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Using previously genotyped controls in genome-wide association studies (GWAS): application to the Stroke Genetics Network (SiGN)
2014
Frontiers in Genetics
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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
2013
Human Genetics
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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
2022
Journal of Genomics
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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)
2014
PLoS ONE
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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
2014
Molecular Plant
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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
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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
2009
PLoS ONE
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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
2010
Genetic Epidemiology
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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
2013
Molecular Psychiatry
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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
2008
Current Opinion in Lipidology
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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
2016
Scientific Reports
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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
2015
Nature Communications
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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
2010
BMC Research Notes
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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
2017
Molecular Plant
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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
2013
Journal of Biomolecular Techniques
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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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