Thermo Fisher Scientific Analysis Note, Axiom Transplant GT Array Owner's manual

Brand: Thermo Fisher Scientific

Model: Analysis Note, Axiom Transplant GT Array

Type: Owner's manual

For Research Use Only. Not for use in diagnostic procedures.

Analysis Workflow for AxiomTM Transplant Genotyping Array

Overview

AxiomTM Transplant Genotyping Array (P/N 902865) enables large scale genotyping of transplant and solid organ related studies.

Designed by leading transplantation and immunogenetic researchers and iGeneTRAiN1, this array provides deep coverage of MHC, KIR,

pharmacogenomic, and metabolic loci as well as regions of copy number variation related to transplantation outcomes2. Modules for the

transplant-specific and genome-wide content were based on the major human populations from the HapMap project. Approximately 296K

markers from the AxiomTM Biobank Array compose the imputation grid. Approximately 50K SNPs from the 1000 Genomes Phase I

reference panel were added to improve coverage in African and other populations. Approximately18K markers were designed to optimize

and standardize genotyping quality control. Additional modules added to the array include: HLA and KIR region markers, known CNVs,

tissue- specific markers, non-HLA MHC region makers, LoF variants, and pharmacogenomic markers.

Data from over 17,000 samples was used to develop library files which provide the latest in biobank data analysis options.

AxiomTM Genotyping Solution Data Analysis Guide (P/N 702961) provides detailed information for analyzing AxiomTM arrays. For best results

users should follow the steps of the Best Practices Genotyping Analysis Workflow. This analysis note provides additional and specific

instructions for the AxiomTM Transplant Genotyping Array.

Analysis of the Axiom Transplant Array and Genotyping with Priors

To improve the reproducibility of genotype calls across multiple batches in very large datasets, improvements to the Axiom Analysis

Guidelines, described in the AxiomTM Genotyping Solution Data Analysis Guide, have been implemented for Axiom Transplant Genotyping

Array. These include (1) the use of SNP-specific priors for any size sample set, (2) the use of only one best probeset to represent each

marker, and (3) a Step2 probe set list recommended for use in the final genotyping step. The library files for Axiom Transplant Genotyping

Array incorporate all of these elements.

The use of generic priors for large batches allows the genotyping algorithm to dynamically adapt to observed cluster locations and tends to

maximize the number of well-clustered SNPs in a given batch, while SNP-specific priors function to anchor the genotype calls to improve

the reproducibility of calls in separate batches and increase the number of SNPs recommended across all batches. Similarly, the dynamic

selection of the best probeset may be different in separate batches and standardization on one probe set per marker improves

reproducibility of recommended SNPs across all batches. The Step2 probe set list removes some probe sets from the final genotyping step

which were included in earlier versions of the analysis library files (.r2 or earlier).

The SNP-specific priors for Axiom Transplant Genotyping Array were generated using data from DNA samples isolated from blood and

tissue and are recommended for use with blood, tissue, and cell line samples (see “Analysis Options” below). For this reason generic priors

are recommended when genotyping DNA isolated from other sample types (e.g., saliva or whole-genome amplified samples).

Analysis Options

The improved analysis workflow for AxiomTM Transplant Genotyping Array requires the use of .r3 version of the analysis library file

package. This package is available for download from within Axiom™ Analysis Suite or from the Technical Documentation tab of Axiom

Biobank Genotyping Array product page, see ”Additional Information” section for more information. Earlier versions of the analysis

library files (.r2 or earlier) do not support the complete improved analysis workflow for this array.

As described in the AxiomTM Genotyping Solution Data Analysis Guide, all steps of the Best Practices Workflow should be completed in

Axiom™ Analysis Suite. The suite is the recommended software system for most Axiom users. Alternatively, Thermo Fisher Power Tools

(APT) and SNPolisher may be used for analysis. For detailed information on these software packages refer to their respective guides and

manuals. For detailed information on these software packages refer to AxiomTM Genotyping Solution Data Analysis Guide (P/N 702961),

Axiom™ Analysis Suite User Guide (P/N 703307), APT Manual: apt-probeset-genotype (1.18.0), and SNPolisher User Guide (Version 1.5 or

greater).

Axiom Transplant Genotyping Array is designed for use with samples from African, Asian, and European populations. Genotyping

samples from these populations will provide the best results.

2 Analysis Workflow for AxiomTM Transplant Genotyping Array

In Axiom Analysis Suite, the Human setting should be selected in the Thresholds Setting drop-down menu. When analyzing blood and

cell line samples, the Axiom_tx_v1_SNPSpecificPriors library files should be selected in the Select Analysis Configuration drop-down

(see Figure 1A). If other sample types are being analyzed the Axiom_tx_v1_GenericPriors should be selected. To genotype the same probe

sets used in earlier versions of the analysis library files, remove the Axiom_tx_v1.r3.step2 file from the SNP List File under Genotyping

(see Figure 1B).

Figure 1. Thresholds Setting drop-down menu.

A) Select priors file in Select Analysis Configuration drop-down

menu. B) Option to remove recommended SNP list file.

Annotation Files

The annotation files include:

 Affy SNP ID

 Probeset ID

 71-mer sequence information

 Chromosome and position information

 rsIDs

 MAF values

In order to export in VCF format from Axiom Analysis Suite, the ref and alt allele columns need to be populated. These annotation files do

contain information in the ref and alt allele columns.

Support

For further support, users should contact their local Thermo Fisher Field Application Specialist or send an email to Support@Thermo

Fisher.com.

Additional Information

For more information about AxiomTM Transplant Genotyping Array and Axiom Genotyping Solution data analysis, please consult the

following resources:

 AxiomTM Transplant Genotyping Array Data Sheet, P/N GGNO0693

 Axiom™ Analysis Suite User Guide, P/N 703307

 AxiomTM Genotyping Solution Data Analysis Guide, P/N 702961

 APT Manual: apt-probeset-genotype

Analysis Workflow for AxiomTM Transplant Genotyping Array 3

 Analysis library files are available on the AxiomTM Biobank Genotyping Arrays product page, Technical Documentation tab:

- AGCC 3.x AxiomTM Transplant GeneTitan MC library files

- AxiomTM Transplant Genotyping Array Analysis Files, r3

- AxiomTM Transplant Array, Annotation Converter

- Axiom_tx_v1 Annotations, CSV format

- Axiom_tx_v1 Annotations, SQLite Format

References

1 B. J. Keating, et al., Design and Implementation of the International Genetics and Translational Research in Transplantation Network.

Transplantation. 99(11):2401–2412. doi: 10.1097/TP.0000000000000913.

2 Li, Y.R., et al, Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies. Genome

Medicine. 2015 Oct 1;7(1):90. doi: 10.1186/s13073-015-0211-x.

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23 January 2017

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Thermo Fisher Scientific Analysis Note, Axiom Transplant GT Array Owner's manual

Thermo Fisher Scientific Analysis Note, Axiom Transplant GT Array Owner's manual

Thermo Fisher Scientific Analysis Note, Axiom Transplant GT Array Owner's manual

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