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Truong VQ, Woerner JA, Cherlin TA, Bradford Y, Lucas AM, Okeh CC, Shivakumar MK, Hui DH, Kumar R, Pividori M, Jones SC, Bossa AC, Turner SD, Ritchie MD, Verma SS. Quality Control Procedures for Genome-Wide Association Studies. Curr Protoc 2022; 2:e603. [PMID: 36441943 DOI: 10.1002/cpz1.603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Genome-wide association studies (GWAS) are being conducted at an unprecedented rate in population-based cohorts and have increased our understanding of the pathophysiology of many complex diseases. Regardless of the context, the practical utility of this information ultimately depends upon the quality of the data used for statistical analyses. Quality control (QC) procedures for GWAS are constantly evolving. Here, we enumerate some of the challenges in QC of genotyped GWAS data and describe the approaches involving genotype imputation of a sample dataset along with post-imputation quality assurance, thereby minimizing potential bias and error in GWAS results. We discuss common issues associated with QC of the GWAS data (genotyped and imputed), including data file formats, software packages for data manipulation and analysis, sex chromosome anomalies, sample identity, sample relatedness, population substructure, batch effects, and marker quality. We provide detailed guidelines along with a sample dataset to suggest current best practices and discuss areas of ongoing and future research. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Van Q Truong
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jakob A Woerner
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Tess A Cherlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Yuki Bradford
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Anastasia M Lucas
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Chelsea C Okeh
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Manu K Shivakumar
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Daniel H Hui
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Rachit Kumar
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Milton Pividori
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - S Chris Jones
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Abigail C Bossa
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Boutaoui N, Puranik S, Zhang R, Wang T, Hui DH, Brehm J, Forno E, Chen W, Celedón JC. Epigenome-wide effects of vitamin D on asthma bronchial epithelial cells. Epigenetics 2019; 14:844-849. [PMID: 31122150 DOI: 10.1080/15592294.2019.1622993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Vitamin D is a nutrient and a hormone with multiple effects on immune regulation and respiratory viral infections, which can worsen asthma and lead to severe asthma exacerbations. We set up a complete experimental and analytical pipeline for ATAC-Seq and RNA-Seq to study genome-wide epigenetic changes in human bronchial epithelial cells of asthmatic subjects, following treatment of these cells with calcitriol (vitamin D3) and Poly (I:C)(a viral analogue). This approach led to the identification of biologically plausible candidate genes for viral infections and asthma, such as DUSP10 and SLC44A1.
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Affiliation(s)
- Nadia Boutaoui
- a Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh , Pittsburgh , PA , USA
| | - Sandeep Puranik
- a Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh , Pittsburgh , PA , USA
| | - Rong Zhang
- a Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh , Pittsburgh , PA , USA.,b Department of Statistics, University of Pittsburgh , Pittsburgh , PA , USA
| | - Ting Wang
- c Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Daniel H Hui
- d Brigham and Women's Hospital, Harvard Medical School, Broad Institute , Boston , MA , USA
| | - John Brehm
- e Division of Pulmonary and Critical Care Medicine, University of Pittsburgh Medical Center- St. Margret's Hospital, University of Pittsburgh , Pittsburgh , PA , USA
| | - Erick Forno
- a Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh , Pittsburgh , PA , USA
| | - Wei Chen
- a Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh , Pittsburgh , PA , USA
| | - Juan C Celedón
- a Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh , Pittsburgh , PA , USA
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