A permutation test for the robust sib-pair linkage method.

Abstract:

:The robust sib-pair method introduced by Haseman & Elston (1972) is one of the most widely circulated allele-sharing methods for linkage analysis. The procedure evaluates linkage by significance testing of a regression coefficient and, hence, a standard t-test has traditionally been applied despite known violations of the statistical assumptions underlying the test. We present a permutation based reference distribution for the estimate of the regression coefficient that is motivated by genetic principles rather than by standard regression testing procedures. The permutation test approximates Mendelian co-segregation under the null hypothesis of no linkage, making it a very natural approach. Theory and simulations show that the conventional t-test approximates the permutation test quite well, even when dependent sib pairs are used for analysis. These results thus indirectly address concerns over the t-test. To illustrate the permutation test using real data we applied the procedure to two lipoprotein systems that have been well characterized.

journal_name

Ann Hum Genet

journal_title

Annals of human genetics

authors

Wan Y,Cohen J,Guerra R

doi

10.1046/j.1469-1809.1997.6110077.x

subject

Has Abstract

pub_date

1997-01-01 00:00:00

pages

79-87

issue

Pt 1

eissn

0003-4800

issn

1469-1809

journal_volume

61

pub_type

杂志文章
  • Multivariate linkage analysis of specific language impairment (SLI).

    abstract::Specific language impairment (SLI) is defined as an inability to develop appropriate language skills without explanatory medical conditions, low intelligence or lack of opportunity. Previously, a genome scan of 98 families affected by SLI was completed by the SLI Consortium, resulting in the identification of two quan...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2007.00361.x

    authors: Monaco AP

    更新日期:2007-09-01 00:00:00

  • The Scianna blood group lies distal to uridine monophosphate kinase on chromosome 1p.

    abstract::Linkage between the Scianna blood group and the Rhesus blood group has been confirmed. Families demonstrating recombinants between U M P K and Sc suggest that U M P K lies between Sc and PGM1. ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1979.tb02004.x

    authors: Noades JE,Corney G,Cook PJ,Putt W,King J,Fisher RA,Spowart G,Lee M,Bowell PJ

    更新日期:1979-10-01 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

  • Very close linkage between D2S1 and ACP1 on chromosome 2p.

    abstract::The genomic DNA-probe L2.30 was used to assign D2S1 to 2p23-pter by in situ hybridization. The RFLP revealed by BglII was then used for linkage studies in the Oslo-NHIK families segregating for the acid phosphatase ACP1 protein polymorphism. Evidence for very close linkage was found by a lod score of +17.17 at recombi...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1986.tb01757.x

    authors: Lothe RA,Gedde-Dahl T,Olaisen B,Bakker E,Pearson P

    更新日期:1986-10-01 00:00:00

  • Using age of onset to distinguish between subforms of breast cancer.

    abstract::Information on family history and age of onset of breast cancer is examined in an attempt to distinguish between postulated early and late onset forms of breast cancer and to estimate the familial correlation between any subforms that may exist. Data are taken from the Cancer and Steroid Hormone Study, a multicentre, ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1990.tb00373.x

    authors: Claus EB,Risch NJ,Thompson WD

    更新日期:1990-05-01 00:00:00

  • An algorithm for Monte Carlo estimation of genotype probabilities on complex pedigrees.

    abstract::Exact probability and likelihood computation on complex pedigrees is often infeasible, since exact methods are too computationally intensive even with today's computing technology. A statistical tool, Markov chain Monte Carlo (MCMC), is increasingly being explored as a technique for estimating probabilities of genotyp...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1994.tb00731.x

    authors: Lin S,Thompson E,Wijsman E

    更新日期:1994-10-01 00:00:00

  • Genetic Obesity Risk and Attenuation Effect of Physical Fitness in Mexican-Mestizo Population: a Case-Control Study.

    abstract::We analyzed commonly reported European and Asian obesity-related gene variants in a Mexican-Mestizo population through each single nucleotide polymorphism (SNP) and a genetic risk score (GRS) based on 23 selected SNPs. Study subjects were physically active Mexican-Mestizo adults (n  =  608) with body mass index (BMI) ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12190

    authors: Costa-Urrutia P,Abud C,Franco-Trecu V,Colistro V,Rodríguez-Arellano ME,Vázquez-Pérez J,Granados J,Seelaender M

    更新日期:2017-05-01 00:00:00

  • PTPN22 gene polymorphism (C1858T) is associated with susceptibility to type 1 diabetes: a meta-analysis of 19,495 cases and 25,341 controls.

    abstract::The protein tyrosine phosphatase N22 (PTPN22) gene C1858T polymorphism has been reported to be associated with susceptibility to type 1 diabetes (T1D) in relatively small sample sizes. This study aimed at investigating the pooled association by carrying out a meta-analysis on the published studies. The Medline, EBSCO,...

    journal_title:Annals of human genetics

    pub_type: 杂志文章,meta分析

    doi:10.1111/ahg.12016

    authors: Xuan C,Lun LM,Zhao JX,Wang HW,Zhu BZ,Yu S,Liu Z,He GW

    更新日期:2013-05-01 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 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

  • On avoiding statistical bias in linkage-based counselling.

    abstract::Using the Succession Rule of Laplace (1795) and related reasoning, this paper shows how to give unbiased counselling to patients when predictions are to be based on small samples. The recombination fraction can be regarded as a probability parameter, theta, which itself has a probability distribution between the limit...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1990.tb00388.x

    authors: Renwick JH

    更新日期:1990-10-01 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

  • 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

  • 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 test...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2011.00683.x

    authors: Hiekkalinna T,Göring HH,Terwilliger JD

    更新日期:2012-01-01 00:00:00

  • Maternal and paternal lineages of the Samaritan isolate: mutation rates and time to most recent common male ancestor.

    abstract::The Samaritan community is a small, isolated, and highly endogamous group numbering some 650 members who have maintained extensive genealogical records for the past 13-15 generations. We performed mutation detection experiments on mitochondrial DNAs and Y chromosomes from confirmed maternal and paternal lineages to es...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.2003.00024.x

    authors: Bonné-Tamir B,Korostishevsky M,Redd AJ,Pel-Or Y,Kaplan ME,Hammer MF

    更新日期:2003-03-01 00:00:00

  • Chromosomal assignment of seven human genomic DNA sequences associated with restriction fragment length polymorphisms.

    abstract::Seven phage clones containing human sequences were picked at random from a human genomic library cloned in Charon 4A. The clones are devoid of repetitive sequences and can be used to recognize restriction fragment length polymorphisms (Feder et al. 1985). The chromosomal locations of the sequences defined by the seven...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1986.tb01033.x

    authors: Spurr NK,Feder J,Bodmer WF,Goodfellow PN,Solomon E,Cavalli-Sforza LL

    更新日期:1986-05-01 00:00:00

  • Analysis of genetic variation in two human thyroxine-binding plasma proteins by immunodetection after isoelectric focusing.

    abstract::An immunological method for the detection of two thyroxine-binding plasma proteins, thyroxine-binding globulin (TBG) and thyroxine-binding prealbumin (TBPA), following polyacrylamide gel isoelectric focusing is described. Both proteins show complex electrophoretic patterns, attributable to post-translational glycosyla...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1985.tb01701.x

    authors: Whitehouse DB,Hopkinson DA,Hill AV,Bowden DK

    更新日期:1985-10-01 00:00:00

  • Origin of triploidy in spontaneous abortuses.

    abstract::Fourteen triploid spontaneous abortuses were studied cytogenetically by sequential Q and C banding and the marker chromosomes were compared with those of the parents. The abortuses comprised all triploid cases in a series of 288 consecutive abortuses of the first 16 weeks of pregnancy occurring in one hospital. In 12 ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1979.tb01542.x

    authors: Lauritsen JG,Bolund L,Friedrich U,Therkelsen AJ

    更新日期:1979-07-01 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

  • 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

  • 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

  • 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

  • From a single whole exome read to notions of clinical screening: primary ciliary dyskinesia and RSPH9 p.Lys268del in the Arabian Peninsula.

    abstract::Primary ciliary dyskinesia (PCD) is a genetic disorder, usually autosomal recessive, causing early respiratory disease and later subfertility. Whole exome sequencing may enable efficient analysis for locus heterogeneous disorders such as PCD. We whole-exome-sequenced one consanguineous Saudi Arabian with clinically di...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2012.00704.x

    authors: Alsaadi MM,Gaunt TR,Boustred CR,Guthrie PA,Liu X,Lenzi L,Rainbow L,Hall N,Alharbi KK,Day IN

    更新日期:2012-05-01 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

  • A mapping function for human chromosomes.

    abstract::The available simple mapping functions are surveyed, and a new mapping function that provides for positive interference within chromosome arms and no interference across the centromere is proposed, together with the corresponding formula for centromeric linkage. This new function is derived by assuming that all chromo...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1976.tb00175.x

    authors: Sturt E

    更新日期:1976-11-01 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

  • 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

  • A study of the population of Paraguay through isonymy.

    abstract::In order to describe the isonymic structure of Paraguay, the distribution of 4,843,868 surnames of 2,882,163 persons was studied in the 18 departments and 237 districts of the nation. The correlations between isonymic and geographic distances for departments were r = 0.713 ± 0.052 for Euclidean distance, 0.597 ± 0.074...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2011.00676.x

    authors: Dipierri J,Rodriguez-Larralde A,Alfaro E,Scapoli C,Mamolini E,Salvatorelli G,Caramori G,De Lorenzi S,Sandri M,Carrieri A,Barrai I

    更新日期:2011-11-01 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

  • 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