Rapid identification of the ABO genotypes by their single-stand conformation polymorphism

Tsai, Li-Chin; Kao, L. G.; Chang, Jan‐Gowth; Lee, Hsien-Hsiung; Linacre, Adrian; Lee, James Chun-I

doi:10.1002/(sici)1522-2683(20000201)21:3<537::aid-elps537>3.0.co;2-1

Cited by 11 publications

(13 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The fourth approach utilizes mutation screening methods that detect both known and unknown SNPs in the assayed PCR products, e.g. denaturing gradient gel electrophoresis (Johnson & Hopkinson, 1992 ;Yip et al 1995Yip et al , 1996 and single strand conformation polymorphism (SSCP) analysis (Akane et al 1996 ;Tsai et al 2000 ;Yip, 2000). Four alleles (A, B, O101 and O201) could be discriminated by SSCP analysis of a single PCR product amplified from exon 6 (Akane et al 1996).…”

Section:     Abo mentioning

confidence: 99%

Sequence variation at the human ABO locus

Yip

2002

Annals of Human Genetics

170

159

View full text Add to dashboard Cite

The ABO blood group is the most important blood group system in transfusion medicine. Since the ABO gene was cloned and the molecular basis of the three major alleles delineated about 10 years ago, the gene has increasingly been examined by a variety of DNA-based genotyping methods and analysed in detail by DNA sequencing. A few coherent observations emerge from these studies. First, there is extensive sequence heterogeneity underlying the major ABO alleles that produce normal blood groups A, B, AB and O when in correct combination with other alleles. Second, there is also extensive heterogeneity underlying the molecular basis of various alleles producing ABO subgroups such as A # , A x and B $ . There are over 70 ABO alleles reported to date and these alleles highlight the extensive sequence variation in the coding region of the gene. A unifying system of nomenclature is proposed to name these alleles. Third, extensive sequence variation is also found in the non-coding region of the gene, including variation in minisatellite repeats in the 5h untranslated region (UTR), 21 single nucleotide polymorphisms (SNPs) in intron 6 and one SNP in the 3h UTR. The haplotypes of these variations reveal a specific relationship with the major ABO alleles. Fourth, excluding the common alleles, about half of the remaining alleles are due to new mutations and the other half can better be explained by intragenic recombination (both crossover and gene conversion) between common alleles. In particular, the recombination sites in hybrid alleles can be quite precisely defined through haplotype analysis of the SNPs in intron 6. This indicates that recombination is equally as important as point mutations in generating the genetic diversity of the ABO locus. Finally, a large number of ABO genotyping methods are available and are based on restriction analysis, allele specific amplification, mutation screening techniques or their combinations. The ABO blood group system (MIM number : 110300) was discovered by K Landsteiner a century ago. It is the most important blood group system in transfusion medicine. The serological and genetic characteristics of the system and the biosynthesis of its antigens have been well established (Daniels, 1995 ;Watkins, 1980 The antigenic determinants of the system are oligosaccharides found on glycoproteins and glycolipids. As such they are not direct gene products of the ABO gene. Instead, the ABO gene encodes enzymes known as glycosyltransferases which transfer specific sugar residues to a precursor substance (the H antigen) to produce the A and B antigens. There are three major alleles at the ABO locus : alleles A, B and O. The A allele encodes α1 4 3 N-acetylgalactosaminyltransferase (A transferase ; EC 2n4.1n40) which adds N-acetylgalactosamine (GalNAc) to the H antigen to form the A antigen. The B allele encodes α1 4 3 galactosyltransferase (B transferase ; EC 2n4.1n37) which transfers galactose

show abstract

Section:     Abo mentioning

confidence: 99%

Sequence variation at the human ABO locus

Yip

2002

Annals of Human Genetics

170

159

View full text Add to dashboard Cite

show abstract

“…analysis parameters that were carried out on DNA extracts prepared from saliva samples with known AB0 phenotypes, revealed fully consistent and reproducible results. Grunnet et al 1994;Nishimukai et al 1996;Ringel et al 2000;Tsai et al 2000), it was not necessary to perform a direct sequencing analysis. 1) and the restriction products that enabled the allelic genotypes to be determined (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The molecular genetics behind human AB0 bloodgroups are defined by a number of sequence polymorphisms located on exon 6 and exon 7 of chromosome 9 (Nishimukai et al 1996;Ringel et al 2000;Grunnet et al 1994;Tsai et al 2000;Yip 2000). At least 13 sequence polymorphisms that code for the different amino acids determining the AB0 serological traits have been well investigated.…”

Section: Ab0 Bloodgroups At the Dna Levelmentioning

confidence: 99%

“…AB0 blood group typing of forensic evidence material by means of PCR was made possible by the description of the molecular genetics of the AB0 blood group system even down to the subgroup level (Yamamoto et al 1990; Lee and Chang 1992;Grunnet et al 1994;Fukumori et al 1995;Nishimukai et al 1996;Ringel et al 2000;Tsai et al 2000;Yip 2000). AB0 genotyping may reveal invaluable data in certain identification cases although genetic typing by short tandem repeats (STRs) generally provides a superior discrimination power.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

AB0 blood group genotyping of ancient DNA by PCR-RFLP

Hummel¹,

Kahle²,

Herrmann³

2002

Int J Legal Med

View full text Add to dashboard Cite

The paper presents an PCR-RFLP-based method to determine AB0 blood groups at the genotype level. In order to ensure the applicability of the method to severely degraded DNA, new sets of primers were designed that amplify 103/104 bp and 64 bp sequences on exon 6 and exon 7 of chromosome 9, respectively. The amplification of the two PCR products and the subsequent RFLP analysis with four endonucleases was revealed to be an effective and reliable way to determine AB0 bloodgroups at the genotype level, distinguishing the alleles A, B, 0 1 , 0 1v , and 0 2 . PCR analysis of severely degraded sample material may possibly require higher cycle numbers. Therefore, the experiments presented here including those on positive control samples, were carried out employing 45 amplification cycles in order to ensure the validity of the amplification and RFLP analysis. As positive controls, small amounts of modern intact DNA extracted from saliva samples of 12 individuals with known AB0 phenotypes were used. The protocols for the AB0 typing were then applied to ancient degraded DNA extracted from 15 archaeological bones and teeth about 250 and 3,000 years old, respectively. The results presented for the archaeological sample material are based on repeated analysis derived from two independently processed DNA extracts of each sample. Moreover, the authentification process for the results derived from the archaeological samples included repeated multiplex STR genotyping of the extracts, showing the genetic uniqueness of the extracts which is the strongest possible indicator for the authenticity of an unknown DNA sample. Additionally, it was possible to compare the STR typing results to those from previous studies using the same material. Both the AB0 typing and the STR typing revealed fully reproducible results in all cases.

show abstract

“…Several DNA‐based methods using the PCR have been developed to detect the SNPs within the ABO gene. These methods include PCR‐RFLP 1, 7, allele‐specific primer PCR (ASP‐PCR) 4, 8, single‐base primer extension reaction 9, 10, mutagenically separated PCR 2 and PCR‐single‐strand conformation polymorphism (PCR‐SSCP) by slab gel electrophoresis 11–13. Analysis of SSCP by CE (SSCP‐CE) has been developed to detect single nucleotide (nt) mutations and shown to be rapid, has a high resolution and be reproducible 14–16.…”

Section: Introductionmentioning

confidence: 99%

ABO genotyping by single strand conformation polymorphism – using CE

et al. 2009

Self Cite

View full text Add to dashboard Cite

This study describes a novel method of ABO genotyping using amplicons generated by PCR-SSCP and separated by CE. We describe four amplicons with sizes of 112, 121, 123 and 160 bp based on SSCP analysis. These amplicons are amplified from exons 6 and 7 and include polymorphic sites of cDNA 261, 297, 467, 526, 646, 657, 681, 703, 1061 and 1096 generated from the ABO gene. The positions of the SSCP alleles, when rescaled using SSCP pattern as the mobility values based on an internal standard ranged, ranged from 146 to 210. The mobility variations of alleles with 1-4 SNPs within the same amplicons were from 1.88 to 12.01. These wide mobility differences allow for unambiguous allele determination. The use of different fluorescent dyes allows for the identification of two fragments with overlapping size ranges. The validity of the test was confirmed based on the SD of the mobility values from the eleven fragments of allelic ladder and it never exceeded 0.37. The mean values of the mobility variation between the samples and the ladders for the four amplicons ranged only from 0.05 to 0.39. This method was shown to successfully identify alleles A(1), A(1v), B, O(1), O(1v) and O(2) in tested samples. Since the largest amplicons are only 160 bp, this method is ideal for the fast screening ABO genotypes from trace, or seriously, degraded samples and may be valuable in clinical transfusion or forensic applications.

show abstract

Rapid identification of the ABO genotypes by their single-stand conformation polymorphism

Cited by 11 publications

References 31 publications

Sequence variation at the human ABO locus

Sequence variation at the human ABO locus

AB0 blood group genotyping of ancient DNA by PCR-RFLP

ABO genotyping by single strand conformation polymorphism – using CE

Contact Info

Product

Resources

About