Full‐length nucleotide sequences of 30 common SLC44A2 alleles encoding human neutrophil antigen‐3

Abstract

Background HNA-3a alloantibodies can cause severe transfusion-related acute lung injury (TRALI). The frequency of the single nucleotide polymorphisms (SNPs) indicative of the two clinically relevant HNA-3a/b antigens are known in many populations. In the present study, we determined the full length nucleotide sequence of common SLC44A2 alleles encoding the choline transporter-like protein-2 (CTL2) that harbors HNA-3a/b antigens. Study design and methods A method was devised to determine the full length coding sequence and adjacent intron sequences from genomic DNA by 8 polymerase chain reaction (PCR) amplifications covering all 22 SLC44A2 exons. Samples from 200 African American, 96 Caucasian, 2 Hispanic and 4 Asian blood donors were analyzed. We developed a decision tree to determine alleles (confirmed haplotypes) from the genotype data. Results A total of 10 SNPs were detected in the SLC44A2 coding sequence. The non-coding sequences harbored an additional 28 SNPs (1 in the 5’-untranslated region (UTR); 23 in the introns; and 4 in the 3’-UTR). No SNP indicative of a non-functional allele was detected. The nucleotide sequences for 30 SLC44A2 alleles (haplotypes) were confirmed. There may be 66 haplotypes among the 604 chromosomes screened. Conclusions We found 38 SNPs, including 1 novel SNP, in 8192 nucleotides covering the coding sequence of the SLC44A2 gene among 302 blood donors. Population frequencies of these SNPs were established for African Americans and Caucasians. Because alleles encoding HNA-3b are more common than non-functional SLC44A2 alleles, we confirmed our previous postulate that African American donors are less likely to form HNA-3a antibodies compared to Caucasians.

Genotype frequency of human neutrophil antigen‐3 polymorphisms in the Yi, Han, and Tibetan populations of China

“…The HNA‐3a/b SNP (461G>A) was detected by both sequencing approaches (Table ). In addition, we detected the two known SNPs 503‐15T>C (rs1560711) located in Intron 7 in Yi and Tibetan populations and 331‐44G>A (rs12972963) located in Intron 5 in the Han population (Table ) . The only other known SNP in these DNA stretches, 457C>T (rs147820753), was not found in the three populations.…”

“…In addition, we detected the two known SNPs 503‐15T>C (rs1560711) located in Intron 7 in Yi and Tibetan populations and 331‐44G>A (rs12972963) located in Intron 5 in the Han population (Table ) . The only other known SNP in these DNA stretches, 457C>T (rs147820753), was not found in the three populations. The SNPs detected in the study were in a Hardy‐Weinberg equilibrium (p > 0.05), with the exception of one SNP pair (503‐15T>C and 461G>A) in the Yi population (p = 0.049).…”

“…The SLC44A2*2 allele frequencies vary among populations and range in the Han population from 38.2% (Nanning) to 26.2% (Guangzhou) . Although TRALI is much less frequently reported in China than in the United States, the susceptible allele SLC44A2*2 is more prevalent in any East Asian population compared to 17% in Caucasians and 7% in African Americans …”

SLC44A2 single nucleotide polymorphisms, isoforms, and expression: Association with severity of Meniere's disease?

“…These differences are sufficient to create the HNA3a epitope. In support of subtle changes having an effect on protein conformation, Chen et al 28 and Flesch et al 29 report a missense SNP rs147820753 position 537C>T (p1) p.151 leu>phe which immediately precedes rs2288904 and alters HNA-3a antibody reactivity with the epitope involving p.152 arg .…”

“…If the proteins from both alleles are expressed in heterozygous individuals and the resulting molecules combine to form a transporter molecule, different folding of the protein containing arginine and the protein containing glutamine at amino acid 152/154 could result in altered function of the complex. Although Chen et al 28 reported that computational predictions of the p.154 arg and p154 gln alleles revealed no deleterious structural or functional differences, this type of analysis does not take into account the subtle conformational change that result from these different amino acids. These differences are sufficient to create the HNA3a epitope.…”