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PubMed1989

BamHI and SacI RFLPs of the human immunoglobulin IGHG genes with reference to the Gm polymorphism in African people. Evidence for a major polymorphism.

In this paper, we extend the study of the IGHG gene RFLPs in black African persons and in some other individuals characterized by a Negroid admixture. We demonstrate a polymorphism that is much more important in black Africans, than in Caucasoids, mainly for the IGHG3 and G1 genes, the most 5' members of the IGHG multigene family. These genes encode for the IgG3 and IgG1 subclasses, which are of crucial biological importance.

Alleles↗
PubMed2000

Single-strand conformational polymorphism and sequence polymorphism of Mhc-DRB in Latxa and Karrantzar sheep: implications for Caprinae phylogeny.

Single-strand conformational polymorphism analysis and DNA sequencing were used to characterize Mhc-DRB second exon variability in the Latxa and Karrantzar breeds of sheep. The presence of more than two sequences in some animals indicates that alleles of two different loci have been amplified. Six new alleles were identified by sequencing. The allele frequency distribution of the DRB1 gene is striking, with two alleles accounting for half of the gene pool in both breeds under study. The most frequent allele in both breeds was the same (named DRB1*0702), with some specific amino acids: Tyr in position 31 and Thr in 51. A species variability analysis was also performed including the entire set of sheep DRB exon 2 sequences. Based on the patchwork patterns of different alleles, interallelic recombination appears to be playing a significant role in the generation of allelic diversity at this locus in sheep. The phylogenetic tree of all known Caprinae DRB sequences shows that certain alleles from one species are more closely related to those from other species than they are to each other. Allele DRB1*0702 merits special attention due to its high similarity to the Mufflon allele. As this is the most frequent in both breeds analyzed, one can hypothesize that in sheep, both Mufflon and Argali have had different influences depending on the sheep breed under study and that the relationship between domestic sheep and Mufflon is greater than previously thought. The data generated in this study can serve as a basis for developing a typing assay for the sheep DRB genes in the Latxa and Karrantzar populations.

Alleles↗
PubMed2003

A linkage map of the basidiomycete Coprinus cinereus based on random amplified polymorphic DNAs and restriction fragment length polymorphisms.

A genetic linkage map of the basidiomycete Coprinus cinereus was constructed on the basis of the segregation of 219 RAPD markers, 28 RFLP markers and the A and B mating-type loci among 40 random basidiospore progeny from a single cross between a wild-type homokaryon, KF(3)#2, and an AmutBmut strain, #326. Thirteen linkage groups covering a total of 1346cM were identified and correlated to the 13 chromosomes of this fungus by hybridization of RFLP and RAPD marker probes to CHEF blots. These probes also revealed chromosome length polymorphisms (CLP), which could be associated with haplotype plots of the progeny. The average kb/cM ratio in this cross was approximately 27.9kb/cM. The AmutBmut strain undergoes sexual development without mating, because of mutations in both A and B mating-type loci, and has been used to identify mutations affecting developmental processes such as dikaryosis, fruit body morphogenesis, and meiosis. The markers in the map, especially the RAPD ones, would facilitate mapping of genes responsible for such mutations induced in the AmutBmut strain.

Chromosome Mapping↗
PubMed2005

5,10-Methylenetetrahydrofolate reductase polymorphisms and pharmacogenetics: a new role of single nucleotide polymorphisms in the folate metabolic pathway in human health and disease.

Knowledge about the role of folate, a water-soluble B vitamin, and single nucleotide polymorphisms (SNPs) in the folate metabolic pathway in human health and disease has been rapidly expanding. Recently, functionally significant SNPs in 5,10-methylenetetrahydrofolate reductase (MTHFR), a critical enzyme for intracellular folate homeostasis and metabolism, have been identified and characterized. An emerging body of in vitro and clinical evidence suggests that these MTHFR SNPs may be an important pharmacogenetic determinant of predicting response to and toxicity of methotrexate and 5-fluorouracil-based cancer and anti-inflammatory treatments because of their well-defined and highly relevant biochemical effects on intracellular folate composition and one-carbon transfer reactions.

5,10-Methylenetetrahydrofolate Reductase (FADH2)↗
PubMed2006

Use of PCR-restriction fragment length polymorphism analysis to identify the main new world Leishmania species and analyze their taxonomic properties and polymorphism by application of the assay to clinical samples.

At least 13 characterized Leishmania species are known to infect humans in South America. Five of these parasites are transmitted in the sylvatic ecotopes of the whole French Guianan territory and responsible for cutaneous leishmaniasis. For the diagnosis of cutaneous leishmaniasis, restriction fragment length polymorphism (RFLP) analyses have shown promising results. Thus, the end of the small subunit and internal transcribed spacer 1 of the rRNA genes were sequenced and targeted by PCR-RFLP analysis in the 10 main New World (NW) Leishmania species from the two subgenera. Then, the procedure was tested on 40 samples from patients with cutaneous leishmaniasis, and its results were compared with those of conventional methods. (i) The results of this simple genus-specific method were in agreement with those of previous isoenzyme analyses. (ii) This method distinguished the most medically relevant Leishmania species with only one enzyme (RsaI). (iii) This method could be performed directly on human biopsy specimens (sensitivity of 85.7%). Performing NW Leishmania species typing rapidly and easily in the field constitutes a very valuable improvement for detection of Leishmania spp. Revealing great diversity with several enzymes, this method could also be useful for taxonomic, ecological, and epidemiological studies in space and time.

Animals↗
PubMed2006

Rapid screening of fluoroquinolone resistance determinants in Streptococcus pneumoniae by PCR-restriction fragment length polymorphism and single-strand conformational polymorphism.

A rapid method, using PCR-restriction fragment length and single-strand conformation polymorphism (SSCP), was applied to screen for mutations of the fluoroquinolone resistance determinants in Streptococcus pneumoniae. One hundred nonduplicate Streptococcus pneumoniae isolates with ciprofloxacin MICs of > or = 4.0 microg/ml from the Prince of Wales Hospital, Hong Kong, years 2000 to 2003, were examined. For each isolate, PCR amplicons of quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, parC, and parE genes were digested with AluI, HinfI, Sau3AI, and MspI, respectively, and analyzed by SSCP. Each SSCP pattern was given a number, and each isolate obtained a four-digit code, e.g., 1111, that represented the SSCP profile. The SSCP patterns were correlated to mutations characterized from sequence analyses of PCR amplicons. The most common SSCP profile obtained was no. 5232 (40%), which included strains with two amino acid substitutions in the ParC (Lys-137-Asn) and ParE (Ile-460-Val) genes, followed by the SSCP profile 5223 (17%), which included strains with amino acid substitutions in the ParE (Ile-460-Val) gene only. Ten isolates (10%) with amino acid substitutions at GyrA and ParE (+/-ParC) genes were resistant to levofloxacin with a MIC of > or = 16 microg/ml. Other SSCP profiles were unique in distinguishing the common amino acid substitutions in GyrA (Ser-81-Phe) and ParC (Lys-137-Asn, Ser-79-Phe plus Lys-137-Asn, Asp-83-Asn plus Lys-137-Asn, Ser-79-Phe, and Glu-96-Asp). SSCP analysis of restricted fragments generated patterns that were highly discriminative for mutations present in the QRDRs of gyrA, gyrB, parC, and parE. This method provides a database of high resolution profiles on these mutations and allows rapid screening for new mutations of the fluoroquinolone resistance genes.

Amino Acid Substitution↗
PubMed1987

Neutrality tests of highly polymorphic restriction-fragment-length polymorphisms.

The allele frequency data of Baird et al. were tested using Ewens-Watterson sampling theory for goodness of fit to the infinite-alleles model of neutral evolution. Although probes of both the HRAS-1 and D14S1 loci identify highly diverse restriction-fragment-length polymorphisms, the observed values of gene identity (F) and the common allele frequency (C) are not significantly different from the neutral expectation. Allele frequency distributions show a tendency toward a deficit in diversity for HRAS-1 and a slight excess diversity for D14S1. The direction of these departures is consistent with potential selective effects of the Harvey-ras oncogene and hitchhiking of the D14S1 locus to closely linked immunoglobulin genes. Direct chi 2-tests of goodness of fit of the observed and expected allele frequency distributions reveal significant departures in the caucasoid and Hispanic HRAS-1 distributions but not in any of the other tests.

Alleles↗
PubMed2001

Analysis of the EPHX1 113 polymorphism and GSTM1 homozygous null polymorphism and oral clefting associated with maternal smoking.

Maternal cigarette smoking during the first trimester of pregnancy is associated with an increased risk of having a child with an oral cleft. Compounds present in cigarette smoke undergo bioactivation and/or detoxication. Phase I of this process results in the formation of reactive epoxides, which can form DNA adducts initiating and promoting mutagenesis, carcinogenesis, or teratogenesis. Microsomal epoxide hydrolase (mEH; gene symbol EPHX1) catalyzes hydrolysis of epoxides. Phase II involves attachment of a moiety (e.g., glutathione) to the compound mediated by a variety of enzymes, including glutathione S-transferase, generally resulting in a decreased reactivity. Recent studies suggest an association between the EPHX1 codon 113 polymorphism or homozygous null GSTM1 allele and the risk of carcinogenesis, emphysema, phenytoin-associated oral clefting, and the risk of spontaneous abortion. This study explores the association between EPHX1 codon 113 and homozygous null GSTM1 genotypes and oral clefting among infants whose mothers smoked during pregnancy. Case infants were diagnosed with isolated cleft lip with or without cleft palate (CL/P). EPHX1 codon 113 allelotyping was performed on 195 samples (85 cases, 110 controls) by PCR/RFLP analysis. 130 samples (79 cases, 51 controls) were tested for the GSTM1 homozygous null genotype using PCR. Using the odds ratio as a measure of association, we did not observe elevated risks of CL/P associated with either allelic comparison. This suggests that when mothers smoke periconceptionally, their infants having these alleles at either (or both) loci were not at substantially increased risk for CL/P compared to infants with the wild-type alleles.

Alleles↗
PubMed2006

Systematic search for single nucleotide polymorphisms in a lymphoid tyrosine phosphatase gene (PTPN22): association between a promoter polymorphism and type 1 diabetes in Asian populations.

The protein tyrosine phosphatase, nonreceptor 22 gene (PTPN22) maps to human chromosome 1p13.3-p13.1 and encodes an important negative regulator of T-cell activation, lymphoid-specific phosphatase (Lyp). Recently, the minor allele of a single-nucleotide polymorphism (SNP) at nucleotide position 1858 (rs2476601, +1858C > T) was found to be associated with type 1 diabetes. However, the degree of the association is variable among ethnic populations, suggesting the presence of other disease-associated variants in PTPN22. To examine this possibility, we carried out a systemic search for PTPN22 using direct sequencing of PCR-amplified products in the Japanese population. Association and linkage studies were also conducted in 1,690 Japanese samples, 180 Korean samples, and 472 Caucasian samples from 95 nuclear families. We identified five novel SNPs, but not the +1858C > T SNP. Of these two frequent SNPs, -1123G > C, and +2740C > T were in strong linkage disequilibrium (LD), and the -1123G > C promoter SNP was associated with acute-onset but not slow-onset type 1 diabetes in the Japanese population (odds ratio [OR] = 1.42, 95% CI = 1.07-1.89, P = 0.015). This association was observed also in Korean patients with type 1 diabetes (Mantel-Haenszel chi2= 6.543, P = 0.0105, combined OR = 1.41 95% CI = 1.09-1.82). Furthermore, the affected family-based control (AFBAC) association test and the transmission disequilibrium analysis of multiplex families of European descent from the British Diabetes Association (BDA) Warren Repository indicated that the association was stronger in -1123G > C compared to +1858C > T. In conclusion, the type 1 diabetes association with PTPN22 is confirmed, but it cannot be attributed solely to the +1858C > T variant. The promoter -1123G > C SNP is a more likely causative variant in PTPN22.

Alleles↗
PubMed1993

An antigen processing polymorphism revealed by HLA-B8-restricted cytotoxic T lymphocytes which does not correlate with TAP gene polymorphism.

In previous studies of antigen presentation through HLA-B27, we identified a healthy person whose lymphoblastoid cells do not present three B27-restricted viral epitopes to specific cytotoxic T lymphocytes (CTL), despite adequate cell surface expression of HLA-B2702 of normal sequence. Similar findings were observed in all members of his family sharing the HLA-A3-B2702 haplotype. The original donor, NW, carries HLA-B8 on his other class I haplotype, which his daughter, HW, has inherited. We now report a failure to present an HLA-B8-restricted epitope from influenza nucleoprotein following viral infection of NW cells, although exogenous added peptide is still presented normally. However, cells from HW, which do not carry the A3-B2702 haplotype, present the expected epitope after viral infection. Another B8-restricted epitope, from human immunodeficiency virus-gag, is presented equally well by both cell lines when infected with gag-vaccinia. This antigen processing phenotype does not correlate with any of the known human TAP-1 and TAP-2 polymorphisms.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1991

Application of silver staining to the rapid typing of the polymorphism of HLA-DQ alleles by enzymatic amplification and allele-specific restriction fragment length polymorphism.

A rapid and highly sensitive silver staining method, originally developed for the detection of proteins, was slightly modified to detect nucleic acids in polyacrylamide gels. The second exons of the histocompatibility antigen HLA-DQA 1 and DQB 1 genes were selectively amplified from genomic DNA by the polymerase chain reaction (PCR). Digestion of the PCR products by endonucleases, followed by their size-separation on polyacrylamide gels and visualization by silver staining, allowed us to define the HLA-DQ alleles of the genomic DNA. The intensity of staining of digested PCR-amplified DNA is linear from at least 8 to 18 ng for fragments of lengths ranging from approximately 40 to 200 bp. Thus, silver staining in combination with PCR and allele-specific restriction fragment length polymorphism provides a simple, safe, and rapid method for accurate definition of HLA-DQ alleles at the nucleotide level in the clinical typing laboratory.

Base Sequence↗
PubMed1987

Adaptive significance of amylase polymorphism in Drosophila. I. The geographical pattern of allozyme polymorphism at the amylase locus in Drosophila subobscura.

Allelic variation at the Amy locus was studied in eight natural populations from the central and northern range of D. subobscura, and the geographical pattern of Amy polymorphism over the range of this species was described. Even though regional and local differences in gene frequencies were found, in general the same alleles occur at high, intermediate and low frequencies, in nearly all populations. There are no significant differences in allele frequencies, but there is significant difference in the degree of heterozygosity among groups of populations from the northern, central and southern range. An analysis of population subdivision indicates that heterogeneity within populations is higher than between populations. Genetic distance values indicate that there is a variable degree of geographical differentiation between local populations. Variability within and between continental and insular populations is also discussed.

Adaptation, Physiological↗
PubMed1991

Detection of frequent BglII polymorphism by polymerase chain reaction and TaqI restriction fragment length polymorphism for 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase at the human HSD beta 3 locus (1p11-p13).

Analysis of amplified polymerase chain reaction products of 575 bp from the fourth exon of the human type I 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase gene at locus HSD beta 3 1p11-p13, reveals a frequent two-allele polymorphism at codon Leu338 due to a silent substitution of T by C, thus creating a BglII site leading to 371- and 204-bp fragments. Southern blot analysis of BglII-digested DNA from 57 individuals using a genomic probe detects two allelic fragments of 5.3 kb and 0.77 kb, respectively, while two allelic fragments of 3.7 kb and 3.4 kb are obtained in TaqI digests with multiple constant bands, as also observed with BglII digests.

Bacterial Proteins↗
PubMed1982

Human chromosomal polymorphism. II. Chromsomal C polymorphism in Mongoloid populations of Central Asia.

C polymorphism of chromosomes 1, 9 and 16 was studied in 447 Mongoloids of Central Asia living under different ecological conditions; two highland (Kirghiz) and three steppe (Kazakh, Mongolian, and Dungan) populations. C band sizes were estimated according to the semiquantitative 5-level method of Patil and Lubs (1977). All the ethnic groups studied showed statistically significant homogeneity in the frequency of C variants. It is suggested that chromosomal C-heterochromatin material has no selective value in the process of human adaptation to extreme high-altitude factors.

Adolescent↗
PubMed1994

New murine polymorphisms detected by random amplified polymorphic DNA (RAPD) PCR and mapped by use of recombinant inbred strains.

Oligonucleotide primers of random sequence that were 12 bases in length, 58% in GC content, and lacking internal palindromes were designed. By random amplified polymorphic DNA (RAPD) PCR, these primers were used to survey for DNA variations between the progenitors of the mouse AXB and BXA recombinant inbred sets (A/J and C57BL/6J). We identified 17 DNA variants detected by 10 primers. Map positions for these variants were determined by comparing their strain distribution patterns in the AXB, BXA recombinant inbred sets with strain distribution patterns of previously published loci. When necessary, BXD and NXSM recombinant inbred sets were also used. These 17 new loci mapped to 12 chromosomes. The 10 primers were also used to survey 20 inbred mouse strains including the progenitors of other recombinant inbred sets and four mouse strains recently inbred from the wild (CAST/Ei, MOLF/Ei, PERA/Ei, and SPRET/Ei).

Animals↗
PubMed1980

An electrophoretic polymorphism that mimics a true genetic polymorphism in Triturus cristatus carnifex (Amiphibia, Urodela).

Phosphoglucomutase electrophoretic patterns have been studied in 60 tail homogenates of Triturus cristatus carnifex. Our results show that the same sample produces a different electrophoretic pattern with homogenate ageing; a new band of intermediate mobility appears, together with the one produced by the fresh preparation. The phenomenon can mimic a true genetic polymorphism when differently stored samples are analyzed.

Animals↗
PubMed1995

Alpha-1-antichymotrypsin bi-allele polymorphism, apolipoprotein-E tri-allele polymorphism and genetic risk of Alzheimer's syndrome.

The alpha1-antichymotrypsin and apolipoprotein-E polymorphisms were investigated in patients suffering from Alzheimer's syndrome and non-demented psychiatric inpatients as controls. The apolipoprotein E allele 4, well known as risk factor, tended to be elevated in the index group. The frequency of the alpha1-antichymotrypsin allele A was significantly increased in patients with Alzheimer's syndrome: 0.647 vs. 0.483 (chi-square test, p < 0.05). We conclude that, apart from the apolipoprotein E allele 4, the alpha1-antichymotrypsin allele A possibly represents a second genetic factor increasing individual's risk for Alzheimer's syndrome.

Aged↗