Literature DB >> 17401150

Online resources for SNP analysis: a review and route map.

Christopher Phillips1.   

Abstract

The major online single nucleotide polymorphism (SNP) databases freely available as research tools for genetic analysis are explained, reviewed, and compared. An outline is given of the search strategies that can be used with the most extensive current SNP databases: National Centre for Biotechnology Information (NCBI) dbSNP and HapMap to help the user secure the most appropriate data for the research needs of clinical genetics and population genetics research. A range of online tools that can be useful in designing SNP genotyping assays are also detailed.

Mesh：

Year:  2007        PMID： 17401150     DOI： 10.1385/mb:35:1:65

Source DB:  PubMed          Journal:  Mol Biotechnol        ISSN： 1073-6085            Impact factor:   2.695


  32 in total

1.  Estimate of the mutation rate per nucleotide in humans.

Authors:  M W Nachman; S L Crowell
Journal:  Genetics       Date:  2000-09       Impact factor: 4.562

2.  Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.

Authors:  M S Phillips; R Lawrence; R Sachidanandam; A P Morris; D J Balding; M A Donaldson; J F Studebaker; W M Ankener; S V Alfisi; F-S Kuo; A L Camisa; V Pazorov; K E Scott; B J Carey; J Faith; G Katari; H A Bhatti; J M Cyr; V Derohannessian; C Elosua; A M Forman; N M Grecco; C R Hock; J M Kuebler; J A Lathrop; M A Mockler; E P Nachtman; S L Restine; S A Varde; M J Hozza; C A Gelfand; J Broxholme; G R Abecasis; M T Boyce-Jacino; L R Cardon
Journal:  Nat Genet       Date:  2003-02-18       Impact factor: 38.330

Review 3.  Using online databases for developing SNP markers of forensic interest.

Authors:  Christopher Phillips
Journal:  Methods Mol Biol       Date:  2005

4.  A haplotype map of the human genome.

Authors: 
Journal:  Nature       Date:  2005-10-27       Impact factor: 49.962

Review 5.  SNPs in forensic genetics: a review on SNP typing methodologies.

Authors:  Beatriz Sobrino; María Brión; Angel Carracedo
Journal:  Forensic Sci Int       Date:  2005-01-11       Impact factor: 2.395

6.  High-density single-nucleotide polymorphism maps of the human genome.

Authors:  Raymond D Miller; Michael S Phillips; Inho Jo; Miriam A Donaldson; Joel F Studebaker; Nicholas Addleman; Steven V Alfisi; Wendy M Ankener; Hamid A Bhatti; Chad E Callahan; Benjamin J Carey; Cheryl L Conley; Justin M Cyr; Vram Derohannessian; Rachel A Donaldson; Carolina Elosua; Stacey E Ford; Angela M Forman; Craig A Gelfand; Nicole M Grecco; Susan M Gutendorf; Cricket R Hock; Mark J Hozza; Soyoung Hur; Sun Mi In; Diana L Jackson; Sangmee Ahn Jo; Sung-Chul Jung; Sook Kim; Kuchan Kimm; Ellen F Kloss; Daniel C Koboldt; Jennifer M Kuebler; Feng-Shen Kuo; Jessica A Lathrop; Jong-Keuk Lee; Kathy L Leis; Stephanie A Livingston; Elizabeth G Lovins; Maria L Lundy; Sima Maggan; Matthew Minton; Michael A Mockler; David W Morris; Eric P Nachtman; Bermseok Oh; Chan Park; Chang-Wook Park; Nicholas Pavelka; Adrienne B Perkins; Stephanie L Restine; Ravi Sachidanandam; Andrew J Reinhart; Kathryn E Scott; Gira J Shah; Jatana M Tate; Shobha A Varde; Amy Walters; J Rebecca White; Yeon-Kyeong Yoo; Jong-Eun Lee; Michael T Boyce-Jacino; Pui-Yan Kwok
Journal:  Genomics       Date:  2005-08       Impact factor: 5.736

7.  CENSOR--a program for identification and elimination of repetitive elements from DNA sequences.

Authors:  J Jurka; P Klonowski; V Dagman; P Pelton
Journal:  Comput Chem       Date:  1996-03

8.  Human genome-wide screen of haplotype-like blocks of reduced diversity.

Authors:  Javier Costas; Antonio Salas; Christopher Phillips; Angel Carracedo
Journal:  Gene       Date:  2005-04-11       Impact factor: 3.688

9.  Human non-synonymous SNPs: server and survey.

Authors:  Vasily Ramensky; Peer Bork; Shamil Sunyaev
Journal:  Nucleic Acids Res       Date:  2002-09-01       Impact factor: 16.971

10.  Perspectives on human genetic variation from the HapMap Project.

Authors:  Gil McVean; Chris C A Spencer; Raphaelle Chaix
Journal:  PLoS Genet       Date:  2005-10       Impact factor: 5.917
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  11 in total

Review 1.  Annotating individual human genomes.

Authors:  Ali Torkamani; Ashley A Scott-Van Zeeland; Eric J Topol; Nicholas J Schork
Journal:  Genomics       Date:  2011-08-02       Impact factor: 5.736

2.  Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses.

Authors:  Shaunna L Clark; Joseph L McClay; Daniel E Adkins; Karolina A Aberg; Gaurav Kumar; Sri Nerella; Linying Xie; Ann L Collins; James J Crowley; Corey R Quakenbush; Christopher E Hillard; Guimin Gao; Andrey A Shabalin; Roseann E Peterson; William E Copeland; Judy L Silberg; Hermine Maes; Patrick F Sullivan; Elizabeth J Costello; Edwin J van den Oord
Journal:  Nicotine Tob Res       Date:  2015-08-17       Impact factor: 4.244

3.  Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence.

Authors:  Shaunna L Clark; Joseph L McClay; Daniel E Adkins; Gaurav Kumar; Karolina A Aberg; Srilaxmi Nerella; Linying Xie; Ann L Collins; James J Crowley; Corey R Quackenbush; Christopher E Hilliard; Andrey A Shabalin; Scott I Vrieze; Roseann E Peterson; William E Copeland; Judy L Silberg; Matt McGue; Hermine Maes; William G Iacono; Patrick F Sullivan; Elizabeth J Costello; Edwin J van den Oord
Journal:  Alcohol Clin Exp Res       Date:  2017-03-24       Impact factor: 3.455

4.  Fine-mapping of the leaf rust Lr34 locus in Triticum aestivum (L.) and characterization of large germplasm collections support the ABC transporter as essential for gene function.

Authors:  Abdulsalam Dakouri; Brent D McCallum; Andrzej Z Walichnowski; Sylvie Cloutier
Journal:  Theor Appl Genet       Date:  2010-03-30       Impact factor: 5.699

5.  HapMap-based study on the association between MPO and GSTP1 gene polymorphisms and lung cancer susceptibility in Chinese Han population.

Authors:  Jun-dong Gu; Feng Hua; Chao-rong Mei; De-jie Zheng; Guo-fan Wang; Qing-hua Zhou
Journal:  Acta Pharmacol Sin       Date:  2014-05       Impact factor: 6.150

6.  Evidence for the role of EPHX2 gene variants in anorexia nervosa.

Authors:  A A Scott-Van Zeeland; C S Bloss; R Tewhey; V Bansal; A Torkamani; O Libiger; V Duvvuri; N Wineinger; L Galvez; B F Darst; E N Smith; A Carson; P Pham; T Phillips; N Villarasa; R Tisch; G Zhang; S Levy; S Murray; W Chen; S Srinivasan; G Berenson; H Brandt; S Crawford; S Crow; M M Fichter; K A Halmi; C Johnson; A S Kaplan; M La Via; J E Mitchell; M Strober; A Rotondo; J Treasure; D B Woodside; C M Bulik; P Keel; K L Klump; L Lilenfeld; K Plotnicov; E J Topol; P B Shih; P Magistretti; A W Bergen; W Berrettini; W Kaye; N J Schork
Journal:  Mol Psychiatry       Date:  2013-09-03       Impact factor: 15.992

7.  Genetic variants of genes in the Notch signaling pathway predict overall survival of non-small cell lung cancer patients in the PLCO study.

Authors:  Yinghui Xu; Yanru Wang; Hongliang Liu; Xiaozheng Kang; Wei Li; Qingyi Wei
Journal:  Oncotarget       Date:  2016-09-20

8.  [Interference of homologous sequences on the SNP study of CYP2A13 gene].

Authors:  Feng Hua; Haisu Wan; Chaorong Mei; Dejie Zheng; Linlin Sun; Jun Chen; Hongyu Liu; Qinghua Zhou
Journal:  Zhongguo Fei Ai Za Zhi       Date:  2010-02

9.  Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes.

Authors:  Jorge Amigo; Christopher Phillips; Antonio Salas; Angel Carracedo
Journal:  BMC Bioinformatics       Date:  2009-03-19       Impact factor: 3.169

10.  Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma.

Authors:  Christine F Skibola; Paige M Bracci; Eran Halperin; Alexandra Nieters; Alan Hubbard; Randi A Paynter; Danica R Skibola; Luz Agana; Nikolaus Becker; Patrick Tressler; Matthew S Forrest; Sriram Sankararaman; Lucia Conde; Elizabeth A Holly; Martyn T Smith
Journal:  PLoS One       Date:  2008-06-30       Impact factor: 3.240
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