The nature of diversity and diversification at the ABO locus

eQTL in diseased colon tissue identifies novel target genes associated with IBD

Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14, and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.

Molecular genetic analysis of two novel a allele to cause Ax phenotype in Chinese

BACKGROUND

Mutations of ABO gene may cause the dysfunction of ABO glycosyltransferase (GT) that can result in weak ABO phenotypes. Here, we identified two novel weak ABO subgroup alleles and explored the mechanism that caused Ax phenotype.

MATERIALS AND METHODS

The ABO phenotyping and genotyping were performed by serological studies and direct DNA sequencing of ABO gene. The role of the mutations was evaluated by 3D model, predicting protein structure changes, and in vitro expression assay. The total glycosyltransferase transfer capacity in supernatant of transfected cells was examined.

RESULTS

The results of serological showed the subject RJ23 and RJ52 both were Ax phenotypes. The novel A alleles, Avar-1 and Avar-2 were identified according to the gene analysis. Both Avar-1 and Avar-2 harbored recombinant heterozygous alleles, specifically A2.05 and O.01.02. These alleles showcased substitutions at positions c.106G > T, c.189C > T, c.220C > T, and c.1009A > G in their respective exons. It is worth noting that the crossing-over regions of these two alleles differed from each other. In vitro expression study showed that GTA mutant impaired H to A antigen conversion, and the mutant did not affect the production of GTA though the Western bolt. In silico analysis showed that GTA mutant may change the local conformation and the stability of GT.

CONCLUSIONS

The Avar-1 and Avar-2 alleles were identified, which could cause the Ax phenotype through changing the local conformation and reducing stability of the GTA.

B-Cell Lymphoma Producing IgM Anti-B Antibody: A Case Report

ABO blood group system is the most important blood group system in transfusion and transplantation medicine. Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphomas (NHLs) worldwide. There have been some studies that lymphoma could affect ABO blood group system and thus affect blood transfusion strategy. However, the mechanisms lymphoma affecting ABO blood group system have not been fully elucidated so far. Here, we report a case of a patient who was a 72-year-old Chinese man came to our hospital for medical advice because of cervical lymphadenophathy. The patient was subsequently diagnosed with diffuse large B-cell lymphoma by lymph-node biopsy. His ABO blood group was initially typed as B on November 7, 2020. He was transfusing B type leukocyte poor RBCs (LPR) before we found the patient’s ABO blood group discrepancy on December 2, 2020 by forward and reverse typing methods, which the discrepancy was verified by genotyping. The patient began to transfuse O type washed RBCs (WRBC) since then. Compared to transfuse B type leukocyte poor RBCs (LPR), the efficiency of transfusing O type washed RBCs (WRBC) was better. Although hemoglobin level did not greatly improve, indirect bilirubin level evidently decreased. Furthermore, we found B-cell lymphoma affected blood transfusion strategy by producing IgM anti-B antibody in this case. Clinicians should need to be aware of the effect of B-cell lymphoma on blood transfusion strategy.

[Genetic analysis of weakened expression of ABO blood group antigen in 20 cases]

OBJECTIVE

To explore the molecular mechanism for weakened expression of ABO blood group antigens in 20 cases.

METHODS

Blood samples were collected from 20 cases with weakened expression of ABO blood group antigens, including 12 children undergoing elective surgery and 8 of their parents or grandparents. Serological identification of the ABO blood group was performed using microcolumn agglutination method and saline test tube method. The PCR products of exons 1-7 and their upstream promoter region of the ABO gene were directly sequenced for genotyping.

RESULTS

In 11 of the cases, the ABO genotype could be determined by pedigree analysis (including 1 case of ABO*A2.01/ABO*B.01, 1 case of ABO*A2.01/ ABO*O01.01, 1 case of A1.02/B3.04, 2 cases of B3.04/O.01.01, 2 cases of B3.02/O.01.02, and 4 cases of Bw.12/O.01.01). Pedigree analysis revealed deletion mutation at -35_-18 nt in the ABO promoter region in 3 cases, indicating that the mutation occurred in the B allele; a C > T mutation occurred at -119 nt in the ABO promoter region in 1 case; a C deletion at 1054 nt in exon 7 was identified in 1 case; no mutation was found in exons 1-7 and their regulatory region of ABO gene in 4 cases.

CONCLUSION

The C > T mutation at-119 nt in the promoter region and the deletion mutation at 1054 nt in exon 7 of ABO gene are probably new mutations leading to abnormal expression of ABO blood group antigens. Some ABO subtypes may be associated with abnormal introns or mRNA synthesis.

A 24-base pair deletion in the ABO gene causes a hereditary splice site defect: a novel mechanism underlying ABO blood group O

BACKGROUND

Blood group A and B antigens are synthesized by glycosyltransferases regulated by a complex molecular genetic background. A multibase deletion in the ABO gene was identified in two related blood donors. To define its hereditary character and to evaluate genotype-phenotype associations, a detailed study including 30 family members was conducted.

METHODS AND MATERIALS

ABO phenotyping was performed with agglutination techniques and adsorption-elution tests. The secretor status was determined. Allele-specific sequencing of ABO and genotyping of family members by a mutation-specific polymerase chain reaction were carried out. Functional analysis included cloning of complementary DNA and transfection experiments in HeLa cells. The antigen expression was investigated by flow cytometry and adsorption-elution method.

RESULTS

Sequencing analysis revealed a 24-bp deletion in Exon 5 and the adjacent intronic region of ABO. The alteration was inherited by 16 family members. Nine of them being heterozygous for the mutated allele failed to express A antigen on their erythrocytes as found by routine typing. In particular samples, however, adsorption-elution studies indicated inconclusive results. HeLa cells transfected with aberrant gene transcripts did not express blood group antigen A.

CONCLUSION

The variation causes defects in messenger RNA splicing, most likely inactivating the transferase as observed by serological typing and in vitro expression analysis. These data suggest a novel mechanism associated with blood group O and extend the knowledge of exceptionally rare ABO splice site mutations and deletions. With increased understanding of the molecular bases of ABO, the diagnostics may be further enhanced to ensure the safest possible use of the blood supply.

Genomic analysis of blood samples with serologic ABO discrepancy identifies 12 novel alleles in a Chinese Han population

OBJECTIVES

This study aimed at identifying new ABO alleles from155 unrelated blood samples with potential ABO discrepancy in a Chinese Han population of 835 144 donors.

BACKGROUND

Serological strategies and genotyping are crucial for the precise determination of ABO discrepancy.

METHODS

Their ABO phenotypes and plasma glycosyltransferase activity were determined by standard forward and reverse typing and dilution tests. The genomic DNA of the ABO gene was amplified by polymerase chain reaction and sequenced. The frequency of ABO subgroup alleles associated with ABO discrepancy was analysed.

RESULTS

Serological analysis indicated that 53, 96 and 6 samples with ABO discrepancy were identified in the A, B and O subgroups, respectively. Genetic analysis revealed 12 novel alleles among the 46 associated with serologic ABO discrepancy. The majority of novel alleles was obtained from point mutations or single base insertion in Exons 6 to 7 of the ABO gene. The most frequent alleles were ABO*cisAB.01 (14/53, 26.42%) and ABO*A2.05 (7/53, 13.2%) in the A subgroup and ABO*BA.02 (34/96, 35.42%) and ABO*BEL.11 (15/96, 15.62%) in the B subgroup. Samples with the same ABO subgroup allele displayed different phenotypes, such as ABO*AX.13, ABO*BW.03, ABO*BW.12, ABO*BW.15, ABO*BEL.03, ABO*BEL.10 and ABO*BEL.11.

CONCLUSION

This study identified 12 novel alleles among the 46 associated with serologic ABO discrepancies. ABO genotyping is needed for the accurate evaluation of blood phenotype to improve the safety of blood transfusion.

Molecular Basis of ABO Variants Including Identification of 16 Novel ABO Subgroup Alleles in Chinese Han Population

Introduction

The characteristic of ABO blood subgroup is crucial for elucidating the mechanisms of such variant phenotypes and offering useful information in blood transfusion.

Methods

In total, 211 ABO variants including part of available family members were investigated in this study. The phenotypes of these individuals were typed with serologic methods. The full coding regions of ABO gene and the erythroid cell-specific regulatory elements in intron 1 of them were amplified with polymerase chain reaction and then directly sequenced. The novel alleles were confirmed by cloning and sequencing. Phylogenetic tree was made using CLUSTAL W software. 3D structural analyses of the glycosyltransferases (GTs) with some typical mutations were performed by PyMOL software.

Results

Forty-eight distinctly rare ABO alleles were identified in 211 Chinese variant individuals, including 16 novel ABO alleles. All of the alleles were categorized as 5 groups: 16 ABO*A alleles, 23 ABO*B alleles, 4 ABO*BA alleles, 4 ABO*cisAB alleles, and 1 ABO*O alleles. ABO*A2.08 and ABO*BA.02 were the relatively predominant A and B subgroup alleles, respectively. According to the phylogenetic tree, 28 alleles (5 common alleles and 23 alleles identified in our laboratory) were classified into 3 major allelic lineages. The structural analysis of 3D homology modeling predicted reduced protein stability of the mutant GTs and may explain the reduced ABO antigen expression.

Conclusions

The molecular basis of ABO variants was analyzed, and 16 novel ABO alleles were identified. The results extended the information of ABO variants and provided a basis for better transfusion strategies and helped to improve blood transfusion safety.

Rapid and Reliable One-Step ABO Genotyping Using Direct Real-Time Allele-Specific PCR and Melting Curve Analysis Without DNA Preparation

ABO genotyping is a molecular diagnostic technique important for transfusion and transplantation in medicine, and human identification in forensic science. Because ABO genotyping are labor intensive and time consuming, the genotyping cannot be firstly used to resolve the serological ABO discrepancy in blood bank. For rapid one-step ABO genotyping, we developed direct, real-time, allele-specific polymerase chain reaction (PCR), and melting curve analysis (DRAM assay) without DNA preparation. In DRAM assay, we used a special PCR buffer for direct PCR, a rapid RBC lysis buffer, white blood cells as template without DNA preparation, allele-specific primers for discriminating three ABO alleles (261G/del, 796C/A, and 803G/C), and melting curve analysis as a detection method. There was 100% concordance among the results of ABO genotyping by the DRAM assay, serologic typing, PCR-RFLP and PCR-direct sequencing of 96 venous blood samples. We were able to reduce the number of manual steps to three and the hands-on time to 12 min, compared to seven steps and approximately 40 min for conventional ABO genotyping using allele-specific PCR with purified DNA and agarose gel electrophoresis. We have established and validated the DRAM assay for rapid and reliable one-step ABO genotyping in a closed system. The DRAM assay with an appropriate number of allele-specific primers could help in resolving ABO discrepancies and should be valuable in clinical laboratory and blood bank.

Establishing Blood Group Genotyping to Resolve ABO Discrepancies in Iran

ABO discrepancies are recognized when the reactions obtained in the forward type do not "match" the reactions obtained in the reverse type. Discrepant results are often caused by a variant ABO gene. Molecular analysis is required to confirm the type of subgroups and discrepancy. In this study ABO genotyping was performed on a series of blood donors and patients to determine their definite blood groups. We examined 100 samples with ABO discrepancies from blood donors and patients referred to Tehran Blood Transfusion Center between October 2015 and August 2016. ABO genotyping was performed on all samples with allele specific PCR for differentiation of A, B and O alleles. Exon 6 and 7 of ABO gene were sequenced to confirm the results. The genotyping of donor/patients samples with discrepant results of ABO blood typing consisted of 61 cases of A₂ and A₂B, 3 cases of B 302 and 4 cases of Aw06. Genotyping of 6 samples that had extra antibody in their serum (AB blood group) confirmed the cell type reaction results. 6 samples that had shown a very weak reaction with anti-AB (similar to O blood group) and had no anti-A in their serum were genotyped as O ₁ O ₂. Blood group genotyping laboratory provides an efficient service for evaluation of ABO discrepancies and resolve the problems encountered in serology reactions.

CDetection: CRISPR-Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity

CRISPR-based nucleic acid detection methods are reported to facilitate rapid and sensitive DNA detection. However, precise DNA detection at the single-base resolution and its wide applications including high-fidelity SNP genotyping remain to be explored. Here we develop a Cas12b-mediated DNA detection (CDetection) strategy, which shows higher sensitivity on examined targets compared with the previously reported Cas12a-based detection platform. Moreover, we show that CDetection can distinguish differences at the single-base level upon combining the optimized tuned guide RNA (tgRNA). Therefore, our findings highlight the high sensitivity and accuracy of CDetection, which provides an efficient and highly practical platform for DNA detection.

Rapid rare ABO blood typing using a single PCR based on a multiplex SNaPshot reaction

BACKGROUND

ABO subgroups would be considered when discrepancies in ABO grouping occur. Serological methods including adsorption-elution test, salivary ABH inhibition test, and anti-A1 (lectin) saline method could be used. However, these serological methods are laboring and obscure. Therefore, reliable and affordable method to assess the ABO subgroups is of particular interest.

METHODS

To solve this problem, the multiplex SNaPshot-based assays were designed to determine rare A and B subgroups. Primers used as probes for determination of rare ABO blood groups known in Taiwanese population were designed. Many ABO subtype samples were used to validate the accuracy and reproducibility of our SNaPshot panel.

RESULTS

A panel of primer probes were successfully designed in determining 8 SNP sites (261, 539, 838, 820, 745, 664, IVS6 +5, and 829 in exon 6 and 7) for A phenotype and 6 SNP sites (261, 796, IVS3 +5, 247, 523, and 502 in exon 2, 6 and 7 and intron 3) for B phenotype. SNaPshot analysis for defining blood group A alleles (A₁, A₂, A₃, A_m and A_el) and blood group B alleles (B₁, B₃, B_w and B_el) was therefore available.

CONCLUSION

SNaPshot analysis could be used in reference laboratories for typing known rare subgroups of A and B without DNA cloning and traditional sequencing. Moreover, this method would help to construct databases of genotyped blood donors, and it potentially plays a role in determining fetal-maternal ABO incompatibility.

ABO blood groups as a prognostic factor for recurrence in ovarian and vulvar cancer

The relationship between ABO blood groups (BG) and risk of incidence in cancers including gynecological cancers has been widely studied, showing increased incidence risk for BG A patients. As available data are inconsistent we investigated whether BG and their anti-glycan antibodies (anti-A and anti-B) have prognostic values in gynecological cancers. We retrospectively evaluated 974 patients with gynecological cancers in three cancer centers (Switzerland and Australia) between 1974 and 2014 regarding the relationships between clinico-pathological findings and the BG. Time to disease recurrence was significantly influenced by BG in patients with ovarian (n = 282) and vulvar (n = 67) cancer. BG O or B patients showed a significantly increased risk for ovarian cancer relapse compared to A, 59% and 82%, respectively (p = 0.045; HR O vs A = 1.59 (CI 1.01-2.51) and (p = 0.036; HR A vs B = 0.55 (CI 0.32-0.96). Median time to relapse for advanced stage (n = 126) ovarian cancer patients was 18.2 months for BG O and 32.2 for A (p = 0.031; HR O vs A = 2.07 (CI 1.07-4.02)). BG also significantly influenced relapse-free survival in patients with vulvar cancer (p = 0.002), with BG O tending to have increased relapse risk compared to A (p = 0.089). Blood groups hence associate with recurrence in ovarian and vulvar cancer: women with BG O seem to have a lower ovarian cancer incidence, however are more likely to relapse earlier. The significance of the BG status as a prognostic value is evident and may be helpful to oncologists in prognosticating disease outcome and selecting the appropriate therapy.

Evolution of technology for molecular genotyping in blood group systems

The molecular basis of the blood group antigens was identified first in the 1980s and 1990s. Since then the importance of molecular biology in transfusion medicine has been described extensively by several investigators. Molecular genotyping of blood group antigens is one of the important aspects and is successfully making its way into transfusion medicine. Low-, medium- and high-throughput techniques have been developed for this purpose. Depending on the requirement of the centre like screening for high- or low-prevalence antigens where antisera are not available, correct typing of multiple transfused patients, screening for antigen-negative donor units to reduce the rate of alloimmunization, etc. a suitable technique can be selected. The present review discusses the evolution of different techniques to detect molecular genotypes of blood group systems and how these approaches can be used in transfusion medicine where haemagglutination is of limited value. Currently, this technology is being used in only a few blood banks in India. Hence, there is a need for understanding this technology with all its variations.

Allelic variance among ABO blood group genotypes in a population from the western region of Saudi Arabia

Background

Characterization of the ABO blood group at the phenotype and genotype levels is clinically essential for transfusion, forensics, and population studies. This study elucidated ABO phenotypes and genotypes, and performed an evaluation of their distribution in individuals from the western region of Saudi Arabia.

Methods

One-hundred and seven samples underwent standard serological techniques for ABO blood group phenotype analysis. ABO alleles and genotypes were identified using multiplex polymerase chain reaction, and electrophoretic analysis was performed to evaluate the highly polymorphic ABO locus.

Results

A phenotype distribution of 37.4%, 30.8%, 24.3%, and 7.5% was found for blood groups O, A, B, and AB respectively in our study cohort. Genotype analysis identified 10 genotype combinations with the O01/O02 and A102/O02 genotypes being the most frequent with frequencies of 33.6% and 14.95%, respectively. Common genotypes such as A101/A101, A101/A102, A101/B101, B101/B101, and O01/O01 were not detected. Similarly, the rare genotypes, cis-AB01/O02, cis-AB01/O01, and cis-AB01/A102 were not found in our cohort. The most frequently observed allele was O02 (35.98%) followed by the A102 allele (17.76%). Furthermore, our findings are discussed in reference to ABO allele and genotype frequencies found in other ethnic groups.

Conclusion

The study has a significant implication on the management of blood bank and transfusion services in Saudi Arabian patients.

Human genetic variation database, a reference database of genetic variations in the Japanese population

Whole-genome and -exome resequencing using next-generation sequencers is a powerful approach for identifying genomic variations that are associated with diseases. However, systematic strategies for prioritizing causative variants from many candidates to explain the disease phenotype are still far from being established, because the population-specific frequency spectrum of genetic variation has not been characterized. Here, we have collected exomic genetic variation from 1208 Japanese individuals through a collaborative effort, and aggregated the data into a prevailing catalog. In total, we identified 156 622 previously unreported variants. The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious. In addition, we have constructed a Japanese-specific major allele reference genome by which the number of unique mapping of the short reads in our data has increased 0.045% on average. Our results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants. All the collected data were centralized to a newly developed database to serve as useful resources for exploring pathogenic variations. Public access to the database is available at http://www.genome.med.kyoto-u.ac.jp/SnpDB/.

Genetic Sequencing Analysis of A307 Subgroup of ABO Blood Group

BACKGROUND The aim of this study was to investigate the serology and gene sequence characteristics of the A307 subgroup of the ABO blood group. MATERIAL AND METHODS Monoclonal anti-A and anti-B antibodies were used to detect the ABO antigens of a proband whose positive blood type was not consistent with the negative blood type of the ABO blood group. Standard A-, B-, and O-negative typing cells were used to test for ABO antibodies in the serum. Additionally, polymerase chain reaction with sequence-specific primer (PCR-SSP) was used to confirm the genotype, and subsequently, exons 6 and 7 of the ABO gene were detected by gene sequencing. Samples from the wife and daughters of the proband were also used for serological and genetic testing. RESULTS Red blood cells of the proband showed weak agglutination reaction with anti-A antibody, while anti-B antibody was detected in the serum. Moreover, PCR-SSP detected A307 and O02 alleles, while gene sequencing revealed mutation of c.745C>T in exon 7, which produced a polypeptide chain p.R249W. The A307 gene of the proband was not inherited by his daughters. CONCLUSIONS A mutation (c.745 C>T) in exon 7 of the ABO blood group gene resulted in low activity of a-1,3-N-acetyl-galactosaminyl transferase, producing A3 phenotype.

BGMUT Database of Allelic Variants of Genes Encoding Human Blood Group Antigens

The Blood group antigen Gene MUTation (BGMUT) database documents variations in genes of human blood group systems. In March 2014, the database, accessible at www.ncbi.nlm.nih.gov/gv/mhc/xslcgi.cgi?cmd=bgmut, listed 1,545 alleles of 44 genes of 34 blood group systems. Besides allelic information, the BGMUT resource also presents comprehensive and current information on blood group systems. This review describes the database and notes its utility for the transfusion medicine and human genetics communities.

Molecular genetic analysis and structure model of a rare B(A)02 subgroup of the ABO blood group system

BACKGROUND

Serological analysis of ABO blood group has been widely applied in transfusion medicine. However, ABO subgroups with different expression of blood group antigens sometimes cannot be determined by serological methods. Therefore, genotyping is useful to understand the variant ABO phenotypes.

MATERIAL AND METHODS

Exon 6 to exon 7 and adjacent introns of the ABO gene from a donor with ABO typing discrepancy were amplified and sequenced. Cloning sequencing was also performed to identify the allele. To explore the effect of mutation, three dimensional model of mutant p.Pro234Ala was built and optimized.

RESULTS

The variant B (c. 700C > G) allele expressed an AweakB phenotype with anti-A in his serum with a ABO*B(A)02/O02 heterozygote genotype. Cloning sequencing confirmed that the c.700C > G single nucleotide polymorphism was associated with a B101 allele. Three dimensional molecular modeling suggested that p.Pro234Ala might affect the conformation of His233, Met266 and Ala268, which were known as critical residues for donor recognition.

CONCLUSION

ABO genotyping is needed for correct identification subgroups to improve accuracy evaluation of blood typing and increase the safety of blood transfusion. Alteration of DNA sequence in the ABO gene resulted in amino acid substitutions and led to a weak or missing expression of ABO antigens.

Analysis of a Larger SNP Dataset from the HapMap Project Confirmed That the Modern Human A Allele of the ABO Blood Group Genes Is a Descendant of a Recombinant between B and O Alleles

The human ABO blood group gene consists of three main alleles (A, B, and O) that encode a glycosyltransferase. The A and B alleles differ by two critical amino acids in exon 7, and the major O allele has a single nucleotide deletion (Δ261) in exon 6. Previous evolutionary studies have revealed that the A allele is the most ancient, B allele diverged from the A allele with two critical amino acid substitutions in exon 7, and the major O allele diverged from the A allele with Δ261 in exon 6. However, a recent phylogenetic network analysis study showed that the A allele of humans emerged through a recombination between the B and O alleles. In the previous study, a restricted dataset from only two populations was used. In this study, therefore, we used a large single nucleotide polymorphism (SNP) dataset from the HapMap Project. The results indicated that the A101-A201-O09 haplogroup was a recombinant lineage between the B and O haplotypes, containing the intact exon 6 from the B allele and the two critical A type sites in exon 7 from the major O allele. Its recombination point was assumed to be located just behind Δ261 in exon 6.

A Novel ABO Gene Variant Leads to Discrepant Results in Forward/Reverse and Molecular Blood Grouping

BACKGROUND

Discrepant results in antigen and reverse ABO blood typing are often caused by a variant ABO gene. Molecular analysis can help to characterize such variants. Here, we describe the identification of a novel ABO gene variant in a patient with aberrant ABO phenotype and discrepant genotyping results.

METHODS

A patient with discrepant results in automated forward and reverse ABO phenotyping was further investigated by serological (gel and tube technique) and molecular (commercial and inhouse PCR-SSP, DNA sequencing) methods. A PCR-SSP system was established to screen the novel mutation in 1,820 blood donors.

RESULTS

Standard serological tests confirmed blood group O, however, only anti-B isoagglutinins were present. A monoclonal anti-AB antibody detected very weak agglutination in gel technique. Standard ABO genotyping using PCR-SSP led to discrepant results (O(1)/O(1) or O(1)/A) depending on the test system used. ABO exon re-sequencing identified a novel missense mutation in exon 6 at position 248A>G (Asp83Gly) in the binding region of PCR-SSP primers for the detection of 261G alleles. Blood donors with regular ABO blood groups were all negative for the 248G allele designated Aw34.

CONCLUSION

The novel ABO gene variant Aw34 is associated with very weak A antigen expression and absent anti-A isoagglutinins. The mutation is located in exon 6 close to the O(1)-specific 261G deletion in the binding region of PCR-SSP primers. Presumably, depending on the primer concentration used in commercial ABO genotyping kits, the mutation could lead to a false-negative reaction.

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

BACKGROUND

A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima's D. These statistics are now often being applied in the analysis of Next Generation Sequencing (NGS) data. However, estimates of frequency spectra from NGS data are strongly affected by low sequencing coverage; the inherent technology dependent variation in sequencing depth causes systematic differences in the value of the statistic among genomic regions.

RESULTS

We have developed an approach that accommodates the uncertainty of the data when calculating site frequency based neutrality test statistics. A salient feature of this approach is that it implicitly solves the problems of varying sequencing depth, missing data and avoids the need to infer variable sites for the analysis and thereby avoids ascertainment problems introduced by a SNP discovery process.

CONCLUSION

Using an empirical Bayes approach for fast computations, we show that this method produces results for low-coverage NGS data comparable to those achieved when the genotypes are known without uncertainty. We also validate the method in an analysis of data from the 1000 genomes project. The method is implemented in a fast framework which enables researchers to perform these neutrality tests on a genome-wide scale.

ABO blood group, hypercoagulability, and cardiovascular and cancer risk

The antigens of the ABO system (A, B, and H determinants, respectively) consist of complex carbohydrate molecules. It has been known for nearly half a century that the ABO blood group exerts a major influence on plasma levels of the von Willebrand factor (VWF)-factor VIII (FVIII) complex and that normal group O individuals have significantly lower levels of VWF and FVIII than do non-O individuals. As a consequence, several investigators have studied the association between ABO blood group and the risk of developing bleeding or thrombotic events. A number of epidemiological studies have also analyzed the biologic relevance of this interaction by assessing whether the ABO blood group could influence human longevity through the regulation of VWF-FVIII plasma levels. In this review, the molecular mechanisms by which the ABO blood group determines plasma VWF and consequently, FVIII levels, the possible clinical implications, and the current knowledge on the association between the ABO blood group and the risk of developing certain cancers will be reviewed.

Blood Group ABO Genotyping in Paternity Testing

BACKGROUND: The ABO blood groups result from DNA sequence variations, predominantly single nucleotide and insertion/deletion polymorphisms (SNPs and indels), in the ABO gene encoding a glycosyltransferase. The ABO blood groups A(1), A(2), B and O predominantly result from the wild type allele A1 and the major gene variants that are characterized by four diallelic markers (261G>del, 802G>A, 803G>C, 1061C>del). Here, we were interested to evaluate the impact of ABO genotyping compared to ABO phenotyping in paternity testing. METHODS: The major ABO alleles were determined by PCR amplification with sequence-specific primers (PCR-SSP) in a representative sample of 1,335 blood donors. The genotypes were compared to the ABO blood groups registered in the blood donor files. Then, the ABO phenotypes and genotypes were determined in 95 paternity trio cases that have been investigated by 12 short tandem repeat (STR) markers before. We compared statistical parameters (PL, paternity likelihood; PE, power of exclusion) of both blood grouping approaches. RESULTS: The prevalence of the major ABO alleles and genotypes corresponded to the expected occurrence of ABO blood groups in a Caucasian population. The low resolution genotyping of 4 diallelic markers revealed a correct genotype-phenotype correlation in 1,331 of 1,335 samples (99.7%). In 60 paternity trios with confirmed paternity of the alleged father based on STR analysis both PL and PE of the ABO genotype was significantly higher than of the ABO phenotype. In 12 of 35 exclusion cases (34.3%) the ABO genotype also excluded the alleged father, whereas the ABO phenotype excluded the alleged father only in 7 cases (20%). CONCLUSION: In paternity testing ABO genotyping is superior to ABO phenotyping with regard to PL and PE, however, ABO genotyping is not sufficient for valid paternity testing. Due to the much lower mutation rate compared to STR markers, blood group SNPs in addition to anonymous SNPs could be considered for future kinship analysis and genetic identity testing.

The functional A allele was resurrected via recombination in the human ABO blood group gene

Functional A and B alleles are distinguished at two critical sites in exon 7 of the human ABO blood group gene. The most frequent nonfunctional O alleles have one-base deletion in exon 6 producing a frameshift, and it has the A type signature in two critical sites in exon 7. Previous studies indicated that B and O alleles were derived from A allele in human lineage. In this study, we conducted a phylogenetic network analysis using six representative haplotypes: A101, A201, B101, O01, O02, and O09. The result indicated that the A allele, possibly once extinct in the human lineage a long time ago, was resurrected by a recombination between B and O alleles less than 300,000 years ago.

The frequency of ABO blood group maternal-fetal incompatibility, maternal iso-agglutinins, and immune agglutinins quantitation in Osogbo, Osun State, South-West of Nigeria

Background:

ABO incompatibility in maternal–fetal relationship has been shown to cause hemolytic disease of the newborn (HDNB); a survey which is not yet done in this locality.

Aim:

Frequency of ABO blood group maternal-fetal incompatibility, maternal iso-agglutinins, and immune agglutinins quantitation was carried out in Osogbo, Osun State, South-West of Nigeria.

Settings and Designs:

A total of 260 subjects comprising 130 postpartum mothers within the age range of 22-35 years having good obstetrics history and normal delivery, with their 130 neonate babies were used for the study.

Materials and Methods:

ABO cell and serum groupings were carried out on the subjects using standard antisera and cells with appropriate controls. Direct Coomb’s Test was carried out on neonate red cells. Antibody quantitation by double dilution on the maternal serum using red cells containing corresponding antigen to the antibody was determined. A titer, which is the reciprocal of the highest dilution showing agglutination by Indirect Coombs Test, was determined. Another batch of sera was pretreated with 2-mecarptoethanol before determining the titer.

Statistical Analysis:

The distribution study results obtained were compared in percentages, whereas the antibodies quantitation was expressed as titers using the mode of the titers for compariso-agglutininsn.

Results and Conclusions:

Thirty-eight percent (50) mothers were ABO incompatible with their babies, whereas 62% (80) mothers were compatible. The distribution of blood groups in the compatible population showed blood group O (45%); A (30%); B (20%); and AB (5%). Mothers O, A, and B carrying incompatible babies had a frequency of 24% each, whereas mothers AB had 28%. Serologist differences occur in maternal ABO antibodies of corresponding incompatible baby ABO antigens. A high incidence of ABO maternal-fetal incompatibility observed without detection of immune agglutinins is indicative of a rare incidence of HDNB due to ABO incompatibility in the population studied.

Blood groups in the Species Survival Plan®, European endangered species program, and managed in situ populations of bonobo (Pan paniscus), common chimpanzee (Pan troglodytes), gorilla (Gorilla ssp.), and orangutan (Pongo pygmaeus ssp.)

Blood groups of humans and great apes have long been considered similar, although they are not interchangeable between species. In this study, human monoclonal antibody technology was used to assign human ABO blood groups to whole blood samples from great apes housed in North American and European zoos and in situ managed populations, as a practical means to assist blood transfusion situations for these species. From a subset of each of the species (bonobo, common chimpanzee, gorilla, and orangutans), DNA sequence analysis was performed to determine blood group genotype. Bonobo and common chimpanzee populations were predominantly group A, which concurred with historic literature and was confirmed by genotyping. In agreement with historic literature, a smaller number of the common chimpanzees sampled were group O, although this O blood group was more often present in wild-origin animals as compared with zoo-born animals. Gorilla blood groups were inconclusive by monoclonal antibody techniques, and genetic studies were inconsistent with any known human blood group. As the genus and, specifically, the Bornean species, orangutans were identified with all human blood groups, including O, which had not been reported previously. Following this study, it was concluded that blood groups of bonobo, common chimpanzees, and some orangutans can be reliably assessed by human monoclonal antibody technology. However, this technique was not reliable for gorilla or orangutans other than those with blood group A. Even in those species with reliable blood group detection, blood transfusion preparation must include cross-matching to minimize adverse reactions for the patient.

Patterns of human genetic variation inferred from comparative analysis of allelic mutations in blood group antigen genes

Comparative analysis of allelic variation of a gene sheds light on the pattern and process of its diversification at the population level. Gene families for which a large number of allelic forms have been verified by sequencing provide a useful resource for such studies. In this regard, human blood group-encoding genes are unique in that differences of cell surface traits among individuals and populations can be readily detected by serological screening, and correlation between the variant cell surface phenotype and the genotype is, in most cases, unequivocal. Here, we perform a comprehensive analysis of allelic forms, compiled in the Blood Group Antigen Gene Mutation database, of ABO, RHD/CE, GYPA/B/E and FUT1/2 gene families that encode the ABO, RH, MNS, and H/h blood group system antigens, respectively. These genes are excellent illustrative examples showing distinct mutational patterns among the alleles, and leading to speculation on how their origin may have been driven by recurrent but different molecular mechanisms. We illustrate how alignment of alleles of a gene may provide an additional insight into the DNA variation process and its pathways, and how this approach may serve to catalog alleles of a gene, simplifying the task and content of mutation databases.

Variant ABO blood group alleles, secretor status, and risk of pancreatic cancer: results from the pancreatic cancer cohort consortium

BACKGROUND

Subjects with non-O ABO blood group alleles have increased risk of pancreatic cancer. Glycosyltransferase activity is greater for the A(1) versus A(2) variant, whereas O01 and O02 variants are nonfunctioning. We hypothesized: 1) A(1) allele would confer greater risk than A(2) allele, 2) protective effect of the O allele would be equivalent for O01 and O02 variants, 3) secretor phenotype would modify the association with risk.

METHODS

We determined ABO variants and secretor phenotype from single nucleotide polymorphisms in ABO and FUT2 genes in 1,533 cases and 1,582 controls from 12 prospective cohort studies. Adjusted odds ratios (OR) for pancreatic cancer were calculated using logistic regression.

RESULTS

An increased risk was observed in participants with A(1) but not A(2) alleles. Compared with subjects with genotype O/O, genotypes A(2)/O, A(2)/A(1), A(1)/O, and A(1)/A(1) had ORs of 0.96 (95% CI, 0.72-1.26), 1.46 (95% CI, 0.98-2.17), 1.48 (95% CI, 1.23-1.78), and 1.71 (95% CI, 1.18-2.47). Risk was similar for O01 and O02 variant O alleles. Compared with O01/O01, the ORs for each additional allele of O02, A(1), and A(2) were 1.00 (95% CI, 0.87-1.14), 1.38 (95% CI, 1.20-1.58), and 0.96 (95% CI, 0.77-1.20); P, O01 versus O02 = 0.94, A(1) versus A(2) = 0.004. Secretor phenotype was not an effect modifier (P-interaction = 0.63).

CONCLUSIONS

Among participants in a large prospective cohort consortium, ABO allele subtypes corresponding to increased glycosyltransferase activity were associated with increased pancreatic cancer risk.

IMPACT

These data support the hypothesis that ABO glycosyltransferase activity influences pancreatic cancer risk rather than actions of other nearby genes on chromosome 9q34.

Genome-wide scans for footprints of natural selection

Detecting recent selected ‘genomic footprints’ applies directly to the discovery of disease genes and in the imputation of the formative events that molded modern population genetic structure. The imprints of historic selection/adaptation episodes left in human and animal genomes allow one to interpret modern and ancestral gene origins and modifications. Current approaches to reveal selected regions applied in genome-wide selection scans (GWSSs) fall into eight principal categories: (I) phylogenetic footprinting, (II) detecting increased rates of functional mutations, (III) evaluating divergence versus polymorphism, (IV) detecting extended segments of linkage disequilibrium, (V) evaluating local reduction in genetic variation, (VI) detecting changes in the shape of the frequency distribution (spectrum) of genetic variation, (VII) assessing differentiating between populations (F_ST), and (VIII) detecting excess or decrease in admixture contribution from one population. Here, we review and compare these approaches using available human genome-wide datasets to provide independent verification (or not) of regions found by different methods and using different populations. The lessons learned from GWSSs will be applied to identify genome signatures of historic selective pressures on genes and gene regions in other species with emerging genome sequences. This would offer considerable potential for genome annotation in functional, developmental and evolutionary contexts.

The M142T mutation causes B3 phenotype: three cases and an in vitro expression study

The B3 phenotype is the most common B subtype in Korea. The B305 allele (425 T>C, M142T) was first reported in 2 Chinese individuals; however, it has not yet been reported in the Koreans, and the impact of the M142T mutation on the expression of the B3 phenotype has also not been studied. To resolve an ABO discrepancy between a group O neonate and her group O father and A(1)B(3) mother, blood samples from these individuals and other family members were referred to our laboratory for ABO gene analysis. The B305 allele was discovered in the neonate (B305/O01), her mother (A102/ B305), and her maternal aunt (B305/O02), while her father was typed as O01/O02. Transient transfection experiments were performed in HeLa cells using the B305 allele synthesized by site-directed mutagenesis; flow cytometric analysis revealed that this transfect expressed 35.5% of the total B antigen produced by the B101 allele transfect. For comparison, Bx01 allele transfects were also created, and they expressed 11.4% of the total B antigen expressed on the surface of B101 transfects. These experiments demonstrate that the M142T (425 T>C) mutation is responsible for the B subtype phenotype produced by the B305 allele.

Distribution of ABO blood group allele and identification of three novel alleles in the Chinese Han population

BACKGROUND

The ABO blood group system is clinically important in blood transfusion. The molecular characterization of ABO blood group has clinical and anthropological importance. Here, we determined the ABO alleles distribution and identified three novel alleles in the Chinese Han population.

STUDY DESIGN AND METHODS

Four hundred and seventeen Chinese Han individuals were determined by standard serologic techniques for the ABO blood group phenotypes. The ABO genotypes and alleles were analysed by polymerase chain reaction sequence-based typing (PCR-SBT) for sequencing exon 6 to 7 of the ABO gene. The polymorphisms of intron 5 and 6 of the ABO gene were also analysed by PCR-SBT. The two haplotypes including new alleles were separated by a Dynabeads M-270 Streptavidin protocol.

RESULTS

All ABO genotypes of the samples were consistent with the phenotypes. Fourteen alleles were identified based on the nucleotide sequences of exon 6 and 7, with five common alleles (A101, A102, B101, O01 and O02), six known rare alleles (A205, B110, O04, O05, O07 and O50) and three novel alleles (B112, CisAB06 and 061). The three new alleles appeared with the frequencies of 0.12%, 0.12% and 0.36%, respectively.

CONCLUSION

The detailed frequencies distribution of ABO alleles was studied in the Chinese Han population. We identified 14 alleles, including 3 novel alleles.