TDT statistics for mapping quantitative trait loci.

Abstract:

:The original transmission disequilibrium test (TDT), was introduced to test for linkage between a marker and a disease-susceptibility locus (Spielman et al. 1993). Allison (1997) extended the TDT procedure to quantitative traits. Allison's test, however, is restrictive in that it requires family trios consisting of one heterozygous parent, one homozygous parent and one child, and considers only the situation where the marker locus is analogous to the quantitative trait locus itself. In this paper, we propose, investigate and apply a general TDT for quantitative traits that permits more than one child per family, does not require only one parent to be heterozygous, and allows for the fact that the various alleles at the marker and trait loci may be at varying degree of linkage disequilibrium. We also show that this TDT for quantitative traits is still a valid test of linkage in the presence of population substructure. To provide guidelines for study design, we develop analytic formulae for calculation of the power of the TDT for mapping quantitative trait loci and investigate the impact of various factors on the power. Power calculations show that the proposed TDT for quantitative traits is more powerful than Allison's basic test statistic and the extreme discordant sib pair linkage method. The proposed TDT statistic for quantitative traits is applied to systolic blood pressure variation in the Rochester Family Heart Study using an extremely discordant sibling pair design.

journal_name

Ann Hum Genet

journal_title

Annals of human genetics

authors

Xiong MM,Krushkal J,Boerwinkle E

doi

10.1046/j.1469-1809.1998.6250431.x

subject

Has Abstract

pub_date

1998-09-01 00:00:00

pages

431-52

issue

Pt 5

eissn

0003-4800

issn

1469-1809

journal_volume

62

pub_type

杂志文章
  • 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

  • Ancient DNA and family relationships in a Pompeian house.

    abstract::Archaeological, anthropological and pathological data suggest that thirteen skeletons found in a house at the Pompeii archaeological site, dated to 79 A.D., belong to one family. To verify this and to identify the relationships between these individuals, we analyzed DNA extracted from bone specimens. Specifically, hyp...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2009.00520.x

    authors: Di Bernardo G,Del Gaudio S,Galderisi U,Cascino A,Cipollaro M

    更新日期:2009-07-01 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

  • 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

  • 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

  • F-statistics and analysis of gene diversity in subdivided populations.

    abstract::It is show that Wright's F-statistics can be defined as ratios of gene diversities of heterozygosities rather than as the correlations of uniting gametes. This definition is applicable irrespective of the number of alleles involved or whether there is selection or not. The relationship between F-statistics and Nei's g...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1977.tb01918.x

    authors: Nei M

    更新日期:1977-10-01 00:00:00

  • Dystrophin nonsense mutations can generate alternative rescue transcripts in lymphocytes.

    abstract::Secondary alterations in splicing have been reported to produce semi-functional mRNA from several nonsense mutations in the dystrophin gene. Disruptions of exonic splicing enhancers by single nucleotide changes are thought to underlie such alterations. The precise frequencies of such nonsense mutation-dependent splici...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2008.00468.x

    authors: Nishiyama A,Takeshima Y,Zhang Z,Habara Y,Tran TH,Yagi M,Matsuo M

    更新日期:2008-11-01 00:00:00

  • Influence of population stratification on population-based marker-disease association analysis.

    abstract::Population-based genetic association analysis may suffer from the failure to control for confounders such as population stratification (PS). There has been extensive study on the influence of PS on candidate gene-disease association analysis, but much less attention has been paid to its influence on marker-disease ass...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2010.00588.x

    authors: Li T,Li Z,Ying Z,Zhang H

    更新日期:2010-07-01 00:00:00

  • 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 a...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12089

    authors: Cao Y,Maxwell TJ,Wei P

    更新日期:2015-01-01 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

  • 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

  • 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

  • Rates of mutant and inherited structural cytogenetic abnormalities detected at amniocentesis: results on about 63,000 fetuses.

    abstract::We report data on diagnoses made on amniotic fluid specimens from 1977 to 1984 as reported to the New York State Chromosome Registry. The rate of all de novo (presumed mutant) abnormalities was about 2 per 1,000 in about 61,000 fetuses in which results are unlikely to be biased by the reason for amniocentesis (except ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1987.tb00864.x

    authors: Hook EB,Cross PK

    更新日期:1987-01-01 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

  • The location of the major bands on chromosome 1 at diakinesis in the human male and the relationship between banding pattern and chiasma localization.

    abstract::Q-banded chromosome 1 bivalents from six human males were measured in order to determine the locations of the major band borders. Chiasma position was also recorded in these bivalents in order to determine whether chiasmata preferentially occurred in Q-bright regions, Q-dark regions or in the interfaces between. The r...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1985.tb01686.x

    authors: Laurie DA,Hultén MA,Palmer RW

    更新日期:1985-05-01 00:00:00

  • Portability of tag SNPs across isolated population groups: an example from India.

    abstract::Isolated population groups are useful in conducting association studies of complex diseases to avoid various pitfalls, including those arising from population stratification. Since DNA resequencing is expensive, it is recommended that genotyping be carried out at tagSNP (tSNP) loci. For this, tSNPs identified in one i...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2006.00383.x

    authors: Sarkar Roy N,Farheen S,Roy N,Sengupta S,Majumder PP

    更新日期:2008-01-01 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

  • Association of CTLA-4 polymorphisms with increased risks of myasthenia gravis.

    abstract::Myasthenia gravis (MG) is considered to be a kind of autoimmune disorder resulting from dysfunction of neuromuscular transmission caused by autoantibodies against the nicotinic acetylcholine receptors. A number of studies have identified Cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) as a candidate gene for MG. ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,meta分析

    doi:10.1111/ahg.12262

    authors: Li F,Yuan W,Wu X

    更新日期:2018-11-01 00:00:00

  • Common variants in KCNQ1 confer increased risk of type 2 diabetes and contribute to the diabetic epidemic in East Asians: a replication and meta-analysis.

    abstract::We aimed to evaluate the effect of four common variants (rs2237892, rs2283228, rs2237895, and rs2237897) in KCNQ1 on susceptibility of type 2 diabetes (T2D) by performing a case-control study as well as a comprehensive meta-analysis. We genotyped these four variants in two sets of Chinese Han population, comprising a ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,meta分析

    doi:10.1111/ahg.12029

    authors: Wang H,Miao K,Zhao J,Liu L,Cui G,Chen C,Wang DW,Ding H

    更新日期:2013-09-01 00:00:00

  • Correlated odour threshold bimodality of two out of three synthetic musks.

    abstract::The odour threshold bimodality for exaltolide described by Whissell-Buechy & Amoore (1973) among American whites is confirmed for a population sample in London. A highly correlated bimodality presumed to be caused by the absence of inactivity of certain receptor sites is shown to exist for another structurally differe...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1975.tb00639.x

    authors: Kalmus H,Seedburgh D

    更新日期:1975-05-01 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

  • Genetic linkage between the Kell blood group system and prolactin-inducible protein loci: provisional assignment of KEL to chromosome 7.

    abstract::The Kell blood group locus (KEL) is tightly linked to the prolactin-inducible protein locus (PIP) with zeta = 9.12 at theta = 0.00 for combined paternal and maternal meioses. In view of the regional localization of PIP to 7q32-q36 (Myal et al. 1989a), a similar assignment for KEL is favoured. ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1991.tb00406.x

    authors: Zelinski T,Coghlan G,Myal Y,Shiu RP,Philipps S,White L,Lewis M

    更新日期:1991-05-01 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

  • 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

  • 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

  • Epidemiological approach to identifying genetic predispositions for atypical hemolytic uremic syndrome.

    abstract::Atypical hemolytic uremic syndrome (aHUS) is caused by several susceptibility genes. A registry including analyses of susceptibility genes, familial occurrence and genotype-phenotype correlation should provide classification insights. Registry data of 187 unrelated index patients included age at onset, gender, family ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2009.00554.x

    authors: Sullivan M,Erlic Z,Hoffmann MM,Arbeiter K,Patzer L,Budde K,Hoppe B,Zeier M,Lhotta K,Rybicki LA,Bock A,Berisha G,Neumann HP

    更新日期:2010-01-01 00:00:00

  • Evidence for a human mitotic mutant with pleiotropic effect.

    abstract::Male and female sibs born to third-cousin parents presented with mental retardation, microcephaly, short stature, juvenile onset limb-girdle muscular dystrophy and multiple chromosome mosaicism in lymphocytes and fibroblasts. Different aneuploidies (mostly trisomies) were found in 15-20% of the cells and trisomies for...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1989.tb01791.x

    authors: Papi L,Montali E,Marconi G,Guazzelli R,Bigozzi U,Maraschio P,Zuffardi O

    更新日期:1989-07-01 00:00:00

  • A new genetic polymorphism in human platelet polypeptides detected by two-dimensional electrophoresis.

    abstract::We described a new genetic polymorphism of human platelet polypeptide, detected by two-dimensional polyacrylamide gel electrophoresis followed by silver-staining. The polymorphism was tentatively designated thrombocyte B (ThB) with a molecular weight of 34 kDa and isoelectric point of 4.7-4.8. In this polypeptide, thr...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1991.tb00402.x

    authors: Kajii E,Iwamoto S,Omi T,Ikemoto S

    更新日期:1991-05-01 00:00:00

  • Genetic history of the population of Crete.

    abstract::The medieval history of several populations often suffers from scarcity of contemporary records resulting in contradictory and sometimes biased interpretations by historians. This is the situation with the population of the island of Crete, which remained relatively undisturbed until the Middle Ages when multiple wars...

    journal_title:Annals of human genetics

    pub_type: 历史文章,杂志文章

    doi:10.1111/ahg.12328

    authors: Drineas P,Tsetsos F,Plantinga A,Lazaridis I,Yannaki E,Razou A,Kanaki K,Michalodimitrakis M,Perez-Jimenez F,De Silvestro G,Renda MC,Stamatoyannopoulos JA,Kidd KK,Browning BL,Paschou P,Stamatoyannopoulos G

    更新日期:2019-11-01 00:00:00

  • Exon deletion in the non-catalytic domain of eIF2Bepsilon due to a splice site mutation leads to infantile forms of CACH/VWM with severe decrease of eIF2B GEF activity.

    abstract::The CACH/VWM syndrome is an autosomal recessive leukodystrophy characterized by a broad spectrum of clinical presentations and by diffuse cavitary degeneration of the white matter on MRI. Mutations responsible for this disorder are missense or frameshift mutations occurring in the five genes (EIF2B1-5) that encode the...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2007.00427.x

    authors: Horzinski L,Gonthier C,Rodriguez D,Scherer C,Boespflug-Tanguy O,Fogli A

    更新日期:2008-05-01 00:00:00