전장유전체 연관분석 (Genome-wide association study). An examination of many common genetic variants in different individuals to see if any variant is associated with a trait. GWAS typically focus on associations between SNPs and traits like major diseases. (http://en.wikipedia.org/wiki/Genome-wide_association_study)

대표적인 Genotype and phenotype 연관 연구

Genotype data can be

• SNP array
• WGS or Exome sequencing

자매품

• PheWAS (Phenome-wide association study)
• EWAS (Epigenome-wide association study)
• EWAS (Environment-wide association study)
• MWAS (Metagenome-wide association study)
• MWAS (Metabolome-wide association study)

관련 논문 #

GWAS 학습용 자료

• Chapter 11: Genome-Wide Association Studies PLOS Computational biology 2012-12-27: GWAS에 대한 학습용 자료

GWAS 사례들

• Insight into the genetic architecture of back pain and its risk factors from a study of 509,000 individuals bioRxiv 2018-08-03: Back pain과 그 Pleiotropy 효과 연구
• GWAS on prolonged gestation (post-term birth): analysis of successive Finnish birth cohorts 2017-10-10: 임신 기간 연구
• Genome-wide association study of offspring birth weight in 86,577 women highlights maternal genetic effects that are independent of fetal genetics bioRxiv 2017-09-08: 출생 체중 GWAS 분석 했더니, 엄마와 독립적인 듯.
• Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders Nature Genetics 2016-12-05: 23andMe 개인의 정신적 특징 5개에 대한 GWAS 연구
  • Extraversion (versus introversion) reflects talkativeness, assertiveness and a high activity level.
  • Neuroticism (versus emotional stability) reflects negative affect, such as anxiety and depression.
  • Agreeableness (versus antagonism) measures cooperativeness and compassion.
  • Conscientiousness (versus undependability) indicates diligence and self-discipline.
  • Openness to experience (versus being closed to experience) captures intellectual curiosity and creativit
• Pathway-Based Genome-Wide Association Studies for Two Meat Production Traits in Simmental Cattle Nature 2015-12-17: Biological pathway based GWAS
• Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height BMC Genetics 2013-06-13

GWAS 연구방법 보완

• From genome-wide associations to candidate causal variants by statistical fine-mapping Nature Reviews Genetics 2018-05-29
• The personal and clinical utility of polygenic risk scores Nature Reviews Genetics 2018-05-22: polygenic risk score에 대한 리뷰 논문
• Including phenotypic causal networks in genome-wide association studies using mixed effects structural equation models bioRxiv 2018-01-22
• Implicit Causal Models for Genome-wide Association Studies arXiv 2017-10-30: GWAS에 대한 추론 모델
• COMBAT: A Combined Association Test for Genes Using Summary Statistics Genetics 2017-09-06: COMBAT이라는 GWAS 보완 연구방법
• Discovering genetic interactions bridging pathways in genome-wide association studies bioRxiv 2017-08-30

관련 정보 #

관련 프로그램

• GCTA: Genome-wide complex trait analysis
• easyGWASCore: C, C++로 알고리즘을 만들고, Python 인터페이스를 만듬. GWAS 및 관련 메타 분석 가능
• PLINK: C++로 만들어진 대표적인 집단유전학 분석 프로그램 (American Journal of Human Genetics, 2007)
• KING: SNP array 데이터로부터 혈연관계 추정 (Kinship analysis)
• adegenet: SNP array 데이터로 GWAS 분석하기 R 패키지
• StAMPP: Mixed polyploid 데이터에 대한 집단유전학 분석 R 패키지
• GAPIT: GWAS and selection R 패키지
• EMMA: R 패키지
• TASSEL: software for association mapping of complex traits in diverse samples Java GUI 프로그램
• GenABEL: R 패키지 (Bioinformatics, 2007)

관련자료

• GWAS(전유전체관련성분석)의 가치를 둘러싼 우려 2017-06-16: 가치가 없으려나
• Genome of the Netherlands: 네덜란드인 770명 GWAS
• 전 게놈 관련 분석으로 배우는 유전 통계학 R users conference in Korea 2014 2014-01-02
• GWAS로 배우는 유전통계학 2012-03-30: 6편까지 있음

Incoming Links #

[Medical Scholarly Articles] About (MedicalScholarlyArticle 0) #

• A GWAS assessment of the contribution of genomic imprinting to the variation of body mass index in mice
• Genome-wide association study identifies 74 loci associated with educational attainment
• Robust relationship inference in genome-wide association studies
• Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

[Codes] About (Code 1) #

• GAPIT
• GCTA
• PLINK
• adegenet

Related Datasets (Dataset 2) #

• ENCODE
• dbGaP

Related Books (Book 3) #

• Epigenetics in Human Disease

[Software Applications] About (SoftwareApplication 4) #

• KING

Related Products (Product 5) #

• Genome-Wide Human SNP Array 6.0

Related Articles (Article 6) #

• DNA profiling
• Epigenome-wide association studies
• Genetic risk index
• Hair loss
• Human genome
• Human leukocyte antigen
• Identity by descent
• Intelligence quotient
• Low back pain
• Metagenomics
• Opportunities and challenges of whole-genome and -exome sequencing
• Personalized medicine
• PheWAS
• QTL
• SNP array

Related Education Events (EducationEvent 7) #

• Genomics and Precision Medicine

[Datasets] About (Dataset 8) #

• GWAS Catalog

Related Medical Conditions (MedicalCondition 9) #

• Ageing
• Attention deficit hyperactivity disorder
• Depression
• Diabetes mellitus
• Headache
• Hypertension
• Parkinson's disease
• Prostate cancer
• Thyroid cancer

Related Medical Scholarly Articles (MedicalScholarlyArticle 10) #

• Complex disease and phenotype mapping in the domestic dog
• Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer
• Genome-wide association study identifies 74 loci associated with educational attainment
• Methods of integrating data to uncover genotype–phenotype interactions
• Robust relationship inference in genome-wide association studies

[Articles] About (Article 11) #

• 잃어버린 유전 가능성(Missing heritability)에 대해

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