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Using previously genotyped controls in genome-wide association studies (GWAS): application to the Stroke Genetics Network (SiGN)

Braxton D. Mitchell, Myriam Fornage, Patrick F. McArdle, Yu-Ching Cheng, Sara L. Pulit, Quenna Wong, Tushar Dave, Stephen R. Williams, Roderick Corriveau, Katrina Gwinn, Kimberly Doheny, Cathy C. Laurie (+2 others)
2014 Frontiers in Genetics  
Genome-wide association studies (GWAS) are widely applied to identify susceptibility loci for a variety of diseases using genotyping arrays that interrogate known polymorphisms throughout the genome.  ...  This strategy, however, requires that careful attention be paid to the choice of "public controls" and to the comparability of genetic data between cases and the public controls to ensure that any allele  ...  This project received partial support from The Mid-Atlantic Nutrition Obesity Research Center (P30 DK072488) from the NIH National Institute of Diabetes and Digestive and Kidney Diseases.  ... 
doi:10.3389/fgene.2014.00095 pmid:24808905 pmcid:PMC4010766 fatcat:rhcjh3hwgze5tf3kxergax6awu

Imputation across genotyping arrays for genome-wide association studies: assessment of bias and a correction strategy

Eric O. Johnson, Dana B. Hancock, Joshua L. Levy, Nathan C. Gaddis, Nancy L. Saccone, Laura J. Bierut, Grier P. Page
2013 Human Genetics  
Biases remained problematic for very similar arrays (550v1 vs. 550v3) and were substantial for dissimilar arrays (Illumina 1M vs. Affymetrix 6.0).  ...  Imputation based on the union of genotyped SNPs across the Illumina 1M and 550v3 arrays showed spurious associations for 0.2 % of SNPs: *2,000 false positives per million SNPs imputed.  ...  Funding support for genotyping, which was performed at the Johns Hopkins University Center for Inherited  ... 
doi:10.1007/s00439-013-1266-7 pmid:23334152 pmcid:PMC3628082 fatcat:6zwhwheshzbrrnpemjngb2ombi

GTQC: Automated Genotyping Array Quality Control and Report

Shilin Zhao, Limin Jiang, Hui Yu, Yan Guo
2022 Journal of Genomics  
Based on previously established protocols and strategies, we developed an R package GTQC (GenoTyping Quality Control) to automate a majority of the quality control steps for general array genotyping data  ...  Quality control of genotyping array is generally a complicated process, as it requires intensive manual labor in implementing the established protocols and curating a comprehensive quality report.  ...  In 2017, Zhao et al. summarized quality control strategies for Illumina Human Exome Bead Chip and extended them to all types of Illumina genotyping arrays [16] .  ... 
doi:10.7150/jgen.69860 pmid:35300047 pmcid:PMC8922302 fatcat:n2cumentkvgzzjmwc3fqlcsqn4

Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

Luca Bianco, Alessandro Cestaro, Daniel James Sargent, Elisa Banchi, Sophia Derdak, Mario Di Guardo, Silvio Salvi, Johannes Jansen, Roberto Viola, Ivo Gut, Francois Laurens, David Chagné (+4 others)
2014 PLoS ONE  
It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application  ...  A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations.  ...  Base calling and quality control were performed using the Illumina RTA sequence analysis pipeline.  ... 
doi:10.1371/journal.pone.0110377 pmid:25303088 pmcid:PMC4193858 fatcat:ip7bbykelzhlhihgrpu6vogoje

A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding

Haodong Chen, Weibo Xie, Hang He, Huihui Yu, Wei Chen, Jing Li, Renbo Yu, Yue Yao, Wenhui Zhang, Yuqing He, Xiaoyan Tang, Fasong Zhou (+2 others)
2014 Molecular Plant  
SNP discovery and development of a high-density genotyping array for sunflower. PLoS One. 7, e29814.  ...  With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays.  ...  Illumina manufacturing processes successfully synthesized 51 478 markers, which were analyzed with respect to genotype clustering using GenomeStudio Genotyping software (v2011.1, Illumina, Inc.).  ... 
doi:10.1093/mp/sst135 pmid:24121292 fatcat:v532l6lbyjanhojyshlxubg7mi

Highly Parallel SNP Genotyping

2003 Cold Spring Harbor Symposia on Quantitative Biology  
Both genomic DNA and total RNA (converted to cDNA) from an ovarian tissue sample were genotyped for 32 SNPs in gene coding regions.  ...  The Sentrix ™ array matrix. Figure 7. Allele-specific expression monitoring.  ...  Besides being important for quality control of complex lab processes, the ability to evaluate objectively the quality of large data sets also enables process improvement to be carried out in a systematic  ... 
doi:10.1101/sqb.2003.68.69 pmid:15338605 fatcat:fza3sgintjbzbbqhp2rqgxh7xy

Exome Sequencing of a Multigenerational Human Pedigree

Dale Hedges, Dan Burges, Eric Powell, Cherylyn Almonte, Jia Huang, Stuart Young, Benjamin Boese, Mike Schmidt, Margaret A. Pericak-Vance, Eden Martin, Xinmin Zhang, Timothy T. Harkins (+2 others)
2009 PLoS ONE  
Applying the conservative genotype calling approach HCDiff, the average rate of detection of a variant allele based on Illumina 1 M BeadChips genotypes was 95.2% at $10x sequence.  ...  Further, we propose an advantageous genotype calling strategy for low covered targets that empirically determines cut-off thresholds at a given coverage depth based on existing genotype data.  ...  Array-Based Genotyping We processed all individuals on the Illumina 1 M Duo BeadChip, following the manufacturer's recommendations (Illumina Inc.).  ... 
doi:10.1371/journal.pone.0008232 pmid:20011588 pmcid:PMC2788131 fatcat:6nmoybxcmzhydcem2bujn25hci

Quality control and quality assurance in genotypic data for genome-wide association studies

Cathy C. Laurie, Kimberly F. Doheny, Daniel B. Mirel, Elizabeth W. Pugh, Laura J. Bierut, Tushar Bhangale, Frederick Boehm, Neil E. Caporaso, Marilyn C. Cornelis, Howard J. Edenberg, Stacy B. Gabriel, Emily L. Harris (+13 others)
2010 Genetic Epidemiology  
The need for careful attention to data quality has been appreciated for some time in this field, and a number of strategies for quality control and quality assurance (QC/QA) have been developed.  ...  Here we extend these methods and describe a system of QC/QA for genotypic data in genome-wide association studies (GWAS).  ...  Additional funding sources for projects are: (1) Genotyping was performed at the Broad Institute of MIT and Harvard, with funding support from the NIH GEI (U01HG04424), and Johns Hopkins University  ... 
doi:10.1002/gepi.20516 pmid:20718045 pmcid:PMC3061487 fatcat:tdeqtcmwqbej3dg6z5ng64suke

Detecting large copy number variants using exome genotyping arrays in a large Swedish schizophrenia sample

J P Szatkiewicz, B M Neale, C O'Dushlaine, M Fromer, J I Goldstein, J L Moran, K Chambert, A Kähler, P K E Magnusson, C M Hultman, P Sklar, S Purcell (+2 others)
2013 Molecular Psychiatry  
We genotyped 9100 Swedish subjects (3962 cases with SCZ and 5138 controls) using both standard genome-wide association study (GWAS) and exome arrays.  ...  Genotyping large numbers of samples is essential for progress.  ...  Funding for the project was provided by the Wellcome Trust. We thank two anonymous reviewers for their helpful comments. All authors reviewed and approved the final version of the manuscript.  ... 
doi:10.1038/mp.2013.98 pmid:23938935 pmcid:PMC3966073 fatcat:6dln3xgfxbci5mmlbnaxzn2q4y

Common statistical issues in genome-wide association studies: a review on power, data quality control, genotype calling and population structure

Yik Y Teo
2008 Current Opinion in Lipidology  
Sim for their helpful comments in improving the article. References and recommended reading  ...  Acknowledgements The author acknowledges support from the Grand Challenges in Global Health and the Wellcome Trust. The author also thanks K.S. Small and X.L.  ...  Quality control Quality control refers to the exploratory procedures used to evaluate the genotyping performance of the samples and the genotyping array.  ... 
doi:10.1097/mol.0b013e3282f5dd77 pmid:18388693 fatcat:q6igmwf3djbnpdmnbptae3bmly

Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples

Jingwen Wang, Tiina Skoog, Elisabet Einarsdottir, Tea Kaartokallio, Hannele Laivuori, Anna Grauers, Paul Gerdhem, Marjo Hytönen, Hannes Lohi, Juha Kere, Hong Jiao
2016 Scientific Reports  
For the WGS study, 56% of the low-frequency variants in Illumina array have identical MAFs and 26% have one allele difference between sequencing and individual genotyping data.  ...  The pooling strategy can thus be a rapid and costeffective approach for the initial screening in large-scale association studies.  ...  of Helsinki, for assistance in genotyping.  ... 
doi:10.1038/srep33256 pmid:27633116 pmcid:PMC5025741 fatcat:rpppubn6c5hm3gymkqwogssytm

Whole-exome SNP array identifies 15 new susceptibility loci for psoriasis

Xianbo Zuo, Liangdan Sun, Xianyong Yin, Jinping Gao, Yujun Sheng, Jinhua Xu, Jianzhong Zhang, Chundi He, Ying Qiu, Guangdong Wen, Hongqing Tian, Xiaodong Zheng (+37 others)
2015 Nature Communications  
Here, we present a large-scale wholeexome array analysis for psoriasis consisting of 42,760 individuals.  ...  Our findings increase the number of genetic risk factors for psoriasis and highlight new and plausible biological pathways in psoriasis.  ...  Acknowledgements We thank the individuals and their families who participated in this project. We also thank the participants contributing to the sample collection from the Genetic Resources  ... 
doi:10.1038/ncomms7793 pmid:25854761 pmcid:PMC4403312 fatcat:yipwp46hwvedlpd7ridkagxdni

Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation

Elizabeth A Tindall, Desiree C Petersen, Stina Nikolaysen, Webb Miller, Stephan C Schuster, Vanessa M Hayes
2010 BMC Research Notes  
Conclusions: We demonstrate the importance of visually inspecting genotype cluster plots generated by the Illumina software and issue warnings regarding commonly accepted quality control parameters.  ...  We highlight applications for interpretation of Illumina generated genotype cluster plots to maximise data inclusion and reduce genotyping errors.  ...  Graham Giles and Dr. Gianluca Severi (The Cancer Council of Victoria, Melbourne, Australia) for coordinations of sample collections for the prostate cancer study, and Dr.  ... 
doi:10.1186/1756-0500-3-39 pmid:20175893 pmcid:PMC2848685 fatcat:6pkple3u6jekpdkc7lysyhcbdu

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

Awais Rasheed, Yuanfeng Hao, Xianchun Xia, Awais Khan, Yunbi Xu, Rajeev K. Varshney, Zhonghu He
2017 Molecular Plant  
In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding.  ...  Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees.  ...  to hundreds of markers as in quality control (QC) analysis for hybrid purity; (c) hundreds of samples for few targets and hundreds of background markers as in MABC; and (d) hundreds to thousands of samples  ... 
doi:10.1016/j.molp.2017.06.008 pmid:28669791 fatcat:6hu6b3dx3bgixivj5qug6hiqje

Development of a Genotyping Microarray for Studying the Role of Gene-Environment Interactions in Risk for Lung Cancer

Don A. Baldwin, Christopher P. Sarnowski, Sabrina A. Reddy, Ian A. Blair, Margie Clapper, Philip Lazarus, Mingyao Li, Joshua E. Muscat, Trevor M. Penning, Anil Vachani, Alexander S. Whitehead
2013 Journal of Biomolecular Techniques  
A microarray (LungCaGxE), based on Illumina BeadChip technology, was developed for high-resolution genotyping of genes that are candidates for involvement in environmentally driven aspects of lung cancer  ...  The iterative array design process illustrates techniques for managing large panels of candidate genes and optimizing marker selection, aided by a new bioinformatics pipeline component, Tagger Batch Assistant  ...  We thank David McGain and Kathakali Addya (Penn Molecular Profiling Facility) and Cecilia Kim (Children's Hospital of Philadelphia Center for Applied Genomics) for technical assistance.  ... 
doi:10.7171/jbt.13-2404-004 pmid:24294113 pmcid:PMC3792704 fatcat:q5wgdekbwrdtzpfnyjivj5gjf4
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