On the validity of the likelihood ratio test and consistency of resulting parameter estimates in joint linkage and linkage disequilibrium analysis under improperly specified parametric models.

Abstract:

:It has been shown that parametric analysis of linkage disequilibrium conditional on linkage using an overly deterministic model can be optimal for family-based association analysis. However, if one applies this strategy carelessly, there is a risk of false inference. We analyse properties of such likelihood ratio tests when the assumed disease mode of inheritance is inaccurate. Under some conditions, problems result if one is not careful to consider what null hypothesis is being tested. We show that: (a) tests for which the null hypothesis assumes the absence of both linkage and association are independent of the true mode of inheritance; (b) likelihood ratio tests assuming either linkage or association under the null hypothesis may depend on the true mode of inheritance, leading to inconsistent parameter estimates, in particular under extremely deterministic models; (c) this problem cannot be eliminated by increasing sample size or adding population controls--as sample size increases, the chance of false positive inference goes to 100%; (d) this issue can lead to systematic false positive inference of association in regions of linkage. This is important because highly deterministic models are often used intentionally in model-based analyses because they can have more power than the true model, and are implicit in many model-free analysis methods.

journal_name

Ann Hum Genet

journal_title

Annals of human genetics

authors

Hiekkalinna T,Göring HH,Terwilliger JD

doi

10.1111/j.1469-1809.2011.00683.x

subject

Has Abstract

pub_date

2012-01-01 00:00:00

pages

63-73

issue

1

eissn

0003-4800

issn

1469-1809

journal_volume

76

pub_type

杂志文章
  • Assignment of the gene for cytosolic alanine aminotransferase (AAT1) to human chromosome 8.

    abstract::The segregation of human cytosolic alanine aminotransferase (AAT1) and the individual human chromosomes has been studied in 27 secondary and tertiary rat hepatoma-human (liver) fibroblast hybrids. The staining solution used to visualize AAT activity on starch gels was specific for AAT since it was visualized only when...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1982.tb00703.x

    authors: Astrin KH,Arredondo-Vega FX,Desnick RJ,Smith M

    更新日期:1982-05-01 00:00:00

  • Search for the PARK3 founder haplotype in a large cohort of patients with Parkinson's disease from northern Germany.

    abstract::A founder haplotype on chromosome 2p for autosomal dominant Parkinson's disease (PD) has been postulated for two families of Northern European descent, and a new mutation in the alpha-synuclein gene (Ala30Pro) has been found in a German PD family. We evaluated 85 German PD patients and 85 ethnically matched controls f...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.1999.6340285.x

    authors: Klein C,Vieregge P,Hagenah J,Sieberer M,Doyle E,Jacobs H,Gasser T,Breakefield XO,Risch NJ,Ozelius LJ

    更新日期:1999-07-01 00:00:00

  • Genetic linkage analysis using lognormal variance components.

    abstract::Typically genetic studies of continuous traits such as cholesterol levels or blood pressure assume that interindividual variability follows a normal distribution. Here we develop methods to analyze positively skewed data by assuming a lognormal distribution. We develop a variance components approach for identifying su...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.1998.6260521.x

    authors: Wan Y,De Andrade M,Yu L,Cohen J,Amos CI

    更新日期:1998-11-01 00:00:00

  • Determination of probability distribution of diplotype configuration (diplotype distribution) for each subject from genotypic data using the EM algorithm.

    abstract::Haplotype analysis is important for mapping traits. Recently, methods for estimating haplotype frequencies from genotypes of unrelated individuals based on the expectation-maximization (EM) algorithm have been developed. Our program estimates haplotype frequencies in the population and determines the posterior probabi...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1017/S0003480002001124

    authors: Kitamura Y,Moriguchi M,Kaneko H,Morisaki H,Morisaki T,Toyama K,Kamatani N

    更新日期:2002-05-01 00:00:00

  • An investigation of the possible influence of neutral alpha-glucosidases on the clinical heterogeneity of glycogenosis type II.

    abstract::The lysosomal storage disorder glycogenosis type II, caused by a deficiency of lysosomal alpha-glucosidase, is very heterogeneous in its clinical presentation. It has been suggested that this heterogeneity may be due to differential expression of neutral alpha-glucosidases. We have therefore analysed the activity of t...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1989.tb01783.x

    authors: Van der Ploeg AT,Kroos MA,Swallow DM,Reuser AJ

    更新日期:1989-05-01 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

  • Tracing quantitative measurements on human chromosomes in family studies.

    abstract::Statistical methods are developed for tracing quantitative measurements on human chromosomes from parents to offspring. Tests for transmission are briefly considered. ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1977.tb01963.x

    authors: Lauder IJ

    更新日期:1977-07-01 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

  • 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

  • Power of variance component linkage analysis-II. Discrete traits.

    abstract::We determine the power of variance component linkage analysis in the case of discrete, dichotomous traits analyzed under a classical liability threshold model. For simplicity we consider randomly ascertained samples and an additive model of variation incorporating a qtl, residual additive genetic factors, and individu...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1529-8817.2004.00128.x

    authors: Williams JT,Blangero J

    更新日期:2004-11-01 00:00:00

  • A speculative model for the Rh blood groups.

    abstract::Two closely linked structural loci, D and 'CcEe', are proposed as the basis of the Rh blood groups. Mutation and unequal crossing-over between the two loci at meiosis are considered as possible explanations for some rare Rh complexes. The theory predicts that complexes arising from unequal crossing-over would be expec...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1986.tb01045.x

    authors: Tippett P

    更新日期:1986-07-01 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

  • Using microarray analysis to identify genes and pathways that regulate fetal hemoglobin levels.

    abstract::Increased levels of fetal hemoglobin (HbF: α2γ2) can ameliorate the clinical severity of the β-hemoglobinopathies. Microarray analysis represents a powerful approach to identify novel genetic factors regulating the γ-globin gene. Gene expression profiling was previously performed on 14 individuals with high or normal ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12346

    authors: Jia S,Jia W,Yu S,Hu Y,He Y

    更新日期:2020-01-01 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

  • Absence of significant autosomal lesions in Huntington's disease.

    abstract::Peripheral blood from six patients with Huntington's disease (HD) and six controls were cultured in three types of media known to produce fragile sites. A total of 3000 metaphases per group were scrutinized in a blind coded study. No significantly specific 'hot-spot' was found capable of differentiating between HD pat...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1985.tb01704.x

    authors: Beverstock GC,Mol A,Wienhofer E

    更新日期:1985-10-01 00:00:00

  • Association of the methylenetetrahydrofolate reductase gene A1298C polymorphism with male infertility: a meta-analysis.

    abstract::Published data on the association between the methylenetetrahydrofolate reductase (MTHFR) gene A1298C (rs1801131) polymorphism and male infertility risk are inconclusive. To derive a more precise estimation of the relationship, a meta-analysis was performed. In this meta-analysis, a total of seven case-control studies...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,meta分析

    doi:10.1111/j.1469-1809.2011.00691.x

    authors: Shen O,Liu R,Wu W,Yu L,Wang X

    更新日期:2012-01-01 00:00:00

  • A family-based robust multivariate association test using maximum statistic.

    abstract::For characterizing the genetic mechanisms of complex diseases familial data with multiple correlated quantitative traits are usually collected in genetic studies. To analyze such data, various multivariate tests have been proposed to investigate the association between the underlying disease genes and the multiple tra...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12054

    authors: Hsieh TJ,Chang SH,Tai JJ

    更新日期:2014-03-01 00:00:00

  • N-ras-like sequences on chromosomes 9, 6 and 22 with a polymorphism at the chromosome 9 locus.

    abstract::Two clones, pCN1 and pCN2, which together form full-length cDNA for N-ras, were used to search for restriction fragment length polymorphisms. pCN2, which entirely consists of 3' non-translated sequences, revealed more bands on DNA transfer hybridizations than could be accounted for using the known restriction map of N...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1988.tb01096.x

    authors: Middleton-Price H,Spurr N,Hall A,Malcolm S

    更新日期:1988-07-01 00:00:00

  • Search for multifactorial disease susceptibility genes in founder populations.

    abstract::The current challenge in biomedical research is to detect genetic risk factors involved in common complex diseases. The power to detect their role is generally poor in populations that have been large for a long time. It has been suggested that the power may be increased by taking advantage of the specificity of found...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.2000.6430255.x

    authors: Bourgain C,Genin E,Quesneville H,Clerget-Darpoux F

    更新日期:2000-05-01 00:00:00

  • Association Patterns of Endothelial Nitric Oxide Synthase Gene (NOS3) Variant Glu298Asp with Blood Pressure and Serum Lipid Levels in Subjects with Coronary Artery Disease from Pakistan.

    abstract::Nitric oxide is an important antiatherosclerotic agent. The main determinant of nitric oxide levels is enzyme nitric oxide synthase encoded by the NOS3 gene, the common variants in this gene may be responsible for variations in plasma enzyme levels. The association of NOS3 variants with coronary artery disease (CAD) v...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12192

    authors: Shahid SU,Shabana.,Rehman A

    更新日期:2017-07-01 00:00:00

  • Sex-specific effects of AGT-6 and ACE I/D on pulse pressure after 6 months on antihypertensive treatment: the GenHAT study.

    abstract::Research suggests pulse pressure (PP) is a predictor of cardiovascular disease, and genes likely influence PP levels. Additionally, gender may be an effect modifier between PP and cardiovascular disease. This study addresses whether two renin-angiotensin-aldosterone system (RAAS) variants are associated with PP in a s...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,多中心研究,随机对照试验

    doi:10.1111/j.1469-1809.2007.00381.x

    authors: Lynch AI,Arnett DK,Davis BR,Boerwinkle E,Ford CE,Eckfeldt JH,Leiendecker-Foster C

    更新日期:2007-11-01 00:00:00

  • Biochemical characterization of the genetic variants of human phosphoglycolate phosphatase (PGP).

    abstract::Phosphoglycolate phosphatase (PGP) exhibits a wide range of activities in normal human red cells. Analysis of blood from 57 individuals of known PGP phenotype revealed no correlation between enzyme activity, electrophoretic phenotype or 2,3-DPG concentration. Neither was there evidence of variation in Km, heat stabili...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1981.tb00313.x

    authors: Turner VS,Hopkinson DA

    更新日期:1981-05-01 00:00:00

  • Genetic association studies in complex disease: disentangling additional predisposing loci from associated neutral loci using a constrained - permutation approach.

    abstract::In the process of genetically mapping a complex disease, the question may arise whether a certain polymorphism is the only causal variant in a region. A number of methods can answer this question, but unfortunately these methods are optimal for bi-allelic loci only. We wanted to develop a method that is more suited fo...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1529-8817.2004.00129.x

    authors: Spijker GT,Nolte IM,Jansen RC,Te Meerman GJ

    更新日期:2005-01-01 00:00:00

  • Assignment of the human cardiac/slow skeletal muscle troponin C gene (TNNC1) between D3S3118 and GCT4B10 on the short arm of chromosome 3 by somatic cell hybrid analysis.

    abstract::We have determined the chromosomal location of the human cardiac/slow skeletal muscle troponin C gene (TNNC1) to the short arm of chromosome 3 using somatic cell hybrids. PCR-based analysis of a 'monochromosomal' hybrid panel identified the presence of the TNNC1 gene on human chromosome 3 and subsequent analysis of th...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.1997.6140375.x

    authors: Townsend PJ,Yacoub MH,Barton PJ

    更新日期:1997-07-01 00:00:00

  • Founder effects for ATM gene mutations in Italian Ataxia Telangiectasia families.

    abstract::We screened ATM gene mutations in 104 Italian Ataxia-Telangiectasia patients from 91 unrelated families (detection rate 90%) and found 21 recurrent mutations in 63 families. The majority (67%) of patients were compound heterozygotes, while 33% were homozygotes. To determine the existence of common haplotypes and poten...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2009.00535.x

    authors: Chessa L,Piane M,Magliozzi M,Torrente I,Savio C,Lulli P,De Luca A,Dallapiccola B

    更新日期:2009-09-01 00:00:00

  • Confirmation of the relationship of HLA (chromosome 6) genes to depression and manic depression. II. The Ontario follow-up and analysis of 117 kindreds.

    abstract::HLA typing was conducted on 577 family members of 86 families having at least two first-degree family members with a lifetime history of major depression or bipolar disorder. The results were combined with a follow-up study of 10 Newfoundland kindreds and with the data obtained from our previous studies, giving a tota...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1988.tb01108.x

    authors: Stancer HC,Weitkamp LR,Persad E,Flood C,Jorna T,Guttormsen SA,Yagnow RL

    更新日期:1988-10-01 00:00:00

  • 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

  • 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

  • Tests of gene-environment interaction for case-parent triads with general environmental exposures.

    abstract::As knowledge of the human genome continues to grow, more progress is being made towards not only identifying the genes involved in disease susceptibility but also in defining the synergistic role genes play with environmental exposures. The detection of gene-environment interactions is important as it can offer clinic...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1529-8817.2003.00073.x

    authors: Lake SL,Laird NM

    更新日期:2004-01-01 00:00:00

  • Identification and regional localization of a highly polymorphic dinucleotide repeat D11S614 to the interval in 11q23.3 flanked by recurrent translocation breakpoints.

    abstract::A highly informative dinucleotide repeat polymorphism has been identified at the D11S614 locus on chromosome 11q23. Ten different alleles have been observed at this locus, and the heterozygosity frequency is approximately 85%. Physical localization of this marker in a panel of somatic cell hybrids containing chromosom...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1993.tb00901.x

    authors: Benham F,Sugiyama R,Hunt D,Gillett G,Smith M

    更新日期:1993-10-01 00:00:00