Whole-genome sequencing in French Canadians from Quebec.

Abstract:

:Genome-wide association studies (GWAS) have had a tremendous success in the identification of common DNA sequence variants associated with complex human diseases and traits. However, because of their design, GWAS are largely inappropriate to characterize the role of rare and low-frequency DNA variants on human phenotypic variation. Rarer genetic variation is geographically more restricted, supporting the need for local whole-genome sequencing (WGS) efforts to study these variants in specific populations. Here, we present the first large-scale low-pass WGS of the French-Canadian population. Specifically, we sequenced at ~5.6× coverage the whole genome of 1970 French Canadians recruited by the Montreal Heart Institute Biobank and identified 29 million bi-allelic variants (31 % novel), including 19 million variants with a minor allele frequency (MAF) <0.5 %. Genotypes from the WGS data are highly concordant with genotypes obtained by exome array on the same individuals (99.8 %), even when restricting this analysis to rare variants (MAF <0.5, 99.9 %) or heterozygous sites (98.9 %). To further validate our data set, we showed that we can effectively use it to replicate several genetic associations with myocardial infarction risk and blood lipid levels. Furthermore, we analyze the utility of our WGS data set to generate a French-Canadian-specific imputation reference panel and to infer population structure in the Province of Quebec. Our results illustrate the value of low-pass WGS to study the genetics of human diseases in the founder French-Canadian population.

journal_name

Hum Genet

journal_title

Human genetics

authors

Low-Kam C,Rhainds D,Lo KS,Provost S,Mongrain I,Dubois A,Perreault S,Robinson JF,Hegele RA,Dubé MP,Tardif JC,Lettre G

doi

10.1007/s00439-016-1702-6

subject

Has Abstract

pub_date

2016-11-01 00:00:00

pages

1213-1221

issue

11

eissn

0340-6717

issn

1432-1203

pii

10.1007/s00439-016-1702-6

journal_volume

135

pub_type

杂志文章
  • Nine novel germline mutations of STK11 in ten families with Peutz-Jeghers syndrome.

    abstract::Peutz-Jeghers Syndrome (PJS) is an autosomal dominant hereditary disease characterized by hamartomatous polyposis involving the entire bowel. Recently STK11, a gene bearing a mutation responsible for PJS, was isolated. We investigated the entire coding region of STK11 in 15 unrelated PJS families by the PCR-SSCP (poly...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050801

    authors: Nakagawa H,Koyama K,Miyoshi Y,Ando H,Baba S,Watatani M,Yasutomi M,Matsuura N,Monden M,Nakamura Y

    更新日期:1998-08-01 00:00:00

  • Molecular genetic epidemiology of human diseases: from patterns to predictions.

    abstract::Databases of disease-associated or disease-causing mutations allow the study, not only of the molecular mechanisms underlying the primary lesions at the DNA level, but also of the functional consequences of mutation at the phenotypic level. The Human Gene Mutation Database (HGMD) and the bioinformatics analyses of its...

    journal_title:Human genetics

    pub_type: 杂志文章,评审

    doi:10.1007/s00439-013-1396-y

    authors: Knecht C,Krawczak M

    更新日期:2014-04-01 00:00:00

  • Mitochondrial DNA polymorphisms as risk factors for Parkinson's disease and Parkinson's disease dementia.

    abstract::The activity of complex I of the mitochondrial respiratory chain has been found to be decreased in patients with Parkinson's disease (PD), but no mutations have been identified in genes encoding complex I subunits. Recent studies have suggested that polymorphisms in mitochondrial DNA (mtDNA)-encoded complex I genes (M...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-004-1123-9

    authors: Autere J,Moilanen JS,Finnilä S,Soininen H,Mannermaa A,Hartikainen P,Hallikainen M,Majamaa K

    更新日期:2004-06-01 00:00:00

  • Transcriptome profile reveals AMPA receptor dysfunction in the hippocampus of the Rsk2-knockout mice, an animal model of Coffin-Lowry syndrome.

    abstract::Coffin-Lowry syndrome (CLS) is a syndromic form of mental retardation caused by loss of function mutations in the X-linked RPS6KA3 gene, which encodes RSK2, a serine/threonine kinase acting in the MAPK/ERK pathway. The mouse invalidated for the Rps6ka3 (Rsk2-KO) gene displays learning and long-term spatial memory defi...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-010-0918-0

    authors: Mehmood T,Schneider A,Sibille J,Marques Pereira P,Pannetier S,Ammar MR,Dembele D,Thibault-Carpentier C,Rouach N,Hanauer A

    更新日期:2011-03-01 00:00:00

  • Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping.

    abstract::Genetic studies in Turkish, Native American, European American, and African American (AA) families have linked chromosome 18q21.1-23 to susceptibility for diabetes-associated nephropathy. In this study, we have carried out fine linkage mapping in the 18q region previously linked to diabetic nephropathy in AAs by genot...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-009-0732-8

    authors: McDonough CW,Bostrom MA,Lu L,Hicks PJ,Langefeld CD,Divers J,Mychaleckyj JC,Freedman BI,Bowden DW

    更新日期:2009-12-01 00:00:00

  • A response to "Personalised medicine and population health: breast and ovarian cancer".

    abstract:: ...

    journal_title:Human genetics

    pub_type: 信件

    doi:10.1007/s00439-019-01984-z

    authors: Antoniou A,Anton-Culver H,Borowsky A,Broeders M,Brooks J,Chiarelli A,Chiquette J,Cuzick J,Delaloge S,Devilee P,Dorval M,Easton D,Eisen A,Eklund M,Eloy L,Esserman L,Garcia-Closas M,Goldgar D,Hall P,Knoppers BM,Kraf

    更新日期:2019-03-01 00:00:00

  • Barrett's oesophagus: an ideal model to study cancer genetics.

    abstract::Chronic gastro-oesophageal reflux disease can induce a metaplastic change of the distal oesophagus called Barrett's oesophagus whereby the normal squamous epithelium is substituted by a columnar epithelium. Patients with Barrett's oesophagus are at increased risk of oesophageal adenocarcinoma which occurs through dysp...

    journal_title:Human genetics

    pub_type: 杂志文章,评审

    doi:10.1007/s00439-009-0665-2

    authors: di Pietro M,Fitzgerald RC

    更新日期:2009-08-01 00:00:00

  • In-frame deletions of BRCA1 may define critical functional domains.

    abstract::The identification of genomic rearrangements involving more than 0.5 kb of the BRCA1 gene has confirmed a more complex mutation spectrum than was initially appreciated. Genomic rearrangements in BRCA1 represent 15% of all mutations in a group of French and American breast and ovarian cancer families and 36% of all mut...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390000372

    authors: Rohlfs EM,Chung CH,Yang Q,Skrzynia C,Grody WW,Graham ML,Silverman LM

    更新日期:2000-10-01 00:00:00

  • Alport syndrome: a genetic study of 31 families.

    abstract::Thirty one families with Alport syndrome including 3 families with associated syndromes were studied. The location of the COL4A5 gene, responsible for the Alport syndrome, was determined by linkage analysis with eight probes of the Xq arm and by a radiation hybrid panel. Concordant data indicated the localization of t...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00220471

    authors: M'Rad R,Sanak M,Deschenes G,Zhou J,Bonaiti-Pellie C,Holvoet-Vermaut L,Heuertz S,Gubler MC,Broyer M,Grunfeld JP

    更新日期:1992-12-01 00:00:00

  • The thymidylate synthase tandem repeat polymorphism is not associated with homocysteine concentrations in healthy young subjects.

    abstract::Thymidylate synthase (TYMS) and 5,10-methylenetetrahydrofolate reductase (MTHFR) may compete for their common cofactor 5,10-methylenetetrahyhdrofolate (5,10-meTHF). Limiting 5,10-meTHF results in elevated homocysteine, especially in individuals homozygous for the T allele of the MTHFR C677T polymorphism. The TYMS gene...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-003-1039-9

    authors: Brown KS,Kluijtmans LA,Young IS,McNulty H,Mitchell LE,Yarnell JW,Woodside JV,Boreham CA,McMaster D,Murray L,Strain JJ,Whitehead AS

    更新日期:2004-01-01 00:00:00

  • A case of Shwachman syndrome with increased spontaneous chromosome breakage.

    abstract::In a patient with Shwachman syndrome, a high incidence of chromosome breakage was found. Chromosome studies done on three occasions on the patient's PHA-stimulated peripheral blood lymphocytes showed elevated frequencies of spontaneous chromosome aberrations compared with those in normal individuals. The patient's lym...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00284489

    authors: Tada H,Ri T,Yoshida H,Ishimoto K,Kaneko M,Yamashiro Y,Shinohara T

    更新日期:1987-11-01 00:00:00

  • The gene for human interleukin 7 (IL7) is at 8q12-13.

    abstract::The gene for human interleukin 7 (IL7) maps to chromosome 8 by Southern analysis of a somatic cell hybrid panel and to 8q12-q13 by in situ hybridization. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00274000

    authors: Sutherland GR,Baker E,Fernandez KE,Callen DF,Goodwin RG,Lupton S,Namen AE,Shannon MF,Vadas MA

    更新日期:1989-07-01 00:00:00

  • Ss blood group associated PAS-staining polymorphism of glycoprotein 3 from human erythrocyte membranes.

    abstract::It is shown by discontinuous sodium dodecylsulfate (SDS) polyacrylamide gel electrophoresis of human red cell membranes, followed by periodic acid Schiff (PAS) staining and densitometry, that the band PAS-3 (monomeric Ss glycoprotein) exhibits a polymorphism with respect to its staining intensity. In membranes of the ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00291494

    authors: Dahr W,Uhlenbruck G,Schmalisch R,Janssen E

    更新日期:1976-05-19 00:00:00

  • Investigations on the polymorphism of glyoxalase I (EC 4.4.1.5) in the population of Hessen, Germany.

    abstract::The phenotypes of glyoxalase I (GLO) were determined in a random population from Hessen (Germany) by high-voltage agarose gel electrophoresis. The gene frequencies in 1150 unrelated individuals were 0.4391 for GLO1 and 0.5609 fro GLO2. Rare phenotypes were not observed. The segregation of phenotypes in 50 families an...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00295812

    authors: Kühnl P,Schwabenland R,Spielmann W

    更新日期:1977-08-31 00:00:00

  • Evidence for chromosome instability in vivo in Bloom syndrome: increased numbers of micronuclei in exfoliated cells.

    abstract::The incidence of exfoliated epithelial cells containing micronuclei was determined in two small human populations, one homozygous and the other heterozygous for the Bloom syndrome gene (bl). The objectives of the study were two: to learn whether the chromosome instability featured so prominently by Bloom syndrome (BS)...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00284570

    authors: Rosin MP,German J

    更新日期:1985-01-01 00:00:00

  • Heterozygous missense variants of LMX1A lead to nonsyndromic hearing impairment and vestibular dysfunction.

    abstract::Unraveling the causes and pathomechanisms of progressive disorders is essential for the development of therapeutic strategies. Here, we identified heterozygous pathogenic missense variants of LMX1A in two families of Dutch origin with progressive nonsyndromic hearing impairment (HI), using whole exome sequencing. One ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-018-1880-5

    authors: Wesdorp M,de Koning Gans PAM,Schraders M,Oostrik J,Huynen MA,Venselaar H,Beynon AJ,van Gaalen J,Piai V,Voermans N,van Rossum MM,Hartel BP,Lelieveld SH,Wiel L,Verbist B,Rotteveel LJ,van Dooren MF,Lichtner P,Kunst HPM,

    更新日期:2018-05-01 00:00:00

  • Dinucleotide (CA/GT) repeat polymorphism in intron 17B of the cystic fibrosis transmembrane conductance regulator (CFTR) gene.

    abstract::We describe a polymorphic microsatellite (IVS17BCA) in intron 17B of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It consists of an 11 to 20 CA/GT dinucleotide repeat, located 424 bp from exon 17B. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00197276

    authors: Morral N,Girbau E,Zielenski J,Nunes V,Casals T,Tsui LC,Estivill X

    更新日期:1992-01-01 00:00:00

  • Malformative syndrome associated with a ring 10 chromosome and a translocated 10q/19 chromosome.

    abstract::A male newborn with a ring 10 chromosome is described. The distal part of the long arm of chromosome 10, deleted during ring formation (10q25), is translocated to the short arm of chromosome 19. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00293602

    authors: Fryns JP,De Boeck K,Jaeken J,van den Berghe H

    更新日期:1978-08-31 00:00:00

  • Linkage analysis identifies the thyroglobulin gene region as a major locus for familial congenital hypothyroidism.

    abstract::Congenital hypothyroidism affects 1/3000-4000 newborns and it has been estimated that 10-20% are familial cases with an autosomal recessive mode of inheritance. Previous studies of mostly individual cases have led to the identification of mutations in a number of genes, indicating that it is a genetically heterogeneou...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-002-0680-z

    authors: Ahlbom BE,Yaqoob M,Gustavsson P,Abbas HG,Annerén G,Larsson A,Wadelius C

    更新日期:2002-02-01 00:00:00

  • Linkage relationships of biochemical markers to Q- and C-band variants in a large black kindred.

    abstract::Lod scores are reported for 86 biochemical to cytogenetic marker comparisons in Black kindred. Analysis with unconfirmed locus assignments resulted in 12 exclusions of close linkage. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00290217

    authors: Fogle TA,Namboodiri KK,Elston RC,McKenzie WH,Hames CG

    更新日期:1980-01-01 00:00:00

  • Genetic polymorphisms associated with rubella virus-specific cellular immunity following MMR vaccination.

    abstract::Rubella virus causes a relatively benign disease in most cases, although infection during pregnancy can result in serious birth defects. An effective vaccine has been available since the early 1970s and outbreaks typically do not occur among highly vaccinated (≥2 doses) populations. Nevertheless, considerable inter-in...

    journal_title:Human genetics

    pub_type: 杂志文章,meta分析

    doi:10.1007/s00439-014-1471-z

    authors: Kennedy RB,Ovsyannikova IG,Haralambieva IH,Lambert ND,Pankratz VS,Poland GA

    更新日期:2014-11-01 00:00:00

  • Mapping of the kinesin-related gene ATSV to chromosome 2q37.

    abstract::The human ATSV (axonal transporter of synaptic vesicles) gene encodes an anterograde axonal motor transport protein and demonstrates homology to the kinesin gene family in several species. The human ATSV gene was mapped to chromosome 2q37 by screening of a human/rodent somatic cell hybrid panel by the polymerase chain...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050944

    authors: Keller MP,Seifried BA,Rabin BA,Chance PF

    更新日期:1999-03-01 00:00:00

  • The identification of two mis-sense mutations at the PAH gene locus in a Turkish patient with phenylketonuria.

    abstract::DNA sequence analysis of the 13 exons and intron/exon boundaries of the phenylalanine hydroxylase (PAH) gene has detected two base transitions, resulting in mis-sense mutations, in the genomic DNA of a Turkish patient (E1) with phenylketonuria (PKU). The Leu48----Ser amino acid substitution was associated with the mut...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00197153

    authors: Konecki DS,Schlotter M,Trefz FK,Lichter-Konecki U

    更新日期:1991-08-01 00:00:00

  • Lactose digestion and the evolutionary genetics of lactase persistence.

    abstract::It has been known for some 40 years that lactase production persists into adult life in some people but not in others. However, the mechanism and evolutionary significance of this variation have proved more elusive, and continue to excite the interest of investigators from different disciplines. This genetically deter...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-008-0593-6

    authors: Ingram CJ,Mulcare CA,Itan Y,Thomas MG,Swallow DM

    更新日期:2009-01-01 00:00:00

  • Linkage analysis of X-linked cleft palate and ankyloglossia in Manitoba Mennonite and British Columbia Native kindreds.

    abstract::A locus (CPX) responsible for X-linked cleft palate and ankyloglossia was previously mapped to the proximal long arm of the X chromosome through DNA marker linkage studies in two large kindred: an Icelandic family and a British Columbia (B.C.) Native family. In this study, additional linkage analyses have been perform...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00202859

    authors: Gorski SM,Adams KJ,Birch PH,Chodirker BN,Greenberg CR,Goodfellow PJ

    更新日期:1994-08-01 00:00:00

  • Detecting genomic clustering of risk variants from sequence data: cases versus controls.

    abstract::As the ability to measure dense genetic markers approaches the limit of the DNA sequence itself, taking advantage of possible clustering of genetic variants in, and around, a gene would benefit genetic association analyses, and likely provide biological insights. The greatest benefit might be realized when multiple ra...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-013-1335-y

    authors: Schaid DJ,Sinnwell JP,McDonnell SK,Thibodeau SN

    更新日期:2013-11-01 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

  • An alpha-spectrin mutation responsible for hereditary elliptocytosis associated in cis with the alpha v/41 polymorphism.

    abstract::The alpha 207 Leu-->Pro mutation in spectrin has recently been identified as a cause of alpha I/50-46a hereditary elliptocytosis (HE) or pyropoikilocytosis among Black people. We have found this mutation in a Moroccan family in both the heterozygous and homozygous states. The mutated alpha-spectrin allele carried, in ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00202482

    authors: Dalla Venezia N,Wilmotte R,Morlé L,Forissier A,Parquet N,Garbarz M,Rousset T,Dhermy D,Alloisio N,Delaunay J

    更新日期:1993-02-01 00:00:00

  • Absence of mutations in the WT1 gene in patients with XY gonadal dysgenesis.

    abstract::The WT1 gene is normally expressed during gonadal development and specific mutations in heterozygous form cause Drash syndrome, characterized by male pseudohermaphroditism and gonadal dysgenesis, renal failure and a predisposition for Wilms' tumour. These observations prompted us to test whether WT1 mutations are invo...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00214195

    authors: Nordenskjöld A,Fricke G,Anvret M

    更新日期:1995-07-01 00:00:00

  • A case of 9p- syndrome.

    abstract::An 8-month-old female child with the 9p- karyotype: 46,XX,del(9) (p22) is presented, being the first case from among Oriental people. She has many clinical features similar to those described in Caucasian cases. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00295813

    authors: Kuroki Y,Yokota S,Nakai H,Yamamoto Y,Matsui I

    更新日期:1977-08-31 00:00:00