ArticleGenome medicine2015
Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies.
Article in Genome medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Steroid-tacrolimus drug-drug interaction and the effect of CYP3A genotypes.British journal of clinical pharmacology · 2024Article
- Genetic versus self-reported African ancestry of the recipient and neighborhood predictors of kidney transplantation outcomes in 2 multiethnic urban cohorts.American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2024Article
- Polygenic risk score for acute rejection based on donor-recipient non-HLA genotype mismatch.PloS one · 2024Article
- Higher number of tacrolimus dose adjustments in kidney transplant recipients who are extensive and intermediate CYP3A5 metabolizers.Clinical transplantation · 2023Article
- Genome-wide copy number variant screening of Saudi schizophrenia patients reveals larger deletions in cases versus controls.Frontiers in molecular neuroscience · 2023Article
- Impact ofTransplantation direct · 2022Article
- Donor and recipient polygenic risk scores influence the risk of post-transplant diabetes.Nature medicine · 2022Article
- Donor-Recipient Non-HLA Variants, Mismatches and Renal Allograft Outcomes: Evolving Paradigms.Frontiers in immunology · 2022Review
- Precision Dosing for Tacrolimus Using Genotypes and Clinical Factors in Kidney Transplant Recipients of European Ancestry.Journal of clinical pharmacology · 2021Observational
- A Multi-Marker Test for Analyzing Paired Genetic Data in Transplantation.Frontiers in genetics · 2021Review
- Pharmacogenomics in kidney transplant recipients and potential for integration into practice.Journal of clinical pharmacy and therapeutics · 2020Observational
- Joint testing of donor and recipient genetic matching scores and recipient genotype has robust power for finding genes associated with transplant outcomes.Genetic epidemiology · 2020Article
- Renoprotective and Immunomodulatory Effects of GDF15 following AKI Invoked by Ischemia-Reperfusion Injury.Journal of the American Society of Nephrology : JASN · 2020Article
- High-activity Classical and Alternative Complement Pathway Genotypes-Association With Donor-specific Antibody-triggered Injury and Renal Allograft Survival.Transplantation direct · 2020Article
- Genetic background and transplantation outcomes: insights from genome-wide association studies.Current opinion in organ transplantation · 2020Review
- Tacrolimus troughs and genetic determinants of metabolism in kidney transplant recipients: A comparison of four ancestry groups.American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2019Observational
- Identification of genetic variants associated with tacrolimus metabolism in kidney transplant recipients by extreme phenotype sampling and next generation sequencing.The pharmacogenomics journal · 2019Observational
- Analysis of 75 Candidate SNPs Associated With Acute Rejection in Kidney Transplant Recipients: Validation of rs2910164 in MicroRNA MIR146A.Transplantation · 2019Article
- Variants in immune-related genes and genital HPV 16 persistence in men.Papillomavirus research (Amsterdam, Netherlands) · 2019Article
- Genetic Variants Associated With Immunosuppressant Pharmacokinetics and Adverse Effects in the DeKAF Genomics Genome-wide Association Studies.Transplantation · 2019Observational
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Authors and funding
66 authors.
Funding
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.
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