从字面意义上来说,G是基因组,P是表型组。G的最小单位可以被视为一个SNP,而P的最小单位则是一个表型,相当于≥1个SNP的集合所代表的性状,可以是疾病,也可以是疾病的某一个病理指标。
今天分享的这篇文章,讲的是孟德尔随机化全表型的聚类研究,刚好还有代码,我们可以学习一下这种新的方法到底是如何实现的——
提出了一种采用孟德尔随机化全关联聚类(PWC-MR)的方法,并用这种方法对肥胖相关的多种表型和受教育程度的关系进行了探索
文章提供了代码:
https://github.com/ LizaDarrous/PheWAS-cluster(https://doi.org/10.5281/zenodo. 10466847)
用到的数据源在这里:
Data | Web resource |
---|---|
Body mass index (BMI) GWAS | [https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/21001_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 21001_irnt.gwas.imputed_v3.both_sexes.tsv.bgz](https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/21001_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 21001_irnt.gwas.imputed_v3.both_sexes.tsv.bgz) |
Educational attainment (EDU) GWAS | [https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/21001_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 21001_irnt.gwas.imputed_v3.both_sexes.tsv.bgz](https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/21001_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 21001_irnt.gwas.imputed_v3.both_sexes.tsv.bgz) |
Systolic bloof pressure (SBP) GWAS | [https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz](https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz) |
childBMI GWAS | [https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz](https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz) |
BMI GWAS 1 | [https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz](https://broad-ukb-sumstats-us-east-1.s3.amazonaws.com/round2/additive-tsvs/4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz -O 4080_irnt.gwas.imputed_v3.both_sexes.tsv.bgz) |
BMI GWAS 2 | https://doi.org/10.5523/bris.pnoat8cxo0u52p6ynfaekeigi |
Adipose cis-eQTL MuTHER | https://doi.org/10.5523/bris.pnoat8cxo0u52p6ynfaekeigi |
Adipose cis-eQTL GTEx v8 | https://www.gtexportal.org/home/datasets |
Brain cis-eQTL | https://yanglab.westlake.edu.cn/software/smr/#DataResource |
感兴趣的小伙伴可以先学习起来~ ps:之前发的青光眼小编还在通关ing,等把代码搞通了就放上来