Analysis workflow for UK Biobank Axiom® Array
Contents
1. affymetrix AnalysisNote A Analysis workflow for UK Biobank Axiom Array Overview UK Biobank Axiom Array is a powerful tool for translational research in the fields of epidemiology human disease and population genetics Designed by leading researchers for use by UK Biobank the highly informative content categories include markers corresponding to observed or expected rare alternate alleles of potentially significant phenotypic interest as well as markers in complex regions of the genome This advanced design requires custom analysis steps to gain full value from the array Axiom Genotyping Solution Data Analysis Guide P N 702961 provides detailed information for analyzing Axiom arrays For best results users should follow the steps of the Best Practices Genotyping Analysis Workflow This Analysis Note provides additional instructions for customized analysis options and unique markers specific to UK Biobank Axiom Array Multi allelic markers UK Biobank Axiom Array content includes a set of 2 881 markers corresponding to 1 360 multi allelic loci each having multiple pairs of A B alleles for the same chromosomal position Some of these markers correspond to observed or expected rare alternate alleles which were added to the array because of their potential phenotypic impact For a number of loci in the Rare variants in cancer predisposition genes and Rare variants in cardiac disease predisposition genes categories it is imp2. Dish QC DQC values Step 3 QC the samples based on DQC values Genotyping is performed on passing samples Step 4 Generate sample QC call rates Steo1 AxiomGT1 see Table 1 for file names Step 5 QC samples based on QC call rate Step 6 QC the plates based on sample pass rate and average QC call rate of passing samples BEEP Ps CENONE Pasing Samples ANG Pia lES Figure 2 Example analysis workflow for UK Biobank Axiom Array Boxes enclose GTC and APT genotyping steps file names A marker list must be selected to perform sample required for each Best Practices Workflow step are detailed in enotvpina It is recommended to select the Bi allelic Table 1 circles enclose output genotypes and curved arrows Ss a unless you have developed advanced indicate output files to be appended before executing SNP QC algorithms to handle the multi allelic markers in the Bi allelic Plus Unsupported Multiallelic markers list Step 4 Sample C call rat Select one of the following two marker list options see e Table 1 for file names Qc sepia E A Bi allelic markers recommended Genotype N B Bi allelic Plus Unsupported Multiallelic markers bi allelic requires user developed advanced algorithm elie only The genotype output includes all markers in the selected option except ApoE SNP rs429358 To genotype this SNP select the appropriate Supplemental Analysis file Step 7 Bi allelic Table 1 The genotype output from Supplem
3. of analysis package UK Biobank Axiom Array r3 for genotyping rs429358 and rs7412 This package Is available for download from within Genotyping Console 4 2 GTC or from the Technical Documentation tab of the Axiom Biobank Genotyping Array product page see the Additional Information section below for more information Earlier versions of the analysis library files r1 and r2 do not support the complete custom analysis workflow As described in the Axiom Genotyping Solution Data Analysis Guide the Best Practices Genotyping Analysis Workflow Steps 1 7 can be performed using either GTC or Affymetrix Power Tools APT The Best Practices Genotyping Analysis Workflow Step 8 SNP QC requires the use of APT or SNPolisher For detailed information on these software packages refer to the Affymetrix Genotyping Console 4 2 User Manual P N 702982 Axiom Genotyping Solution Data Analysis Guide P N 702961 APT Manual apt probeset genotype 1 16 1 and the SNPolisher User Guide Version 1 5 or greater There are two options for executing Best Practices Genotyping Step 7 for UK Biobank Axiom Array Option one is the standard analysis option which produces genotype calls for the bi allelic markers only The genotypes for these markers are called using the Axiom genotyping algorithm AxiomGT1 and are thus supported This option is enabled by selecting the Bi allelic markers list Figure 1 and Table 1 A second option is provided to ge
4. Manual P N 702982 Axiom Genotyping Solution Data Analysis Guide P N 702961 APT Manual apt probeset genotype Analysis library files are available on the Axiom Biobank Genotyping Arrays product page Technical Documentation tab UK Biobank Axiom Array Analysis Files r3 UK Biobank Axiom Array Annotation Converter r3 Affymetrix Inc Tel 1 888 362 2447 Affymetrix UK Ltd Tel 44 0 1628 552550 Affymetrix Japan K K Tel 81 0 3 6430 4020 Panomics Solutions Tel 1 877 726 6642 panomics affymetrix com USB Products Tel 1 800 321 9322 usb affymetrix com www affymetrix com Please visit our website for international distributor contact information For Research Use Only Not for use in diagnostic procedures P N 703267 Rev 1 2014 Affymetrix Inc All rights reserved Affymetrix Axiom Command Console CytoScan DMET GeneAtlas GeneChip GeneChip compatible GeneTitan Genotyping Console myDesign NetAffx OncoScan Powered by Affymetrix PrimeView Procarta and QuantiGene are trademarks or registered trademarks of Affymetrix Inc All other trademarks are the property of their respective owners
5. ental markers multiallelic markers Analysis includes only ApoE SNP rs429358 Manually append the output files from Supplemental Selected Analysis to the corresponding output files from the PA selected marker list Bi allelic markers or Bi Allelic Plus coca Unsupported Multiallelic markers to produce genotypes for all selected markers This must be done for each of the following output files AxiomGT1 calls txt AxiomGT1 contidences txt AxiomGT1 snp posteriors txt and AxiomGT1 summary txt To append the Tiles remove oe the header lines those that begin with from the appropriate output file produced by the Supplemental Analysis step After header removal append the file to the file with same name produced by the Step 7 for genotyping Bi allelic markers or Bi allelic Plus rs429358 Unsupported Multiallelic markers Step 8 Execute SNP QC on the appended output file including all markers Refer to the Axiom Genotyping Solution i Data Analysis Guide P N 702961 for details on SNP QC All genotypes Genotypes when genotyping in GTC Chapter 7 and APT Chapter 8 Step 8 SNP QC affymetrix Biology for a better world Table 1 Files used in GTC and APT for QC and a genotyping Batch size Step lt 96 samples Step 4 a _Step1_AxiomGT1 Axiom_UKB_WCSG_LessThan96_Step1 r3 apt probeset genotype AxiomGT 1 Step 7 LessThan96_Step2_AxiomGT1 Axiom_UKB_WCSG_LessThan96_Step2_Bi Bi allelic markers only Bi alle
6. lic markers allelic r3 apt probeset genotype AxiomGT1 xml Step 7 LessThan96_Step2_AxiomGT1 Axiom_UKB_WCSG_LessThan96_Step2_Bi alle Bi allelic multiallelic markers Bi allelic Plus Unsupported Multiallelic markers licPlusUnsupportedMultiallelic r3 apt probeset genotype AxiomGT1 xml Step 7 LessThan96_Step2_AxiomGT1 Axiom_UKB_WCSG_LessThan96_Step2_ Supplemental Analysis Supplemental Analysis Supplemental_Analysis r3 AxiomGT1 xml gt 96 samples Step 4 96o0rMore_Step1_AxiomGT 1 Axiom_UKB_WCSG_96orMore_Step1 r3 apt probeset genotype AxiomGT 1 Step 7 96o0rMore_Step2_AxiomGT1 Axiom_UKB_WCSG_96orMore_Step2_Bi allelic Bi allelic markers only Bi allelic markers r3 apt probeset genotype AxiomGT1 xml Step 7 96orMore_Step2_AxiomGT1 Axiom_UKB_WCSG_96orMore_Step2_Bi alle Bi allelic multiallelic markers Bi allelic Plus Unsupported Multiallelic markers icPlusUnsupportedMultiallelic r3 apt probeset genotype AxiomGT 1 xml Step 7 960rMore_Step2_AxiomGT1 Axiom_UKB_WCSG_96orMore_Step2_ Supplemental Analysis Supplemental Analysis Supplemental_Analysis r3 AxiomGT1 xml Support Users should contact their local Affymetrix Field Application Specialist or send an email to Support attymetrix com Additional information For more information about UK Biobank Axiom Array and Axiom Genotyping Solution data analysis please consult the following resources UK Biobank Axiom Array Data Sheet P N GGNO03529 Genotyping Console 4 2 User
7. notype all markers on the array including the unsupported multi allelic markers This option is enabled by selecting the Bi allelic Plus Unsupported Multiallelic markers list Figure 1 and Table 1 Note The AxiomGT1 algorithm is not designed to handle multi allelic markers therefore the genotype calls from the multi allelic markers in this option are not Supported by Affymetrix Users of this option should exclude output for probe sets not in the bi allelic marker list for any routine downstream analysis New algorithms must be developed by the user to call these multi allelic markers A complete list of markers is included in the annotation file Axiom_UKB_WCSG na34 annot db The identity of probe sets associated with multi allelic markers is also provided Note There are 267 bi allelic markers whose best probe set selected by the SNPolisher Classification step may change between the Bi allelic markers and Bi allelic Plus Unsupported Multiallelic markers options Complete instructions for executing the Best Practices Workflow are detailed in the Axiom Genotyping Solution Data Analysis Guide P N 702961 for GTC Chapter 7 and APT Chapter 8 Genotyping fewer than 96 unique individuals requires the use of SNP specific priors select the appropriate options in Table 1 section LessThan96 when genotyping fewer than 96 unique samples Select the appropriate options in Table 1 section 96orMore when genotyping 96 or more uniq
8. ortant to know the exact number of each possible A C G T allele Thus specific probes were added to the array for each of these alleles Multi allelic markers require additional calculations for interpretation and the development of new genotype calling algorithms is necessary to analyze them The current Axiom analysis software does not support multi allelic marker genotyping and these markers are excluded from the standard analysis option however an option for genotyping these markers is provided for users who would like to develop their own methods to interpret the calls SNP rs429358 and rs7412 in the ApoE gene UK Biobank Axiom Array interrogates two challenging SNPs in the ApoE gene rs429358 and rs7412 These SNPs are important in the study of Alzheimer s disease coronary heart disease Rheumatoid Arthritis as well as other conditions Due to high GC content in the flanking regions genotyping these SNPs reliably requires a variation from the standard genotyping method Therefore the probe set for rs429358 marker is removed from both the standard and optional marker lists and a supplemental option is provided to genotype this one marker separately SNP specific priors see Axiom Genotyping Solution Data Analysis Guide Chapter 2 What is a SNP Cluster Plot for AxiomGT1 Genotypes for more details have been included for both rs429358 and rs7412 Analysis options The customized UK Biobank Axiom Array workflow requires use of the r3 version
9. ue samples Figure 1 Genotyping Analysis Options in GTC Analysis configuration options available for genotyping various marker lists in GTC Marker lists are available for QC genotyping Step1 and sample genotyping Step2 Sample genotyping includes options for Bi allelic markers only Bi allelic Plus Unsupported Multiallelic markers and Supplemental Analysis for genotyping rs429358 S60orMore Step AxiomGT 1 960rMore_Step2_AsxdomGT 1 Bi allelic markers 960rMore_Step2_AxiomGT 1 Bi allelic Plus Unsupported Muttiallelic markers 960rMore_Step2_AxiomGT1 Supplemental Analysis Less Than96_Step1_AxiomGT1 Less Than96_Step2_AxiomGT1 Bi allelic markers Less Than96_Step2_AxiomGT 1 Bi allelic Plus Unsupported Multiallelic markers Less Than96_Step2_AxiomGT1 Supplemental Analysis Best Practices Genotyping Analysis Workflow for UK Biobank Axiom Array The steps listed below can be applied to analysis performed in GTC or APT Refer to the Axiom Genotyping Solution Data Analysis Guide P N 702961 see Chapter 3 Best Practices Genotyping Analysis Workflow for a description of each step An example workflow is provided in Figure 2 Table 1 lists the files used by each software package Ensure the correct sample size option is also selected There are no changes from the instructions provided in the Axiom Genotyping Solution Data Analysis Guide P N 702961 for Steps 1 6 Step 1 Group samples plates into batches Step 2 Generate sample
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