Evaluation of coverage variation of SNP chips for genome-wide association studies
Mingyao Li,Chun Li,Weihua Guan +2 more
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TLDR
Detailed evaluation of SNP chip coverage is conducted, including a map of local coverage – calculated over small consecutive genomic regions and gene Coverage – calculated for each known gene in the genome to reveal the degree of variation of each SNP chip in covering the genome.Abstract:
Genome-wide association (GWA) studies for complex human diseases are now feasible. Many GWA studies rely on commercial SNP chips, for which a common evaluation criterion is global coverage of the genome. Although providing an overall evaluation of an SNP chip, the global coverage does not tell us how the coverage varies across the genome, an important feature that should be taken into consideration, as coverage variation often results in power variation and potentially biased search in subsequent association analysis. To achieve a fuller understanding of SNP chip coverage, we conducted detailed evaluation of coverage, including (1) a map of local coverage - calculated over small consecutive genomic regions and (2) gene coverage - calculated for each known gene in the genome. These evaluations can reveal the degree of variation of each SNP chip in covering the genome and can facilitate SNP chip comparisons at a finer scale.read more
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Chapter 11: Genome-wide association studies.
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A haplotype map of the human genome
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TL;DR: A public database of common variation in the human genome: more than one million single nucleotide polymorphisms for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted.
Journal ArticleDOI
Complement Factor H Polymorphism in Age-Related Macular Degeneration
Robert J. Klein,Caroline J. Zeiss,Emily Y. Chew,Jen-yue Tsai,Richard S. Sackler,Chad Haynes,A. K. Henning,John Paul SanGiovanni,Shrikant Mane,Susan T. Mayne,Michael B. Bracken,Frederick L. Ferris,Jurg Ott,Colin J. Barnstable,Josephine Hoh +14 more
TL;DR: A genome-wide screen for polymorphisms associated with age-related macular degeneration revealed a polymorphism in linkage disequilibrium with the risk allele representing a tyrosine-histidine change at amino acid 402 in the complement factor H gene.
Journal ArticleDOI
Global variation in copy number in the human genome
Richard Redon,Shumpei Ishikawa,Karen R. Fitch,Lars Feuk,George H. Perry,T. Daniel Andrews,Heike Fiegler,Michael H. Shapero,Andrew R. Carson,Wenwei Chen,Eun Kyung Cho,Stephanie Dallaire,Jennifer L. Freeman,Juan R. González,Mònica Gratacòs,Jing Huang,Dimitrios Kalaitzopoulos,Daisuke Komura,Jeffrey R. MacDonald,Christian R. Marshall,Rui Mei,Lyndal Montgomery,Keunihiro Nishimura,Kohji Okamura,Fan Shen,Martin J. Somerville,Joelle Tchinda,Armand Valsesia,Cara Woodwark,Fengtang Yang,Junjun Zhang,Tatiana Zerjal,Jane Zhang,Lluís Armengol,Donald F. Conrad,Xavier Estivill,Chris Tyler-Smith,Nigel P. Carter,Hiroyuki Aburatani,Charles Lee,Keith W. Jones,Stephen W. Scherer,Matthew E. Hurles +42 more
TL;DR: A first-generation CNV map of the human genome is constructed through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia, underscoring the importance of CNV in genetic diversity and evolution and the utility of this resource for genetic disease studies.
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Finishing the euchromatic sequence of the human genome
Chris P. Ponting,Daniel Barker +1 more
TL;DR: The current human genome sequence (Build 35) as discussed by the authors contains 2.85 billion nucleotides interrupted by only 341 gaps and is accurate to an error rate of approximately 1 event per 100,000 bases.
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A genome-wide association study identifies novel risk loci for type 2 diabetes
Robert Sladek,Ghislain Rocheleau,Johan Rung,Christian Dina,Lishuang Shen,David Serre,Philippe Boutin,Daniel Vincent,Alexandre Belisle,Samy Hadjadj,Beverley Balkau,Barbara Heude,Guillaume Charpentier,Thomas J. Hudson,Thomas J. Hudson,Alexandre Montpetit,Alexey V. Pshezhetsky,Marc Prentki,Barry I. Posner,David J. Balding,David Meyre,Constantin Polychronakos,Philippe Froguel,Philippe Froguel +23 more
TL;DR: Four loci containing variants that confer type 2 diabetes risk are identified and constitute proof of principle for the genome-wide approach to the elucidation of complex genetic traits.
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