A family-based joint test for mean and variance heterogeneity for quantitative traits.

Abstract:

:Traditional quantitative trait locus (QTL) analysis focuses on identifying loci associated with mean heterogeneity. Recent research has discovered loci associated with phenotype variance heterogeneity (vQTL), which is important in studying genetic association with complex traits, especially for identifying gene-gene and gene-environment interactions. While several tests have been proposed to detect vQTL for unrelated individuals, there are no tests for related individuals, commonly seen in family-based genetic studies. Here we introduce a likelihood ratio test (LRT) for identifying mean and variance heterogeneity simultaneously or for either effect alone, adjusting for covariates and family relatedness using a linear mixed effect model approach. The LRT test statistic for normally distributed quantitative traits approximately follows χ(2)-distributions. To correct for inflated Type I error for non-normally distributed quantitative traits, we propose a parametric bootstrap-based LRT that removes the best linear unbiased prediction (BLUP) of family random effect. Simulation studies show that our family-based test controls Type I error and has good power, while Type I error inflation is observed when family relatedness is ignored. We demonstrate the utility and efficiency gains of the proposed method using data from the Framingham Heart Study to detect loci associated with body mass index (BMI) variability.

journal_name

Ann Hum Genet

journal_title

Annals of human genetics

authors

Cao Y,Maxwell TJ,Wei P

doi

10.1111/ahg.12089

subject

Has Abstract

pub_date

2015-01-01 00:00:00

pages

46-56

issue

1

eissn

0003-4800

issn

1469-1809

journal_volume

79

pub_type

杂志文章
  • A note on assortative mating, linkage and genotypic frequencies.

    abstract::It is shown that in the equilibrium position with respect to the assortative mating process given by Fisher's (1918) model, the population is in linkage disequilibrium, contrary to a result given by Vetta (1975). ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1978.tb00937.x

    authors: Wilson SR

    更新日期:1978-07-01 00:00:00

  • Interrelationship and familiality of dyslexia related quantitative measures.

    abstract::Dyslexia is a complex gene-environment disorder with poorly understood etiology that affects about 5% of school-age children. Dyslexia occurs in all languages and is associated with a high level of social and psychological morbidity for the individual and their family; approximately 40-50% have persistent disability i...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,多中心研究

    doi:10.1111/j.1469-1809.2006.00312.x

    authors: Schulte-Körne G,Ziegler A,Deimel W,Schumacher J,Plume E,Bachmann C,Kleensang A,Propping P,Nöthen MM,Warnke A,Remschmidt H,König IR

    更新日期:2007-03-01 00:00:00

  • Bantu and European Y-lineages in Sub-Saharan Africa.

    abstract::Ancient diversity in Sub-Saharan Africa is known to have been re-modulated to a large extent by Bantu migrations in the sub-Sahel region, in two southwards waves of advance through both the west and east coasts. Haplotype matching performed for Y-STR haplotypes in several sub-Saharan populations, both inside and outsi...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1017/S0003480002001306

    authors: Pereira L,Gusmão L,Alves C,Amorim A,Prata MJ

    更新日期:2002-11-01 00:00:00

  • Linkage and association study of late-onset Alzheimer disease families linked to 9p21.3.

    abstract::A chromosomal locus for late-onset Alzheimer disease (LOAD) has previously been mapped to 9p21.3. The most significant results were reported in a sample of autopsy-confirmed families. Linkage to this locus has been independently confirmed in AD families from a consanguineous Israeli-Arab community. In the present stud...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2008.00474.x

    authors: Züchner S,Gilbert JR,Martin ER,Leon-Guerrero CR,Xu PT,Browning C,Bronson PG,Whitehead P,Schmechel DE,Haines JL,Pericak-Vance MA

    更新日期:2008-11-01 00:00:00

  • Genetics of Hunter syndrome: carrier detection, new mutations, segregation and linkage analysis.

    abstract::We have investigated 31 families segregation for Hunter Syndrome in order to advance our understanding of the genetics of this disease. The hair root test for the diagnosis of carriers of Hunter Syndrome was improved by the adoption of a new diagnostic index that distinguishes between carrier and normal females better...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1986.tb01756.x

    authors: Chase DS,Morris AH,Ballabio A,Pepper S,Giannelli F,Adinolfi M

    更新日期:1986-10-01 00:00:00

  • Assignment of the human locus determining phosphoglycolate phosphatase (PGP) to chromosome 16.

    abstract::The segregation of human phosphoglycolate phosphatase has been studied in 52 independent human-rodent hybrids and 69 subclones. The results suggest that human PGP is on chromosome 16. Family data suggest that PGP is not close to 16qh or alpha Hp. The most likely regional assignment for PGP would appear to be 16p13 or ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1980.tb01557.x

    authors: Povey S,Jeremiah SJ,Barker RF,Hopkinson DA,Robson EB,Cook PJ,Solomon E,Bobrow M,Carritt B,Buckton KE

    更新日期:1980-01-01 00:00:00

  • Disease-Causing Variants in the ATL1 Gene Are a Rare Cause of Hereditary Spastic Paraplegia among Czech Patients.

    abstract::Variants in the ATL1 gene have been repeatedly described as the second most frequent cause of hereditary spastic paraplegia (HSP), a motor neuron disease manifested by progressive lower limb spasticity and weakness. Variants in ATL1 have been described mainly in patients with early onset HSP. We performed Sanger seque...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12206

    authors: Mészárosová AU,Grečmalová D,Brázdilová M,Dvořáčková N,Kalina Z,Čermáková M,Vávrová D,Smetanová I,Staněk D,Seeman P

    更新日期:2017-11-01 00:00:00

  • Genotype-phenotype correlation and the size of microdeletion or microduplication of 7q11.23 region in patients with Williams-Beuren syndrome.

    abstract::Williams-Beuren syndrome (WBS) is a chromosomal microdeletion syndrome with variable phenotypic features such as supravalvular aortic stenosis (SVAS), facial appearance characteristics, growth retardation, and infantile hypercalcemia. This study aimed to detect the 7q11.23 microdeletion in 10 patients with early clini...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12278

    authors: Ghaffari M,Tahmasebi Birgani M,Kariminejad R,Saberi A

    更新日期:2018-11-01 00:00:00

  • Differential growth of human foetal gonads with respect to sex and body side.

    abstract::Measurements have been carried out on the gonads of 54 human foetuses, 29 males and 25 females. Crown-rump lengths ranged between 140 and 212 mm. The criteria used were fresh weight, total protein contents and total DNA contents. It was found that for any given crown-rump length class, the mean values of testes exceed...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1976.tb00171.x

    authors: Mittwoch U

    更新日期:1976-07-01 00:00:00

  • Loci contributing to adult height and body mass index in African American families ascertained for type 2 diabetes.

    abstract::Height and body mass index (BMI) have high heritability in most studies. High BMI and reduced height are well-recognized as important risk factors for a number of cardiovascular diseases. We investigated these phenotypes in African American families originally ascertained for studies of linkage with type 2 diabetes us...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1529-8817.2005.00176.x

    authors: Sale MM,Freedman BI,Hicks PJ,Williams AH,Langefeld CD,Gallagher CJ,Bowden DW,Rich SS

    更新日期:2005-09-01 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

  • Evolution of the apolipoprotein B gene and coronary artery disease: a study in low and high risk Asians.

    abstract::This study traces the evolutionary pathways of the apolipoprotein B gene in the low risk Chinese and high risk Asian Indians in relation to coronary artery disease (CAD). Haplotypes were constructed from six apoB polymorphisms sp24/27, Ag(c/g), Ag(a1/d), XbaI, Ag(h/i) and, Ag(t/z). These were genotyped from 474 Chines...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.1999.6310045.x

    authors: Heng CK,Saha N,Low PS

    更新日期:1999-01-01 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

  • Genetic polymorphism of human deoxyribonuclease II (DNase II): low activity levels in urine and leukocytes are due to an autosomal recessive allele.

    abstract::The objectives of this study were to elucidate the genetic basis of human deoxyribonuclease II (DNase II) and to evaluate its usefulness as a genetic and/or diagnostic marker. We have devised a novel, specific and highly sensitive assay method for the urinary and leukocytic enzymes (Yasuda et al. 1991). The distributi...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1992.tb01125.x

    authors: Yasuda T,Nadano D,Sawazaki K,Kishi K

    更新日期:1992-01-01 00:00:00

  • The European-specific mitochondrial cluster J/T could confer an increased risk of insulin-resistance and type 2 diabetes: an analysis of the m.4216T > C and m.4917A > G variants.

    abstract::The aims of this study were to investigate the contributions of the mitochondrial DNA m.4216T > C and m.4917A > G variants, and also of the European-specific mitochondrial cluster J/T, to the development of type 2 diabetes mellitus in Caucasian-Brazilian patients from Southern Brazil. We analyzed 347 type 2 diabetes p...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,多中心研究

    doi:10.1111/j.1469-1809.2005.00249.x

    authors: Crispim D,Canani LH,Gross JL,Tschiedel B,Souto KE,Roisenberg I

    更新日期:2006-07-01 00:00:00

  • Delineation of subtelomeric deletion of the long arm of chromosome 6.

    abstract::Pure subtelomeric deletion of the long arm of chromosome 6 is rare. The frequency of this deletion accounts for approximately 0.05% of subjects with intellectual disability and developmental delay with or without dysmorphic features. Common phenotypes associated with this deletion include intellectual disability, deve...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,评审

    doi:10.1111/j.1469-1809.2011.00675.x

    authors: Lee JY,Cho YH,Hallford G

    更新日期:2011-11-01 00:00:00

  • The TCF7L2 diabetes risk variant is associated with HbA₁(C) levels: a genome-wide association meta-analysis.

    abstract::Genome-wide association (GWA) studies have identified around 20 common genetic variants influencing the risk of type 2 diabetes (T2D). Likewise, a number of variants have been associated with diabetes-related quantitative glycaemic traits, but to date the overlap between these genes and variants has been low. The majo...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,meta分析

    doi:10.1111/j.1469-1809.2010.00607.x

    authors: Franklin CS,Aulchenko YS,Huffman JE,Vitart V,Hayward C,Polašek O,Knott S,Zgaga L,Zemunik T,Rudan I,Campbell H,Wright AF,Wild SH,Wilson JF

    更新日期:2010-11-01 00:00:00

  • Ancestry Informative Marker Panel to Estimate Population Stratification Using Genome-wide Human Array.

    abstract::Case-control studies are a powerful strategy to identify candidate genes in complex diseases. In admixed populations, association studies can be affected by population stratification, leading to spurious genetic associations. Ancestry informative markers (AIMs) can be used to minimise this effect. The aim of this work...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12208

    authors: Barbosa FB,Cagnin NF,Simioni M,Farias AA,Torres FR,Molck MC,Araujo TK,Gil-Da-Silva-Lopes VL,Donadi EA,Simões AL

    更新日期:2017-11-01 00:00:00

  • Recurrence risks in an oligogenic threshold model: the effect of alterations in allele frequency.

    abstract::The polygenic threshold model assumes that the distribution of the underlying liability is approximately normal. This paper examines the impact of deviations from normality in the underlying liability distribution when the number of loci affecting liability is finite, but large (e.g. 5-10). Skewness and kurtosis of th...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1986.tb01941.x

    authors: Kendler KS,Kidd KK

    更新日期:1986-01-01 00:00:00

  • The association of HLA-linked genes with systemic lupus erythematosus.

    abstract::The reported associations between HLA antigen DR3 and null (QO) alleles at the C4A and C4B loci and systemic lupus erythematosus are here analysed. The empirical logistic method has been applied to a body of data which included the relevant genotypes. The analysis suggests that the association with null alleles at the...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1986.tb01942.x

    authors: Green JR,Montasser M,Woodrow JC

    更新日期:1986-01-01 00:00:00

  • Similarity-based multimarker association tests for continuous traits.

    abstract::Testing multiple markers simultaneously not only can capture the linkage disequilibrium patterns but also can decrease the number of tests and thus alleviate the multiple-testing penalty. If a gene is associated with a phenotype, subjects with similar genotypes in this gene should also have similar phenotypes. Based o...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2012.00706.x

    authors: Lin WY,Tiwari HK,Gao G,Zhang K,Arcaroli JJ,Abraham E,Liu N

    更新日期:2012-05-01 00:00:00

  • A genome-wide association study of autism reveals a common novel risk locus at 5p14.1.

    abstract::Although autism is one of the most heritable neuropsychiatric disorders, its underlying genetic architecture has largely eluded description. To comprehensively examine the hypothesis that common variation is important in autism, we performed a genome-wide association study (GWAS) using a discovery dataset of 438 autis...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2009.00523.x

    authors: Ma D,Salyakina D,Jaworski JM,Konidari I,Whitehead PL,Andersen AN,Hoffman JD,Slifer SH,Hedges DJ,Cukier HN,Griswold AJ,McCauley JL,Beecham GW,Wright HH,Abramson RK,Martin ER,Hussman JP,Gilbert JR,Cuccaro ML,Haines JL

    更新日期:2009-05-01 00:00:00

  • Genetic diversity of a late prehispanic group of the Quebrada de Humahuaca, northwestern Argentina.

    abstract::This palaeogenetic study focused on the analysis of a late prehispanic Argentinean group from the Humahuaca valley, with the main aim of reconstructing its (micro)evolutionary history. The Humahuaca valley, a natural passageway from the eastern plains to the highlands, was the living environment of Andean societies wh...

    journal_title:Annals of human genetics

    pub_type: 历史文章,杂志文章

    doi:10.1111/ahg.12075

    authors: Mendisco F,Keyser C,Seldes V,Rivolta C,Mercolli P,Cruz P,Nielsen AE,Crubezy E,Ludes B

    更新日期:2014-09-01 00:00:00

  • A small number of candidate gene SNPs reveal continental ancestry in African Americans.

    abstract::Using genetic data from an obesity candidate gene study of self-reported African Americans and European Americans, we investigated the number of Ancestry Informative Markers (AIMs) and candidate gene SNPs necessary to infer continental ancestry. Proportions of African and European ancestry were assessed with STRUCTURE...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2012.00738.x

    authors: Kodaman N,Aldrich MC,Smith JR,Signorello LB,Bradley K,Breyer J,Cohen SS,Long J,Cai Q,Giles J,Bush WS,Blot WJ,Matthews CE,Williams SM

    更新日期:2013-01-01 00:00:00

  • 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

  • Genomic testing and counseling: The contribution of next-generation sequencing to epilepsy genetics.

    abstract:INTRODUCTION:Currently, next-generation sequencing (NGS) technology is more accessible and available to detect the genetic causation of diseases. Though NGS technology benefited some clinical phenotypes, for some clinical diagnoses such as seizures and epileptic disorders, adaptation occurred slowly. The genetic diagno...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12397

    authors: Alsubaie L,Aloraini T,Amoudi M,Swaid A,Eyiad W,Al Mutairi F,Ababneh F,Alrifai MT,Baarmah D,Altwaijri W,Alotaibi N,Harthi A,Rumayyan A,Alanazi A,Qrimli M,Alfadhel M,Alfares A

    更新日期:2020-11-01 00:00:00

  • Variation in 5' promoter region of the APOE gene contributes to predicting ischemic heart disease (IHD) in the population at large: the Copenhagen City Heart Study.

    abstract::The objective of this study was to evaluate whether an increased hazard of developing ischemic heart disease (IHD) is associated with any of the three genotypes A560T832/A560T832, A560T832/A560G832 and A560T832/T560T832, defined by variations in two non-coding SNPs in the 5' promoter region of the apolipoprotein E (AP...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2007.00370.x

    authors: Stengård JH,Frikke-Schmidt R,Tybjaerg-Hansen A,Nordestgaard BG,Sing CF

    更新日期:2007-11-01 00:00:00

  • New variants of Ps salivary polymorphic proteins.

    abstract::Electrophoretic analysis of the Ps protein demonstrated the existence of phenotypes additional to those described by Azen & Denniston (1980). A hypothesis that the polymorphism of the Ps protein is determined by five expressed and one unexpressed alleles was supported by family studies. The gene frequencies in a Japan...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1988.tb01073.x

    authors: Minaguchi K,Shirotani T,Suzuki K

    更新日期:1988-01-01 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

  • Racial heterogeneity of DNA polymorphisms linked to the A and the O alleles of the ABO blood group gene.

    abstract::Except for subgroup A2 and minor A, O and B alleles (Ax, O2 and B(A)), which occur at low frequencies in the population, the major ABO alleles are considered to be homogeneous entities. The present study is the first demonstration of an extensive variability linked to the more common alleles of the blood A and O genes...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1996.tb01173.x

    authors: Zago MA,Tavella MH,Simões BP,Franco RF,Guerreiro JF,Santos SB

    更新日期:1996-01-01 00:00:00