Analysis of the Genomic Sequence of ABO Allele Using Next-Generation Sequencing Method

Comprehensive Annotation of Complete ABO Alleles and Resolution of ABO Variants by an Improved Full-Length ABO Haplotype Sequencing

BACKGROUND

Full-length ABO haplotype sequencing is crucial for accurate genotyping, reference gene annotation, and molecular mechanism analysis of its variants. However, there is currently a deficiency of comprehensive annotation for full-length ABO haplotypes, spanning from the 5' untranslated region (UTR) to the 3' UTR.

METHODS

Two sets of specimens (79 random blood donors and 47 ABO variants) were tested. The full-length ABO gene spanning the 5' UTR to the 3' UTR was amplified using an improved one-step ultra-long-range PCR with a pair of PCR suppression primers. A single-molecule real-time library was constructed, and ABO haplotype sequencing was performed. Data analysis including basecalling, aligning, variant calling, clustering, and variant annotation were performed.

RESULTS

The amplicon measured 26.1 kb without splicing, representing the most complete ABO gene reported to date. The complete ABO haplotype sequence was obtained via long-read sequencing. The comprehensive ABO reference alleles were obtained and the ABO sequence patterns within each allele in a Chinese population were further classified. The full-length ABO gene haplotype analysis technique effectively resolved ABO variants with structural variations (SVs), including large fragment deletions, inversions, recombination, and chimeras.

CONCLUSIONS

Full-length ABO haplotype sequencing filled a gap that was missing with respect to the 3' UTR sequences of ABO alleles and can advance blood group genomic analysis, aiding in ABO gene function analysis, evolutionary studies, and the resolution of ABO variants.

Characterization of a novel AEL allele harboring a c.28 + 5G>A mutation on the ABO*A2.01 background: a study utilizing PacBio third-generation sequencing and functional assays

Background

Mutations in the ABO gene, including base insertions, deletions, substitutions, and splicing errors, can result in blood group subgroups associated with the quantity and quality of blood group antigens. Here, we employed third-generation PacBio sequencing to uncover a novel AEL allele arising from an intron splice site mutation, which altered the expected A2 phenotype to manifest as an Ael phenotype. The study aimed to characterize the molecular mechanism underlying this phenotypic switch.

Methods

A 53-year-old healthy male blood donor with an atypical agglutination pattern was investigated. PacBio sequencing was used to sequence the entire ABO gene of the proband. In silico analysis predicted aberrant splicing, which was experimentally verified using a minigene splicing assay.

Results

Based on serological characteristics, the proband was determined to have an Ael phenotype. Sequencing revealed heterozygosity for ABO*O.01.02 and a novel ABO*A2.01-like allele with an additional c.28 + 5G>A mutation in intron 1. In silico predictions also indicated that this mutation is likely to cause aberrant splicing. Minigene analysis suggested that this mutation disrupted the 5'-end canonical donor splice site in intron 1, activated a cryptic donor site, and resulted in a 167 bp insertion, producing a truncated glycosyltransferase (p.Lys11Glufs*66). Meanwhile, a small amount of the wild type transcript was also generated through normal splicing, contributing to the Ael phenotype.

Conclusion

A novel AEL allele was identified in a Chinese male blood donor on the ABO*A2.01 background, characterized by the c.28 + 5G>A variant. This study provides insights into the molecular basis of blood group antigen variation.

Detecting serologically difficult ABO blood groups using single-molecule real-time sequencing technology

BACKGROUND AND OBJECTIVES

Recently, third-generation long-read sequencing technology has been increasingly applied to the detection of various blood group systems. Because of its long read length and use of single-molecule sequencing, it is capable of obtaining the sequences of blood group genes in their entirety as well as of distinguishing haplotypes. Therefore, here, we collected ABO blood group samples that were difficult to classify serologically and analysed the sequences of the coding regions of the ABO genes as well as the sequences upstream and downstream of the coding regions.

MATERIALS AND METHODS

Samples with ABO antigen typing and reverse serum typing discrepancies were screened in a total of 21 patients. All samples were subjected to serological testing and preliminary ABO genotyping (polymerase chain reaction with sequence-specific primers [PCR-SSP]), followed by single-molecule real-time (SMRT) sequencing to obtain complete ABO gene sequences. PCR sequence-based typing (PCR-SBT) was performed to validate the results.

RESULTS

Of the 21 samples, 15 had common ABO types, and 6 had rare ABO subtypes. One new allele, ABO*B.NEW (c.861C>T), and one allelic base recombination event was identified. Forty-two haplotype sequences were obtained via SMRT sequencing with intronic single-nucleotide variants (SNVs) specific to the ABO allele, and all of the exon region sequences were consistent with the PCR-SBT results.

CONCLUSION

SMRT sequencing is capable of accurately obtaining complete ABO gene sequences, distinguishing haplotypes and identifying allelic recombination.

Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets

Polymorphisms in the human ABO gene determine the major blood classification system based on the three well-known forms: A; B; and O. In pigs that carry only two main alleles in this gene (A and O), we still need to obtain a more comprehensive distribution of variants, which could also impact its function. In this study, we mined more than 500 whole-genome sequencing datasets to obtain information on the ABO gene in different Suidae species, pig breeds, and populations and provide (i) a comprehensive distribution of the A and O alleles, (ii) evolutionary relationships of ABO gene sequences across Suidae species, and (iii) an exploratory evaluation of the effect of the different ABO gene variants on production traits and blood-related parameters in Italian Large White pigs. We confirmed that allele O is likely under balancing selection, present in all Sus species investigated, without being fixed in any of them. We reported a novel structural variant in perfect linkage disequilibrium with allele O that made it possible to estimate the evolutionary time window of occurrence of this functional allele. We also identified two single nucleotide polymorphisms that were suggestively associated with plasma magnesium levels in pigs. Other studies can also be constructed over our results to further evaluate the effect of this gene on economically relevant traits and basic biological functions.