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GCAT:a tool for Genome-wide Complex Trait Analysis  

2011-10-25 18:46:14|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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       GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits. GCTA was developed by Jian Yang, Hong Lee, Mike Goddard and Peter Visscher and is maintained in Peter Visscher's lab at the Queensland Institute of Medical Research . GCTA currently supports the following functionalities:

  • Estimate the genetic relationship from genome-wide SNPs;
  • Estimate the inbreeding coefficient from genome-wide SNPs;
  • Estimate the variance explained by all the autosomal SNPs;
  • Partition the genetic variance onto individual chromosomes;
  • Estimate the genetic variance associated with the X-chromosome;
  • Test the effect of dosage compensation on the X-chromosome;
  • Predict the genome-wide additive genetic effects for individual subjects and for individual SNPs;
  • Estimate the LD structure encompassing a list of target SNPs;
  • Simulate GWAS data based upon the observed genotype data.
  • Convert Illumina raw genotype data into PLINK PED format.
  • Citations

    Methodology:

    Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, Goddard ME, Visscher PM. Common SNPs explain a large proportion of the heritability for human height. Nat Genet. 2010 Jul 42(7): 565-9. [PubMed ID: 20562875]. 

    Lee SH, Wray NR, Goddard ME and Visscher PM. Estimating Missing Heritability for Disease from Genome-wide Association Studies. Am J Hum Genet. 2011 Mar 88(3): 294-305. [PubMed ID: 21376301]

    Yang J, Manolio TA, Pasquale LR, Boerwinkle E, Caporaso N, Cunningham JM, de Andrade M, Feenstra B, Feingold E, Hayes MG, Hill WG, Landi MT, Alonso A, Lettre G, Lin P, Ling H, Lowe W, Mathias RA, Melbye M, Pugh E, Cornelis MC, Weir BS, Goddard ME, Visscher PM: Genome partitioning of genetic variation for complex traits using common SNPs. Nat Genet. 2011 Jun 43(6): 519-525. [PubMed ID: 21552263]

    Software tool:

    Yang J, Lee SH, Goddard ME and Visscher PM. GCTA: a tool for Genome-wide Complex Trait Analysis. Am J Hum Genet. 2011 Jan 88(1): 76-82. [PubMed ID: 21167468]

  • VIA:http://gump.qimr.edu.au/gcta/
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