Biomedical subjects

Sanjay Shete

Publications and source records attributed to Sanjay Shete.

At least 19 recordsLinked to original sources

PubMed2006

Exploring joint effects of genes and the clinical efficacy of morphine for cancer pain: OPRM1 and COMT gene.

Pain is a complex human trait. It is likely that the interaction of multiple genes, each with a small individual effect, along with the effect of environmental factors, influences the clinical efficacy of opioids rather than a single gene alone. Polymorphisms in genes coding for the mu-opioid receptor (A118G) and catechol-O-methyl transferase (Val158Met) may be important modulators of opioid efficacy. We assessed joint effects of the OPRM1 and COMT genes in predicting morphine dose for cancer pain relief. We used genotype and clinical data from a pharmacokinetic study of morphine in 207 inpatients treated with stable morphine dose for at least 3 days by Palliative Medicine Specialists. Results showed significant variation in morphine dose requirement by genotype groups: carriers of COMT Val/Val and Val/Met genotype required 63% and 23%, respectively, higher morphine dose compared to carriers of Met/Met genotype (p=0.02). Carriers of OPRM1 GG genotype required 93% higher morphine dose compared to carriers of AA genotypes (p=0.012). When we explored for joint effects, we found that carriers of the OPRM1 AA and COMT Met/Met genotype required the lowest morphine dose to achieve pain relief (87 mg/24 h; 95%CI=57,116) and those with neither Met/Met nor AA genotype needed the highest morphine dose (147 mg/24 h; 95%CI=100,180). The significant joint effects for the Met/Met and AA genotypes (p<0.012) persisted, even after controlling for demographic and clinical variables in the multivariable analyses. Future studies are needed to further characterize the joint effects of multiple genes, along with demographic and clinical variables, in predicting opioid dose.

Adult↗

PubMed2006

Promoter polymorphism (-786t>C) in the endothelial nitric oxide synthase gene is associated with risk of sporadic breast cancer in non-Hispanic white women age younger than 55 years.

BACKGROUND: Nitric oxide (NO) is constitutively synthesized in the endothelium by endothelial nitric oxide synthase (eNOS) and acts as a pleiotropic regulator involved in carcinogenesis. Most breast cancers develop from mammary epithelial cells; therefore, NO may play a role in their development. It was hypothesized that eNOS polymorphisms are associated with risk of breast cancer. METHODS: In the current hospital-based case-control study of 421 non-Hispanic white women with sporadic breast cancer and 423 frequency-matched control subjects, we genotyped 3 polymorphisms of eNOS (i.e., -786T>C, the 27-base pair [bp] variable number of tandem repeats [VNTR] in intron 4, and 894G>T [Glu298Asp]) and assessed their associations with risk of breast cancer. RESULTS: It was found that, compared with -786TT, the -786C variant genotypes were associated with a significantly increased risk of breast cancer in an allele dose-dependent manner (adjusted odds ratio [OR], 1.33 [95% confidence interval (95% CI)], 0.99-1.77 for -786TC; and OR, 1.79 [95% CI, 1.11-2.87] for -786CC; P(trend) = .007), but 27-bp VNTR and 894G>T genotypes were not. Stratification analysis demonstrated that the risk associated with -786C variant genotypes (-786TC/CC) was more pronounced in smokers and in those 50 years or older (OR, 1.82 [95% CI, 1.19-2.80] and OR, 2.08 [95% CI, 1.25-3.45], respectively), and in the estrogen and progesterone receptor-negative cases (OR, 1.70 [95% CI, 1.10-2.62] and OR, 1.57 [95% CI, 1.07-2.32], respectively). Furthermore, the C4G haplotype derived from the observed genotypes was also associated with a significantly increased risk of breast cancer (OR, 2.16; 95% CI, 1.07-4.36). CONCLUSIONS: The results suggest that eNOS polymorphisms (especially -786T>C) may play a role in the development of sporadic breast cancer.

Adult↗

PubMed2006

uPAR and HER-2 gene status in individual breast cancer cells from blood and tissues.

Overexpression of urokinase plasminogen activator system or HER-2 (erbB-2) in breast cancer is associated with a poor prognosis. HER-2 overexpression is caused by HER-2 gene amplification. The anti-HER-2 antibody trastuzumab significantly improves clinical outcome for HER2-positive breast cancer. Drugs that target the uPA system are in early clinical trials. The aims of this study were to determine whether urokinase plasminogen activator receptor (uPAR) gene amplification occurs and whether analysis of individual tumor cells (TCs) in the blood or tissue can add information to conventional pathological analysis that could help in diagnosis and treatment. Analysis of individual TCs indicates that uPAR amplification occurs in a significant portion of primary breast cancers and also circulating tumor cells (CTCs) from patients with advanced disease. There was complete concordance between touch preps (TPs) and conventional pathological examination of HER-2 and uPAR gene status in primary tumors. There was also excellent concordance of HER-2 gene status between primary tumors and CTCs provided that acquisition of HER-2 gene amplification in CTCs was taken into account. Unexpectedly, gene amplification of HER-2 and uPAR occurred most frequently in the same TC and patient, suggesting a biological bias and potential advantage for coamplification. Expression of HER-2 and uPAR in primary tumors predicted gene status in 100 and 92% of patients, respectively.

Breast Neoplasms↗

PubMed2006

TLINKAGE-IMPRINT: a model-based approach to performing two-locus genetic imprinting analysis.

OBJECTIVES: Imprinting refers to the expression of only one copy of a gene pair, which is determined by the parental origin of the copy. Imprinted genes play a role in the development of several complex diseases, including cancers and mental disorders. In certain situations, two-trait-loci models are shown to be more powerful than one-trait-locus models. However, no current methods use pedigree structure efficiently and perform two-locus imprinting analyses. In this paper, we apply the Elston-Stewart algorithm to the parametric two-trait-loci imprinting model used by Strauch et al. [2000] to obtain a method for qualitative trait linkage analyses that explicitly models imprinting and can be applied to large pedigrees. METHODS: We considered a parametric approach based on 4 x 4 penetrance matrix to account for imprinting and modified TLINKAGE software to implement this approach. We performed simulation studies using a small and a large pedigree under dominant and imprinted and dominant or imprinted scenarios. Furthermore, we developed a likelihood ratio-based test for imprinting that compares the logarithm of odds (LOD) score obtained using the two-locus imprinting model with that obtained using the standard two-locus model that does not allow for imprinting. RESULTS: In simulation studies of three scenarios where the true mode of inheritance included imprinting, accurate modeling through the proposed approach yielded higher LOD scores and better recombination fraction estimates than the traditional two-locus model that does not allow for imprinting. CONCLUSIONS: This imprinting model will be useful in identifying the genes responsible for several complex disorders that are potentially caused by a combination of imprinted and non-imprinted genes.

Algorithms↗

PubMed2006

Joint effects of germ-line p53 mutation and sex on cancer risk in Li-Fraumeni syndrome.

Germ-line p53 mutations have been identified in most families with Li-Fraumeni syndrome (LFS). For germ-line p53 mutation carriers, there is considerable variability with respect to age of cancer onset and tumor type, suggesting that additional genetic effects influence the clinical severity and tumor spectrum. To identify factors that might contribute to the observed heterogeneity in time to onset, we used segregation analysis to analyze the joint effects of germ-line p53 mutations and risk modifier(s) on cancer incidence. We studied 159 kindreds, ascertained through probands who had been diagnosed with childhood soft-tissue sarcoma before 16 years of age, survived >3 years after diagnosis, and treated at The University of Texas M.D. Anderson Cancer Center (Houston, TX) from 1944 to 1975. This unique cohort has been followed systematically for >20 years and has had germ-line p53 mutation testing in probands and extended family members. The analyses revealed that germ-line p53 mutations and sex had significant effects on cancer risk: men with p53 mutations had 151-fold higher odds of developing cancer than did those without mutations [95% confidence interval (95% CI), 60-380], and women with p53 mutations had 1,075-fold higher odds than did those without mutations (95% CI, 358-3,229) and 7.1-fold higher odds of having cancer than did men with mutations (95% CI, 2.5-20.3). These findings provide quantitative cancer risk assessments for LFS families.

Adolescent↗

PubMed2006

Familial thoracic aortic aneurysms and dissections: three families with early-onset ascending and descending aortic dissections in women.

Ascending thoracic aortic aneurysms leading to type A dissections can be inherited in an autosomal dominant manner with variable age of onset and decreased penetrance, primarily in women. Three families are described with autosomal dominant inheritance of either ascending aortic aneurysms leading to type A dissections or type B dissections, and a young age of onset of aortic dissections in both men and women. Pedigree analysis suggests that a de novo mutation is responsible for the disease in one family. The discordant age of onset of aortic disease in a monozygotic twin pair in a different family indicates that environmental or stochastic factors may influence the variable expression of disease. Genetic analysis of one family excluded linkage to known loci for TAAD (TAAD1, TAAD2, FAA1, or FBN1) and sequence analysis failed to identify mutations in TGFBR2, the gene encoding transforming growth factor beta receptor type II. Thus, a novel unidentified loci may be responsible for the phenotype in these three families.

Adolescent↗

PubMed2006

Polymorphisms and haplotypes of the NBS1 gene are associated with risk of sporadic breast cancer in non-Hispanic white women <or=55 years.

DNA double-strand breaks (DSBs) may lead to genomic instability and cancer if unrepaired. Nijmegen breakage syndrome 1 (NBS1) protein is one of the key proteins that participates in recognition and repair of DSBs in humans. We hypothesized that polymorphisms of NBS1 are associated with breast cancer risk. We selected three NBS1 haplotype-tagging polymorphisms (i.e. 924T>C, 8360G>C and 30537G>C) to represent all common (>or=5%) haplotypes reported in the National Institute of Environmental Health Sciences database and to reconstruct haplotypes. In a hospital-based case-control study of 421 non-Hispanic white patients with sporadic breast cancer ( C polymorphism. Furthermore, the derived haplotypes were associated with risk in a dose-response manner as the number of variant (risk) alleles (i.e. 8360C, 924C or 30537C) increased (adjusted OR = 1.07, 95% CI = 0.78-1.46 for 1-2 variant alleles; adjusted OR = 2.47, 95% CI = 1.48-4.14 for 3-6 variant alleles; P(trend) = 0.006). These findings suggest that NBS1 polymorphisms and haplotypes may contribute to the etiology of sporadic breast cancer in young non-Hispanic white women. Large studies are warranted to confirm these findings.

Aged↗

PubMed2006

The role of MMP-2 and MMP-9 polymorphisms in sporadic intracranial aneurysms.

OBJECT: Matrix metalloproteinases (MMPs) are a family of endopeptidases that mediate vascular remodeling by degrading extracellular matrix components, such as collagen and elastin. On the basis of accumulating evidence that implicates increased MMP-2 (gelatinase A) and MMP-9 (gelatinase B) amounts and activity in the pathogenesis of aneurysms, the authors investigated the genetic association between polymorphisms in MMP-2 and MMP-9 and sporadic intracranial aneurysms. METHODS: Eight polymorphisms located in MMP-2 and MMP-9 were genotyped, and the association of these variations with disease was assessed in a Caucasian population consisting of 125 patients with intracranial aneurysms and 234 ethnically matched healthy volunteers. Polymorphisms in the MMP-2 gene and the haplotypes generated from these polymorphisms were not associated with the occurrence of intracranial aneurysms. However, a polymorphism located in the 3' untranslated region of MMP-9 showed a significant association with disease in the study population, with individuals carrying the TT genotype at increased risk for developing intracranial aneurysms (odds ratio 1.91, p = 0.005). Haplotypes containing the T allele of this polymorphism also showed a comparable association with disease. Similar results were obtained in an analysis of these polymorphisms in a subgroup of patients who presented with ruptured aneurysms. CONCLUSIONS: The study findings support a role for MMP-9, but not MMP-2, in the pathogenesis of intracranial aneurysms.

Female↗

PubMed2005

Effects of population structure on genetic association studies.

Population-based case-control association is a promising approach for unravelling the genetic basis of complex diseases. One potential problem of this approach is the presence of population structure in the samples. Using the Collaborative Study on the Genetics of Alcoholism (COGA) single-nucleotide polymorphism (SNP) datasets, we addressed three questions: How can the degree of population structure be quantified, and how does the population structure affect association studies? How accurate and efficient is the genomic control method in correcting for population structure? The amount of population structure in the COGA SNP data was found to inflate the p-value in association tests. Genomic control was found to be effective only when the appropriate number of markers was used in the control group in order to correctly calibrate the test. The approach presented in this paper could be used to select the appropriate number of markers for use in the genomic control method of correcting population structure.

Databases, Genetic↗

PubMed2005

Analysis of alcoholism data using support vector machines.

A supervised learning method, support vector machine, was used to analyze the microsatellite marker dataset of the Collaborative Study on the Genetics of Alcoholism Problem 1 for the Genetic Analysis Workshop 14. Twelve binary-valued phenotype variables were chosen for analyses using the markers from all autosomal chromosomes. Using various polynomial kernel functions of the support vector machine and randomly divided genome regions, we were able to observe the association of some marker sets with the chosen phenotypes and thus reduce the size of the dataset. The successful classifications established with the chosen support vector machine kernel function had high levels of correctness for each prediction, e.g., 96% in the fourfold cross-validations. However, owing to the limited sample data, we were not able to test the predictions of the classifiers in the new sample data.

Alcoholism↗

PubMed2005

Analysis of genes for alcoholism using two-disease-locus models.

Using model-based two-locus methods for mapping genes, we analyzed the family data from the Collaborative Study on the Genetics of Alcoholism. Microsatellite data from 143 families ascertained through having three or more individuals affected with alcohol dependence were used for this investigation. Four regions showing evidence for linkage were identified using single-locus models from previous investigations. We investigated the genetic linkage, pattern of disease inheritance, and pair-wise genetic epistasis of these loci using the TLINKAGE program for two-disease-locus analysis.

Alcoholism↗

PubMed2005

Genetic imprinting analysis for alcoholism genes using variance components approach.

Genomic imprinting, which is also known as the parent-of-origin effect, is a mechanism that only expresses one copy of a gene pair depending upon the parental origin. Although many chromosomal regions in the human genome are likely to be imprinted, imprinting is not accounted for in the usual linkage analysis. In this study, using a variance-components approach with a quantitative phenotype ttth-FP1, we found significant evidence of imprinting at two loci, D7S1790 and D1S1631, on chromosome 1 and chromosome 7, respectively. Our results suggest that allowing for the possibility of imprinting can increase the power to detect linkage for localizing genes for alcoholism.

Alcoholism↗

PubMed2005

Examining the effect of linkage disequilibrium on multipoint linkage analysis.

Most linkage programs assume linkage equilibrium among multiple linked markers. This assumption may lead to bias for tightly linked markers where strong linkage disequilibrium (LD) exists. We used simulated data from Genetic Analysis Workshop 14 to examine the possible effect of LD on multipoint linkage analysis. Single-nucleotide polymorphism packets from a non-disease-related region that was generated with LD were used for both model-free and parametric linkage analyses. Results showed that high LD among markers can induce false-positive evidence of linkage for affected sib-pair analysis when parental data are missing. Bias can be eliminated with parental data and can be reduced when additional markers not in LD are included in the analyses.

Genetic Markers↗

PubMed2005

Mutations in transforming growth factor-beta receptor type II cause familial thoracic aortic aneurysms and dissections.

BACKGROUND: A genetic predisposition for progressive enlargement of thoracic aortic aneurysms leading to type A dissection (TAAD) is inherited in an autosomal-dominant manner in up to 19% of patients, and a number of chromosomal loci have been identified for the condition. Having mapped a TAAD locus to 3p24-25, we sequenced the gene for transforming growth factor-beta receptor type II (TGFBR2) to determine whether mutations in this gene resulted in familial TAAD. METHODS AND RESULTS: We sequenced all 8 coding exons of TGFBR2 by using genomic DNA from 80 unrelated familial TAAD cases. We found TGFBR2 mutations in 4 unrelated families with familial TAAD who did not have Marfan syndrome. Affected family members also had descending aortic disease and aneurysms of other arteries. Strikingly, all 4 mutations affected an arginine residue at position 460 in the intracellular domain, suggesting a mutation "hot spot" for familial TAAD. Despite identical mutations in the families, assessment of linked polymorphisms suggested that these families were not distantly related. Structural analysis of the TGFBR2 serine/threonine kinase domain revealed that R460 is strategically located within a highly conserved region of this domain and that the amino acid substitutions resulting from these mutations will interfere with the receptor's ability to transduce signals. CONCLUSIONS: Germline TGFBR2 mutations are responsible for the inherited predisposition to familial TAAD in 5% of these cases. Our results have broad implications for understanding the role of TGF-beta signaling in the pathophysiology of TAAD.

Adult↗

PubMed2005

Methylenetetrahydrofolate reductase polymorphisms and risk of squamous cell carcinoma of the head and neck: a case-control analysis.

Folate deficiency is implicated in cancer risk that may be modulated by a genetic variation in the methylenetetrahydrofolate reductase (MTHFR) gene in folate metabolism. We hypothesized that genetic variants in MTHFR are associated with risk of squamous cell carcinoma of the head and neck (SCCHN). We genotyped 3 MTHFR polymorphisms (C677T, A1298C and G1793A) and estimated their haplotypes in a hospital-based case-control study of 537 SCCHN cases and 545 cancer-free controls. The controls were frequency-matched to the cases by age (+/- 5 years), sex, ethnicity and smoking status. We found that the MTHFR 1298AC/CC genotypes were associated with an approximately 35% reduction in risk of SCCHN (adjusted odds ratio = 0.65; 95% CI = 0.51-0.82) compared to the AA genotype. The MTHFR 677CT and 1793GA/AA genotypes were associated with nonsignificant increased risk of SCCHN compared to the 677CC and 1793GG genotypes, respectively. We estimated that there were 8 haplotypes and 16 haplotype genotypes based on these 3 variants. When we used the haplotypes and assumed that the 677T, 1298A and 1793A alleles were risk alleles, the adjusted odds ratios increased as the number of risk alleles increased: 1.00 for 0-1 variant, 1.85 (1.3-2.5) for any 2 risk alleles and 1.93 (1.4-2.7) for any 3 risk alleles. These results suggest that all 3 MTHFR polymorphisms may play a role in the susceptibility to SCCHN among non-Hispanic whites. Future studies should incorporate detailed data on alcohol consumption, dietary folate intake and related serologic measurements.

Adult↗

PubMed2005

Parametric approach to genomic imprinting analysis with applications to Angelman's syndrome.

Genomic imprinting is a mechanism by which only one copy of a gene pair is expressed, and this expression is determined by the parental origin of the copy. The deregulation of imprinted genes has been implicated in a number of human diseases. The Imprinted Gene Catalogue now has more than 200 genes listed, and estimates based on mouse models suggest many more may exist in humans. Therefore, the development of methods to identify such genes is important. In this communication, we present a parametric model-based approach to analyzing arbitrary-sized pedigree data for genomic imprinting. We have modified widely used LINKAGE program to incorporate our proposed approach. In addition, our approach allows for the use of sex-specific recombinations in the analysis, which is of particular importance in a genome-wide analysis for imprinted genes. We compared our imprinting analysis approach to that implemented in the GENEHUNTER-IMPRINT program using simulation studies as well as by analyzing causal genes in Angelman's syndrome families, which are known to be imprinted. These analyses showed that the proposed approach is very powerful for detecting imprinted genes in large pedigrees.

Angelman Syndrome↗

PubMed2005

Genetic mapping of a third Li-Fraumeni syndrome predisposition locus to human chromosome 1q23.

Li-Fraumeni syndrome (LFS) is a clinically and genetically heterogeneous inherited cancer syndrome. Most cases ( approximately 70%) identified and characterized to date are associated with dominantly inherited germ line mutations in the tumor suppressor gene TP53 (p53) in chromosome 17p13.1. In a subset of non-p53 patients with LFS, CHEK2 in chromosome 22q11 has been identified as another predisposing locus. Studying a series of non-p53 LFS kindred, we have shown that there is additional genetic heterogeneity in LFS kindred with inherited predisposition at loci other than p53 or CHEK2. Using a genome-wide scan for linkage with complementing parametric and nonparametric analysis methods, we identified linkage to a region of approximately 4 cM in chromosome 1q23, a genomic region not previously implicated in this disease. Identification ofa third predisposing gene and its underlying mutation(s) should provide insight into other genetic events that predispose to the genesis of the diverse tumor types associated with LFS and its variants.

Checkpoint Kinase 2↗

PubMed2005

Linkage analysis of affected sib pairs allowing for parent-of-origin effects.

Parent-of-origin effects, also known as genomic imprinting, exist for many mammalian genes. For imprinted genes the expression of an allele depends upon the sex of the transmitting parent. Here we have developed a method based on alleles that are shared identical by descent by affected sib pairs, that allows for parent-of-origin effects. Our method allows for sex-specific recombination rates, an important consideration in studying imprinted genes. We have also derived a tetrahedron for the true identical-by-descent frequencies accounting for parent-of-origin effects. Using this tetrahedron, we propose a robust generalized minmax test for linkage and discuss its properties in the presence of genomic imprinting. We have also performed power comparisons of various allele sharing tests and provide regions of the tetrahedron in which the different tests are optimal. We also provide useful strategies to determine the optimal tests to use while performing a genome scan.

Alleles↗