Literature DB >> 21546396

famCNV: copy number variant association for quantitative traits in families.

Hariklia Eleftherohorinou1, Johanna C Andersson-Assarsson, Robin G Walters, Julia S El-Sayed Moustafa, Lachlan Coin, Peter Jacobson, Lena M S Carlsson, Alexandra I F Blakemore, Philippe Froguel, Andrew J Walley, Mario Falchi.   

Abstract

UNLABELLED: A program package to enable genome-wide association of copy number variants (CNVs) with quantitative phenotypes in families of arbitrary size and complexity. Intensity signals that act as proxies for the number of copies are modeled in a variance component framework and association with traits is assessed through formal likelihood testing.
AVAILABILITY AND IMPLEMENTATION: The Java package is made available at www.imperial.ac.uk/medicine/people/m.falchi/. CONTACT: m.falchi@imperial.ac.uk.

Entities:  

Mesh：

Year:  2011        PMID： 21546396      PMCID： PMC3117380          DOI： 10.1093/bioinformatics/btr264

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  16 in total

1.  A general test of association for quantitative traits in nuclear families.

Authors:  G R Abecasis; L R Cardon; W O Cookson
Journal:  Am J Hum Genet       Date:  2000-01       Impact factor: 11.025

2.  cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs.

Authors:  Lachlan J M Coin; Julian E Asher; Robin G Walters; Julia S El-Sayed Moustafa; Adam J de Smith; Rob Sladek; David J Balding; Philippe Froguel; Alexandra I F Blakemore
Journal:  Nat Methods       Date:  2010-05-30       Impact factor: 28.547

3.  High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping.

Authors:  Daniel A Peiffer; Jennie M Le; Frank J Steemers; Weihua Chang; Tony Jenniges; Francisco Garcia; Kirt Haden; Jiangzhen Li; Chad A Shaw; John Belmont; Sau Wai Cheung; Richard M Shen; David L Barker; Kevin L Gunderson
Journal:  Genome Res       Date:  2006-08-09       Impact factor: 9.043

Review 4.  Copy-number variation and association studies of human disease.

Authors:  Steven A McCarroll; David M Altshuler
Journal:  Nat Genet       Date:  2007-07       Impact factor: 38.330

5.  Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis.

Authors:  Yurii S Aulchenko; Dirk-Jan de Koning; Chris Haley
Journal:  Genetics       Date:  2007-07-29       Impact factor: 4.562

6.  On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test.

Authors:  Iuliana Ionita-Laza; George H Perry; Benjamin A Raby; Barbara Klanderman; Charles Lee; Nan M Laird; Scott T Weiss; Christoph Lange
Journal:  Genet Epidemiol       Date:  2008-04       Impact factor: 2.135

7.  PLINK: a tool set for whole-genome association and population-based linkage analyses.

Authors:  Shaun Purcell; Benjamin Neale; Kathe Todd-Brown; Lori Thomas; Manuel A R Ferreira; David Bender; Julian Maller; Pamela Sklar; Paul I W de Bakker; Mark J Daly; Pak C Sham
Journal:  Am J Hum Genet       Date:  2007-07-25       Impact factor: 11.025

8.  Robust variance-components approach for assessing genetic linkage in pedigrees.

Authors:  C I Amos
Journal:  Am J Hum Genet       Date:  1994-03       Impact factor: 11.025

9.  Relative impact of nucleotide and copy number variation on gene expression phenotypes.

Authors:  Barbara E Stranger; Matthew S Forrest; Mark Dunning; Catherine E Ingle; Claude Beazley; Natalie Thorne; Richard Redon; Christine P Bird; Anna de Grassi; Charles Lee; Chris Tyler-Smith; Nigel Carter; Stephen W Scherer; Simon Tavaré; Panagiotis Deloukas; Matthew E Hurles; Emmanouil T Dermitzakis
Journal:  Science       Date:  2007-02-09       Impact factor: 47.728

10.  Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations.

Authors:  David Meyre; Jérôme Delplanque; Jean-Claude Chèvre; Cécile Lecoeur; Stéphane Lobbens; Sophie Gallina; Emmanuelle Durand; Vincent Vatin; Franck Degraeve; Christine Proença; Stefan Gaget; Antje Körner; Peter Kovacs; Wieland Kiess; Jean Tichet; Michel Marre; Anna-Liisa Hartikainen; Fritz Horber; Natascha Potoczna; Serge Hercberg; Claire Levy-Marchal; François Pattou; Barbara Heude; Maithé Tauber; Mark I McCarthy; Alexandra I F Blakemore; Alexandre Montpetit; Constantin Polychronakos; Jacques Weill; Lachlan J M Coin; Julian Asher; Paul Elliott; Marjo-Riitta Järvelin; Sophie Visvikis-Siest; Beverley Balkau; Rob Sladek; David Balding; Andrew Walley; Christian Dina; Philippe Froguel
Journal:  Nat Genet       Date:  2009-01-18       Impact factor: 38.330
View more
  8 in total

1.  Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity.

Authors:  Julia S El-Sayed Moustafa; Hariklia Eleftherohorinou; Adam J de Smith; Johanna C Andersson-Assarsson; Alexessander Couto Alves; Eleni Hadjigeorgiou; Robin G Walters; Julian E Asher; Leonardo Bottolo; Jessica L Buxton; Rob Sladek; David Meyre; Christian Dina; Sophie Visvikis-Siest; Peter Jacobson; Lars Sjöström; Lena M S Carlsson; Andrew Walley; Mario Falchi; Philippe Froguel; Alexandra I F Blakemore; Lachlan J M Coin
Journal:  Hum Mol Genet       Date:  2012-05-16       Impact factor: 6.150

2.  Signatures of TSPAN8 variants associated with human metabolic regulation and diseases.

Authors:  Tisham De; Angela Goncalves; Doug Speed; Philippe Froguel; Daniel J Gaffney; Michael R Johnson; Marjo-Riitta Jarvelin; Lachlan Jm Coin
Journal:  iScience       Date:  2021-07-22

3.  Copy number variation genotyping using family information.

Authors:  Jen-Hwa Chu; Angela Rogers; Iuliana Ionita-Laza; Katayoon Darvishi; Ryan E Mills; Charles Lee; Benjamin A Raby
Journal:  BMC Bioinformatics       Date:  2013-05-09       Impact factor: 3.169

4.  Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans.

Authors:  August Blackburn; Marcio Almeida; Angela Dean; Joanne E Curran; Matthew P Johnson; Eric K Moses; Lawrence J Abraham; Melanie A Carless; Thomas D Dyer; Satish Kumar; Laura Almasy; Michael C Mahaney; Anthony Comuzzie; Sarah Williams-Blangero; John Blangero; Donna M Lehman; Harald H H Göring
Journal:  Eur J Hum Genet       Date:  2015-01-14       Impact factor: 4.246

5.  VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions.

Authors:  Jianxin Shi; Xiaohong R Yang; Neil E Caporaso; Maria T Landi; Peng Li
Journal:  Front Genet       Date:  2014-03-18       Impact factor: 4.599

6.  Haplotype phasing and inheritance of copy number variants in nuclear families.

Authors:  Priit Palta; Lauris Kaplinski; Liina Nagirnaja; Andres Veidenberg; Märt Möls; Mari Nelis; Tõnu Esko; Andres Metspalu; Maris Laan; Maido Remm
Journal:  PLoS One       Date:  2015-04-08       Impact factor: 3.240

7.  Low copy number of the salivary amylase gene predisposes to obesity.

Authors:  Mario Falchi; Julia Sarah El-Sayed Moustafa; Petros Takousis; Francesco Pesce; Amélie Bonnefond; Johanna C Andersson-Assarsson; Peter H Sudmant; Rajkumar Dorajoo; Mashael Nedham Al-Shafai; Leonardo Bottolo; Erdal Ozdemir; Hon-Cheong So; Robert W Davies; Alexandre Patrice; Robert Dent; Massimo Mangino; Pirro G Hysi; Aurélie Dechaume; Marlène Huyvaert; Jane Skinner; Marie Pigeyre; Robert Caiazzo; Violeta Raverdy; Emmanuel Vaillant; Sarah Field; Beverley Balkau; Michel Marre; Sophie Visvikis-Siest; Jacques Weill; Odile Poulain-Godefroy; Peter Jacobson; Lars Sjostrom; Christopher J Hammond; Panos Deloukas; Pak Chung Sham; Ruth McPherson; Jeannette Lee; E Shyong Tai; Robert Sladek; Lena M S Carlsson; Andrew Walley; Evan E Eichler; Francois Pattou; Timothy D Spector; Philippe Froguel
Journal:  Nat Genet       Date:  2014-03-30       Impact factor: 38.330

8.  Investigating the effects of copy number variants on reading and language performance.

Authors:  Alessandro Gialluisi; Alessia Visconti; Erik G Willcutt; Shelley D Smith; Bruce F Pennington; Mario Falchi; John C DeFries; Richard K Olson; Clyde Francks; Simon E Fisher
Journal:  J Neurodev Disord       Date:  2016-05-15       Impact factor: 4.025
  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.