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Results for “common variants”

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PubMed2006

A common genetic variant is associated with adult and childhood obesity.

Obesity is a heritable trait and a risk factor for many common diseases such as type 2 diabetes, heart disease, and hypertension. We used a dense whole-genome scan of DNA samples from the Framingham Heart Study participants to identify a common genetic variant near the INSIG2 gene associated with obesity. We have replicated the finding in four separate samples composed of individuals of Western European ancestry, African Americans, and children. The obesity-predisposing genotype is present in 10% of individuals. Our study suggests that common genetic polymorphisms are important determinants of obesity.

Adult↗

PubMed1997

Human thiopurine methyltransferase pharmacogenetics: gene sequence polymorphisms.

Thiopurine methyltransferase (TPMT) catalyzes the S-methylation of thiopurine drugs. TPMT activity is regulated by a common genetic polymorphism that is associated with large individual variations in thiopurine toxicity and efficacy. We previously cloned the functional gene for human TPMT and reported a common variant allele for low enzyme activity, TPMT*3A, that contains point mutations at cDNA nucleotides 460 and 719. In the present study, we set out to determine the number, types, and frequencies of TPMT variant alleles associated with low enzyme activity in clinical laboratory samples in the United States and to compare those results with data obtained from two different ethnic groups. We identified a total of six different variant alleles for low TPMT activity in the 283 clinical laboratory samples studied. The most common variant was *3A; the second most frequent variant allele, *3C, contained only the nucleotide 719 polymorphism; and four other variant alleles were detected. TPMT*3A also appeared to be the most common variant allele in a Norwegian white population sample, but it was not found in a population sample of Korean children. However, *3C was present in samples from the Korean children, as was novel allele, *6. Characterization of variant alleles for low TPMT enzyme activity will help make it possible to assess the potential clinical utility of deoxyribonucleic acid-based diagnostic tests for determining TPMT genotype.

Alleles↗

PubMed1996

Common sequence variants of lipoprotein lipase: standardized studies of in vitro expression and catalytic function.

We have assessed the functional activity of three common sequence variants of human lipoprotein lipase (LPL). Two of these, Asn291Ser and Asp9Asn arise from missense mutations while the third, Ser447Ter, derives from a nonsense mutation, truncating LPL by two residues. As previous in vitro studies have produced conflicting results, we have re-analyzed the catalytic function of these variants using the COS cell transfection system, under optimized and standardized experimental protocols. We found the Asn291Ser variant to manifest with a decrease in catalytic activity (57% of normal) due to a reduction in secretion and stability of the active homodimeric form. The Asp9Asn variant also showed a significant decrease in catalytic activity (85% of normal), but this was found to be due to a decreased rate of secretion only, as the homodimeric form was stable. The findings for these mutants contrasted with those of the Ser447Ter truncation variant which proved to be catalytically normal; this variant also manifested normal homodimer stability. The truncated variant did however, present with a higher total secreted mass level (131%) than control LPL. This was most likely due to enhanced secretion of the monomeric form. None of these mutations exhibited defects in binding affinity to cell surface proteoglycans. Each of these variants deviated significantly from normal as regards to their secreted activity or mass levels in the COS cell transfection system.

Catalysis↗

PubMed1997

Worldwide frequency of a common genetic variant of luteinizing hormone: an international collaborative research. International Collaborative Research Group.

OBJECTIVE: To determine the worldwide frequency of a common immunological LH variant because of two point mutations in the LH beta-subunit gene (Trp8Arg and Ile15Thr). DESIGN: Cross-sectional study on LH status (variant and wild-type) in serum (or DNA) samples from Finland (Finns and Lapps), Estonia, Poland, Sweden, The Netherlands, United Kingdom, Italy, South Africa (blacks), Thailand, China, Japan, and the United States (Hispanics and blacks). SETTING: Academic research environment. PATIENT(S): Ambulatory adult men and women (n = 2,936) with minor illnesses and no known endocrinological disorders. INTERVENTION: A single blood sample was collected from each subject. MAIN OUTCOME MEASURE(S): The LH status was determined by two immunofluorometric assays using monoclonal antibodies. One (assay 1) only recognizes the wild-type LH, the other (assay 2) recognizes equally variant and wild-type LH. The ratio of assay 1 to assay 2 indicates the LH status: wild-type, > 0.9; heterozygote, 0.2 to 0.9; and homozygote, < 0.15. One population (Lapps) was studied by DNA analysis using polymerase chain reaction and allele-specific oligonucleotide hybridization. RESULT(S): The carrier frequency of the variant LH beta allele varied from 7.1% in U.S. Hispanics to 41.9% in Lapps of northern Finland. The variant LH beta allele tended to be more common in populations from Northern Europe as compared with those from Asia. CONCLUSION(S): The high frequency of the LH beta variant worldwide makes it an important confounding factor when obtaining disproportionately low LH levels with some immunometric assays. The LH variant may contribute to some pathologies of the pituitary-gonadal function.

Adolescent↗

PubMed1979

Properties of the two common electrophoretic variants of phosphoglucomutase in Drosophila melanogaster.

Phosphoglucomutase (PGM) of adult stage in Drosophilia melanogaster has been characterized by gel filtration, ion-exchange chromatography, and isoelectric focusing. The two common electrophoretic variants, PGMA and PGMB, differ with respect to their kinetic and stability parameters. PGMA is more thermostable than PGMB but shows the same pH optimum, equal dependence on Mg2+, and identical molecular weight. There is no significant kinetic difference between the two allozymes at the optimum pH values, but at pH 6.0 the Km value for glucose-1,6-diphosphate of PGMB is significantly higher than that of PGMA. This difference might explain the observed selective advantage of the PgmA allele in population studies.

Alleles↗

PubMed2006

A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization.

Extremes of the electrocardiographic QT interval, a measure of cardiac repolarization, are associated with increased cardiovascular mortality. We identified a common genetic variant influencing this quantitative trait through a genome-wide association study on 200 subjects at the extremes of a population-based QT interval distribution of 3,966 subjects from the KORA cohort in Germany, with follow-up screening of selected markers in the remainder of the cohort. We validated statistically significant findings in two independent samples of 2,646 subjects from Germany and 1,805 subjects from the US Framingham Heart Study. This genome-wide study identified NOS1AP (CAPON), a regulator of neuronal nitric oxide synthase, as a new target that modulates cardiac repolarization. Approximately 60% of subjects of European ancestry carry at least one minor allele of the NOS1AP genetic variant, which explains up to 1.5% of QT interval variation.

Adaptor Proteins, Signal Transducing↗

PubMed1987

A rare variant of common arterial trunk.

A 13 day old baby was admitted to hospital with multiple abnormalities, increasing cyanosis, and cardiac failure. Cardiac catheterisation was performed on the day of admission and he died shortly after the procedure. A rare variant of common arterial trunk, in which the pulmonary arteries arose directly from the underside of the aortic arch, was found at necropsy.

Humans↗

PubMed2001

Neonatal screening for haemoglobinopathies: the results of a 10-year programme in an English Health Region.

Neonatal identification of sickle cell disease can significantly reduce mortality and morbidity during the first 5 years of life. During a 10-year period, 414,801 neonates were screened by isoelectric focusing. The most common variants detected were haemoglobins S, C, D and E. Two hundred and fifty of the samples tested were homozygotes or compound heterozygotes, and 6554 samples were heterozygotes for the common variants. The gene frequencies in the population tested were calculated from this data for the most common variants. They were: S, 0.0057; C, 0.0014; D(Punjab(Los Angeles)), 0.0007; E, 0.0005. Additionally, 16 babies had beta thalassaemia major and 405 had rarer variants, of which six had never previously been described. Knowledge of the distribution of these inherited diseases is useful in healthcare planning and appropriate allocation of resources, while counselling targeted at appropriate couples enables informed parental choice and may prevent disease.

Anemia, Sickle Cell↗

PubMed2005

A common missense variant in BRCA2 predisposes to early onset breast cancer.

INTRODUCTION: Mutations in the BRCA2 gene are one of the two major causes of hereditary breast cancer. Protein-truncating mutations of BRCA2 are usually deleterious and increase the risk of breast cancer up to 80% over a lifetime. A few missense mutations in BRCA2 are believed to have a similarly high penetrance, apart from more common neutral polymorphisms. It is often difficult to classify a particular sequence variant as a mutation or a polymorphism. For a deleterious variant, one would expect a greater allele frequency in breast cancer cases than in ethnic-matched controls. In contrast, neutral polymorphic variants should be equally frequent in the two groups. METHODS: We genotyped 3,241 cases of breast cancer diagnosed at under 51 years of age, unselected for family history, from 18 hospitals throughout Poland and 2,791 ethnic-matched controls for a single BRCA2 C5972T variant. RESULTS: The variant was present in approximately 6% of the Polish population. In the study, 13 women (11 cases and two controls (OR = 4.7; p = 0.02)) were homozygous for the variant allele. The overall odds ratio for breast cancer in women with a single copy of the BRCA2 C5972T variant was 1.1 (p = 0.7); however, the effect was significant for patients diagnosed at or before age 40 (OR = 1.4; p = 0.04). We reviewed the association between the BRCA2 variant in different histologic subgroups and found the effect most pronounced in women who had ductal carcinoma in situ (DCIS) with micro-invasion (OR = 2.8; p < 0.0001). CONCLUSION: The BRCA2 C5972T allele is a common variant in Poland that increases the risk of DCIS with micro-invasion. The homozygous state is rare but increases the risk of breast cancer five-fold.

Adult↗

PubMed2004

Characterization of common genetic variants in cathepsin K and testing for association with bone mineral density in a large cohort of perimenopausal women from Scotland.

UNLABELLED: BMD values in approximately 3000 perimenopausal Scottish women were adjusted by regression to identify and account for nongenetic factors. Adjusted BMD values were not associated with simple tandem repeat (STR) markers or single nucleotide polymorphisms (SNPs) at the Cathepsin K (CTSK) locus. We present a thorough analysis of common CTSK polymorphisms and genetic relatedness among CTSK haplotypes. INTRODUCTION: CTSK is a cysteine protease of the papain family and is thought to play a critical role in osteoclast-mediated bone degradation. Rare, inactivating mutations in CTSK cause pychodysostosis, an autosomal recessive osteochondrodysplasia characterized by osteosclerosis and short stature. However, there have been no studies of common genetic variants in CTSK and their possible association with bone density in the general population. MATERIALS AND METHODS: To identify common single nucleotide polymorphisms (SNPs) and simple tandem repeat (STR) polymorphisms in and around CTSK, we screened all CTSK exons, intron A, all intron-exon boundaries, and the putative CTSK promoter region in 130 random whites using both high-performance liquid chromatography (HPLC) and DNA sequencing. CTSK markers were genotyped in approximately 3000 perimenopausal Scottish women whose hip and spine bone mineral density (BMD) had been measured by DXA. We performed linear regression analysis to identify and adjust for nongenetic predictors of BMD, and adjusted BMD values (regression residuals) were tested for association with individual CTSK markers and haplotypes by ANOVA and the composite haplotype method of Zaykin et al. RESULTS AND CONCLUSIONS: We discovered two intronic SNPs (8% and 9% frequency), but no common exonic SNPs (> 1% frequency), and found that three STRs at the immediate 5' end of the CTSK locus are highly polymorphic. The population frequencies of haplotypes defined by these five polymorphisms were estimated, and a cladogram was derived showing proximity of relationship and likely descent of the 30 most common CTSK haplotypes. Regression analyses revealed that approximately 39% of spine and 19% of hip rate of change in BMD was accounted for by nongenetic factors. For baseline BMD values in premenopausal women, nongenetic predictors explained 11% of the variance at the spine and 13% at the hip. Adjusted BMD values showed no statistically significant association with any of the individual CTSK polymorphisms or CTSK haplotypes.

Analysis of Variance↗

PubMed2001

Immunological characterization of human luteinizing hormone with special regard to a common genetic variant.

Immunoassays are widely used for measuring gonadotropins, including luteinizing hormone (LH), as these are both specific and sensitive. Because LH is microheterogeneous it has been claimed that the specificity of monoclonal antibodies used in two-site immunoassays can limit their clinical utility. Furthermore, we reported earlier a common genetic variant form of LH due to amino acid alterations in the LHbeta gene that is poorly or not recognized by antibodies directed against epitopes present in the intact molecule. We here report the result of an LH epitope mapping using 30 different monoclonal antibodies. The antigenic area affected by the amino acid alterations is fairly large, as antibodies to the two intact domains are able to sandwich each other. Combinations of alpha-beta or beta-beta antibodies generally provide alternatives for unbiased detection of circulating LH and some have reasonably good discrimination of human chorionic gonadotropin. The beta-beta combinations exhibit a peculiarity in urine determinations as they detect the urinary beta-core fragment. Our aims were to study the altered immunoreactivity caused by the amino acid changes and to design two-site LH assays fully capable of recognizing the biologically active LH variant. We also conclude that the variability in recognizing the universally occurring LH variant is the most important factor contributing to the widely documented LH immunoassay discrepancies.

Antibodies, Monoclonal↗

PubMed1997

Common and variant gene fusions predict distinct clinical phenotypes in rhabdomyosarcoma.

PURPOSE: We evaluated the clinical features of the common PAX3-FKHR and variant PAX7-FKHR gene fusions observed in rhabdomyosarcoma. PATIENTS AND METHODS: Reverse-transcriptase polymerase chain reaction (RT-PCR) assays were used to detect the gene fusions in 34 cases of rhabdomyosarcoma. Clinical data were obtained retrospectively and compared with the molecular results. RESULTS: The PAX3-FKHR and PAX7-FKHR gene fusions were present in tumors from 18 and 16 patients, respectively. The group with a PAX7-FKHR fusion was younger (P = .01) and presented more often with an extremity lesion (82% v 22%; P = .001). PAX7-FKHR tumors were more often localized than PAX3-FKHR tumors (P = .03). In patients with metastatic disease at diagnosis, the patterns were different: PAX7-FKHR patients had metastatic disease that involved only bone (n = 2) and distant nodes (n = 2), while the PAX3-FKHR group had multiple sites involved, including bone (n = 7), marrow (n = 7), lungs (n = 3), distant nodes (n = 2), skin (n = 1), and brain (n = 1). No significant difference in relapse rate was observed. A trend toward improved overall survival in the PAX7-FKHR group was noted (P = .09). Event-free survival for this PAX7-FKHR group was significantly longer (P = .04). CONCLUSION: Our results suggest that the common PAX3-FKHR and the variant PAX7-FKHR fusions are associated with distinct clinical phenotypes. Identification of fusion gene status may be a useful diagnostic tool in rhabdomyosarcoma.

Adolescent↗

PubMed2006

Meta-analysis of association of rare mutations and common sequence variants in the MSR1 gene and prostate cancer risk.

BACKGROUND: MSR1 has been reported to be associated with increased risk of prostate cancer (PCa). METHODS: We performed a meta-analysis of all eight published studies to evaluate the pooled effect of three rare mutations (R293X, S41T, and D174Y) and five common sequence variants (PRO3, INDEL1, IVS5-59, P275A, and INDEL7), stratified by race and sporadic/hereditary cancer. RESULTS: Several variants were significantly or marginally significantly associated with sporadic, not hereditary PCa risk, including R293X in white men (random effect OR = 1.34, P = 0.09) and D174Y in black men (random effect OR = 2.41, P = 0.04). The associations were not significant when the initial study was excluded. However, the frequency of the D174Y mutation was consistently higher among cases in all three studies that examined black men. CONCLUSIONS: Overall, this meta-analysis suggests the MSR1 gene does not independently confer a major risk to PCa but may confer a moderate risk to PCa, especially in black men.

Black or African American↗

PubMed2005

Common genetic variants in the interleukin-6 and chitotriosidase genes are associated with the risk for serious infection in children undergoing therapy for acute myeloid leukemia.

Infectious complications represent a substantial cause of morbidity and mortality in children undergoing therapy for acute myeloid leukemia (AML). Since it has been shown that alterations in innate immune pathways contribute to the risk for serious infections, we analyzed well-characterized variants in innate immune genes (TNF, IL6, IL8, MPO, CHIT, FCGR2A, TLR2, and TLR4) to determine their possible contribution to infectious complications during therapy for pediatric AML. The study population consisted of 168 North European Caucasian children enrolled on the clinical trial AML-BFM 93. We found an association between Gram-negative bacterial infection and common, functional variants in two genes, IL6 and CHIT. The risk for infection was significantly higher in children with the G allele in the IL6 promoter at -174 bp (P=0.026) and in patients with the H allele of CHIT (P=0.033). The promoter variant in IL6 has been shown to increase expression while the H allele disrupts both function and circulating levels. Our data suggest that variant alleles of both IL6 and CHIT could influence susceptibility to infection with Gram-negative bacteria in children undergoing therapy for AML. Follow-up studies, namely replication association studies and in vitro investigation of these common polymorphisms, are warranted to confirm these observations.

Acute Disease↗

PubMed2003

Cytologic and immunocytochemical findings of anaplastic large cell lymphoma: analysis of ten fine-needle aspiration specimens over a 9-year period.

BACKGROUND: Anaplastic large cell lymphoma (ALCL) has raised much controversy in the field of hematolymphoid pathology. Its nature is becoming better characterized with recent advances in molecular genetics. However, to the authors' knowledge, a detailed description of the fine-needle aspiration (FNA) cytology of ALCL is lacking and the application of immunocytochemical study, including immunostaining for anaplastic lymphoma kinase (ALK) protein, to cytology samples has not been studied to date. METHODS: The authors reviewed 10 FNA specimens of ALCL from 8 patients encountered at Pamela Youde Nethersole Eastern Hospital and Queen Mary Hospital in Hong Kong over a 9-year period from early 1993 to the end of 2001. The cytologic and immunocytochemical findings (including ALK protein overexpression) of the specimens were correlated with histologic and immunohistochemical findings of surgical biopsy specimens. RESULTS: Six of the eight patients had ALCL of the common variant, whereas the remaining two patients had ALCL of the small cell variant. FNA specimens of ALCL of the common variant yielded many loosely dispersed "hallmark" cells that contained eccentric kidney-shaped or embryo-like nuclei, several prominent rod-shaped or angulated basophilic nucleoli, and abundant amphophilic cytoplasm. "Doughnut" cells, tumor cells with multilobated nuclei, and multinucleated giant cells with a wreath-like arrangement of nuclei occasionally were found. A small number of "plasmacytoid" tumor cells, nondescript small round tumor cells, and reactive polymorphs also was present. In contrast, "plasmacytoid" cells and nondescript small to medium-sized tumor cells represented the predominant cell population in ALCL of the small cell variant. The "plasmacytoid" appearance was exaggerated further in air-dried smears. In air-dried smears, small intracytoplasmic vacuoles and scanty azurophilic granules also were noted. On immunocytochemical study performed using the cell block materials, the majority of tumor cells demonstrated membranous and paranuclear "dot-like" positivity for CD30. The staining for epithelial membrane antigen, leukocyte common antigen, and T-cell markers was variable. Positive staining for ALK protein was demonstrated beautifully in two of the cases. CONCLUSIONS: Despite the wide morphologic spectrum of ALCL, a definitive diagnosis on the basis of FNA cytology is possible on careful interpretation of the cytologic features and a high index of suspicion. The cytologic diagnosis can be confirmed further with proper application of immunostaining to cell block sections. Immunocytochemical study for ALK protein, which provides useful prognostic information, also can be demonstrated satisfactorily using cytology samples.

Adolescent↗

PubMed2005

No association of serotonin transporter gene (SLC6A4) with schizophrenia and bipolar disorder in Japanese patients: association analysis based on linkage disequilibrium.

Serotonin transporter gene (SLC6A4) is one of the most promising candidate genes for psychiatric disorders such as schizophrenia (SCZ) and bipolar disorder (BP). Two functional polymorphisms, 5HTTLPR and 5HTTVNTR, have been a focus for genetic association analyses; however, no conclusive results have been obtained. We conducted, 1) a mutation search of SLC6A4, 2) LD mapping to select 'tagging' markers (10 SNPs and 5HTTVNTR, while 5HTTLPR was treated as an independent marker because of its allelic form), and 3) association analysis of these 'tagging' markers and independent markers (5HTTLPR and Asn605Lys) with SCZ and BP in Japanese patients. In this mutation search, a nonsynonymous SNP, Asn605Lys, was detected. No associations of 'tagging' markers and independent markers with such conditions were found. These results indicate that SLC6A4 might not play a major role in SCZ and BP in Japanese patients, a finding that agrees with both the common disease-common variant hypothesis and common disease-rare variant hypothesis.

Adult↗

PubMed2004

Studies of the neuromedin U-2 receptor gene in human obesity: evidence for the existence of two ancestral forms of the receptor.

Central administration of neuromedin U (NMU) suppresses food intake acting through the NMU-2 receptor (NMU2R), which is expressed in the hypothalamus. We screened the NMU2R gene in 96 patients with severe early-onset obesity. A common variant haplotype was found (f-0.21). This common variant haplotype was unusual in nature, consisting of four non-contiguous missense changes in complete linkage disequilibrium, and across two separate exons. The variant haplotype resulted in four amino acid substitutions (S295T/F312L/P380L/ M385 V) and was present in several other Europid populations and in subjects of South Asian, East Asian and African American origin, but not in eleven African Pygmies. This variant haplotype was not associated with obesity or related traits in 500 subjects from a prospective population-based cohort. In summary, we have identified two markedly different isoforms of the NMU-2 receptor, presumably arising through an ancient and complex mutational event; no genetic associations between this haplotype and obesity-related traits were, however, discerned. Further investigation of the pharmacogenomic consequences of NMU2R variation in humans is warranted.

Amino Acid Sequence↗

PubMed1996

Improved method to create the common ostium variant of the distal arteriovenous fistula for enhancing crural prosthetic graft patency.

PURPOSE: Successful use of the distal adjunctive arteriovenous fistula (dAVF) for the enhancement of prosthetic graft patency rates in the crural position is critically dependent on the qualitative and quantitative aspects of the arterial and venous runoff. Precise technical performance of the fistula is equally vital to secure optimal results. The purpose of this study was to determine current prosthetic graft patency and limb salvage rates using a modified version of the common ostium dAVF. METHODS: The standard method to create the common ostium variant of dAVF has been modified to improve apposition of the "otomy" sites of the artery and vein, avoid twisting and stenosis by terminating the fistula suture line at the artery-vein junctures, reshaping the ovoid ostium to a rectangular shape, and finally, use of multiple interrupted heel-toe sutures. RESULTS: Since 1979 we have created 290 fistulas in 281 patients who required leg revascularization procedures. In different time periods we have documented improving graft patency and limb salvage rates. Fistula patency, reflected by annual attrition rates of 13% to 26% per year, continues as a challenge for long-term results. Current 3-year secondary cumulative graft patency and limb salvage rates by life table analysis are 61% and 74%, respectively. The conduit material may play a role with regard to steal phenomena and the need for banding techniques. CONCLUSION: Configuration of the adjunctive dAVF may impact on prosthetic graft patency in the crural position. In addition, the type of graft material used for bypass may be instrumental in preventing or precipitating the steal phenomenon. These issues require further study to better understand flow dynamics, patterns of intimal hyperplasia, and blood distribution as a function of conduit material and impedance of the arterial and venous runoff.

Adult↗