Development and evaluation of a transfusion medicine genome wide genotyping array

Abstract

BACKGROUND: Many aspects of transfusion medicine are affected by genetics. Current single-nucleotide polymorphism (SNP) arrays are limited in the number of targets that can be interrogated and cannot detect all variation of interest. We designed a transfusion medicine array (TM-Array) for study of both common and rare transfusion-relevant variations in genetically diverse donor and recipient populations.STUDY DESIGN AND METHODS: The array was designed by conducting extensive bioinformatics mining and consulting experts to identify genes and genetic variation related to a wide range of transfusion medicine clinical relevant and research-related topics. Copy number polymorphisms were added in the alpha globin, beta globin, and Rh gene clusters. RESULTS:The final array contains approximately 879,000 SNP and copy number polymorphism markers. Over 99% of SNPs were called reliably. Technical replication showed the array to be robust and reproducible, with an error rate less than 0.03%. The array also had a very low Mendelian error rate (average parent-child trio accuracy of 0.9997). Blood group results were in concordance with serology testing results, and the array accurately identifies rare variants (minor allele frequency of 0.5%). The array achieved high genome-wide imputation coverage for African-American (97.5%), Hispanic (96.1%), East Asian (94.6%), and white (96.1%) genomes at a minor allele frequency of 5%. CONCLUSIONS: A custom array for transfusionmedicine research has been designed and evaluated. It gives wide coverage and accurate identification of rare SNPs in diverse populations. The TM-Array will be useful for future genetic studies in the diverse fields of transfusion medicine research. T ransfusion medicine encompasses diverse medical services and fields of research including blood donation, component processing, immunohematology, infectious disease, recipient outcomes, ABBREVIATIONS: BGMUT = blood group antigen gene mutation; CNPs = copy number polymorphisms; GWASs = genome-wide association studies; MAF = minor allele frequency; NHLBI = National Heart, Lung, and Blood Institute; RBC-Omics = Red Blood Cell Omics; REDS-III = Recipient Epidemiology Donor Evaluation Study-III; SCD = sickle cell disease; SNP = single-nucleotide polymorphism

Blood, sweat, and tears: Red Blood Cell‐Omics study objectives, design, and recruitment activities

“…8,12,13 For example, some blood donors can donate repeatedly without hemoglobin deferral, yet others are deferred for low hemoglobin after one or a few donations. Investigating whether there are DNA polymorphism(s) that enable high-intensity donation without low hemoglobin deferral or are associated with pica and RLS will contribute to understanding the physiologic mechanisms of iron absorption and metabolism.…”

“…Questions about diet were not included because previous studies among donors revealed that dietary differences do not significantly alter iron status in a manner that can be reliably detected by a self-reported dietary history. 12,13 …”

“…The array includes SNPs to provide good imputation coverage (approximately 95% of markers had R 2 > 0.8 down to a minor allele frequency of 5%) in populations of European, African, and East Asian descent. Further details are in our companion article, “Development and Evaluation of a Transfusion Medicine Genome Wide Genotyping Array.” 13 …”

“…Questions about diet were not included because previous studies among donors revealed that dietary differences do not significantly alter iron status in a manner that can be reliably detected by a self-reported dietary history. 12,13 During the enrollment visit, a whole blood unit and ethylenediaminetetraacetic acid (EDTA) retention tube were collected from each participant. The whole blood donor units were processed into LR-RBC components according to each blood center's standard operating procedures.…”

Genetic and behavioral modification of hemoglobin and iron status among first‐time and high‐intensity blood donors

“…20 This cohort was genotyped using a customized Affymetrix Axiom Array with approximately 879,000 single nucleotide polymorphisms (SNPs). 22 Participants were stratified by sex and categorized into six groups that approximated the longitudinal groups ( Figure 1B), differing by selection of females with a previous low hemoglobin deferral, instead of frequent first-time females, who could not be defined because of the crosssectional study design. Groups 1 (2198 females) and 2 (1800 males) consisted of first-time or reactivated donors.…”