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SNP analysis of the inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP) gene by a fluorescence-adapted SSCP method.

Tozaki T, Choi-Miura NH, Taniyama M, Kurosawa M, Tomita M - BMC Med. Genet. (2002)

Bottom Line: One of the SNPs was a new SNP resulting in an amino acid substitution, while the other SNPs have already been reported in the public databases.Six SNPs of the IHRP were associated with two haplotypes.The fluorescence-adapted SSCP was useful for detecting and genotyping SNPs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Physiological Chemistry, School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa, Tokyo 142-8555, Japan. ttozaki@nyc.odn.ne.jp

ABSTRACT

Background: Single-nucleotide polymorphisms (SNPs) are considered to be useful polymorphic markers for genetic studies of polygenic traits. Single-stranded conformational polymorphism (SSCP) analysis has been widely applied to detect SNPs, including point mutations in cancer and congenital diseases. In this study, we describe an application of the fluorescent labeling of PCR fragments using a fluorescent-adapted primer for SSCP analysis as a novel method.

Methods: Single-nucleotide polymorphisms (SNPs) of the inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP) gene were analyzed using a fluorescence-adapted SSCP method. The method was constructed from two procedures: 1) a fluorescent labeling reaction of PCR fragments using fluorescence-adapted primers in a single tube, and 2) electrophoresis on a non-denaturing polyacrylamide gel.

Results: This method was more economical and convenient than the single-stranded conformational polymorphism (SSCP) methods previously reported in the detection of the labeled fragments obtained. In this study, eight SNPs of the IHRP gene were detected by the fluorescence-adapted SSCP. One of the SNPs was a new SNP resulting in an amino acid substitution, while the other SNPs have already been reported in the public databases. Six SNPs of the IHRP were associated with two haplotypes.

Conclusions: The fluorescence-adapted SSCP was useful for detecting and genotyping SNPs.

No MeSH data available.


Related in: MedlinePlus

Relationship between genomic structure and the location of single-nucleotide polymorphisms (SNPs) in the IHRP gene
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Figure 3: Relationship between genomic structure and the location of single-nucleotide polymorphisms (SNPs) in the IHRP gene

Mentions: A total of 20 Japanese individuals were genotyped for sequence variations of all 24 exons and the surrounding regions of the IHRP gene. A total of eight SNPs were found in the gene by this method. The locations of these SNPs are shown in Figure 3. Five of the SNPs found in the IHRP gene were located within exons: a T/C at nucleotide (nt) position 24 in exon 1, a T/C at nt position 75 in exon 1, a T/A at nt position 3448 in exon 3, a G/A at nt position 3723 in exon 4, and a G/A at nt position 3843 in exon 4. Three SNPs of the IHRP gene were located within introns: a G/C at nt position 10912 near exon 16, a A/G at nt position 12599 near exon 20, a A/G at nt position 13522 near exon 21. One of the five exon-based SNPs, the T/A at nt position 3448 in exon 3, resulted in an amino acid substitution from Ile to Asn. This is a newly identified SNP, while the remaining seven SNPs have already been reported in the NCBI dbSNP database and the JSNP db SNP database . Table 2 summarizes the SNPs and their allelic frequencies detected in our samples of 20 Japanese subjects.


SNP analysis of the inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP) gene by a fluorescence-adapted SSCP method.

Tozaki T, Choi-Miura NH, Taniyama M, Kurosawa M, Tomita M - BMC Med. Genet. (2002)

Relationship between genomic structure and the location of single-nucleotide polymorphisms (SNPs) in the IHRP gene
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC117798&req=5

Figure 3: Relationship between genomic structure and the location of single-nucleotide polymorphisms (SNPs) in the IHRP gene
Mentions: A total of 20 Japanese individuals were genotyped for sequence variations of all 24 exons and the surrounding regions of the IHRP gene. A total of eight SNPs were found in the gene by this method. The locations of these SNPs are shown in Figure 3. Five of the SNPs found in the IHRP gene were located within exons: a T/C at nucleotide (nt) position 24 in exon 1, a T/C at nt position 75 in exon 1, a T/A at nt position 3448 in exon 3, a G/A at nt position 3723 in exon 4, and a G/A at nt position 3843 in exon 4. Three SNPs of the IHRP gene were located within introns: a G/C at nt position 10912 near exon 16, a A/G at nt position 12599 near exon 20, a A/G at nt position 13522 near exon 21. One of the five exon-based SNPs, the T/A at nt position 3448 in exon 3, resulted in an amino acid substitution from Ile to Asn. This is a newly identified SNP, while the remaining seven SNPs have already been reported in the NCBI dbSNP database and the JSNP db SNP database . Table 2 summarizes the SNPs and their allelic frequencies detected in our samples of 20 Japanese subjects.

Bottom Line: One of the SNPs was a new SNP resulting in an amino acid substitution, while the other SNPs have already been reported in the public databases.Six SNPs of the IHRP were associated with two haplotypes.The fluorescence-adapted SSCP was useful for detecting and genotyping SNPs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Physiological Chemistry, School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa, Tokyo 142-8555, Japan. ttozaki@nyc.odn.ne.jp

ABSTRACT

Background: Single-nucleotide polymorphisms (SNPs) are considered to be useful polymorphic markers for genetic studies of polygenic traits. Single-stranded conformational polymorphism (SSCP) analysis has been widely applied to detect SNPs, including point mutations in cancer and congenital diseases. In this study, we describe an application of the fluorescent labeling of PCR fragments using a fluorescent-adapted primer for SSCP analysis as a novel method.

Methods: Single-nucleotide polymorphisms (SNPs) of the inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP) gene were analyzed using a fluorescence-adapted SSCP method. The method was constructed from two procedures: 1) a fluorescent labeling reaction of PCR fragments using fluorescence-adapted primers in a single tube, and 2) electrophoresis on a non-denaturing polyacrylamide gel.

Results: This method was more economical and convenient than the single-stranded conformational polymorphism (SSCP) methods previously reported in the detection of the labeled fragments obtained. In this study, eight SNPs of the IHRP gene were detected by the fluorescence-adapted SSCP. One of the SNPs was a new SNP resulting in an amino acid substitution, while the other SNPs have already been reported in the public databases. Six SNPs of the IHRP were associated with two haplotypes.

Conclusions: The fluorescence-adapted SSCP was useful for detecting and genotyping SNPs.

No MeSH data available.


Related in: MedlinePlus