Genotyping complex structural variation at the malaria-associated human glycophorin locus using a PCR-based strategy.
copy number variation
genotyping
glycophorin
malaria
structural variation
Journal
Annals of human genetics
ISSN: 1469-1809
Titre abrégé: Ann Hum Genet
Pays: England
ID NLM: 0416661
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
17
06
2020
revised:
23
07
2020
accepted:
15
08
2020
pubmed:
9
9
2020
medline:
7
5
2021
entrez:
8
9
2020
Statut:
ppublish
Résumé
Structural variation in the human genome can affect risk of disease. An example is a complex structural variant of the human glycophorin gene cluster, called DUP4, which is associated with a clinically significant level of protection against severe malaria. The human glycophorin gene cluster harbours at least 23 distinct structural variants, and accurate genotyping of this complex structural variation remains a challenge. Here, we use a polymerase chain reaction-based strategy to genotype structural variation at the human glycophorin gene cluster, including the alleles responsible for the U- blood group. We validate our approach, based on a triplex paralogue ratio test, on publically available samples from the 1000 Genomes project. We then genotype 574 individuals from a longitudinal birth cohort (Tori-Bossito cohort) using small amounts of DNA at low cost. Our approach readily identifies known deletions and duplications, and can potentially identify novel variants for further analysis. It will allow exploration of genetic variation at the glycophorin locus, and investigation of its relationship with malaria, in large sample sets at minimal cost, using standard molecular biology equipment.
Substances chimiques
Glycophorins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7-17Informations de copyright
© 2020 The Authors. Annals of Human Genetics published by University College London (UCL) and John Wiley & Sons Ltd.
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