GWAS研究现状及资源下载

研究现状

GWAS研究是非常火的， NHGIR 还专门为它开辟了专栏来介绍，下面这个图片也是来自于NHGIR组织，是GWAS近年来发表文章的状况。

图片1

可以在该文章上面下载这个所有的数据

wget http://www.genome.gov/admin/gwascatalog.txt

截至目前为止。2015年5月8日21:08:34

这个文档有19603行的数据，但是只有2113篇pubmed文献，共涉及到七千多个基因。

有293种杂志都发过GWAS的文章，总共有2113篇文献，发表关联分析突变位点最多的是这篇文献23251661 在PLoS One杂志上面，共 949个rs突变。

杂志排序

cut -f 2,5 gwascatalog.txt |perl -alne '{$hash{_}++}END{print "$$_" foreach sort {$hash{$a} <=> $hash{$b}} keys %hash}' |cut -f 2 |perl -alne '{$hash{$_}++}END{print "$_\t$hash{$_}" foreach sort {$hash{$a} <=> $hash{$b}} keys %hash}'

Hum Genet	41
Am J Hum Genet	62
Mol Psychiatry	64
PLoS One	132
PLoS Genet	145
Hum Mol Genet	168
Nat Genet	397

文章的rs突变点排序

cut -f 2,5 gwascatalog.txt |perl -alne '{$hash{_}++}END{print "$$_ $hash{$_}" foreach sort {$hash{$a} <=> $hash{$b}} keys %hash}'

24324551	PLoS One	241
24097068	Nat Genet	245
24816252	Nat Genet	299
23382691	PLoS Genet	699
23251661	PLoS One	949

数据

我取了表头和第一行数据，然后把它转置了，这样方便查看

Date Added to Catalog	10/22/2014
PUBMEDID	24528284
First Author	Ji Y
Date	08/01/2014
Journal	Br J Clin Pharmacol
Link	http://www.ncbi.nlm.nih.gov/pubmed/24528284
Study	Citalopram and escitalopram plasma drug and metabolite concentrations: genome-wide associations.
Disease/Trait	Response to serotonin reuptake inhibitors in major depressive disorder (plasma drug and metabolite levels)
Initial Sample Description	300 European ancestry Escitalpram treated individuals, 130 European ancestry Citalopram treated individuals
Replication Sample Description	NA
Region	17q25.3
Chr_id	17
Chr_pos	79831041
Reported Gene(s)	CBX4
Mapped_gene	CBX8 - CBX4
Upstream_gene_id	57332
Downstream_gene_id	8535
Snp_gene_ids
Upstream_gene_distance	33.93
Downstream_gene_distance	2.12
Strongest SNP-Risk Allele	rs9747992
SNPs	rs9747992
Merged	0
Snp_id_current	9747992
Context	Intergenic
Intergenic	1
Risk Allele Frequency	0.086
p-Value	2.00E-07
Pvalue_mlog	6.698970004
p-Value (text)	(S-DCT concentration)
OR or beta	NR
95% CI (text)	NR
Platform [SNPs passing QC]	Illumina [7,537,437] (Imputed)
CNV	N

上面这个文件是由tab键分割的，每一列的意义如下！

Note: The SNP data in the catalog has been mapped to dbSNP Build 142 and Genome Assembly,
GRCh38/hg37.p13.
DATE ADDED TO CATALOG: Date added to catalog
PUBMEDID: PubMed identification number
FIRST AUTHOR: Last name of first author
DATE: Publication date (online (epub) date if available)
JOURNAL: Abbreviated journal name
LINK: PubMed URL
STUDY: Title of paper (linked to PubMed abstract)
DISEASE/TRAIT: Disease or trait examined in study
INITIAL SAMPLE SIZE: Sample size for Stage 1 of GWAS
REPLICATION SAMPLE SIZE: Sample size for subsequent replication(s)
REGION: Cytogenetic region associated with rs number (NCBI)
CHR_ID: Chromosome number associated with rs number (NCBI)
CHR_POS: Chromosomal position associated with rs number (dbSNP Build 132,
NCBI)
REPORTED GENE (S): Gene(s) reported by author
MAPPED GENE(S): Gene(s) mapped to the strongest SNP (NCBI). If the SNP is
located within a gene, that gene is listed. If the SNP is intergenic, the upstream and
downstream genes are listed, separated by a hyphen. UPSTREAM_GENE_ID:
Entrez Gene ID for nearest upstream gene to rs number, if not within gene (NCBI)
DOWNSTREAM_GENE_ID: Entrez Gene ID for nearest downstream gene to rs
number, if not within gene (NCBI)
SNP_GENE_IDS: Entrez Gene ID, if rs number within gene; multiple genes
denotes overlapping transcripts (NCBI)
UPSTREAM_GENE_DISTANCE: distance in kb for nearest upstream gene to rs
number, if not within gene (NCBI)
DOWNSTREAM_GENE_DISTANCE: distance in kb for nearest downstream
gene to rs number, if not within gene (NCBI)
STRONGEST SNP-RISK ALLELE: SNP(s) most strongly associated with trait +
risk allele (? for unknown risk allele). May also refer to a haplotype.
SNPS: Strongest SNP; if a haplotype is reported above, may include more than one
rs number (multiple SNPs comprising the haplotype)
MERGED: denotes whether the SNP has been merged into a subsequent rs record
(0 = no; 1 = yes; NCBI)
SNP_ID_CURRENT: current rs number (will differ from strongest SNP when
merged = 1)
CONTEXT: SNP functional class (NCBI)
INTERGENIC: denotes whether SNP is in intergenic region (0 = no; 1 = yes;
NCBI)
RISK ALLELE FREQUENCY: Reported risk allele frequency associated with
strongest SNP
P-VALUE: Reported p-value for strongest SNP risk allele (linked to dbGaP
Association Browser)
PVALUE_MLOG: -log(p-value)
P-VALUE (TEXT): Information describing context of p-value (e.g. females,
smokers).
Note that p-values are rounded to 1 significant digit (for example, a published pvalue of 4.8 x 10-7 is rounded to 5 x 10-7).
OR or BETA: Reported odds ratio or beta-coefficient associated with strongest
SNP risk allele
95% CI (TEXT): Reported 95% confidence interval associated with strongest SNP
risk allele
PLATFORM (SNPS PASSING QC): Genotyping platform manufacturer used in
Stage 1; also includes notation of pooled DNA study design or imputation of
SNPs, where applicable
CNV: Study of copy number variation (yes/no)
Updated: January 13, 2015