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- Title
Development and evaluation of a transfusion medicine genome wide genotyping array.
- Authors
Guo, Yuelong; Busch, Michael P.; Seielstad, Mark; Endres‐Dighe, Stacy; Westhoff, Connie M.; Keating, Brendan; Hoppe, Carolyn; Bordbar, Aarash; Custer, Brian; Butterworth, Adam S.; Kanias, Tamir; Mast, Alan E.; Kleinman, Steve; Lu, Yontao; Page, Grier P.; Endres-Dighe, Stacy; National Heart, Lung, and Blood Institute Recipient Epidemiology Donor Evaluation Study (REDS)-III
- Abstract
<bold>Background: </bold>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.<bold>Study Design and Methods: </bold>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.<bold>Results: </bold>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%.<bold>Conclusions: </bold>A custom array for transfusion medicine 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.
- Subjects
BLOOD transfusion; GENOTYPES; SINGLE nucleotide polymorphisms; BLOOD donors; BLOOD banks; BLACK people; GENES; GENETIC polymorphisms; HUMAN genome; RESEARCH funding; WHITE people; BIOINFORMATICS; SEQUENCE analysis
- Publication
Transfusion, 2019, Vol 59, p101
- ISSN
0041-1132
- Publication type
journal article
- DOI
10.1111/trf.15012