Long-range haplotype analysis of the malaria parasite receptor gene ACKR1 in an East-African population

Abstract

The human ACKR1 gene encodes a glycoprotein expressing the Duffy blood group antigens (Fy). The Duffy protein acts as a receptor for distinct pro-inflammatory cytokines and malaria parasites. We determined the haplotypes of the ACKR1 gene in a population inhabiting a malaria-endemic area. We collected blood samples from 60 healthy volunteers in Ethiopia’s southwestern low-altitude tropical region. An assay was devised to amplify the ACKR1 gene as a single amplicon and determine its genomic sequence. All haplotypes were resolved at 5178 nucleotides each, covering the coding sequence (CDS) of the ACKR1 gene and including the 5′- and 3′-untranslated regions (UTR), intron 1, and the 5′- and 3′-flanking regions. When necessary, allele-specific PCR with nucleotide sequencing or length polymorphism analysis was applied. Among the 120 chromosomes analyzed, 18 ACKR1 alleles were confirmed without ambiguity. We found 18 single-nucleotide polymorphisms (SNPs); only one SNP was novel. The non-coding sequences harbored 14 SNPs. No SNP, other than c.-67T>C, indicative of a non-functional allele, was detected. We described haplotypes of the ACKR1 gene in an autochthonous East-African population and found 18 distinct ACKR1 alleles. These long-range alleles are useful as templates to phase and analyze next-generation sequencing data, thus enhancing the reliability of clinical diagnostics.

Molecular analysis of the ICAM4 gene in an autochthonous East African population

“…This low degree of genetic variation in ICAM4 gene may be due to the small size of the ICAM4 gene or its importance in human development and cellular function. The data generated in our study will be useful in determining the evolutionary history of the ICAM4 gene and can be applied to develop, evaluate, and validate next‐generation sequencing techniques and precision medicine …”

“…The data generated in our study will be useful in determining the evolutionary history of the ICAM4 gene and can be applied to develop, evaluate, and validate next-generation sequencing techniques and precision medicine. 3,6 Table S1. ICAM4 genotypes observed in 60 Ethiopian individuals, 57 from Gambela and 3 from Addis Ababa.…”

“…Nucleotide sequences were aligned (CodonCode Aligner; CodonCode) to NCBI RefSeq NG_007728.1 and nucleotide positions defined using the first nucleotide of the coding sequence (CDS) of NM_001544.5 (ICAM4 isoform 1). For comparison, three Ethiopian samples drawn in Addis Ababa were also tested.…”

“…DNA was extracted from EDTA‐anticoagulated whole blood samples from 57 individuals from Gambela, a southwestern region of Ethiopia, and the 1920 nucleotides of ICAM4 gene were sequenced as described previously . Nucleotide sequences were aligned (CodonCode Aligner; CodonCode) to NCBI RefSeq NG_007728.1 and nucleotide positions defined using the first nucleotide of the coding sequence (CDS) of NM_001544.5 (ICAM4 isoform 1).…”

Developments beyond blood group serology in the genomics era

“…Meanwhile, long-range PCR applications for RHD have been described and studies for the FY (Duffy) alleles were described above (Halawani et al, 2014;Lopez et al, 2018;Yin et al, 2018). A recent study describes an important advance whereby the complete RHD sequence was provided using MPS technology (Tounsi et al, 2018).…”