Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Abstract

BackgroundIn addition to HLA genetic incompatibility, non-HLA difference between donor and recipients of transplantation leading to allograft rejection are now becoming evident. We aimed to create a unique genome-wide platform to facilitate genomic research studies in transplant-related studies. We designed a genome-wide genotyping tool based on the most recent human genomic reference datasets, and included customization for known and potentially relevant metabolic and pharmacological loci relevant to transplantation.MethodsWe describe here the design and implementation of a customized genome-wide genotyping array, the ‘TxArray’, comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples on the array, including eight trios.ResultsWe show low Mendelian error rates and high concordance rates for HapMap samples (average parent-parent-child heritability of 0.997, and concordance of 0.996). We performed genotype imputation across autosomal regions, masking directly genotyped SNPs to assess imputation accuracy and report an accuracy of >0.962 for directly genotyped SNPs. We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms. Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms.ConclusionsWe have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0211-x) contains supplementary material, which is available to authorized users.

Tacrolimus trough and dose intra‐patient variability and CYP3A5 genotype: Effects on acute rejection and graft failure in European American and African American kidney transplant recipients

“…Pre‐transplant recipient DNA was obtained at the time of transplant from peripheral blood lymphocytes after red blood cell lysis and isolation by centrifugation. A customized exome‐plus Affymetrix TxArray SNP chip (Affymetrix, Santa Clara, CA, USA) was used to genotype DNA for genetic variants . This chip contains approximately 782 000 genetic markers including 168 000 exonic or coding variants and over 16 000 putative loss‐of‐function variants.…”

“…A customized exome-plus Affymetrix TxArray SNP chip (Affymetrix, Santa Clara, CA, USA) was used to genotype DNA for genetic variants. 34 This chip contains approximately 782 000 genetic markers including 168 000 exonic or coding variants and over 16 000 putative loss-of-function variants. The CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272), and CYP3A5*7 (rs41303343) loss-of-function variants were used in this study and taken from this chip.…”

Tacrolimus troughs and genetic determinants of metabolism in kidney transplant recipients: A comparison of four ancestry groups

“…Genotyping was conducted on an exome-plus Affymetrix Transplant Array chip (Affymetrix, Santa Clara, CA) with ~800 000 high-quality genomic markers after quality control and >34 M markers after imputation using the 1000 Genomes phase 3 and Genome of the Netherlands v5. [27][28][29][30][31] Data quality control was carried out with PLINK software (version 1.90b1a, Harvard University, Cambridge, MA). 32 Genotypes were phased using SHAPEIT2 (v2.r644, University of Oxford, UK) 33 ; and imputed with IMPUTE2 (University of Oxford, UK) 34 Imputed variants with information score more than 0.8 were considered of good quality and used in the analysis.…”

Development and evaluation of a transfusion medicine genome wide genotyping array

“…GWASs have been applied to numerous hematologic endpoints and have advanced our knowledge of the genetic underpinnings of modifiers of complete blood count, hematopoiesis, cardiovascular diseases, and sickle cell anemia . Transplant research has benefitted from GWASs by identifying novel genes and alleles that are associated with kidney transplant rejection and clinical outcomes in patients with renal and lung transplants . Although advances in whole genome sequencing have made it possible to interrogate causal variants directly as opposed to evaluating variants that are in linkage disequilibrium with causal variants, array‐based genotyping remains a cost‐effective method for genotyping large cohorts, such as the UK Biobank cohort, in which half a million participants have been enrolled and genotyped .…”