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At least 865 records · Page 48Linked to original sources
PubMed2004

Association of protein tyrosine phosphatase 1B gene polymorphisms with type 2 diabetes.

The PTPN1 gene codes for protein tyrosine phosphatase 1B (PTP1B) (EC 3.1.3.48), which negatively regulates insulin signaling by dephosphorylating the phosphotyrosine residues of the insulin receptor kinase activation segment. PTPN1 is located in 20q13, a genomic region linked to type 2 diabetes in multiple genetic studies. Surveys of the gene have previously identified only a few uncommon coding single nucleotide polymorphisms (SNPs). We have carried out a detailed association analysis of 23 noncoding SNPs spanning the 161-kb genomic region, which includes the PTPN1 gene. These SNPs have been assessed for association with type 2 diabetes in two independently ascertained collections of Caucasian subjects with type 2 diabetes and two control groups. Association is observed between multiple SNPs and type 2 diabetes. The most consistent evidence for association occurred with SNPs spanning the 3' end of intron 1 of PTPN1 through intron 8 (P values ranging from 0.043 to 0.004 in one case-control set and 0.038-0.002 in a second case-control set). Analysis of the combined case-control data increased the evidence of SNP association with type 2 diabetes (P = 0.005-0.0016). All of the associated SNPs lie in a single 100-kb haplotype block that encompasses the PTPN1 gene. Analysis of haplotypes indicates a significant difference between haplotype frequencies in type 2 diabetes case and control subjects (P = 0.0035-0.0056), with one common haplotype (36%) contributing strongly to the evidence for association with type 2 diabetes. Odds ratios calculated from single SNP or haplotype data are in the proximity of 1.3. Haplotype-based calculation of population-attributable risk (PAR) results in an estimated PAR of 17-20% based on different models and assumptions. These results suggest that PTPN1 is a significant contributor to type 2 diabetes susceptibility in the Caucasian population. This risk is likely due to noncoding polymorphisms.

Diabetes Mellitus, Type 2↗
PubMed2005

Polymorphisms in IGF-binding protein 1 are associated with impaired renal function in type 2 diabetes.

The dysregulation of the IGF system has been implicated in the pathogenesis of obesity, diabetes, and diabetes complications such as nephropathy, but little is known about the genomics of the IGF system in health and disease. We genotyped 13 single nucleotide polymorphisms (SNPs) in IGFBP1 gene in 732 representative type 2 diabetic patients from the Salford Diabetes Register. Of the 13 SNPs, 8 were polymorphic and 7 of those had minor allele frequencies >0.1, one of which was in the gene promoter and one of which was nonsynonymous in exon 4. The minor alleles of these SNPs and two others were associated with a reduced prevalence of diabetic nephropathy. Haplotype analysis revealed that 97% of the genetic variation for IGFBP1 in the population sample could be accounted for using two of the "reno-protective" SNPs, with other SNPs adding little extra information. One of these two SNPs was the nonsynonymous mutation in exon 4, lying close to the integrin-binding RGD motif, which is thought to affect tissue delivery of IGF-I by IGF-binding protein 1 (IGFBP-1), possibly suggesting a "reno-protective" effect via altered IGFBP-1 binding. In conclusion, we have described the first genomic markers to be associated with diabetic microvascular complications within the human IGFBP1 gene.

Base Sequence↗
PubMed2023

The genetic basis of adaptation to copper pollution in Drosophila melanogaster.

Introduction: Heavy metal pollutants can have long lasting negative impacts on ecosystem health and can shape the evolution of species. The persistent and ubiquitous nature of heavy metal pollution provides an opportunity to characterize the genetic mechanisms that contribute to metal resistance in natural populations. Methods: We examined variation in resistance to copper, a common heavy metal contaminant, using wild collections of the model organism Drosophila melanogaster. Flies were collected from multiple sites that varied in copper contamination risk. We characterized phenotypic variation in copper resistance within and among populations using bulked segregant analysis to identify regions of the genome that contribute to copper resistance. Results and Discussion: Copper resistance varied among wild populations with a clear correspondence between resistance level and historical exposure to copper. We identified 288 SNPs distributed across the genome associated with copper resistance. Many SNPs had population-specific effects, but some had consistent effects on copper resistance in all populations. Significant SNPs map to several novel candidate genes involved in refolding disrupted proteins, energy production, and mitochondrial function. We also identified one SNP with consistent effects on copper resistance in all populations near CG11825, a gene involved in copper homeostasis and copper resistance. We compared the genetic signatures of copper resistance in the wild-derived populations to genetic control of copper resistance in the Drosophila Synthetic Population Resource (DSPR) and the Drosophila Genetic Reference Panel (DGRP), two copper-naïve laboratory populations. In addition to CG11825, which was identified as a candidate gene in the wild-derived populations and previously in the DSPR, there was modest overlap of copper-associated SNPs between the wild-derived populations and laboratory populations. Thirty-one SNPs associated with copper resistance in wild-derived populations fell within regions of the genome that were associated with copper resistance in the DSPR in a prior study. Collectively, our results demonstrate that the genetic control of copper resistance is highly polygenic, and that several loci can be clearly linked to genes involved in heavy metal toxicity response. The mixture of parallel and population-specific SNPs points to a complex interplay between genetic background and the selection regime that modifies the effects of genetic variation on copper resistance.

Drosophila↗
PubMed2001

Single nucleotide polymorphisms in the methylenetetrahydrofolate reductase gene are common in US Caucasian and Hispanic American populations.

To investigate the prevalence of the C677T and A1298C single nucleotide polymorphisms (SNPs) in the methylenetetrahydrofolate reductase (MTHFR) gene in Caucasian and Hispanic populations, EDTA-anticoagulated whole blood specimens were collected from a total of 100 random patients, 50 Caucasians and 50 Hispanics of Puerto Rican dissent. The prevalence of the two MTHFR SNPs was determined by polymerase chain reaction (PCR) mediated restriction fragment length polymorphism analysis. In the Caucasian population, homozygosity for the MTHFR A1298C SNP was detected in 4% (2/50) of the individuals tested, while 42% (21/50) were heterozygous for this SNP. Among Hispanics, 4% (2/50) were homozygous and 38% (19/50) heterozygous for the A1298C SNP. Homozygosity for the C677T MTHFR SNP was detected in 16% (8/50) and 10% (5/50) of Caucasians and Hispanics, respectively. In this study, the frequency of the C677T heterozygotes was very high at 56% (28/50) and 52% (26/50) Caucasians and Hispanics, respectively. C677T and A1298C are common SNPs in the MTHFR gene. The high prevalence of these SNPs in both Caucasian and Hispanic populations demonstrates the possibility of compounding effects of these SNPs in the pathogenesis of human diseases. While subgroups of patients may exhibit some clinical phenotype linked to these SNPs, our analysis demonstrates the need for careful interpretation of SNP data in the context of population screening.

DNA↗
PubMed2003

High-throughput SNP analysis for genetic association studies.

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation, and millions of SNPs are now documented. Because of their dense distribution across the genome, SNPs are viewed as ideal markers for large-scale genome-wide association studies to discover genes in common complex diseases, such as cancer. To enable such studies, researchers have constructed appropriate sets of SNP markers, by selecting SNPs that are common in major human populations and by charting the patterns of co-occurrence of SNPs, which could further guide marker selection. High-throughput SNP analysis technologies have also been developed, which can analyze thousands of SNPs in thousands of samples. As SNP analysis techniques and SNP marker sets are improving, researchers have begun to carry out large-scale genome scans for disease genes, with encouraging first results.

Animals↗
PubMed2002

[Linkage disequilibrium analysis of the single nucleotide polymorphisms in the PRKCZ gene].

OBJECTIVE: To search for the disease-associated haplotype in the PRKCZ gene, a susceptibility gene for type 2 diabetes in Han population of North China, by case-control study and linkage disequilibrium (LD) analysis using single nucleotide polymorphisms (SNPs). METHODS: SNPs located in the PRKCZ gene were chosen from public SNP domain by bioinformatic methods and single base extension (SBE) method was used to genotype the loci in 173 sporadic type 2 diabetes patients and 152 normal individuals to perform case-control study and LD analysis. Haplotype block were constructed in these populations. RESULTS: Several SNPs in the PRKCZ gene were found to be associated with the disease. The SNPs formed different haplotype block pattern in case and control groups. The frequencies of the haplotypes formed by 5 SNPs were statistically different between the two groups. CONCLUSION: The haplotype formed by 5 SNPs in the PRKCZ gene may be associated with type 2 diabetes in Han population of China, which is confirmed from statistics to be a susceptibility gene for the disease.

Alleles↗
PubMed2003

[Exploration of methodology for assay of single nucleotide polymorphism in thiopurine methyltransferase gene].

The aim of the present study was to gain an insight into the thiopurine methytransferase (TPMT) genotyping assay, which was based on polymerase chain reaction (PCR), allele-specific PCR, restriction digestion of PCR products, denaturing high-performance liquid chromatography (DHPLC) and SNaPshot sequencing and in combination with direct DNA sequencing. Among the f our methods to test TPMT genetic SNPs based on PCR, allele specific PCR was not able to differentiate wild type from varied type. BsiYI, MwoI and AccI to digest PCR products were used so that SNP in TPMT exon 5, 7 and 10 tested. It showed that there were no differences between the results of digestion of PCR products and those of DNA sequence analysis. Therefore, this method was reliable. But some other methods were still needed to look for a compensation, because no restriction map changing resulted from the 2 SNPs in TPMT promotor was found. As to the results of DHPLC, those for the screening of TPMT exon-5 and -10 for SNPs were the same as restriction analysis of PCR products and direct DNA sequencing. But the variation of the heterozygotes in exon-7 was high, which was different from the results of direct DNA sequencing. After changing the Tm of DNA step by step, It was found that all the samples showed single peak when the temperature was 54 degrees C. But this result was unbelievable because a heterozygote in exon 7 as positive control could not be found. Therefore, it was necessary to test the sensitivity and accuracy of DHPLC, though DHPLC could be used as an effective method of SNPs screening. The results of the SNaPshot sequencing were also same as those of restriction analysis of PCR products and direct DNA sequencing. And the results showed that the bases of TPMT promoter -91 and -168 were G, instead of A and T. The results of the four methods to detect TPMT genetic SNPs based on PCR showed that SNPs analysis technique should be a combination of the techniques above-mentioned. One technique alone could not satisfy the need in clinics and research. The compensation of each other was very important.

Chromatography, High Pressure Liquid↗
PubMed2004

Polymorphisms near a chromosome 6q QTL area are associated with modulation of fetal hemoglobin levels in sickle cell anemia.

In patients with sickle cell anemia, fetal hemoglobin (HbF) concentrations vary by 2 orders of magnitude. This variance may be a result of heterogeneity in gene regulatory elements; accordingly, we searched for single nucleotide polymorphisms (SNPs) that might identify this variation. More than 180 SNPs were studied in 38 genes in 280 sickle cell anemia patients. The strongest association with HbF was found with SNPs near a QTL previously localized on chromosome 6q22.3-q23.2. Initially, two SNPs were identified in intergenic portions of this QTL and were associated with about a 20% difference in percent HbF. Subsequently, we genotyped 44 additional SNPs in the genomic region between 136.1 Mb and 137.5 Mb on chromosome 6q. Twelve SNPs, associated with a 20%-30% difference in HbF concentrations, were located in the introns of four genes, PDE7B, MAP7, MAP3K5 and PEX7. In K562 cells, the p38-MAPK pathway has been associated with the activation of gamma-globin gene expression by histone deacetylase inhibitors. Haplotypes C-T-T-T in MAP7 and T-C-C in PEX7 were significantly associated with increases in concentration of HbF, both showing strong dominance. Genetic elements abutting the 6q22.3-q23.2 QTL, may harbor trans-acting elements that help modulate baseline HbF level in sickle cell anemia.

Black or African American↗
PubMed2004

[The genetic polymorphism of melanoma-associated antigen 1 in Chinese normal donors and hepatoma patients].

OBJECTIVES: To investigate the expression of melanoma-associated antigen 1 (MAGE-1) in Chinese hepatocellular carcinoma (HCC) patients and to determine the existence and distribution of single nucleotide polymorphisms (SNP) of MAGE-1 gene. METHODS: Total RNA was extracted from cancer tissues and adjacent tissues from 19 HCC patients and the expression of MAGE-1 mRNA was examined by using RT-PCR. The PCR products were sequenced to analysis the gene variation. Genomic DNA was extracted from cancer tissues, adjacent tissues and peripheral blood cells of 19 HCC patients, as well as from peripheral blood cells of 23 healthy donors. The PCR product of MAGE-1 DNA was sequenced to determine the existence and distribution of SNPs of MAGE-1 gene. RESULTS: 9 of 19 (47.4%) tumor tissues and none of adjacent tissue from HCC patients expressed MAGE-1 mRNA. There were three kinds of gene variations of cDNA in 9 MAGE-1 mRNA positive patients. One type was named type I including 1 patient, which sequence is as same as that of the GenBank M77481. The other was named TGA type including 5 patients, which involved three nucleotide changes (C159T, A272G and G393A) and result in two amino acid changes (T32A and R72Q). Another one was named GTG type including 3 patients, which involved three nucleotide changes (A272G, C991T, A1125G) and result in only one amino acid changes (T32A). According to the analysis of genomic DNA, above three types were not specific mutations of tumor tissue, but were SNPs. These SNPs types were distributed in HCC patients and normal donors with the frequencies of 26.3% (5/19) and 60.9% (14/23) for type I, 57.9% (11/19) and 47.8% (11/23) for TGA type, and 21.1% (4/19) and 21.7% (5/23) for GTG type, respectively. The sequences of two new SNPs had been deposited in GenBank with the accession numbers of AF463515 and AY148486. In male population, the distributions of SNPs were not correlated to HCC suffering or MAGE-1 expression. Several new HLA-restricted epitopes were probably resulted from SNPs existing. The three-dimensional models of MAGE-1 proteins of type I and TGA type was established by using computer software. CONCLUSION: The expression rate of MAGE-1 gene in Chinese HCC patients is high. Three SNP types of MAGE-1 gene exist in Chinese population. The three-dimensional models of MAGE-1 proteins were obtained by computer processing. These results will be helpful to developing MAGE-1 peptide-vaccine for HCC immunotherapy.

Adult↗
PubMed2004

[Polymorphism analysis of 5' promotor region of BCR gene].

BACKGROUND & OBJECTIVE: BCR-ABL fusion gene is regarded as the molecular hallmark of chronic myelogenous leukemia (CML), and its expression is controlled by the BCR gene promoter. This study was designed to investigate the polymorphism of the promoter region of BCR gene, and its possible correlation with the disease. METHODS: A 1.13 kb fragment of BCR gene 5' promotor region was amplified and sequenced from 30 CML patients and 19 controls. Transcription factor binding sites and repeat sequences in this region were analyzed using softwares and online tools. RESULTS: Four novel single nucleotide polymorphisms (SNPs) and 3 bases different from the reference sequence were detected in the region studied. Among these 2 novel SNPs and 1 different base were located in or near several bases of binding sites. The gene frequencies of the novel SNPs had no significant difference between CML and control people. CONCLUSION: Sequence polymorphisms were found in the 5' promotor region of BCR gene, most of them being SNPs. No relativity can be validated between the SNPs and the disease. But it appears that some SNPs might have the probability of bringing influence to the transcription and expression of the gene.

Base Sequence↗
PubMed2004

[Relationship between polymorphism of IRF-3 gene codon 427 and esophageal cancer in Anyang population of China].

OBJECTIVE: To investigate the association between the single nucleotide polymorphisms (SNPs) of interferon regulatory factor 3 (IRF-3) gene and the susceptibility of esophageal cancer in Anyang area, Henan Province. METHODS: The genomic DNAs of 152 esophageal cancer patients and 191 health controls were extracted from the peripheral blood leukocytes. Three fragments covering codons 96, 194, 377, and 427 of the IRF-3 gene were amplified by polymerase chain reaction (PCR). The SNPs were revealed by DNA sequencing and the genotype of every sample was determined accordingly. The frequency distribution of the SNPs was analyzed by chi(2) test. RESULTS: There were no IRF-3 gene SNPs at codons 96, 194, or 377 in Anyang participants. There was significant difference in the SNPs at codon 427 between the healthy controls and esophageal cancer patients in Anyang area OR=2.38 (95%CI=1.15-4.95,P<0.05). CONCLUSION: The SNPs at codon 427 of the IRF-3 gene may relate to the susceptibility of esophageal cancer. The risk of esophageal cancer in participants with C allele is 2.38-fold compared to those with G allele.

Adult↗
PubMed2005

[Study on single nucleotide polymorphism of TLR4 in Chinese population].

OBJECTIVE: To identify the single nucleotide polymorphisms(SNPs) in the regulatory and coding regions of human Toll-like receptor 4(TLR4) gene and to search for its new genetic makers. METHODS: The 5' flank region, exons, parts of the introns, as well as 3' flank region of TLR4 gene were sequenced to identify and characterize the SNPs in Chinese population. SNP genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism for 2 highly distributed SNPs. RESULTS: Five novel SNPs were identified through a 4.98 kb sequencing of TLR4 gene. Among them, three were in 5'flank region, two in 3'UTR. In the sample of Han population from Chongqing, the minor allele frequencies of two highly distributed SNPs were 0.266 and 0.404 respectively. CONCLUSION: Sampling analysis in Han population of Chongqing showed that the two highly distributed SNPs of TLR4 were common in Chinese population and could be used for genetic marker of TLR4 gene.

Adult↗
PubMed2002

Automated identification of single nucleotide polymorphisms from sequencing data.

Single nucleotide polymorphisms (SNPs) provide abundant information about genetic variation. Large scale discovery of high frequency SNPs is being undertaken using various methods. However, the publicly available SNP data are not always accurate, and therefore should be verified. If only a particular gene locus is concerned,locus-specific polymerase chain reaction amplification may be useful. Problem of this method is that the secondary peak has to be measured. We have analyzed trace data from conventional sequencing equipment and found an applicable rule to discern SNPs from noise. We have developed software that integrates this function to automatically identify SNPs. The software works accurately for high quality sequences and also can detect SNPs in low quality sequences. Further, it can determine allele frequency, display this information as a bar graph and assign corresponding nucleotide combinations. It is very useful for identifying de novo SNPs in a DNA fragment of interest.

Algorithms↗
PubMed2005

[No association between 3 polymorphisms of transforming growth factor beta3 gene and essential hypertension in Chinese].

OBJECTIVE: To investigate possible association between the single nucleotide polymorphisms (SNPs) of transforming growth factor beta3 (TGF-beta3) gene and essential hypertension (EH) in Chinese. METHODS: The promoter region, exons, as well as part of the introns of TGF-beta3 gene were sequenced by a fluorescent labeling automatic sequencing method to detect and characterize the SNPs in 24 DNA samples from a Chinese population. Then we conducted a case-control study using 396 patients with hypertension (case) and 214 nomortensive subjects (control). The three SNPs including Thr63Asn, SS5608219 and SS5608220 were genotyped by PCR-RFLP or real-time allele-specific PCR in subjects studied. RESULTS: Seven SNPs in the exons, introns and 3'untranslated region (3'UTR) of TGF-beta3 gene were identified. Among them, 2 SNPs were found to be novel genetic variants and one of the two located in the exon 1 and produced substitution of amino acid. However, no differences were found between hypertensives and nomortensives in genotype distribution and allele frequency of SS5608219, Thr63Asn or SS5608220 polymorphisms. CONCLUSIONS: Two novel SNPs of TGF-beta3 gene were identified in Chinese. One of them produces a threonine to asparagines substitution in codon 63 (Thr63Asn). But no association was found between TGF-beta3 gene polymorphisms and EH in Chinese.

Aged↗
PubMed2006

[Haplotypes of four single nucleotide polymorphisms in caspase-8, -10 genes in Han nationality of Zhejiang province in China].

OBJECTIVE: To investigate single nucleotide polymorphisms (SNPs) and the distribution of their haplotypes in caspase-8, -10 genes in Zhejiang Han nationality in China. METHODS: PCR, denaturing high-performance liquid chromatography (DHPLC) and DNA sequencing were used to detect the SNPs in the 2nd-5th exons of caspase-10 gene, the 8th-10th exons of caspase-8 and their flanking sequences. Expectation Maximization (EM) algorithm was used for haplotype frequencies analysis and pairwise linkage disequilibrium (LD) test. RESULTS: (1) Two SNPs, A2823G and A12799G, were identified in caspase-10 gene, located in exon 2 and exon 5 respectively. A12799G was newly found with low informativeness. Three SNPs were identified in caspase-8 gene; A43466G, G51484A and G52951A were located in exon 8, exon 9 and intron 9, respectively. They do not change the primary structure of the encoded protein. (2) Linkage equilibrium was observed between A2823G in caspase-10 gene and the three sites in caspase-8 gene. A43466G and G52951A, and G51484A and G52951A in caspase-8 gene were also in linkage equilibrium. Their coefficients of disequilibrium were near 0. Whereas strong linkage disequilibrium was observed between A43466G and G51484A, because its coefficient of disequilibrium was near 1. (3) A total of 11 haplotypes were estimated within A2823G in caspase-10 gene and three sites in caspase-8 gene. A-2823/A-43466/G-51484/G-52951 was the main haplotype with a frequency of 0.3811. A-2823/A-43466/G-51484/A-52951 was the second haplotype with a frequency of 0.2536. The polymorphism information content of their haplotypes was 0.7106. CONCLUSION: The SNPs of caspase-8, -10 genes in Han Chinese of Zhejiang could be parsed into at least three different haplotype blocks. The polymorphism information content can be improved by using haplotype analysis of several SNPs.

Alleles↗
PubMed2006

[Association of single nucleotide polymorphism of megsin gene with IgA nephropathy].

OBJECTIVE: To investigate whether the single nucleotide polymorphisms (SNPs) in the gene of megsin, a novel serine protease inhibitor, account for the pathogenicity of IgA nephropathy (IgAN). METHODS: A comprehensive megsin gene survey, including the entire coding region, part of the regulatory region, and exon-intron connection region, was performed by PCR-direct sequencing on the DNA samples of peripheral blood from 12 randomly selected IgAN patients and 12 randomly selected healthy persons. Eight SNPs with moderate or high frequencies (with the frequency > 5%) selected from the 11 SNPs found were used as candidate SNPs. Then 210 IgAN patients proven by renal-biopsy, all of Chinese Han nationality, and 103 normal volunteers were recruited. The 8 candidate SNPs were genotyped by direct sequencing or PCR-RFLP and a case-control association study was carried out. RESULTS: The SNP of 267G/A in 5'untranslated region within exon1 was significantly associated with IgAN. The frequency of AG/AA genotype of the IgA patients was 29.0%, significantly higher than that of the controls (16.5%, P < 0.05). The frequency of A allele of the IgA patients was 14.8%, significantly higher than that of the controls (8.7%, P < 0.05). The odds ratio of AG/AA genotype versus GG genotype was 2.07 with the 95% confidence interval of 1.15 - 3.74. The linkage disequilibrium between two SNPs existed commonly within one gene. CONCLUSION: 267G/A in megsin gene is associated with IgAN susceptibility. AG and AA genotypes are the risk factors of pathogenesis of IgAN.

Adolescent↗
PubMed2006

[Polymorphisms of hsp 60 gene in Chinese Han people].

OBJECTIVE: To identify the single nucleotide polymorphisms (SNPs) in the regulatory and coding regions of heat shock protein 60 gene and search for its genetic makers in Chinese Han people. METHODS: The 5' flank region, parts of the exons and introns of hsp60 gene were resequenced to identify the SNPs in Chinese Han people, and then the sequenced results to the Japanese, European and African's data in National Center for Biotechnology Information (NCBI) and HapMap databases were compared. RESULTS: One novel SNP was identified in exon 2 resulting in synonymous variant and the G allele frequency was 0.025. There were 11 reported SNPs in the sequenced region. The minor allele frequencies of rs1116734, rs3749095, rs1050347, rs8539 were 0.51, 0.30, 0.29, 0.49. The heterozygosity of the other 7 SNPs was 0. The distributions of rs1116734, rs1050347, rs8539, rs3749095 in Chinese Han people were similar to the Japanese's. The hsp60 rs3749095 which was not found in Japanese people was a high-frequency SNP in Chinese Han people; the distribution of rs8539 in Chinese Han people was quite different from European and African's (P < 0.01). CONCLUSION: The SNPs of hsp60 in Chinese Han people are different from the other peoples. The SNPs of hsp60 gene rs1116734, rs3749095, rs1050347, rs8539 are very common in Chinese Han people and might be used for candidate genetic markers of hsp60 gene.

Adolescent↗
PubMed2006

Effect of the peroxisome proliferators-activated receptor (PPAR) gamma 3 gene on BMI in 1,210 school students from Morelos, Mexico.

UNLABELLED: Little research has been undertaken on risk factors for obesity in young people in Latin America, including Mexico, despite the fact that obesity constitutes the number one public health problem in Mexico. Our objective was to investigate the effect of the Peroxisome proliferators-activated receptor (PPAR)_3 gene on BMI measured among adolescents collected from a cohort study originally designed for epidemiological studies. METHODS: Blood samples and anthropometric measurements were collected from 1,210 out of 13,294 public school students of both sexes, aged 11-24 years in Morelos, Mexico. In this study, we genotyped 7 selected SNPs of the PPAR_ transcript variant 3 (including Pro12Ala) in a group of unrelated 717 males and 493 females (age range 11-24), including 3 SNPs located in the 5' untranslated region. These 7 SNPs were selected by the tagging algorithm implemented in the program haploview to scan the whole gene. We tested each of the 7 SNPs individually for association with the body mass index (BMI), and two SNPs (rs2938392 and rs1175542) revealed significant associations with BMI (p-value=0.008 and 0.029, respectively). The SNP rs2938392 is roughly 41.5 Kb from rs1801282 (Pro12Ala in PPAR_2). Furthermore, we examined the association between haplotypes built from 7 SNPs and BMI using a score statistic implemented in the program haplo.stats. While the permutation based global p-value was 0.544, one individual haplotype with a frequency of 0.279 gave a p-value of 0.089 (permutation based). However, when the analyses were conducted in males only, the permutation based global p-value was 0.055 and one individual haplotype with a frequency of 0.28 gave a significant p-value of 0.013.

5' Untranslated Regions↗