全基因组关联分析GWAS

• 基础概念

reference genome, consensus sequence
"global reference genome track hub" (UCSC)
（目前的序列比对算法需要考虑同一个位点有多种核苷酸的情况）

somatic and germline SNV/SNP（略）
allele, allele frequency（略）

haplotype

homozygous, heterozygous

linkage disequilibrium (LD)

Tag SNP

correlation and causation

QTL, eQTL/expression QTL, eQTL analysis
https://www.cnblogs.com/Acceptyly/p/3904108.html

• GWAS流程

Marees, A. T., de Kluiver, H., Stringer, S., Vorspan, F., Curis, E., Marie-Claire, C., & Derks, E. M. (2018). A tutorial on conducting genome-wide association studies: Quality control and statistical analysis. International journal of methods in psychiatric research, 27(2), e1608. https://doi.org/10.1002/mpr.1608https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001694/

• alignment to a reference
• variant calling
• quality control
• imputation
• association analysis
• multiple hypothesis testing
• replication in an independent cohort
• further correlative analysis

• GotCloud分析流程

施工中

• 相关性和因果性

施工中