HindIII Polymorphism Research Articles

Lack of association between the MHC linked OTF3 gene and systemic lupus erythematosus

The objective of this study was to investigate whether an octamer transcription factor gene (OTF3) located within the MHC region of chromosome 6 is involved in determining susceptibility to systemic lupus erythematosus (SLE) in a Spanish population. An OTF3 HindIII polymorphism was characterized by restriction fragment length polymorphism analysis of polymerase chain reaction amplified genomic DNA in 69 patients with SLE and 60 controls. No differences in the OTF3 allelic or genotypic distribution between healthy controls and patients with SLE were found. In the group of patients with diffuse proliferative glomerulonephritis, where we have previously detected the strongest MHC association, we did not observe OTF3 linkage either. In conclusion, the OTF3 gene does not appear to be associated with SLE in the Spanish population. This might be due to the distance of the gene from the HLA class II-III region where more relevant autoimmune-related genes are located.

The lipoprotein lipase HindIII polymorphism modulates plasma triglyceride levels in visceral obesity.

The aim of this study was to investigate the potential interaction between the lipoprotein lipase (LPL) HindIII polymorphism and visceral adipose tissue (AT) accumulation in the modulation of triglyceride levels in visceral obesity. The LPL-HindIII genotype was determined by polymerase chain reaction in 52 min. Twenty-three subjects were heterozygous (+/-) and 28 were homozygous (+/+) for the presence of the restriction site. One subject who was homozygous for the--allele was excluded from analysis. Body mass index (BMI), fasting insulin level, and visceral AT area as measured by computed tomography were positively correlated with triglyceride levels only in subjects homozygous for the + allele. Furthermore, whereas these variables were negatively correlated with plasma HDL2 cholesterol concentrations in the +/+ group, these associations were not found in +/- heterozygotes, with the exception of BMI. To further investigate the interaction of the LPL-HindIII polymorphism with visceral obesity and hyperinsulinemia, the two genotype groups were further subdivided on the basis of BMI (low versus high), fasting insulin level (low versus high), and visceral AT area (low versus high), and their lipoprotein profiles were compared. Elevated levels of abdominal visceral AT were significantly associated with increased triglyceride concentrations in +/+ homozygous men, suggesting that visceral obesity may lead to hypertriglyceridemia in the presence of the +/+ genotype. In the +/- group, variation in the amount of visceral AT was not associated with differences in triglyceride concentration. However, hypertriglyceridemia and an increased cholesterol-to-HDL cholesterol ratio were observed in the hyperinsulinemic state irrespective of LPL-HindIII genotype status.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA polymorphisms at the lipoprotein lipase gene are associated with macroangiopathy in type 2 (non-insulin-dependent) diabetes mellitus

We studied the effect of variation at the lipoprotein lipase (LPL) gene locus on the susceptibility of individuals with Type 2 diabetes mellitus to atherosclerotic vascular disease in a population of 126 male and 114 female patients. The prevalence of any evidence of coronary heart disease (CHD) (presence of ischaemic ECG changes or definite myocardial infarction) was low in the patients who were homozygous for the presence of the PvuII restriction site (genotype 2−2) (40.9%) compared with those who were heterozygous (genotype 1−2) (57.9% P = 0.05) or homozygous for the absence of it (genotype 1−1) (61.9%; P < 0.04). In men, a clear gene dosage effect on CHD was seen, the genotype 2−2 patients having the lowest (39.1%), the 1−2 patients an intermediate (49.3%) and the 1−1 patients the highest (61.1%) frequency of coronary disease. Patients with the genotype 2−2 of the HindIII polymorphism (absence of the restriction site) had the highest prevalence of any evidence of CHD (90.0%) compared with the genotype 1−2 (heterozygotes for the presence of the restriction site) (55.4%) or 1−1 (presence of the restriction site) (54.6%; P < 0.03). Stepwise discriminant analysis revealed that in the whole diabetic population the PvuII genotype of the LPL gene was independently and significantly associated with CHD but its effect decreased when the plasma lipids were taken into account. Overall, this study demonstrates the role of the PvuII polymorphism in the LPL gene to modulate the risk for diabetic macroangiopathy in patients with Type 2 diabetes mellitus. The data also confirm a role for the apolipoprotein E and cholesteryl ester transfer protein (CETP) EcoNI polymorphisms as important determinants of macroangiopathy in Type 2 diabetes mellitus.

Chromosomal mapping of the human smooth muscle actin gene (enteric type, ACTA3) to 2p13.1 and molecular nature of the HindIII polymorphism

The human gene for smooth muscle actin (enteric type, ACTA3) has been isolated, and three overlapping clones, λHACTSG-17, -2, and -112, were used as probes for fluorescence in situ hybridization of human chromosomes. The gene was localized to chromosome 2p13.1. To clarify the molecular nature of the HindIII RFLP present in the first intron of the gene, the 1105-bp EcoRI— BamHI fragment contained in λHACTSG-17 was sequenced. PCR with primers designed from the determined sequence yielded either the 463- or the 439-bp product or both, using human DNA as template. The 463-bp product was cleavable with HindIII, but the 439-bp product was not. Comparison of their nucleotide sequences revealed that they differ in the presence/absence of a 24-bp sequence harboring a HindIII restriction site. Therefore, analysis of PCR products by size has been shown to be sufficient to detect the RFLP. The allelic frequency on 156 chromosomes was determined by PCR to be 45 (439 bp, corresponding to the formerly designated A1 allele):55 (463 bp, A2 allele) in the Japanese population.

Polymorphisms of the Beta Fibrinogen Gene and Plasma Fibrinogen Concentration in Caucasian and Japanese Population Samples

We reported previously that plasma fibrinogen was significantly higher in U.S. Caucasians than in Japanese, which may contribute to the higher mortality rate of coronary heart disease in the United States than in Japan. To examine the contribution of genetic variations to the race difference in plasma fibrinogen levels, restriction fragment length polymorphisms (RFLPs) of the beta fibrinogen gene were examined in 293 nonsmoking Caucasians and Japanese men and women aged 47-69 years. Three RFLPs were detected by digestion of genomic DNA using the BclI restriction enzyme, polymerase chain reaction (PCR) products using HaeIII and HindIII. The alleles B2 (4.2 kb, BclI digestion), H2 (957 b, HaeIII) and Hd2 (465 b. HindIII) were associated with higher fibrinogen concentrations in previous studies. Because of a strong linkage disequilibrium between HaeIII and HindIII polymorphisms, the data of HindIII was presented. The frequency of the B2 allele was 22% (95% Cl: 17-27%) for Caucasians and 13% (10-17%) for Japanese (the difference: p < 0.01). The respective frequency of the Hd2 allele was 26% (21-31%) and 12% (8-16%) (p < 0.001). After controlling for age, body mass index, alcohol intake, triglycerides, fish intake, and for women, menopausal status and hormone replacement therapy, the adjusted mean fibrinogen level among Caucasians was 289 mg/dl for genotype B1B1 and 301 mg/dl for genotype B1B2 or B2B2 combined (p = 0.18), and 285 mg/dl for Hd1Hd1 and 306 mg/dl for Hd1Hd2 or Hd2Hd2 combined (p = 0.03).(ABSTRACT TRUNCATED AT 250 WORDS)

Lipoprotein lipase HindIII polymorphism in relation to hypertriglyceridemia and visceral obesity

Lipoprotein lipase HindIII polymorphism in relation to hypertriglyceridemia and visceral obesity

Identification of three RFLPs at the HCK locus on chromosome 20

New HindIII, RsaI and TaqI restriction fragment length polymorphisms (RFLPs) within the haemopoietic cell kinase gene in chromosome band 20q11.2 are described. These RFLPs provide a useful marker for linkage analysis in proximal 20q.

Follicle-stimulating hormone beta gene structure in premature ovarian failure

To determine whether mutations in the gene for FSH beta are present, and possibly etiologic, in some patients with 46,XX premature ovarian failure (POF). DNA samples obtained from 18 study patients with POF and two menopausal fertile controls were studied by Southern blot analysis. DNA sequencing was performed in one patient. Patients were seen in a reproductive endocrinology clinic and studied in a medical school laboratory setting at the Medical College of Georgia and Tufts University. Restriction fragment sizes on autoradiographs were compared between the study group and controls. DNA sequencing radiographs were compared between one study patient and five controls. Fragment sizes obtained with the restriction enzymes EcoRI, DraI, HincII, PstI, KpnI, BglI, BamHI, and BglII were similar size in both study subjects and controls using the probes pFSH beta-1.4 and pFSH beta-1.2. A previously described HindIII polymorphism was present using pFSH beta-1.2, but HindIII fragment sizes were identical in patients with ovarian failure and controls using pFSH beta-1.4. DNA sequencing of the FSH beta gene in one patient was normal. No mutations in the gene for FSH beta were identified in women with POF. DNA sequencing of the exons and promoter region of the FSH beta gene in one woman with POF was normal. This does not entirely exclude the possibility that smaller deletions, insertions, or point mutations of the FSH beta could be etiologic in some women with POF. The HindIII polymorphism does not appear to segregate with 46,XX POF.

An interleukin-8 (IL-8) cDNA clone identifies a frequent HindIII polymorphism.

An interleukin-8 cDNA probe detects a biallelic HindIII polymorphism. This frequent restriction fragment length polymorphism (RFLP) provides a new genetic marker for the long arm of chromosome 4.

Two DNA polymorphisms in the lipoprotein lipase gene and their associations with factors related to cardiovascular disease.

Lipoprotein lipase (LPL) plays a crucial role in plasma lipoprotein processing by catalyzing the hydrolysis of core triglycerides of chylomicrons and very low density lipoproteins. Several polymorphic restriction sites have been reported in the LPL gene, including those identified by the enzymes HindIII and PvuII. We have determined the HindIII and PvuII polymorphisms in diabetic (D) and non-diabetic (ND) Hispanics (D = 195; ND = 384) and non-Hispanic Whites (D = 76; ND = 539) from the San Luis Valley, Colorado. Both polymorphisms showed comparable gene frequencies between diabetics and non-diabetics, and between the two ethnic groups. The HindIII and PvuII polymorphisms were in strong linkage disequilibrium in both Hispanics and non-Hispanic Whites (P < 0.001). We estimated whether the two DNA polymorphisms have significant impact in determining interindividual differences in plasma levels of total cholesterol, HDL-cholesterol, LDL-cholesterol, triglycerides, fasting glucose, and fasting insulin. Plasma triglyceride levels varied significantly among the HindIII genotypes in the normoglycemic sample. There was a clear gene dosage effect among the three HindIII genotypes, with the (-/-) genotype having the lowest and the (+/+) genotype having the highest triglyceride levels; these levels were intermediate in the (+/-) genotype. The average effect of the (-) allele of the HindIII polymorphism was to lower triglycerides by 12.85 mg/dl in non-Hispanic White males, 8.06 mg/dl in non-Hispanic White females, 10.91 mg/dl in Hispanic males, and 12.47 mg/dl in Hispanic females. The HindIII polymorphism also showed a significant association with HDL-cholesterol levels in the normoglycemic sample.(ABSTRACT TRUNCATED AT 250 WORDS)

HindIII polymorphism in the BCL6 gene.

HindIII polymorphism in the BCL6 gene.

A new negroid-specific HindIII polymorphism in the serum amyloid A1 (SAA1) gene increases the usefulness of the SAA locus in linkage studies.

The cDNA probe pSAA82 detects three serum amyloid A (SAA) loci on chromosome 11p. SAA1 and SAA2 have 90% nucleotide identity in exon and intron sequences (1), whereas SAA3 has an average of 70% identity with SAA1 and SAA2 (3). The chromosomal organization of the loci is not yet known. A two-allele polymorphic HindIII site was found within intron 2 of the SAA2 locus (1) with fragments of 3.0 (a2) and 5.0 kb (a1) (previously sized as 2.8 and 4.6 kb, respectively) which occur in Caucasoids, Negroids, and San (formerly [open quote]Bushmen[close quotes]) (2). The discovery of a further, Negroid-specific, polymorphic HindIII restriction site, detected with the same probe, increases its usefulness. This RFLP is associated with the SAA1 locus (6) and is characterized by the presence of two allelic fragments of 3.6 (b1) and 1.4 kb (b2). This HindIII site is also thought to occur within intron 2 because of the strong evolutionary conservation between the SAA1 and SAA2 genes. The polymorphism may therefore either predate the gene duplication event or be present as a result of gene conversion. 6 refs., 1 fig.

Associations between lipoprotein lipase gene polymorphisms and plasma correlations of lipids, lipoproteins and lipase activities in young myocardial infarction survivors and age-matched healthy individuals from Sweden.

Association studies were carried out on a sample of 87 patients from Sweden who had survived a myocardial infarction (MI) at a young age and 93 age-matched healthy individuals, to compare the impact of polymorphisms (PvuII, HindIII and Serine447-Stop) at the lipoprotein lipase (LPL) gene locus on among-individual differences in plasma lipid traits and progression of atherosclerosis. Significant linkage disequilibrium was detected between any two of these polymorphisms, with the Stop447 allele being only found on the same chromosome as the rare alleles (no cutting sites) of the PvuII and HindIII polymorphisms. In the healthy individuals, weak associations were found between genotypes of the HindIII polymorphism and triglycerides and the PvuII polymorphism and high density lipoprotein cholesterol explaining 7.4% and 5.6% of sample variance (P = 0.03 and 0.09), respectively. No associations were found between these traits and genotypes of the Serine447-Stop substitution, and thus it is unlikely to be the cause of the associations seen with the PvuII and HindIII polymorphisms even though it truncates the enzyme amino acid sequence. The presence of the rare allele, H-, of the HindIII polymorphism was associated with a smaller variance in triglycerides and both cholesterol and triglycerides in the very low density lipoprotein fraction, and with larger interdependent variation between these lipid traits, and also between LPL activity and these lipid traits. This implies that the H- allele, rather than the Stop447 allele, has the major impact on interdependence between traits which are directly or indirectly influenced by LPL activity. In the healthy individuals who were carriers of the apolipoprotein E2 allele, the inter-dependence between LPL activity and lipid traits was significantly smaller, and that between high density lipoprotein cholesterol and both cholesterol and triglycerides in the very low density lipoprotein fraction was much larger compared with non-carriers (P < 0.05). No significant associations were found between lipid traits or lipase activity and genotypes of the Serine447-Stop substitution. However, in the patients, global severity of coronary atherosclerosis at the first angiography was significantly associated with haplotype combinations of the HindIII and the Serine447-Stop polymorphisms, with the H-Stop haplotype being associated with the highest median score (P = 0.02). The data suggest that variation at the LPL gene locus is associated with a pleiotropic effect, that is not directly mediated by changes in lipids, on severity of coronary atherosclerosis.

Homeobox DNA polymorphisms (RFLPs) in subterranean mammals of theSpalax ehrenbergi superspecies in Israel: Patterns, correlates, and evolutionary significance

Homeobox DNA polymorphisms (restriction fragment length polymorphisms, RFLPs) were first found in 13 individuals, and then in 121 subterranean mole rats of the Spalax ehrenbergi superspecies in Israel. Spalacidae are adapted morphologically to life underground apparently since Oligocene times, 30 million years ago. The superspecies S. ehrenbergi comprises four chromosomal species (2n = 52, 54, 58, and 60) displaying active speciation and dynamic adaptive radiation into four climatic regimes. A Hox-1.1 and -1.5 polymorphism was found with EcoRI, where three of four individuals of the species 2n = 60 were lacking the diagnostic locus-specific band present in all other nine individuals tested in the first stage. Next we found monomorphism in 121 animals in Hox-2.1 digested with five six-base recognition endonucleases (EcoRI, HindIII, BstEII, KpnI, BamHI, and one four-base enzyme, TaqI). However, we found in the same 121 animals from 13 populations of the four species in Hox-3.1 species-specific TaqI polymorphism in two populations of 2n = 54, and HindIII polymorphism in five populations, three of 2n = 54 and two of 2n = 58. The homeobox polymorphisms found display significant correlations with the burrow microclimates of mole rats. Furthermore, they are significantly correlated primarily with diverse morphological variables, and secondarily with protein (allozyme) and DNA polymorphisms, but very little with physiological and behavioral variables. We suggest that in subterranean mole rats, the variation in microclimatic factors, particularly in more unpredictable xeric regions, may maintain genetic polymorphisms by diversifying selection in the developmental control homeobox genes Hox-1.1, -1.5, and Hox-3.1, affecting regulatory morphogenetic processes in evolution. By contrast, the Hox-2.1 monomorphism suggests strong purifying selection for conservation across the superspecies over long periods of evolutionary times. © 1992 Wiley-Liss, Inc.

DNA polymorphisms of the human CD46 gene in fetal and adult tissues

DNA polymorphisms of the CD46 gene were investigated using a full length cDNA probe and five different restriction enzymes in genomic DNA samples from human fetal tissues and adult peripheral blood leukocytes. A HindIII polymorphism was observed and was classed as Types I, II and III at a ratio of approximately 3.5:2:1, depending on the presence or absence of two polymorphic fragments of 4.5 and 2.0 kb. No variation of polymorphic distribution was evident between the fetal and adult samples. Whether variation in CD46 expression between maternal and fetal tissue is relevant to fetal viability in pregnancy remains to be established.

Molecular analysis of the androgen receptor gene in 52 patients with complete or partial androgen insensitivity syndrome: a collaborative study.

In patients with androgen insensitivity syndrome (AIS), RFLP study of the androgen receptor gene made it possible to analyze whether deletions or mutations could be responsible for abnormalities in androgen responsiveness. We studied RFLPs of DNA from 25 46,XY patients with partial AIS (PAIS), defined as a concentration of androgen receptor in genital-skin fibroblasts less than 340 fmol/mg DNA, and DNA from 27 46,XY patients with complete AIS (CAIS) with no detectable androgen receptor site. DNA samples were digested with BamHI, EcoRI, HindIII and TaqI restriction enzymes and hybridized with three cDNA probes covering the three domains of the androgen receptor. When we had the maternal and an unaffected brother's DNA, we analyzed the two androgen receptor gene polymorphisms described, the HindIII and the exon 1 CAG repeat polymorphisms, in order to distinguish the two maternal X chromosomes, and to detect carriers of AIS. We did not find any large deletion among the 52 patients. We observed a heterozygous mother in 3 of 14 families studied with the HindIII polymorphism, and in 12 of 25 families using the exon 1 CAG repeat polymorphism. This study suggests that in AIS, abnormalities in androgen receptor response could be related to point mutations or microdeletions rather than to gross structural alterations of the androgen receptor gene. Furthermore, unless the point mutation has been described, exon 1 and HindIII polymorphism studies would enable the identification of carriers in 50% of families, and the prenatal diagnosis of AIS.

Genetic linkage between Huntington disease and the D4S10 locus in South African families: further evidence against non-allelic heterogeneity

A study of genetic linkage between Huntington disease (HD) and the D4S10 locus (G8) has been undertaken in 10 South African (SA) families originating from the black, white and mixed acestry population groups. Allele frequencies at the D4S10 locus have been established in the non-Caucasoid population groups. There are significant differences in the allele frequencies at the D4S10 locus between the various SA populations. Clearly, information about population-specific frequencies for all polymorphisms is essential prior to the implementation of predictive testing in different population groups. Linkage has been demonstrated within this mixed group of HD families in SA using the HindIII, EcoRI and MspI polymorphisms, detected by G8. A maximum lod score of 8.14 at a recombination fraction of 0.00 (confidence limit 0-0.058) has been calculated using a combined haplotype of the HindIII and MspI polymorphisms. Taking into account the diverse ethnic backgrounds of the different SA population groups in this investigation, the data obtained from the study provide further evidence that there is probably only a single HD locus.

Membrane cofactor protein of the complement system. A HindIII restriction fragment length polymorphism that correlates with the expression polymorphism.

An RFLP was found in the DNA of 25 unrelated persons, two families, and five cell lines that correlated with their membrane cofactor protein phenotype. If restricted with HindIII, DNA derived from upper band predominant protein (U) phenotypes had a band at 2 kb, whereas DNA of lower band predominant (L) phenotypes had a 4-kb band. The equal band protein phenotype, in which equal quantities of the two species are expressed, had bands at both 4 and 2 kb. The polymorphic HindIII site was localized to an intron within the membrane cofactor protein gene between exon 1 (codes for 5'UT/signal peptide) and exon 2 (codes for the first short consensus repeat). Using the polymerase chain reaction (PCR), sequences around this site were amplified and a single band of 260 bp was produced. In the U phenotype, the PCR product was restricted with HindIII into 200- and 60-bp fragments. In the L phenotype, there was no change in the size of 260 bp upon restriction with HindIII. For the equal band protein phenotype, the PCR product was partially cleaved. The 260-bp PCR product was subcloned and sequenced. DNA from the U phenotype demonstrated an intact HindIII site (AAGCTT), whereas in the DNA of the L phenotype, this site was altered because a "G" was substituted for a "C" (AAGGTT).

Genomic determination of the CR1 (CD35) density polymorphism on erythrocytes using polymerase chain reaction amplification and HindIII restriction enzyme digestion

The density of CR1 (the C3b receptor, CD35) on erythrocytes from normal individuals is determined by a codominant bi-allelic system associated with a single base mutation within an intron of the CR1 structural gene, leading to an additional polymorphic HindIII endonuclease site. The CR1 genotype is determined by HindIII digestion of genomic DNA and Southern blotting. We have developed a method based on polymerase chain reaction (PCR) amplification of the genomic DNA fragment of interest followed by HindIII endonuclease digestion and agarose gel electrophoresis which permits a more rapid and reliable determination of the CR1 genotype. The method is suitable for large scale clinical studies in diseases with altered expression of CR1 on erythrocytes.

PCR detection of a HindIII polymorphism in the human gene for type II procollagen (COL2A1)

PCR detection of a HindIII polymorphism in the human gene for type II procollagen (COL2A1)