Goldstein 2022 Feb 18;13:818574. doi: 10.3389/fgene.2022.818574. In this protocol, we have used that experience to provide suggestions for the quality control, imputation and analysis of data from this microarray, assuming careful recalling of the raw intensity data has been performed. The second database is required only for local imputation, and downloading the latest release of the 1,000 Genomes Project data. KL However, many other programs exist, and it is worthwhile investigating whether a piece of software particularly suited to the planned analysis is available. Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications. 2022 Aug 19;12(1):337. doi: 10.1038/s41398-022-02093-8. 2015 Sep 15;5(11):2365-73. doi: 10.1534/g3.115.022111. Clark et al. Hum. PLoS One. To determine the identity of the alleles at these sites, the raw intensity data must be calledclusters of samples with similar intensities are identified, and the clusters are labelled according to the design of the microarray. Fig. There are three major scenarios in which imputation is usually applied: First, imputation can be used to fill the gaps of missing genotypes or to correct for genotyping errors in a self-content SNP dataset without an external reference panel ("hole filling without an external reference panel"). official website and that any information you provide is encrypted The presence of structure is inferred from examining genome-wide genotype data. Principal component regression and linear mixed model in association analysis of structured samples: competitors or complements? At the most extreme level, if all but one variant cluster together, it is difficult to assess whether the lone variant is truly a different genotype, or whether it is a missed call. T Amos Folarin is a senior software developer and bioinformatician at the NIHR BRC MH Bioinformatics Core, using bioinformatics for drug screening, target identification and disease analysis. In short, filter at the point of analysis not the imputated files. Testing Hardy-Weinberg disequilibrium using the generalized linear model. Jonathan Coleman is a PhD student at the MRC Social, Genetic and Developmental Psychiatry Centre (SGDP), using genomic methods to explore differential response to psychological treatments for anxiety disorders. Am. marker . In addition, publicly available scripts from Mike Weale and from Timothe Flutre are used in the protocol. 10.1186/1471-2105-11-134 -. As such, some clusters must be identified by manual recalling by a bioinformatician. Stephen Newhouse is a senior bioinformatician at the NIHR BRC MH Bioinformatics Core, with a focus on translational bioinformatics and the genetics of complex disorders. CM Ramnarine S, Zhang J, Chen LS, Culverhouse R, Duan W, Hancock DB, Hartz SM, Johnson EO, Olfson E, Schwantes-An TH, Saccone NL. Bethesda, MD 20894, Web Policies Use of this site constitutes acceptance of our User Agreement and Privacy Transl Psychiatry. Lippert J A POWERFUL METHOD FOR INCLUDING GENOTYPE UNCERTAINTY IN TESTS OF HARDY-WEINBERG EQUILIBRIUM. The site is secure. 2020 Dec 25;2(1):100018. doi: 10.1016/j.xhgg.2020.100018. If you have the 95% C.I of beta, then calculating the SE (beta) is quite simple! . 2022 Jan 24;23(1):50. doi: 10.1186/s12859-022-04568-3. The value of the array in smaller cohorts is in providing an inexpensive means to assay thousands of variants that are in high LD with a considerably greater number. Post Imputation Quality Control (QC) Post imputation QC was previously completed for a cross-disorder genome-wide study on the OCD dataset. As a result, including closely related individuals can skew analysis; genetic variants shared because of close relatedness can become falsely associated with phenotypic similarity that also results from close relatedness. All credit for Ricopili goes to its creators. et al. The main benefits of the HumanCoreExome as a low-cost microarray are twofold. et al. HHS Vulnerability Disclosure, Help Histograms of the info metric of imputed variants on chromosome 9, split by MAF at 0.01. eCollection 2017. A number of challenges were encountered due to the complexity of using two different imputation software packages, multiple ancestral populations, and many different genotyping platforms. Missing data imputation and haplotype phase inference for genome-wide association studies. Hum Hered. Contribute to transbioZI/Gimpute development by creating an account on GitHub. Hofker J Additive genetic effect of GCKR, G6PC2, and SLC30A8 variants on fasting glucose levels and risk of type 2 diabetes. His interests include developing new methods to understand the genetic architecture of, and epidemiological relationship between, psychiatric and other medical disorders. (post-imputation) . The protocol provided with this article provides a straightforward introduction to the basics of GWAS that will increase standardization of GWAS studies between different groups. for example if beta = 0.5 and the upper C.I is 0.6 then upper C.I of beta = beta + se (beta) x 1.96 0.6 = 0.5 + se x. httpsgithubcomfolk ehelseinstituttetmobagen We conducted post imputation quality from NURSING HLTINFOO1 at Aibt International Institute of Americas-Val Ferreira Post-imputation quality control. Aulchenko N Therefore, post-imputation quality control (QC) is indispensable and critically important to distinguish well-imputed variants from poorly imputed ones. The steps are likely to be applicable to data from other arrays, with the caveat that differences in array content may require alteration of the various thresholds discussed. There is a relationship between MAF and info, and it is valuable to examine these metrics togetherrarer variants usually show lower info scores, and often the appropriate cut-off is obvious from plotting info in MAF bins ( Figure 3 ). PLoS Genet 5:e1000529, Article You can check the position in the queue on the job summary page. This leads to reduced power, as the sample's genotype becomes effectively randomized in respect to the phenotype. M The poster from the ASHG 2016 meeting that describes this program, and the pre-imputation checking , can be downloaded here (3.8MB). Pac Symp Biocomput. 2013 Sep;132(9):1073-5. doi: 10.1007/s00439-013-1336-x. SH A variety of methods exist to control for population stratification, of which the most common is to perform principal component analysis on the genome-wide data, and then use the resulting components as covariates in association analysis. The choices made in conducting the analysis of genotype data affect the final result. C Example scripts are provided at https://github.com/JoniColeman/gwas_scripts . An official website of the United States government. FH Pan Pre-analytical steps partly inform these thresholds. ic, a post-Imputation data checking program Background ic is a set of programs designed to produce a single html page visual summary of one or more imputed data sets from the most common imputation programs. The precise pairwise relationships will differ subtly depending on whether the GRM is made using the genotype data before or after imputation (as well as on the programme used), and so the results of the association study will also differ slightly. The threshold chosen should fall between these two. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Calus MP, Bouwman AC, Hickey JM, Veerkamp RF, Mulder HA. Please enable it to take advantage of the complete set of features! Quality control after genotype imputation, Traffic: 1734 users visited in the last hour, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137601, A: Beagle imputation results quality control, User Agreement and Privacy 8600 Rockville Pike Methods 7, 331331 10.1038/nmth0510-331 Tellier PubMedGoogle Scholar. ME Post-imputation QC was done by extracting SNPs with MAF 0.001, info score 0.5, and HWE p -value 1 10 7 in controls, to identify quality SNPs for further analysis. The first is the core reference database, which is sufficient for the human genome build conversion, sample and variant quality control, population stratification, pre-imputation, post-imputation, and GWAS workflows. At worst, poor quality control can lead to systematic biases in outcome and increased false-positive (and false-negative) associations [ 4 ]. A BMC Bioinformatics 11:134. Nyholt Marchini Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray Jonathan R. I. Coleman,Jonathan Colemanis a PhD student at the MRC Social, Genetic and Developmental Psychiatry Centre (SGDP), using genomic methods to explore differential response to psychological treatments for anxiety disorders. Goddard For the results of a study to be valid and replicable, multiple biases must be addressed in the course of data preparation and analysis. SH Sullivan FOIA Here, I illustrate the con- This result is also supported by a previous experiment that similarly demonstrated. Chang GM PR PMC Hamel Patel is a PhD student at the SGDP and the National Institute for Health Research Biomedical Research Centre for Mental Health (NIHR BRC MH) Bioinformatics Core, South London and Maudsley NHS Trust. For the smallest studies, where fewer than 1000 individuals are investigated, a cut-off of 5% should be consideredthis is in line with the analysis program GenAbel, for example, which uses a minor allele count of 5 as its cut-off [ 18 ]. Bulik-Sullivan . BK 1000 Genomes Imputation Cookbook 2.3.1. . Genome-wide association studies (GWAS) are widely used to assess the impact of common genetic variation on a variety of phenotypes [ 1 , 2 ]. Learn more about Institutional subscriptions, Howie BN, Donnelly P, Marchini J (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. Pre-phasing done with Eagle 2.3. The value of any finding in molecular genetics is reliant on the ability to replicate it in an independent cohort, and the first step to successful replication is to minimize the likelihood that reported findings are false positives. As such, it is recommended that the<0.2 F threshold for females (as used by PLINK) is treated as guidance, and that further checks (such as counting the number of Y chromosome SNPs with data) are made, and that the phenotypic gender of discordant samples is confirmed with the collecting site where possible [ 20 , 23 ]. 10.1007/s00439-008-0568-7 MH Front. 2.4. (2014). However, there is a paucity of information on best practice for using the data resulting from microarray-based genotyping. 2.1 Quality Control of Genotype Data 2.2 Convert Genotype Data to Build 37 2.3 Convert Genotype Files Into IMPUTE format 3 Pre-Phasing (autosomal chromosomes only) 3.1 Sliding Window Analyses 3.2 Pre-Phasing using IMPUTE2 4 Pre-Phasing using SHAPEIT (recommended) 5 Imputation 6 X-Chromosome Imputation 7 Association Analysis Introduction Authors Post-imputation QC might be more important if the initial imputation results are less accurate. JH Epub 2014 Jul 21. Neither choice in this context is wrong, but the choice made has consequences, and as such needs to be considered and reported [ 11 ]. ME As the accessibility of genome-wide data increases, so must the accessibility of advice on its analysis. Chang Clipboard, Search History, and several other advanced features are temporarily unavailable. This study presents independent research part-funded by the National Institute for Health Research Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and Kings College London. MeSH This can be achieved using a pairwise comparison method, comparing each possible pair of variants in a given window of variants and removing one of the pair if the LD between them is above a given cut-off. Samples whose reported gender differs from that suggested by their genes are likely to have been assigned the wrong identity. Goddard HGG Adv. Author Daniel Shriner. All data sets are not perfect. Ethics approval for the Howard University Family Study was obtained from the Howard University Institutional Review Board and written informed consent was obtained from each participant. government site. Any reference papers or site describing post imputation quality control would be highly appreciated. Following genotyping and the recalling of genotypes, most GWAS studies begin by filtering the variants by the frequency of the less-common allele (minor allele frequency or MAF). PF eCollection 2022. The ADHD sample was cleaned prior to upload to the site 7. Human Genetics Deviations from hardy-weinberg equilibrium in parental and unaffected sibling genotype data. ME . If info file is missing we can run SNPTEST with -summary_stats_only flag, which gives you the info score. PubMed Jonathan R. I. Coleman, Jack Euesden, Hamel Patel, Amos A. Folarin, Stephen Newhouse, Gerome Breen, Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray, Briefings in Functional Genomics, Volume 15, Issue 4, July 2016, Pages 298304, https://doi.org/10.1093/bfgp/elv037. 1 Scatterplot of \hat {r}^ {2} and HWE p values. BMC Bioinformatics. DR The authors would like to acknowledge the work of the developmental teams behind PLINK2, GCTA and IMPUTE2. de Bakker 2012 Dec;94(6):319-30. doi: 10.1017/S0016672312000511. Gimpute includes processing steps for genotype liftOver, quality control, population outlier detection, haplotype pre-phasing, imputation, post imputation, data management and the extension to . This site needs JavaScript to work properly. Y volume132,pages 10731075 (2013)Cite this article. We present lessons learned and describe the pipeline implemented here to impute and merge genomic data sets. For example, the graphs below show most of the worst-performing variants have info<0.15, and there is an enrichment of high-quality variants with info>0.85. Controlling for population structure and genotyping platform bias in the eMERGE multi-institutional biobank linked to Electronic Health Records. The development of association analysis software is an active area of research, with programs such as FasT-LMM and BOLT-LMM providing alternative implementations to GCTA [ 31 , 32 ]. The chances of an error in genotype calling increase with decreasing MAF, as the certainty of manual and automatic clustering falls with fewer variants in each cluster [ 17 ]. Aulchenko The imputed data that result from these methods are provided in a probabilistic dosage' format, which is an attractive format from a statistical perspective, as it allows for the variable certainty of each imputed call to be considered within the association model. 8600 Rockville Pike Thresholds that identify missing variants do not necessarily exclude miscalled variants. . and transmitted securely. To make effective use of the array in this manner requires imputation of the data to a reference population, most commonly the 1000 Genomes Reference [ 27 ]. C imputation quality control comprised the input datasets for imputation, which used IMPUTE224 with 1000 Genomes25 Phase 1 v3 as the reference panel. Zuvich RL, Armstrong LL, Bielinski SJ, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, de Andrade M, Doheny KF, Haines JL, Hayes MG, Jarvik GP, Jiang L, Kullo IJ, Li R, Ling H, Manolio TA, Matsumoto ME, McCarty CA, McDavid AN, Mirel DB, Olson LM, Paschall JE, Pugh EW, Rasmussen LV, Rasmussen-Torvik LJ, Turner SD, Wilke RA, Ritchie MD. The confidence index threshold for post-imputation information measures was set either between 0.3 and 0.4 or at a more conservative score of 0.7-0.9 6, 11, 12. The complexities of genotyping and recalling are beyond the scope of this protocol, but guidance is available from array manufacturers and as referenced in the Supplementary Data [ 13 ]. Tucker For example, clustering algorithms can incorrectly define a group of samples as heterozygous. a Common variants (minor allele frequency 0.05). Females are expected to have lower values of F , distributed normally around 0 [ 22 ]. . FOIA This site needs JavaScript to work properly. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. Steemers Much as it confounds estimates of IBD, patterns of LD will also impair chromosome-specific (and genome-wide) tests of homozygosity, and so it is necessary to perform this test following pruning for LD. L However, the effects can be more nuanced; for example, association testing using a mixed linear model may use a genetic relatedness matrix (GRM) to control for gross genetic similarity between individuals [ 9 , 10 ]. Lorraine Southam1, Kalliope Panoutsopoulou2,NWilliamRayner3,4,KayChapman1, Caroline Durrant3, Teresa Ferreira3, Nigel Arden5,6,AndrewCarr1,PanosDeloukas2, Michael Doherty7, John Loughlin8, Andrew McCaskie8,9,WilliamEROllier10 . CAS Although such deviations can be caused by processes that may be of interest within the study, such as selection pressure, the expected size of such deviations is small. Disclaimer, National Library of Medicine Accordingly, it is necessary to prune the data for LD before assessing IBD and population stratification. Odyssey is a pipeline that integrates Howie In this example, a MAF cut-off of 0.01 appears to remove most of the SNPs with low info scores. -, Browning B. L., Browning S. R. (2009). In smaller cohorts, a more stringent MAF cut-off is recommended, as the minor allele count will be lower, which limits the value of conclusions from the analysis of these variants. The Checks tab describes the reproducibility checks that were applied when the results were created. Shriner, D. Impact of HardyWeinberg disequilibrium on post-imputation quality control. GTOOL 6. Anderson With increasing computational sophistication, it is likely that the use of dosage data as an input file type will become possible and commonplace; to this end, readers are advised to consult the PLINK2 website ( https://www.cog-genomics.org/plink2/ ). As such, there is a necessity to perform post-imputation quality control. Impact of Hardy-Weinberg disequilibrium on post-imputation quality control Hum Genet. eCollection 2022. For permissions, please email: journals.permissions@oup.com, Multifactorial feature extraction and site prognosis model for protein methylation data, Core promoter in TNBC is highly mutated with rich ethnic signature, Recent insights into crosstalk between genetic parasites and their host genome, Role of gut-microbiota in disease severity and clinical outcomes, Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines, Pre-analytical procedures: genotyping, calling and recalling, Quality control: selecting variants by allele frequency, Quality control: removing variants and samples with missing data, Quality control: assessing deviation from Hardy-Weinberg equilibrium, Quality control: pruning for LD and removing related samples, Quality control: confirming sample gender and assessing the inbreeding coefficient, Quality control: controlling for population stratification, Imputation to the 1000 Genomes reference population, Post-imputation quality control: monomorphic, rare and missing variants, https://github.com/JoniColeman/gwas_scripts, https://www.cog-genomics.org/plink2/basic_stats, https://mathgen.stats.ox.ac.uk/genetics_software/snptest/old/snptest.html, Receive exclusive offers and updates from Oxford Academic. 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