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PubMed2004

Restriction fragment length polymorphism of L1 amplicon using Rsa 1 detects five different human papillomavirus types and their co-infections among women attending a gynaecological outpatient department.

Detection of human papillomavirus (HPV) types 6, 11, 16, 18, and 33 including co-infections among females attending gynaecological outpatient department and cancer clinics, was done by restriction fragment length polymorphism (using Rsa-1), of approximately 450bp amplicon, obtained by the amplification of the L1 region of HPV genome with consensus primers MY09/11 [Cancer Cells 7 (1989) 209]. The results were further tested with HPV type specific primers [J. Med. Virol. 29 (1989) 20]. The technique was found to be low-cost and less time consuming. The advantage of Rsa 1 over other enzymes was that it detects the five most prevalent HPV types commonly associated with warts, cervical dysplasia, and cancer.

Bacteriophage phi X 174↗

PubMed1987

Ha-ras-1 restriction fragment length polymorphism and susceptibility to colon adenocarcinoma.

It is not yet clear whether some polymorphic variants of the Ha-ras-1 gene confer genetic predisposition to cancer. However, recent data on myelodysplasia and lung cancer are controversial. To clarify this point, 62 colorectal adenocarcinoma patients were examined for the Ha-ras-1 gene restriction fragment length polymorphism and results were compared with those of 108 healthy blood donors. No Ha-ras-1 polymorphic variants specifically associated with the cancer patients were detected. However, a specific genotype was significantly more frequent in the healthy donors than in the cancer patients (16% versus 5%), suggesting an interaction between the two alleles of the gene.

Adenocarcinoma↗

PubMed1998

[Tuberculosis in AIDS patients: the contribution of an analysis of the restriction fragment length polymorphism of Mycobacterium tuberculosis isolates].

BACKGROUND: In this report we study tuberculosis transmission in HIV infected patients using molecular epidemiological methods. PATIENTS AND METHODS: We have studied 60 M. tuberculosis isolates from 30 HIV infected cases, and their clinical-epidemiological data. Susceptibility to tuberculostatic agents and electrophoretic patterns using RFLPs (restriction fragment length polymorphisms) method were evaluated. Dice's coefficient was used for the similarity analysis. RESULTS: Over 73% studied patients were included in clusters using RFLPs analysis. This data show that nearly 60% of the tuberculosis cases in our area have a recent transmission. Forty per cent of these cases were included in the main cluster. The frequency of tuberculostatic-resistant strains in HIV infected patients was similar to the that of observed in other patients. We did not find correlation between RFLPs clusters and clinical-epidemiological data. CONCLUSIONS: Tuberculosis transmission in HIV-positive patients using RFLPs as molecular marker shows that 60% of the cases are caused by recently acquired strains. We did not find multi-drug resistant strains in our isolates. However due to the high transmissibility of these circulating clones, control disease measures in this group of risk population are required.

AIDS-Related Opportunistic Infections↗

PubMed1992

HLA gene analysis in a Japanese family with hypertrophic cardiomyopathy by restriction fragment length polymorphism.

A large Japanese family with hypertrophic cardiomyopathy (HCM) was examined (n = 61). Ten of 14 affected family members who showed HCM on the basis of electrocardiography and two-dimensional echocardiography were subjected to human leukocyte antigen (HL-A)-A,B,C typing by the lymphocyte cytotoxicity test and D, DR typing by restriction fragment length polymorphism (RFLP). As control, the HLA genotype of 14 non-affected family members was analyzed. HLA typing of the affected subjects with HCM revealed a very close association (67%) of HLA-DR (4w8) among A,B,C,D and DR. However, the LOD scores of HLA-DR4 and -DR w8 were 0.693 (theta = 0.35) and 0.642 (theta = 0.30) respectively. These data suggest that HLA-loci, analyzed on the basis of RFLP, may not be related with familial HCM with or without obstruction.

Cardiomyopathy, Hypertrophic↗

PubMed1987

Determination of clonality in acute nonlymphocytic leukemia by restriction fragment length polymorphism and methylation analysis.

Determination of cellular clonality in hematological malignancies provides fundamental information that is important in understanding the pathogenesis of these disorders. We present here an extension of one approach to accomplish this that is based on the interpretation of different methylation patterns on active and inactive X chromosomes within the region of the hypoxanthine-guanine phosphoribosyltransferase gene spanned by a restriction fragment length polymorphism. The successful application of the method to determine clonality is described for three female patients with acute nonlymphocytic leukemia.

Acute Disease↗

PubMed1993

Restriction fragment length polymorphism analysis of Fusobacterium necrophorum using a novel repeat DNA sequence and a 16S rRNA gene probe.

A repeated DNA sequence was isolated from Fusobacterium necrophorum biotype AB, strain FnS1. The repeated sequence shared considerable homology with the transposase gene from the Pseudomonas syringiae insertion sequence IS801. The repeat sequence was used together with a 16S ribosomal RNA gene probe to type F. necrophorum isolates using restriction fragment length polymorphisms. The probes revealed differences between several clinical isolates and will be useful tools to study the epidemiology of ovine foot abscess and other diseases caused by F. necrophorum.

Amino Acid Sequence↗

PubMed1993

Lack of disease associated HLA-DQ restriction fragment length polymorphisms in families with autoimmune thyroid disease.

Autoimmune thyroid disease (AITD) is often familial and serological HLA disease associations have been described in many different populations. However, such HLA disease associations are weak and the precise molecular contribution of HLA antigens to thyroid disease susceptibility remains unknown. Much of the data available are cross-sectional and few studies have explored familial inheritance of AITD at the molecular level. We have, therefore, examined the inheritance of AITD in multiplex and multi-generational families using restriction fragment length polymorphism (RFLP) analysis of DNA digested with the restriction enzyme BamH1 and probed with a full length human HLA-DQ beta cDNA probe. Thirty seven subjects in 7 informative families were available for study. Eleven subjects had Graves' disease and 4 were diagnosed as having Hashimoto's thyroiditis. Segregation of polymorphic fragments enabled genotyping of each individual to produce fully informative families. LOD scores were computed, using the LIPED program, for dominant and recessive models of inheritance, for recombination fractions of 0.01 to 0.5 for each sex, and for penetrances of 0.1 to 1.0. The results showed that maximum LOD scores were negative for all of the inheritance models tested. If the primary locus for AITD were in the HLA region, LOD scores would be highly positive. These data, therefore, provide strong evidence against a disease locus for AITD in linkage disequilibrium with the HLA-DQ beta locus.

Adult↗

PubMed1991

Human CYP1A1 (cytochrome P(1)450) gene: lack of association between the Msp I restriction fragment length polymorphism and incidence of lung cancer in a Norwegian population.

In this study of 221 lung cancer patients and 212 controls, no association between a Msp I polymorphism in the CYP1A1 gene and an increased risk of lung cancer was found. Histological type, smoking habits and family history were also examined. No associations between the Msp I restriction fragment length polymorphism in the CYP1A1 gene and any of these parameters were found. These results are in contrast to a previous report by a Japanese group (Kawajiri et al., 1990) who found an association between the less common allele and an increased susceptibility to lung cancer in their population. The frequency of the less common Msp I 1.9 kb fragment allele (C2) appears to be three times greater in the Japanese population than in the Norwegian population and a Caucasian population of North America. It is possible that in the Asian population this Msp I polymorphism is in linkage disequilibrium with another mutation important for CYP1A1 gene expression, whereas in the Caucasian population these mutations are in equilibrium.

Adenocarcinoma↗

PubMed1987

The coding sequence for the 32,000-dalton pulmonary surfactant-associated protein A is located on chromosome 10 and identifies two separate restriction-fragment-length polymorphisms.

The primary protein component of human pulmonary surfactant is a 32,000-dalton glycoprotein called surfactant-associated protein A. This protein is important for normal lung function, and its expression is developmentally regulated. Using a mapping panel of somatic-cell hybrids, we have localized the coding sequence for pulmonary surfactant-associated protein A to chromosome 10. Additionally, this sequence identifies two separate MspI restriction-fragment-length polymorphisms. Since there is a relative lack of polymorphic markers for chromosome 10, this sequence may be useful in linkage analysis.

Animals↗

PubMed1994

C6 haplotypes: associations of a Dde I site polymorphism to complement deficiency genes and the Msp I restriction fragment length polymorphism (RFLP)

Complement C6 has a common charge polymorphism designated A and B with gene frequencies of 0.65 and 0.35. The probable molecular basis for this is a Glu (C6A) for Ala (C6B) substitution at amino acid position 98, and is detected by digestion with the restriction enzyme Dde I of a polymerase chain reaction (PCR)-amplified fragment of genomic DNA. C6A was found to be Dde I-positive and C6B corresponds to Dde I-negative. We have applied our Dde I A/B polymorphism genotyping method to the investigation of C6-deficient individuals with complete (C6Q0) and sub-total deficiency (C6SD) protein phenotypes, including members of four families. We have also investigated the RFLP detected by digestion of genomic DNA with the enzyme Msp I, which is due to a polymorphic site located in the 5' section of the gene, the variable sequence of which has yet to be determined. Sixteen out of seventeen unrelated C6Q0 subjects were found to be genotypically Dde I B/Msp I-negative; the remaining subject was heterozygous at both the loci under investigation. The C6SD phenotype was found to be associated with the Dde I A/Msp I-positive genotype in two families with combined C6/C7 subtotal deficiency and two with C6SD. It can be concluded that the two forms of C6 deficiency, C6Q0 and C6SD, arose independently on two different C6 allelic backgrounds. These associations have allowed the genotyping of the rare families that contain both types of deficiency. We have also defined a number of normal C6 Dde I/Msp I haplotypes in Caucasians and Cape Coloured populations.

Adult↗

PubMed1999

Possible susceptibility of the HLA-DPB10402 and HLA-DPB104 alleles to unexplained recurrent abortion: analysis by means of polymerase chain reaction-restricted fragment length polymorphism method.

PROBLEM: To clarify whether HLA-DP antigens are associated with patient population of unexplained recurrent abortion. METHOD OF STUDY: The frequency of HLA-DPB1 alleles in patients with unexplained recurrent abortion, and the compatibility of HLA-DPB1 alleles between patient couples, were studied using a polymerase chain reaction (PCR)-restricted fragment length polymorphism (RFLP) method. Thirty patients who had a history of unexplained primary recurrent abortion, and their husbands, were typed for HLA-DPB1 genotype. Two hundred and ninety-nine base pair fragments from the second exon of HLA-DPB1 genes were selectively amplified using the PCR-primers. After amplification, the DNAs were digested with restriction endonucleases, and subjected to electrophoresis in a 12% polyacrilamide gel to determine HLA-DPB1 genotype. RESULTS: The frequency of HLA-DPB1*0402 and DPB1*04 alleles in the patient group (n = 30) was significantly increased, as compared to that in the normal fertile women (n = 30). The frequency of HLA-DPB1*04 allele in the patient group was significantly increased, as compared to that in the general population (n = 112). No significant compatibility of HLA-DPB1 alleles could be observed between patient couples and normal fertile couples. CONCLUSION: These findings suggest a possible new class II association with patient population of unexplained recurrent abortion.

Abortion, Habitual↗

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↗

PubMedDate not supplied

Molecular and genetic characterization and physical mapping of 11 new markers detecting multiallele restriction fragment length polymorphisms on the short arm of human chromosome 3.

Genetic markers with high degrees of polymorphisms are of vital importance in the construction of high resolution (2-4 cM) linkage maps of human chromosomes as specified in the short-term goals of the Human Genome Initiative. In this paper, we report on molecular and genetic characterization and physical localization of 11 new multiallele restriction fragment length polymorphism markers on human chromosome 3p. Ten of these represent three- and four-allele polymorphisms of the base substitution type probably at two adjacent restriction sites. One has been identified as a novel mini-satellite sequence comprising a variable copy number tandem repeat array of a G/T-rich 79-bp sequence. This collection of multiallele polymorphic (PIC values: 0.40-0.60) markers should prove valuable and increase the resolution power of the available chromosome 3p genetic markers.

Alleles↗

PubMed2004

Molecular differentiation of Angiostrongylus costaricensis, A. cantonensis, and A. vasorum by polymerase chain reaction-restriction fragment length polymorphism.

Angiostrongylus cantonensis, A. costaricensis, and A. vasorum are etiologic agents of human parasitic diseases. Their identification, at present, is only possible by examining the adult worm after a 40-day period following infection of vertebrate hosts with the third-stage larvae. In order to obtain a diagnostic tool to differentiate larvae and adult worm from the three referred species, polymerase chain reaction-restriction fragment length polymorphism was carried out. The rDNA second internal transcribed spacer (ITS2) and mtDNA cytochrome oxidase I regions were amplified, followed by digestion of fragments with the restriction enzymes RsaI, HapII, AluI, HaeIII, DdeI and ClaI. The enzymes RsaI and ClaI exhibited the most discriminating profiles for the differentiation of the regions COI of mtDNA and ITS2 of rDNA respectively. The methodology using such regions proved to be efficient for the specific differentiation of the three species of Angiostrongylus under study.

Angiostrongylus↗

PubMed1987

Heterogeneity in the structural basis of the human complement C4A null allele (C4A Q0) as revealed by HindIII restriction fragment length polymorphism analysis.

The highly polymorphic fourth component of human complement (C4) is usually encoded by two genes. C4A and C4B, adjacent to the 21-hydroxylase (21-OH) genes, 21-OHA and 21-OHB, and is also remarkable in the high frequency of the 'null' alleles, C4A Q0 and C4B Q0. The molecular basis for the C4A Q0 allele was studied in 26 families through restriction fragment length polymorphism (RFLP) analysis with C4 and 21-OH cDNA probes after digestion of the DNA with the endonuclease HindIII. The individuals expressing the extended haplotype HLA-A1 (of A2) Cw7 B8 C2C BfS C4AQ0B1 DR3 have a large deletion taking off the C4A and 21-OHA genes.

Alleles↗

PubMed1991

Severe von Willebrand disease due to a defect at the level of von Willebrand factor mRNA expression: detection by exonic PCR-restriction fragment length polymorphism analysis.

von Willebrand disease (vWD), the most common inherited bleeding disorder in humans, results from abnormalities in the plasma clotting protein von Willebrand factor (vWF). Severe (type III) vWD is autosomal recessive in inheritance and is associated with extremely low or undetectable vWF levels. We report a method designed to distinguish mRNA expression from the two vWF alleles by PCR analysis of peripheral blood platelet RNA using DNA sequence polymorphisms located within exons of the vWF gene. This approach was applied to a severe-vWD pedigree in which three of eight siblings are affected and the parents and additional siblings are clinically normal. Each parent was shown to carry a vWF allele that is silent at the mRNA level. Family members inheriting both abnormal alleles are affected with severe vWD, whereas individuals with only one abnormal allele are asymptomatic. The maternal and paternal silent alleles are identical at two coding sequence polymorphisms as well as an intron 40 variable number tandem repeat, suggesting a possible common origin. Given the frequencies of the two exon polymorphisms reported here, this analysis should be applicable to approximately 70% of type I and type III vWD patients. This comparative DNA and RNA PCR-restriction fragment length polymorphism approach may also prove useful in identifying defects at the level of gene expression associated with other genetic disorders.

Alleles↗

PubMed1990

Restriction fragment length polymorphism analysis of HLA haplotypes in families with type I diabetes mellitus.

HLA Class II polymorphisms were analysed in 27 families with at least one Type I diabetic proband using Southern blotting technique according to 10th Histocompatibility Workshop Standards. The probes used were DRB, DQA1, DQB1 and DOB. We have studied 108 haplotypes and performed segregation analysis with HLA serology and restriction fragment length polymorphism (RFLP) data and compared "affected" with "non-affected" haplotypes (not inherited by IDDM patients). RFLPs correlated well with DR and DQ serology and detected additional polymorphisms. In particular, DQB polymorphism analysis showed segregation of the DQw3 splits with 88.5% of the DR4 affected haplotypes bearing the DQw3.2 split (now DQw8) and 11.5% the DQw3.1 split (now DQw7) while in the non-affected DR4 haplotypes 33.3% were DQw3.2 and 66.6% were DQw3.1. Haplotype analysis showed that DR4-DQw3.2 was in strong linkage with the U fragment (2.1 kb Taq I) of DQA2 (DX alpha) and with the L fragment (5.4 kb BamH I) of DOB. This study confirms previous observations of DQB polymorphisms in heterozygous IDDM patients, supports the protective effect of DQw3.1 (DQw7) against the development of the disease and demonstrates the importance of DQw3.2 (DQw8) for susceptibility to Type I diabetes.

Diabetes Mellitus, Type 1↗

PubMedDate not supplied

HLA-DRB and DQB typing by a combination of serology, restriction fragment length polymorphism analysis and oligonucleotide probing.

DNA sequencing has revealed extensive polymorphism within the HLA-DRB and DQB genes of the major histocompatibility complex. At least 43 alleles of the DRB loci and 13 alleles of the DQB1 locus are currently recognized. Identification of these alleles can be performed phenotypically by cellular and serological techniques or genotypically by restriction fragment length polymorphism (RFLP) analysis and sequence-specific oligonucleotide (SSO) probing of DNA amplified by the polymerase chain reaction (PCR). However, each method has its technical limitations so the tissue typing laboratory must therefore choose from the range of available techniques to maximize the efficiency and accuracy of HLA typing. In this paper we describe a scheme for the accurate determination of all the serologically defined DRB and DQB allotypes using a combination of serology, RFLP analysis and PCR-SSO probing. The efficiencies of serology versus RFLP analysis for the DR typing of 800 individuals, and RFLP analysis versus PCR-SSO probing for the DQB typing of 317 individuals, are compared and the merits of each technique discussed. This scheme, which types for both HLA-DRB and DQB with an accuracy approaching 100%, is now routinely employed in all HLA studies of disease and transplantation in our laboratory.

Adult↗