Data mining of SNP databases for the selection of intragenic SNPs
AssigneeJanssen Pharmaceutica NV
InventorsJan Aerts, Yves Wetzels, Nadine Cohen, Jeroen Aerssens
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Abstract
The present invention relates to data mining of SNP databases for the selection of intragenic SNPs. The present invention provides methodologies for annotating SNPs onto candidate genes based on appropriate sequence comparison software or algorithms such as a BLAST search of SNP databases. Additionally, the present invention provides methodologies useful in the selection of intragenic SNPs for genotyping in genetic studies.
Claims164
A method for annotating SNPs onto candidate nucleic acid sequences comprising the steps of:
- (a) generating subsequences of nucleic acid from said candidate nucleic acid sequences;
- (b) comparing each of said subsequences against one or more SNP databases to obtain relevant SNP output files;
- (c) analyzing said relevant SNP output files for relevant valid SNPs;
- and
- (d) annotating said relevant valid SNPs.
A system for annotating SNPs onto candidate nucleic acid sequences comprising the steps of:
- (a) generating subsequences of nucleic acid from said candidate nucleic acid sequences;
- (b) comparing each of said subsequences against one or more SNP databases to obtain relevant SNP output files;
- (c) analyzing said relevant SNP output files for relevant valid SNPs;
- and
- (d) annotating said relevant valid SNPs.
A computer-implemented method for annotating SNPs onto candidate nucleic acid sequences comprising the steps of:
- (a) generating subsequences of nucleic acid from said candidate nucleic acid sequences;
- (b) comparing each of said subsequences against one or more SNP databases to obtain relevant SNP output files;
- (c) analyzing said relevant SNP output files for relevant valid SNPs;
- and
- (d) annotating said relevant valid SNPs.
A computer-implemented system for annotating SNPs onto candidate nucleic acid sequences comprising the steps of:
- (a) importing or having stored nucleic acid sequence data information from one or more databases;
- (b) generating relevant SNP output files by comparing nucleic acid subsequences obtained from said candidate nucleic acid sequences against said one or more databases using BLAST;
- (c) storing said relevant SNP output files;
- (d) analyzing said relevant SNP output files based on stored criteria for relevant valid SNPs;
- (e) annotating said relevant valid SNPs.
A method for determining an association between a SNP and a pathological condition comprising the steps of:
- (a) importing or having stored nucleic acid sequence data information from one or more databases;
- (b) generating relevant SNP output files by comparing nucleic acid subsequences obtained from candidate nucleic acid sequences against said one or more databases using BLAST;
- (c) storing said relevant SNP output files;
- (d) analyzing said relevant SNP output files based on stored criteria for relevant valid SNPs;
- and
- (e) annotating said relevant valid SNPs.
A method for determining an association between a SNP and a pathological condition comprising the steps of:
- (a) generating subsequences of nucleic acid from candidate nucleic acid sequences;
- (b) comparing each of said subsequences against one or more SNP databases to obtain relevant SNP output files;
- (c) analyzing said relevant SNP output files for relevant valid SNPs;
- and
- (d) annotating said relevant valid SNPs.
A method for determining an association between a SNP and a drug response comprising the steps of:
- (a) importing or having stored nucleic acid sequence data information from one or more databases;
- (b) generating relevant SNP output files by comparing nucleic acid subsequences obtained from candidate nucleic acid sequences against said one or more databases using BLAST;
- (c) storing said relevant SNP output files;
- (d) analyzing said relevant SNP output files based on stored criteria for relevant valid SNPs;
- (e) annotating said relevant valid SNPs;
- (f) recalculating nucleic acid positions for said relevant valid SNPs in said candidate nucleic acid sequence;
- and
- (g) comparing said SNP with said drug response.
A method for determining an association between a SNP and a drug response comprising the steps of:
- (a) generating subsequences of nucleic acid from candidate nucleic acid sequences;
- (b) comparing each of said subsequences against one or more SNP databases to obtain relevant SNP output files;
- (c) analyzing said relevant SNP output files for relevant valid SNPs;
- (d) annotating said relevant valid SNPs;
- and
- (e) comparing said SNP with said drug response.
Dependencies are inferred from the claim text.