Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies

Autor: Jonathan W. Arthur, Scott M. Lippman, Florence S.G. Cheung, Lucia Musumeci, Ashraful Hoque, Juergen K. V. Reichardt
Rok vydání: 2010
Předmět:
Zdroj: Human Mutation. 31:67-73
ISSN: 1098-1004
1059-7794
DOI: 10.1002/humu.21137
Popis: This file contains a complete list of single nucleotide differences (SNDs) identified in the research described in the paper: "Single Nucleotide Differences (SNDs) in the dbSNP Database May Lead to Errors in Genotyping and Haplotyping Studies" Lucia Musumeci[1,6,*], Jonathan W. Arthur[2,3,*], Florence SG Cheung[1], Ashraful Hoque[4], Scott Lippman[4], and Juergen KV Reichardt[1,5] [1] Plunkett Chair of Molecular Biology (Medicine) Bosch Institute The University of Sydney Medical Foundation Building (K25) 92–94 Parramatta Road Camperdown, NSW 2006 Australia [2] Discipline of Medicine, Sydney Medical School The University of Sydney Camperdown, NSW 2006 Australia [3] Sydney Bioinformatics The University of Sydney Camperdown, NSW 2006 Australia [4] The University of Texas M. D. Anderson Cancer Center Houston, TX 77030 USA [5] Corresponding Author: jreichardt@med.usyd.edu.au [*] LM and JWA contributed equally to this work [6] Current Affiliation: Immunology and Infectious Diseases Unit, GIGA-R, Liege University, Liege, Belgium This paper has been accepted for publication in the journal Human Mutation, September 2009. Each row of the data file corresponds to a reported SNP in the dbSNP database subsequently identified in the paper as a SND. The columns contain the following information (in column order): 1) The RefSNP id (rs#) for the SND. 2) The base pair position of the reported polymorphic residue within the full sequence up- and down-stream of the SNP contained in the dbSNP database 3) The reported polymorphic alleles 4) The number of times the SNP and its surrounding sequence aligned to the genome within the criteria of sequence identity and sequence coverage defined in the Materials and Methods section of the paper. 5) Whether this SNP has been identified as a SND or not. (Note: this data file contains only SNDs, so all entries in this column are listed as "SND") 6) The heterozygosity of this SND as reported in the dbSNP chromosome report. The quantity is used to determine "very strong" or "strong" subgroups of SNDs according to the procedure outlined in the Materials and Methods section. 7) The standard error of the heterozygosity of this SND as reported in the dbSNP chromosome report. This quantity is not used in this study. 8) The maximum reported probability of this SND being real as reported in the dbSNP chromosome report. This quantity is not used in this study. 9) The validation codes of this SND as reported in the dbSNP chromosome report. The quantity is used to determine "very strong" or "strong" subgroups of SNDs according to the procedure outlined in the Materials and Methods section. 10) The positions in the genome sequence where the SND aligns. This is a string containing multiple entries separated by a pipe (|). Each entry (position) includes four pieces of information, separated by colons. This information is: * The chromosome number to which the SND aligns * The strand the SND aligns to, where 1 = sense and -1 = antisense * The base pair position to which the SND aligns in the chromosome * The allele found at that position
Databáze: OpenAIRE
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