oncogene c-erbA1 immediately proximal to the acute promyelocytic leukaemia breakpoint on chromosome 17.

    abstract::Using in situ hybridization, c-erbA1 has been mapped immediately distal to the translocation breakpoint on chromosome 17 in fibroblasts with a karyotype 46,XX, t(15;17)(q22;q11). Previous work has shown that c-erbA1 is proximal to the translocation breakpoint on chromosome 17 in the t(15;17)(q22;q12-21) in acute promy...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1985.tb01690.x

    authors: Sheer D,Sheppard DM,le Beau M,Rowley JD,San Roman C,Solomon E

    更新日期:1985-07-01 00:00:00

  • Validation study of genetic associations with coronary artery disease on chromosome 3q13-21 and potential effect modification by smoking.

    abstract::The CATHGEN study reported associations of chromosome 3q13-21 genes (KALRN, MYLK, CDGAP, and GATA2) with early-onset coronary artery disease (CAD). This study attempted to independently validate those associations. Eleven single nucleotide polymorphisms (SNPs) were examined (rs10934490, rs16834817, rs6810298, rs928923...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2009.00540.x

    authors: Horne BD,Hauser ER,Wang L,Muhlestein JB,Anderson JL,Carlquist JF,Shah SH,Kraus WE

    更新日期:2009-11-01 00:00:00

  • Mapping of RXRB to human chromosome 6p21.3.

    abstract::Retinoid X Receptor beta (RXRB) is a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). We have confirmed the localization of RXRB to chromosome 6 and we have mapped the gene to chromosome 6p21.3-p21.1 by PCR amplification of 5' untran...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1993.tb01596.x

    authors: Fitzgibbon J,Gillett GT,Woodward KJ,Boyle JM,Wolfe J,Povey S

    更新日期:1993-07-01 00:00:00

  • Studies on N-Acetyltransferase (NAT2) Genotype Relationships in Emiratis: Confirmation of the Existence of Phenotype Variation among Slow Acetylators.

    abstract:BACKGROUND AND PURPOSE:Individuals with slow N-acetylation phenotype often experience toxicity from drugs such as isoniazid, sulfonamides, procainamide, and hydralazine, whereas rapid acetylators may not respond to these medications. The highly polymorphic N-acetyltransferase 2 enzyme encoded by the NAT2 gene is one of...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12198

    authors: Al-Ahmad MM,Amir N,Dhanasekaran S,John A,Abdulrazzaq YM,Ali BR,Bastaki S

    更新日期:2017-09-01 00:00:00

  • Application of multi-locus analytical methods to identify interacting loci in case-control studies.

    abstract::To identify interacting loci in genetic epidemiological studies the application of multi-locus methods of analysis is warranted. Several more advanced classification methods have been developed in the past years, including multiple logistic regression, sum statistics, logic regression, and the multifactor dimensionali...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2007.00360.x

    authors: Vermeulen SH,Den Heijer M,Sham P,Knight J

    更新日期:2007-09-01 00:00:00

  • The mitochondrial DNA 4977-bp deletion and copy number alteration in Han Chinese samples with uterine fibroids.

    abstract::Uterine fibroids (UFs) are the most common benign neoplasms, but their pathogenesis is not completely understood. Thus far, alterations in the mitochondrial DNA (mtDNA) content and the mtDNA 4977-bp deletion level in UFs, as well as the corresponding nontumorous tissue, have remained elusive. To test whether large mtD...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12303

    authors: Luo Y,Zou Y,Wu J,Zhang ZY,Liu FY,Li LP,Huang OP

    更新日期:2019-07-01 00:00:00

  • Association study of M235T and A-6G polymorphisms in angiotensinogen gene with risk of developing preeclampsia in Iranian population.

    abstract:OBJECTIVE:Preeclampsia (PE) is a life-threatening complication of pregnancy that accounts for 12% of all maternal deaths worldwide. The aim of this study is to investigate the relationships between the polymorphisms of angiotensinogen (AGT) gene and preeclampsia. MATERIAL AND METHODS:In this study, 240 unrelated preec...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12323

    authors: Alaee E,Mirahmadi M,Ghasemi M,Kashani E,Attar M,Shahbazi M

    更新日期:2019-11-01 00:00:00

  • The complex and diversified mitochondrial gene pool of Berber populations.

    abstract::The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitoc...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2008.00493.x

    authors: Coudray C,Olivieri A,Achilli A,Pala M,Melhaoui M,Cherkaoui M,El-Chennawi F,Kossmann M,Torroni A,Dugoujon JM

    更新日期:2009-03-01 00:00:00

  • Bayesian inference in multipoint gene mapping.

    abstract::The problem of ordering and mapping genes on the basis of recombinant data and radiation hybrid data is formulated as a problem of Bayesian inference for an unknown permutation. The challenging computational problems posed by this approach are shown to be resolvable using Markov chain Monte Carlo methods. ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1993.tb00887.x

    authors: Stephens DA,Smith AF

    更新日期:1993-01-01 00:00:00

  • G-protein beta-3 subunit C825T polymorphism, sodium and arterial blood pressure: a community-based study of Japanese men and women.

    abstract::Epidemiological evidence on gene-environment effects of the G-protein beta-3 subunit C825T polymorphisms and sodium on blood pressure in the free-living general population is limited. We examined the associations between the C825T polymorphism and blood pressure levels, stratified by the sodium variables estimated by ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2006.00276.x

    authors: Yamagishi K,Tanigawa T,Cui R,Tabata M,Ikeda A,Yao M,Shimamoto T,Iso H

    更新日期:2006-11-01 00:00:00

  • Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations.

    abstract::We describe a novel method for analysis of marker genotype data from admixed populations, based on a hybrid of Bayesian and frequentist approaches in which the posterior distribution is generated by Markov chain simulation and score tests are obtained from the missing-data likelihood. We analysed data on unrelated ind...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1017/S0003480000008022

    authors: McKeigue PM,Carpenter JR,Parra EJ,Shriver MD

    更新日期:2000-03-01 00:00:00

  • A G-band study of chromosomes in liveborn infants.

    abstract::The results of a chromosome survey of 3993 liveborn infants, the majority of which have been studied using G-banding, are reported. The frequency of all types of chromosome abnormalities detected was similar to that found in previous newborn surveys, which were carried out on different socio-economic structure, but th...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1980.tb01556.x

    authors: Buckton KE,O'Riordan ML,Ratcliffe S,Slight J,Mitchell M,McBeath S,Keay AJ,Barr D,Short M

    更新日期:1980-01-01 00:00:00

  • Asymptotic behaviour of the mean of a continuous phenotypic diffusion process with overlapping generations.

    abstract::The equilibrium position is determined for the phenotypic distribution o f a continuous characteristic in a population which reproduces both randomly and assortatively, and wherein generations are overlapping. It is shown that the major assortative mating models so far proposed for continuous traits are not particular...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1978.tb01903.x

    authors: Wilson SR

    更新日期:1978-01-01 00:00:00

  • The distribution of Q: a powerful sibship test of association.

    abstract::Non-random inheritance of the two parental haplotypes among siblings affected by certain diseases has long been used to provide evidence of the presence of disease susceptibility genes. The distribution of a powerful test, called Q, based on haplotype concordance and discordance, is derived under the null hypothesis o...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1994.tb01885.x

    authors: Shah S,Green JR

    更新日期:1994-05-01 00:00:00

  • X-linkage and genetic heterogeneity in bipolar-related major affective illness: reanalysis of linkage data.

    abstract::It has been suggested that an X-linked dominant allele operates in the genetic transmission of bipolar (manic-depressive) illness. Linkage studies with X-chromosome markers have remained inconclusive, showing both positive and negative results. Some of the ambiguity may be attributed to imprecise analytic methods and ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1982.tb00706.x

    authors: Risch N,Baron M

    更新日期:1982-05-01 00:00:00

  • Report on the Fifth International Workshop on Chromosome 9 held at Eynsham, Oxfordshire, UK, September 4-6, 1996.

    abstract::The Fifth International workshop on chromosome 9 comprised a gathering of 36 scientists from seven countries and included a fairly even distribution of interests along chromosome 9 as well as a strong input from more global activities and from comparative mapping. At least eight groups had participated in the goal set...

    journal_title:Annals of human genetics

    pub_type:

    doi:10.1046/j.1469-1809.1997.6130183.x

    authors: Povey S,Attwood J,Chadwick B,Frezal J,Haines JL,Knowles M,Kwiatkowski DJ,Olopade OI,Slaugenhaupt S,Spurr NK,Smith M,Steel K,White JA,Pericak-Vance MA

    更新日期:1997-05-01 00:00:00

  • The fate of 12 recessive mutations in a single village.

    abstract::In a Muslim Arab village, relatively isolated because of the preference of consanguineous marriages, we studied the fate of 12 mutations in 5 different genes. The study was based on carriers detected among relatives of affected patients and of carriers discovered in a random sample of 424 adults. Most of the mutations...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2006.00308.x

    authors: Zlotogora J,Hujerat Y,Barges S,Shalev SA,Chakravarti A

    更新日期:2007-03-01 00:00:00

  • Superiority of denaturing high performance liquid chromatography over single-stranded conformation and conformation-sensitive gel electrophoresis for mutation detection in TSC2.

    abstract::We evaluated denaturing high pressure liquid chromatography (DHPLC) as a scanning method for mutation detection in TSC2, and compared it to conformation-sensitive gel electrophoresis (CSGE) and single-stranded conformation polymorphism analysis (SSCP). The first 20 exons of TSC2 were amplified from 84 TSC patients and...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.1999.6350383.x

    authors: Choy YS,Dabora SL,Hall F,Ramesh V,Niida Y,Franz D,Kasprzyk-Obara J,Reeve MP,Kwiatkowski DJ

    更新日期:1999-09-01 00:00:00

  • Regression-based multivariate linkage analysis with an application to blood pressure and body mass index.

    abstract::Multivariate linkage analysis has been suggested for the analysis of correlated traits, such as blood pressure (BP) and body mass index (BMI), because it may offer greater power and provide clearer results than univariate analyses. Currently, the most commonly used multivariate linkage methods are extensions of the un...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2006.00303.x

    authors: Wang T,Elston RC

    更新日期:2007-01-01 00:00:00

  • The phenotypic consequences of CFTR mutations.

    abstract::Cystic fibrosis is a common autosomal recessive disorder that primarily affects the epithelial cells in the intestine, respiratory system, pancreas, gall bladder and sweat glands. Over one thousand mutations have currently been identified in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene that are ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,评审

    doi:10.1046/j.1469-1809.2003.00028.x

    authors: Rowntree RK,Harris A

    更新日期:2003-09-01 00:00:00

  • Update of spectrum c.35delG and c.-23+1G>A mutations on the GJB2 gene in individuals with autosomal recessive nonsyndromic hearing loss.

    abstract::Hearing loss (HL) is the most common birth defect and the most prevalent sensorineural condition worldwide. It is associated with more than 1,000 mutations in at least 90 genes. Mutations of the gap junction beta-2 protein (GJB2) gene located in the nonsyndromic hearing loss and deafness (DFNB1) locus (chromosome 13q1...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,评审

    doi:10.1111/ahg.12284

    authors: Azadegan-Dehkordi F,Ahmadi R,Koohiyan M,Hashemzadeh-Chaleshtori M

    更新日期:2019-01-01 00:00:00

  • Common glucose-6-phosphate dehydrogenase (G6PD) variants from the Italian population: biochemical and molecular characterization.

    abstract::By biochemical characterization of glucose-6-phosphate dehydrogenase (G6PD) from the red cells of seventeen subjects of the population of Matera (Southern Italy) we have identified six genetically determined common variants. Among these, G6PD Metaponto and G6PD A(-) Matera had been already fully characterized. We have...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1990.tb00355.x

    authors: Viglietto G,Montanaro V,Calabrò V,Vallone D,D'Urso M,Persico MG,Battistuzzi G

    更新日期:1990-01-01 00:00:00