Physical mapping: integrating computational and molecular genetic data.

Abstract:

:A crucial step beyond the identification of genetic linkage of a disease to a chromosomal region is the production of a physical map that will allow the identification of candidate genes. Although the process of physical map building has been facilitated by the flow of data released by the Human Genome Project, gathering all the information together requires significant effort. In a previous study, we reported linkage between Bipolar Affective Disorder and the chromosomal location 4p15.3--p16.1. In this review we use this example to describe how to collect publicly available sequence, DNA fingerprint, and genetic marker data and integrate these with empirical data to build a large scale high resolution physical map of a region. Methods used to identify new genetic markers and candidate genes within a circumscribed region are also presented.

journal_name

Ann Hum Genet

journal_title

Annals of human genetics

authors

Le Hellard S,Semple CA,Morris SW,Porteous DJ,Evans KL

doi

10.1017/S0003480001008594

subject

Has Abstract

pub_date

2001-05-01 00:00:00

pages

221-8

issue

Pt 3

eissn

0003-4800

issn

1469-1809

pii

S0003480001008594

journal_volume

65

pub_type

杂志文章,评审
  • Significance levels in genome-wide interaction analysis (GWIA).

    abstract::Interaction between genetic variants is hypothesized to be one of several putative explanations for the 'case of missing heritability.' Therefore, Genome-Wide Interaction Analysis (GWIA) has recently gained substantial interest. GWIA is computationally challenging and respective power type I error studies are particul...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2010.00610.x

    authors: Becker T,Herold C,Meesters C,Mattheisen M,Baur MP

    更新日期:2011-01-01 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

  • 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

  • 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

  • Regression-based multivariate linkage analysis with an application to blood pressure and body mass index.

    abstract::Multivariate linkage analysis has been suggested for the analysis of correlated traits, such as blood pressure (BP) and body mass index (BMI), because it may offer greater power and provide clearer results than univariate analyses. Currently, the most commonly used multivariate linkage methods are extensions of the un...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2006.00303.x

    authors: Wang T,Elston RC

    更新日期:2007-01-01 00:00:00

  • Drug addiction and stress-response genetic variability: association study in African Americans.

    abstract::Stress is a significant risk factor in the development of drug addictions and in addiction relapse susceptibility. This hypothesis-driven study was designed to determine if specific SNPs in genes related to stress response are associated with heroin and/or cocaine addiction in African Americans. The analysis included ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12064

    authors: Levran O,Randesi M,Li Y,Rotrosen J,Ott J,Adelson M,Kreek MJ

    更新日期:2014-07-01 00:00:00

  • Mapping of RXRB to human chromosome 6p21.3.

    abstract::Retinoid X Receptor beta (RXRB) is a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). We have confirmed the localization of RXRB to chromosome 6 and we have mapped the gene to chromosome 6p21.3-p21.1 by PCR amplification of 5' untran...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1993.tb01596.x

    authors: Fitzgibbon J,Gillett GT,Woodward KJ,Boyle JM,Wolfe J,Povey S

    更新日期:1993-07-01 00:00:00

  • The effect of genetic admixture in an association study: genetic polymorphisms and chromosome aberrations in a Colombian population exposed to organic solvents.

    abstract::The human population is heterogeneous in genetic susceptibility, chromosomal instability and disease risk; all factors which depend on inherited genetic constitution and acquired nongenetic environmental and occupational factors. Recently, special attention has been directed to the identification of sources of potenti...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12019

    authors: Hoyos-Giraldo LS,Escobar-Hoyos LF,Reyes-Carvajal I,García JJ,Córdoba L,Gómez AS,García-Vallejo F,Cajas-Salazar N,Carvajal S,Bedoya G

    更新日期:2013-07-01 00:00:00

  • Phylogenetic analysis of mtDNA lineages in South American mummies.

    abstract::Some studies of mtDNA propose that contemporary Amerindians have descended from four haplotype groups, each defined by specific sets of polymorphisms. One recent study also found evidence of other potential founder haplotypes. We wanted to determine whether the four haplotypes in modern populations were also present i...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1996.tb01193.x

    authors: Monsalve MV,Cardenas F,Guhl F,Delaney AD,Devine DV

    更新日期:1996-07-01 00:00:00

  • The complex and diversified mitochondrial gene pool of Berber populations.

    abstract::The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitoc...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2008.00493.x

    authors: Coudray C,Olivieri A,Achilli A,Pala M,Melhaoui M,Cherkaoui M,El-Chennawi F,Kossmann M,Torroni A,Dugoujon JM

    更新日期:2009-03-01 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

  • Comprehensive Genome Profiling of Single Sperm Cells by Multiple Annealing and Looping-Based Amplification Cycles and Next-Generation Sequencing from Carriers of Robertsonian Translocation.

    abstract::Robertsonian translocation (RT) is a common cause for male infertility, recurrent pregnancy loss, and birth defects. Studying meiotic recombination in RT-carrier patients helps decipher the mechanism and improve the clinical management of infertility and birth defects caused by RT. Here we present a new method to stud...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12187

    authors: Sha Y,Sha Y,Ji Z,Ding L,Zhang Q,Ouyang H,Lin S,Wang X,Shao L,Shi C,Li P,Song Y

    更新日期:2017-03-01 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

  • 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

  • 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 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

  • 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

  • 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

  • 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

  • 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

  • Testing association with interactions by partitioning chi-squares.

    abstract::Gene-gene interaction plays an important role in association studies for complex diseases. There have been different approaches to incorporating gene-gene interactions in candidate gene or genome-wide association studies, especially for those genes with no marginal effects but with interaction effects. However, there ...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2008.00480.x

    authors: Yang Y,He C,Ott J

    更新日期:2009-01-01 00:00:00

  • 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...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1046/j.1469-1809.1997.6110077.x

    authors: Wan Y,Cohen J,Guerra R

    更新日期:1997-01-01 00:00:00

  • A possible mutation of a fluorescence polymorphism.

    abstract::The segregation of the Q-band polymorphisms in 32 families have been studied. From 90 matings in these families, there were a total of 208 offspring. In one of these offspring it could be shown that there had been a change of a fluorescent polymorphism, resulting in the loss of fluorescent intensity in the satellite o...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1978.tb01899.x

    authors: Robinson JA,Buckton KE,Evans HJ

    更新日期:1978-01-01 00:00:00

  • Homozygous in-frame variant of SCL6A3 causes dopamine transporter deficiency syndrome in a consanguineous family.

    abstract::The human dopamine transporter (hDAT) participates in dopamine homeostasis by clearing dopamine from the extracellular space using secondary active transport. Dysregulation of hDAT has been reported to be associated with different neuropsychiatric disorders. Dopamine transporter deficiency syndrome (DTDS) is a complex...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12378

    authors: Heidari E,Razmara E,Hosseinpour S,Tavasoli AR,Garshasbi M

    更新日期:2020-07-01 00:00:00

  • Homozygous sequence variants in the NPR2 gene underlying Acromesomelic dysplasia Maroteaux type (AMDM) in consanguineous families.

    abstract::Acromesomelic dysplasia Maroteaux type (AMDM) is an autosomal recessive skeletal disorder characterized by disproportionate short stature with shortening of the acromesomelic sections of the limbs. AMDM is caused by mutations in the NPR2 gene located on chromosome 9p21-p12. The gene encodes the natriuretic peptide rec...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12116

    authors: Irfanullah,Umair M,Khan S,Ahmad W

    更新日期:2015-07-01 00:00:00

  • Posterior probability of linkage and maximal lod score.

    abstract::To detect linkage between a trait and a marker, Morton (1955) proposed to calculate the lod score z(theta 1) at a given value theta 1 of the recombination fraction. If z(theta 1) reaches +3 then linkage is concluded. However, in practice, lod scores are calculated for different values of the recombination fraction bet...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1995.tb01610.x

    authors: Génin E,Martinez M,Clerget-Darpoux F

    更新日期:1995-01-01 00:00:00

  • Testing candidate loci on chromosomes 1 and 6 for genetic linkage to Peutz-Jeghers' disease.

    abstract::Peutz-Jeghers' syndrome (PJS) is a disease with autosomal dominant inheritance, which is characterised by gastrointestinal hamartomata and characteristic melanin pigmentation. Three candidate sites for a PJS locus have recently been proposed, chromosomes 1p31-p32, 6q25 and 6p11-cen. At the first of these sites, a mult...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.1996.tb00435.x

    authors: Tomlinson IP,Olschwang S,Abelovitch D,Nakamura Y,Bodmer WF,Thomas G,Markie D

    更新日期:1996-09-01 00:00:00

  • Analysis of sports-relevant polymorphisms in a large Brazilian cohort of top-level athletes.

    abstract::In recent years, there have been an increasing number of genetic variants associated with athletic phenotypes. Here, we selected a set of sports-relevant polymorphisms that have been previously suggested as genetic markers for human physical performance, and we examined their association with athletic status in a larg...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/ahg.12248

    authors: Guilherme JPLF,Bertuzzi R,Lima-Silva AE,Pereira ADC,Lancha Junior AH

    更新日期:2018-09-01 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

  • Genetic Polymorphism of CYP2C19 gene in the Stanislas cohort. A link with inflammation.

    abstract::CYP2C19, a member of the cytochrome P450 family, metabolises arachidonic acid to produce epoxyeicosanoid acids, which are involved in vascular tone and inflammation. Thus, this study describes the possible relationship between a CYP2C19 polymorphism (681G>A) and three inflammatory markers: interleukin (IL)-6, tumor ne...

    journal_title:Annals of human genetics

    pub_type: 杂志文章

    doi:10.1111/j.1469-1809.2007.00417.x

    authors: Bertrand-Thiébault C,Berrahmoune H,Thompson A,Marie B,Droesch S,Siest G,Foernzler D,Visvikis-Siest S

    更新日期:2008-03-01 00:00:00