Development and evaluation of a transfusion medicine genome wide genotyping array.
Journal
Transfusion
ISSN: 1537-2995
Titre abrégé: Transfusion
Pays: United States
ID NLM: 0417360
Informations de publication
Date de publication:
01 2019
01 2019
Historique:
received:
28
02
2018
revised:
11
07
2018
accepted:
11
07
2018
pubmed:
21
11
2018
medline:
7
5
2019
entrez:
21
11
2018
Statut:
ppublish
Résumé
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. 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. 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%. 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.
Sections du résumé
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 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.
Identifiants
pubmed: 30456907
doi: 10.1111/trf.15012
pmc: PMC7032526
mid: NIHMS1069174
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
101-111Subventions
Organisme : British Heart Foundation
ID : RG/13/13/30194
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/L003120/1
Pays : United Kingdom
Organisme : NHLBI NIH HHS
ID : HHSN268201100005I
Pays : United States
Organisme : NHLBI NIH HHS
ID : HHSN268201100008I
Pays : United States
Organisme : NHLBI NIH HHS
ID : HHSN268201100002I
Pays : United States
Organisme : NHLBI NIH HHS
ID : HHSN268201100009I
Pays : United States
Organisme : WHI NIH HHS
ID : HHSN268201100001C
Pays : United States
Organisme : NHLBI NIH HHS
ID : HHSN268201100007I
Pays : United States
Organisme : NHLBI NIH HHS
ID : HHSN268201100001I
Pays : United States
Organisme : NHLBI NIH HHS
ID : HHSN268201100004I
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2018 AABB.
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