Residual linkage: why do linkage peaks not disappear after an association study?

Abstract:

:Family-based candidate gene and genome-wide association studies are a logical progression from linkage studies for the identification of gene and polymorphisms underlying complex traits. An efficient way to analyse phenotypic and genotypic data is to model linkage and association simultaneously. An important result from such an analysis is whether any evidence for linkage remains after fitting polymorphisms at candidate genes (residual linkage), because this may indicate locus and allelic heterogeneity in the population and will influence subsequent molecular strategies. Here we report that substantial residual linkage is to be expected, even under genetic homogeneity and when the underlying causal polymorphisms are genotyped and fitted in the model. We simulated a powerful design to detect linkage to quantitative trait loci, with 5, 10 or 20 causal SNPs spread throughout the genome. These SNPs were responsible for all genetic variation, and hence for both linkage and association. Residual linkage at the largest linkage peak from a genome-wide scan was substantial, with mean LOD scores of 0.4, 0.7, and 1.4 for the case of 5, 10 and 20 underlying causal SNPs, respectively. For less powerful designs, the proportion of the original LOD scores that remains after association will be even larger. All cases of 'significant' residual linkage are false positives. The reason for the apparent paradox of detecting residual linkage after fitting causal polymorphisms is that the linkage signals at the largest peaks in a genome-scan are severely inflated, even if all peaks correspond to true linkage. Our findings are general and apply to linkage mapping of any phenotype and to any pedigree structure.

journal_name

Hum Genet

journal_title

Human genetics

authors

Gordon S,Visscher PM

doi

10.1007/s00439-006-0278-y

subject

Has Abstract

pub_date

2007-03-01 00:00:00

pages

77-82

issue

1

eissn

0340-6717

issn

1432-1203

journal_volume

121

pub_type

杂志文章
  • Estimation of the male to female ratio of mutation rates from the segregation of X-chromosomal DNA haplotypes in Duchenne muscular dystrophy families.

    abstract::A novel procedure is presented to estimate the ratio of male to female mutation rates for Duchenne muscular dystrophy (DMD). X-specific restriction fragment length polymorphisms are used to establish DNA haplotypes in three-generation DMD families. From the proportion of DMD patients who have inherited their maternal ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00282088

    authors: Müller CR,Grimm T

    更新日期:1986-10-01 00:00:00

  • Lack of association between human longevity and genetic polymorphisms in drug-metabolizing enzymes at the NAT2, GSTM1 and CYP2D6 loci.

    abstract::In the present study, the possible role of genetic polymorphism of three drug-metabolizing enzymes, debrisoquine/sparteine hydroxylase (CYP2D6), glutathione S-transferase mu (GSTM1), and N-acetyltransferase (NAT2), as a putative genetic component of human longevity, was explored. A total of 817 DNA samples from a cent...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050735

    authors: Muiras ML,Verasdonck P,Cottet F,Schächter F

    更新日期:1998-05-01 00:00:00

  • Incomplete penetrance in primary immunodeficiency: a skeleton in the closet.

    abstract::Primary immunodeficiencies (PIDs) comprise a diverse group of over 400 genetic disorders that result in clinically apparent immune dysfunction. Although PIDs are classically considered as Mendelian disorders with complete penetrance, we now understand that absent or partial clinical disease is often noted in individua...

    journal_title:Human genetics

    pub_type: 杂志文章,评审

    doi:10.1007/s00439-020-02131-9

    authors: Gruber C,Bogunovic D

    更新日期:2020-06-01 00:00:00

  • Two new Gaucher disease mutations.

    abstract::Recently, a mutation at nucleotide 1193 of the glucocerebrosidase gene was described in a patient with type 1 Gaucher disease. This mutation destroys a TaqI site in a polymerase chain reaction (PCR)-amplified fragment. We used digestion with this enzyme to screen DNA samples from Gaucher disease patients representing ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00210614

    authors: Beutler E,Gelbart T

    更新日期:1994-02-01 00:00:00

  • EagI and NotI linking clones from human chromosomes 11 and Xp.

    abstract::EagI and NotI linking libraries were prepared in the lambda vector, EMBL5, from the mouse-human somatic cell hybrid 1W1LA4.9, which contains human chromosomes 11 and Xp as the only human component. Individual clones containing human DNA were isolated by their ability to hybridise with total human DNA and digested with...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF02346183

    authors: Pook MA,Thakrar R,Pottinger B,Harding B,Porteous D,van Heyningen V,Cowell J,Jones C,Povey S,Davies KE,Thakker RV

    更新日期:1996-06-01 00:00:00

  • Rapid detection of alpha-1-antitrypsin deficiency by analysis of a PCR-induced TaqI restriction site.

    abstract::A single base substitution is responsible for the PI-Z mutation in alpha-1-antitrypsin (AAT) deficiency. The Z mutation, which is in exon V of the AAT gene, was analysed directly using a primer designed with a single base substitution in the DNA sequence. During the polymerase chain reaction with this primer, a restri...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00201739

    authors: Dry PJ

    更新日期:1991-10-01 00:00:00

  • Exclusion of a p53 germline mutation in a classic Li-Fraumeni syndrome family.

    abstract::Li-Fraumeni syndrome (LFS) is characterized by a high risk of sarcomas, early onset of breast cancer, and a diversity of other cancers occurring as multiple primary tumors in multiple family members. In many families with LFS, germline mutations within the tumor-suppressor gene p53 have been identified. However, mutat...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050761

    authors: Evans SC,Mims B,McMasters KM,Foster CJ,deAndrade M,Amos CI,Strong LC,Lozano G

    更新日期:1998-06-01 00:00:00

  • Familial double pericentric inversion of chromosome 5 with some features of cri-du-chat syndrome.

    abstract::Fluorescence in situ hybridization analysis was performed to characterize a complex pericentric inversion involving chromosome 5 in a mother and son. The mother had hypertelorism, epicanthal folds, and mild mental deficiency while the son had additional anomalies that have been observed in patients with cri-du-chat sy...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF02346193

    authors: Goodart SA,Butler MG,Overhauser J

    更新日期:1996-06-01 00:00:00

  • The French Canadian Tay-Sachs disease deletion mutation: identification of probable founders.

    abstract::Tay-Sachs disease (TSD) is an inherited neurodegenerative ganglioside storage disorder caused by deficiency of the hexosaminidase A enzyme. A deletion allele (FCD) at the HEXA locus has attained high frequency in the French Canadian population. The distribution of affected probands shows a likely center of diffusion f...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00207048

    authors: De Braekeleer M,Hechtman P,Andermann E,Kaplan F

    更新日期:1992-04-01 00:00:00

  • A new missense mutation (Cys297-->Phe) of the low density lipoprotein receptor in Italian patients with familial hypercholesterolemia (FHTrieste).

    abstract::During a survey of the mutations of the low density lipoprotein receptor (LDL-R) gene in Italian patients with familial hypercholesterolemia (FH), we identified a novel point mutation, that creates a new EcoRI site at the 5' end of exon 7, in a heterozygous FH subject (FH-100). The sequence of a cDNA fragment encompas...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00202819

    authors: Lelli N,Garuti R,Pedrazzi P,Ghisellini M,Simone ML,Tiozzo R,Cattin L,Valenti M,Rolleri M,Bertolini S

    更新日期:1994-05-01 00:00:00

  • Meiotic segregation analysis of a 14;21 Robertsonian translocation carrier by fluorescence in situ hybridization.

    abstract::Meiotic segregation of chromosomes 14 and 21 in sperm from a 14;21 Robertsonian translocation carrier was analyzed with dual-color FISH using two locus-specific DNA probes (Tel 14q and LSI 21). The frequency of normal or chromosomally balanced sperm, resulting from alternate segregation, was 88.42%. The frequency of u...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390051027

    authors: Honda H,Miharu N,Samura O,He H,Ohama K

    更新日期:2000-02-01 00:00:00

  • Amplified product length polymorphism (APLP): a novel strategy for genotyping the ABO blood group.

    abstract::We present a simple rapid reproducible polymerase chain reaction based technique, termed amplified product length polymorphism (APLP), as a new strategy for primer design for ABO genotyping. The method involves the use of primers differing in length and permits the identification of the major ABO genotypes (A1, A2, B,...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050306

    authors: Watanabe G,Umetsu K,Yuasa I,Suzuki T

    更新日期:1997-01-01 00:00:00

  • The advantages of dense marker sets for linkage analysis with very large families.

    abstract::Dense sets of hundreds of thousands of markers have been developed for genome-wide association studies. These marker sets are also beneficial for linkage analysis of large, deep pedigrees containing distantly related cases. It is impossible to analyse jointly all genotypes in large pedigrees using the Lander-Green Alg...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-007-0323-5

    authors: Thomson R,Quinn S,McKay J,Silver J,Bahlo M,FitzGerald L,Foote S,Dickinson J,Stankovich J

    更新日期:2007-05-01 00:00:00

  • Molecular detection of a translocation (Y;15) in a 45,X male.

    abstract::A 45,X male individual was shown to have a translocation of Y-chromosome material to the short arm or proximal long arm of chromosome 15. This translocation was detected by genomic DNA blotting and in situ hybridization with Y-chromosome-specific DNA probes. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00280488

    authors: Disteche CM,Brown L,Saal H,Friedman C,Thuline HC,Hoar DI,Pagon RA,Page DC

    更新日期:1986-12-01 00:00:00

  • Isoelectric focusing of rare transferrin (Tf) variants and common TfC subtypes.

    abstract::TransferrinC (TfC) subtypes were determined by isoelectric focusing (PAGIF) on samples from 90 carriers of the TFB and TfD alleles. In all cases of CB and CD heterozygotes only one of the two common subtypes of the TfC allele, TfC1 or TfC2, was observed. This is considered strong support for the hypothesis of two comm...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00278905

    authors: Kühnl P,Spielmann W,Weber W

    更新日期:1979-01-19 00:00:00

  • Ring chromosome 15 syndrome.

    abstract::Two new cases of ring chromosome 15 are reported. A review of the nine cases described in the literature shows that ring chromosomes 15 are associated with a rather uniform phenotype characterized by slight to moderate mental retardation, marked pre- and postnatal growth failure, triangular face, and short hands and f...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00278290

    authors: Fryns JP,Timmermans J,Hondt FD,François B,Emmery L,van den Berghe H

    更新日期:1979-09-02 00:00:00

  • Blastomere karyotyping and transfer of chromosomally selected embryos. Implications for the production of specific animal models and human prenatal diagnosis.

    abstract::A method is described that permits the generation of four isolated blastomeres after embryo splitting of murine four-cell eggs and the subsequent chromosomal analysis of one of the obtained 1/4-blastomeres. According to the karyograms obtained, embryos can be selected for reimplantation and furthermore triplicated via...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00273646

    authors: Bacchus C,Buselmaier W

    更新日期:1988-12-01 00:00:00

  • Variability in expression of common fragile sites: in search of a new criterion.

    abstract::Fragile sites are nonrandom, heritable sites on chromosomes that can be induced to form gaps, breaks, and rearrangements under specific conditions. There is currently no established criterion to define a common fragile site. We applied seven published criteria to our data from three groups of subjects: (1) three pairs...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00194217

    authors: Jordan DK,Burns TL,Divelbiss JE,Woolson RF,Patil SR

    更新日期:1990-10-01 00:00:00

  • Sex-reversed XY females with campomelic dysplasia are H-Y negative.

    abstract::Three families with infants affected with campomelic dysplasia, a genetically determined mesenchymal disease frequently associated with sex reversal were studied. Two XY females with ovarian gonadal differentiation and typical clinical features of campomelic dysplasia could be tested for H-Y antigen and were found to ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00271160

    authors: Bricarelli FD,Fraccaro M,Lindsten J,Müller U,Baggio P,Carbone LD,Hjerpe A,Lindgren F,Mayerová A,Ringertz H,Ritzén EM,Rovetta DC,Sicchero C,Wolf U

    更新日期:1981-01-01 00:00:00

  • Pooled genome linkage scan of aggressive prostate cancer: results from the International Consortium for Prostate Cancer Genetics.

    abstract::While it is widely appreciated that prostate cancers vary substantially in their propensity to progress to a life-threatening stage, the molecular events responsible for this progression have not been identified. Understanding these molecular mechanisms could provide important prognostic information relevant to more e...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-006-0219-9

    authors: Schaid DJ,McDonnell SK,Zarfas KE,Cunningham JM,Hebbring S,Thibodeau SN,Eeles RA,Easton DF,Foulkes WD,Simard J,Giles GG,Hopper JL,Mahle L,Moller P,Badzioch M,Bishop DT,Evans C,Edwards S,Meitz J,Bullock S,Hope Q,G

    更新日期:2006-11-01 00:00:00

  • Subtyping of haptoglobin--presentation of a new method.

    abstract::A method is described for large scale routine phenotyping of haptoglobin (Hp) which allows complete subtyping without prior purification of the Hp molecule. The procedure includes polyacrylamide gel isoelectric focusing of reduced, neuraminidase treated serum or plasma samples, and nitrocellulose blots developed with ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00273075

    authors: Teige B,Olaisen B,Pedersen L

    更新日期:1985-01-01 00:00:00

  • A mosaic 45,X/46,X,r(?) karyotype investigated with X and Y centromere-specific probes using a non-autoradiographic in situ hybridization technique.

    abstract::The sex-chromosomal origin of the ring chromosome in a pre-pubertal non-virilized female patient presenting with a 45,X/46,X,r(?) karyotype could not be resolved by conventional cytogenetic (including G11) methods. Non-autoradiographic in situ hybridization of biotinylated X and Y centromere-specific alphoid repetitiv...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00283735

    authors: Crolla JA,Llerena JC Jr

    更新日期:1988-12-01 00:00:00

  • X-linked adrenal hypoplasia in a large Greenlandic family. Detection of a missense mutation (N4401) in the DAX-1 gene; implication for genetic counselling and carrier diagnosis.

    abstract::X-linked congenital adrenal hypoplasia (AHC) is a developmental disorder of the human adrenal gland that results in profound hormonal deficiencies, which are lethal if untreated. Hypogonadotropic hypogonadism (HHG) is frequently associated with this disorder. The gene (DAX-1) responsible for the disease has recently b...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050316

    authors: Schwartz M,Blichfeldt S,Müller J

    更新日期:1997-01-01 00:00:00

  • Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

    abstract::Nitric oxide (NO) mediates host resistance to severe malaria and other infectious diseases. NO production and mononuclear cell expression of the NO producing enzyme-inducible nitric oxide synthase (NOS2) have been associated with protection from severe falciparum malaria. The purpose of this study was to identify sing...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-009-0753-3

    authors: Levesque MC,Hobbs MR,O'Loughlin CW,Chancellor JA,Chen Y,Tkachuk AN,Booth J,Patch KB,Allgood S,Pole AR,Fernandez CA,Mwaikambo ED,Mutabingwa TK,Fried M,Sorensen B,Duffy PE,Granger DL,Anstey NM,Weinberg JB

    更新日期:2010-02-01 00:00:00

  • Replication status of the fragile X chromosome, fra(X)(q27), in three heterozygous females.

    abstract::Investigation of lymphocyte cultures from three females heterozygous for fra(X)(q27) shows widely differing proportions of early and late replicating X chromosomes having the fragile site, and suggests that the replication status of the fragile X may be related to the mental capacity of the patient. The study has util...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00333538

    authors: Howell RT,McDermott A

    更新日期:1982-01-01 00:00:00

  • Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer.

    abstract::Every author has erroneously been assigned to the affiliation "62". The affiliation 62 belongs to the author Graham Casey. ...

    journal_title:Human genetics

    pub_type: 已发布勘误

    doi:10.1007/s00439-019-02030-8

    authors: Bien SA,Su YR,Conti DV,Harrison TA,Qu C,Guo X,Lu Y,Albanes D,Auer PL,Banbury BL,Berndt SI,Bézieau S,Brenner H,Buchanan DD,Caan BJ,Campbell PT,Carlson CS,Chan AT,Chang-Claude J,Chen S,Connolly CM,Easton DF,Fesk

    更新日期:2019-07-01 00:00:00

  • Genetic background of apparently idiopathic sporadic cerebellar ataxia.

    abstract::Disease-causing mutations have been identified in various entities of autosomal dominant ataxia and in Friedreich's ataxia. However, no molecular pathogenic factor is known to cause idiopathic cerebellar ataxias. We investigated the CAG/CTG trinucleotide repeats causing spinocerebellar ataxia types 1, 2, 3, 6, 7, 8 an...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390000346

    authors: Schöls L,Szymanski S,Peters S,Przuntek H,Epplen JT,Hardt C,Riess O

    更新日期:2000-08-01 00:00:00

  • PGC-1alpha Thr394Thr and Gly482Ser variants are significantly associated with T2DM in two North Indian populations: a replicate case-control study.

    abstract::The recent observations that Peroxisome proliferator activated receptor gamma coactivator 1 alpha (PGC1A) is responsible for the induction of reactive oxygen species (ROS) detoxifying agents and that ROS triggers insulin resistance, support the role that this gene could play in the onset of Type 2 diabetes mellitus (T...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-007-0352-0

    authors: Bhat A,Koul A,Rai E,Sharma S,Dhar MK,Bamezai RN

    更新日期:2007-06-01 00:00:00

  • Studies on steroid hormone receptors (5alpha-dihidrotesterone, estradiol, and dexamethasone) in cultured human fibroblasts and amniotic fluid cells.

    abstract::Cultured human fibroblasts and amniotic fluid cells (AF cells) were examined for the presence of steroid hormone receptors. In both cell types, the androgen (DHT) or glucocorticoid (dexamethasone) receptor was detected, but not the estrogen receptor. Binding parameters in fibroblasts were: for androgen: KD = 3.7 X 10(...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00295427

    authors: Bauknecht T

    更新日期:1977-12-23 00:00:00

  • Menkes kinky hair disease: a search for closely linked restriction fragment length polymorphism.

    abstract::In a large kindred with X-linked Menkes disease, linkage studies were performed with a restriction fragment length polymorphism (RFLP) that had been found with a cloned hybridisation probe from the proximal short arm of the X chromosome. This RFLP was considered as a potential genetic marker since the Menkes gene seem...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00327110

    authors: Wieacker P,Horn N,Pearson P,Wienker TF,McKay E,Ropers HH

    更新日期:1983-01-01 00:00:00