Investigating shared genetic architecture between inflammatory bowel diseases and primary biliary cholangitis - ScienceDirect
炎症性肠病（IBD）是一组慢性免疫介导的胃肠道特发性炎症，有两种形式，包括克罗恩病（CD）和溃疡性结肠炎（UC）。IBD的患病率在全球范围内呈上升趋势，并且与高昂的医疗费用有关。原发性胆汁性胆管炎 （PBC） 是一种罕见的免疫介导的慢性进行性炎症性肝病，其特征是循环抗线粒体抗体 （AMA） 升高，可引起肝脏慢性和持续性胆汁淤积，如果不及时治疗，可能导致胆管炎和肝功能衰竭。近年来，越来越多的证据支持PBC和IBD之间存在相互共病。已经报道了几例 PBC 相关 IBD 同时发生的病例。
孟德尔随机化分析：
We selected six MR methods including Generalized Summary-data-based Mendelian Randomization (GSMR),54 weighted median,55 MR-Egger,56 weighted mode,57 inverse variance weighting (IVW)58 and Causal Analysis Using Summary Effect estimates (CAUSE)59 to test the causality between PBC and IBD (including UC and CD), from the R packages “TwoSample MR”60 and “GSMR”54 (P≤ 8.3 × 10−3).
数据代码获取：
Data source
GWAS summary statistics for PBC are available by application from:
GWAS Catalog.
GWAS summary statistics for IBD are available by application from:
GWAS Catalog.
GTEx-seq:
https://alkesgroup.broadinstitute.org/LDSCORE/LDSC_SEG_ldscores.
scRNA-seq data:
Whole blood: GEO Accession viewer.
Lung and Spleen: https://doi.org/10.1186/s13059-019-1906-x;
Small Intestinal Epithelium:
Small intestinal epithelium - Single Cell Portal.
Code availability
LDSC: GitHub - bulik/ldsc: LD Score Regression (LDSC).
GNOVA: GitHub - xtonyjiang/GNOVA: A principled framework to estimate annotation-stratified genetic covariance using GWAS summary statistics.
PLINK: PLINK 1.9.
HESS: HESS
MTAG: GitHub - JonJala/mtag: Python command line tool for Multi-Trait Analysis of GWAS (MTAG).
CPASSOC: http://hal.case.edu/∼xxz10/zhuweb/
GSMR: http://cnsgenomics.com/software/gsmr/
TwoSampleMR: Two Sample MR Functions and Interface to MR Base Database • TwoSampleMR
LDSC-SEG: Cell type specific analyses · bulik/ldsc Wiki · GitHub.
MAGMA Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics • MAGMA.Celltyping.
SMR: https://yanglab.westlake.edu.cn/software/smr/#Overview.
