Two new JK silencing alleles identified by single molecule sequencing with 20‐Kb long‐reads

Abstract

BackgroundThe Kidd blood group gene SLC14A1 (JK) accounts for approximately 20 Kb from initiation codon to stop codon in the genome. In genomic DNA analysis using Sanger sequencing or short‐read‐based next generation sequencing, it is difficult to determine the cis or trans positions of single nucleotide variations (SNVs), which are occasionally more than 1 Kb away from each other. We aimed to determine the complete nucleotide sequence of a 20‐Kb genomic DNA amplicon to characterize the JK allelic variants associated with Kidd antigen silencing in a blood donor.Study Design and MethodsThe Jk(a–b–) phenotype was identified in this donor by standard serological typing. A DNA sample obtained from whole blood was amplified by long‐range PCR to obtain a 20‐Kb fragment of the SLC14A1 gene, including the initiation and stop codons. The fragment was then analyzed by Sanger sequencing and single‐molecule sequencing. Transfection and expression studies were performed in CHO cells using the expression vector construct of JK alleles.ResultsSanger sequencing and single‐molecule sequencing revealed that the donor was heterozygous with JK*01 having c.276G>A (rs763262711, p.Trp92Ter) and JK*02 having c.499A>G (rs2298719, p.Met167Val), c.588A>G (rs2298718, p.Pro196Pro), and c.743C>A (p.Ala248Asp). The two JK alleles identified have not been previously described. Transfection and expression studies indicated that the CHO cells transfected with JK*02 having c.743C>A did not express the Jkb and Jk3 antigens.ConclusionsWe identified new JK silencing alleles and their critical SNVs by single‐molecule sequencing and the findings were confirmed by transfection and expression studies.

Resolving Genotype–Phenotype Discrepancies of the Kidd Blood Group System Using Long-Read Nanopore Sequencing

“…The latest advancements in third-generation long-read sequencing (TGS) technologies offer notable advantages, including the capacity to elucidate extensive haplotypes and characterize genomic regions that pose challenges for Sanger sequencing or next-generation short-read sequencing [1]. In the specific field of transfusion medicine, TGS complements traditional approaches used for the blood group assessment of samples with complex or discordant serological and genetic results [2][3][4][5][6]. Such cases include serological reactions Biomedicines 2024, 12, 225 2 of 12 exhibiting unexpected weak agglutination or null phenotypes, often resulting from rare or unknown genetic variants that are not typed in routine genotyping workflows [7].…”

Resolving genotype-phenotype discrepancies of the Kidd blood group system using long-read nanopore sequencing

“…The latest advancements in third-generation long-read sequencing (TGS) technologies offer notable advantages, including the capacity to elucidate extensive haplotypes and characterize genomic regions that pose challenges to Sanger sequencing or next-generation short-read sequencing [1]. In the specific field of transfusion medicine, TGS complements traditional approaches used for the blood group assessment of samples with complex or discordant serological and genetic results [2][3][4][5][6]. Such cases include serological reactions exhibiting unexpected weak agglutination or null phenotypes, often resulting from rare or unknown genetic variants that are not typed in routine genotyping workflows [7].…”