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Literature DB >> 16418238

TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits.

Bradley M Hemminger¹, Billy Saelim, Patrick F Sullivan.

Abstract

UNLABELLED: Investigators conducting studies of the molecular genetics of complex traits in humans often need rationally to select a set of single nucleotide polymorphisms (SNPs) from the hundreds or thousands available for a candidate gene. Accomplishing this requires integration of genomic data from distributed databases and is both time-consuming and error-prone. We developed the TAMAL (Technology And Money Are Limiting) web site to help identify promising SNPs for further investigation. For a given list of genes, TAMAL identifies SNPs that meet user-specified criteria (e.g. haplotype tagging SNPs or SNP predicted to lead to amino acid changes) from current versions of online resources (i.e. HapMap, Perlegen, Affymetrix, dbSNP and the UCSC genome browser). AVAILABILITY: TAMAL is a platform independent web-based application available free of charge at http://neoref.ils.unc.edu/tamal. SUPPLEMENTARY INFORMATION: http://neoref.ils.unc.edu/tamal/.

Entities: Species

Mesh：

Year: 2006 PMID： 16418238 DOI： 10.1093/bioinformatics/btk025

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

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Cited

30 in total

1. Natural selection at genomic regions associated with obesity and type-2 diabetes: East Asians and sub-Saharan Africans exhibit high levels of differentiation at type-2 diabetes regions.

Authors: Yann C Klimentidis; Marshall Abrams; Jelai Wang; Jose R Fernandez; David B Allison
Journal: Hum Genet Date: 2010-12-28 Impact factor: 4.132

2. Voxelwise gene-wide association study (vGeneWAS): multivariate gene-based association testing in 731 elderly subjects.

Authors: Derrek P Hibar; Jason L Stein; Omid Kohannim; Neda Jahanshad; Andrew J Saykin; Li Shen; Sungeun Kim; Nathan Pankratz; Tatiana Foroud; Matthew J Huentelman; Steven G Potkin; Clifford R Jack; Michael W Weiner; Arthur W Toga; Paul M Thompson
Journal: Neuroimage Date: 2011-04-08 Impact factor: 6.556

3. Analysis of 94 candidate genes and 12 endophenotypes for schizophrenia from the Consortium on the Genetics of Schizophrenia.

Authors: Tiffany A Greenwood; Laura C Lazzeroni; Sarah S Murray; Kristin S Cadenhead; Monica E Calkins; Dorcas J Dobie; Michael F Green; Raquel E Gur; Ruben C Gur; Gary Hardiman; John R Kelsoe; Sherry Leonard; Gregory A Light; Keith H Nuechterlein; Ann Olincy; Allen D Radant; Nicholas J Schork; Larry J Seidman; Larry J Siever; Jeremy M Silverman; William S Stone; Neal R Swerdlow; Debby W Tsuang; Ming T Tsuang; Bruce I Turetsky; Robert Freedman; David L Braff
Journal: Am J Psychiatry Date: 2011-04-15 Impact factor: 18.112

4. Genetic association of recovery from eating disorders: the role of GABA receptor SNPs.

Authors: Cinnamon S Bloss; Wade Berrettini; Andrew W Bergen; Pierre Magistretti; Vikas Duvvuri; Michael Strober; Harry Brandt; Steve Crawford; Scott Crow; Manfred M Fichter; Katherine A Halmi; Craig Johnson; Allan S Kaplan; Pamela Keel; Kelly L Klump; James Mitchell; Janet Treasure; D Blake Woodside; Enrica Marzola; Nicholas J Schork; Walter H Kaye
Journal: Neuropsychopharmacology Date: 2011-07-13 Impact factor: 7.853

5. Variants in the CD36 gene associate with the metabolic syndrome and high-density lipoprotein cholesterol.

Authors: Latisha Love-Gregory; Richard Sherva; Lingwei Sun; Jon Wasson; Timothy Schappe; Alessandro Doria; D C Rao; Steven C Hunt; Samuel Klein; Rosalind J Neuman; M Alan Permutt; Nada A Abumrad
Journal: Hum Mol Genet Date: 2008-02-27 Impact factor: 6.150

6. Geographical structure and differential natural selection among North European populations.

Authors: Brian P McEvoy; Grant W Montgomery; Allan F McRae; Samuli Ripatti; Markus Perola; Tim D Spector; Lynn Cherkas; Kourosh R Ahmadi; Dorret Boomsma; Gonneke Willemsen; Jouke J Hottenga; Nancy L Pedersen; Patrik K E Magnusson; Kirsten Ohm Kyvik; Kaare Christensen; Jaakko Kaprio; Kauko Heikkilä; Aarno Palotie; Elisabeth Widen; Juha Muilu; Ann-Christine Syvänen; Ulrika Liljedahl; Orla Hardiman; Simon Cronin; Leena Peltonen; Nicholas G Martin; Peter M Visscher
Journal: Genome Res Date: 2009-03-05 Impact factor: 9.043

TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits.

1. Natural selection at genomic regions associated with obesity and type-2 diabetes: East Asians and sub-Saharan Africans exhibit high levels of differentiation at type-2 diabetes regions.

2. Voxelwise gene-wide association study (vGeneWAS): multivariate gene-based association testing in 731 elderly subjects.

3. Analysis of 94 candidate genes and 12 endophenotypes for schizophrenia from the Consortium on the Genetics of Schizophrenia.

4. Genetic association of recovery from eating disorders: the role of GABA receptor SNPs.

5. Variants in the CD36 gene associate with the metabolic syndrome and high-density lipoprotein cholesterol.

6. Geographical structure and differential natural selection among North European populations.

7. Global similarity with local differences in linkage disequilibrium between the Dutch and HapMap-CEU populations.

8. Genomewide association for schizophrenia in the CATIE study: results of stage 1.

9. Genome-wide pharmacogenomic analysis of response to treatment with antipsychotics.

10. MAVEN: a tool for visualization and functional analysis of genome-wide association results.