Genetics Research
rs3788205
Population Frequencies12
African
T 0.06997C 0.93003TT 0.005434TC/CT 0.12908CC 0.865485pop=52,262
African American
T 0.07166C 0.92834TT 0.005587TC/CT 0.132152CC 0.86226pop=50,472
African Others
T 0.0223C 0.9777TT 0.001117TC/CT 0.042458CC 0.956425pop=1,790
Asian
T 0.1996C 0.8004TT 0.045793TC/CT 0.307586CC 0.646621pop=7,250
East Asian
T 0.1961C 0.8039TT 0.045973TC/CT 0.300336CC 0.653691pop=5,960
European
T 0.302799C 0.697201TT 0.092554TC/CT 0.420489CC 0.486957pop=385,266
Latin American 1
T 0.2357C 0.7643TT 0.056804TC/CT 0.357862CC 0.585334pop=7,746
Latin American 2
T 0.30952C 0.69048TT 0.094225TC/CT 0.430598CC 0.475177pop=17,766
Other
T 0.27909C 0.72091TT 0.084786TC/CT 0.388601CC 0.526613pop=12,738
Other Asian
T 0.2155C 0.7845TT 0.044961TC/CT 0.341085CC 0.613953pop=1,290
South Asian
T 0.2538C 0.7462TT 0.069572TC/CT 0.368363CC 0.562065pop=5,462
Studies20
Unread Studies20 ▼
1
The disruption of craniofacial developmental pathways during early embryogenesis can lead to conditions such as nonsyndromic cleft lip with or without cleft palate (NSCL/…
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The disruption of craniofacial developmental pathways during early embryogenesis can lead to conditions such as nonsyndromic cleft lip with or without cleft palate (NSCL/P). Several lines of evidence indicate that inadequate maternal nutrition causes low folate levels during the periconceptional period, resulting in NSCL/P. Although substantial research has been conducted on the possible link between SLC19A1 genetic variants and NSCL/P, the association between SLC19A1 80G>A (rs1051266) and NSCL/P remains unclear. In the present study, the associations of SLC19A1 80G>A with NSCL/P risk were assessed by calculating the pooled odds ratios (ORs) and 95% confidence intervals (CIs) by meta-analyses.
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Bei der vorliegenden Dissertation handelt es sich um eine systematische Übersichtarbeit. Diese wurde durch eine selektive Literaturrecherche erstellt. Die Literaturquellen lieferte die englischsprachige Datenbank PubMed. Ergänzend dazu wurde medizinische Fachliteratur herangezogen.
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En la etiología de las fisuras orofaciales no sindrómicas (FOFNS) el metabolismo de los folatos jugaría un importante rol, en donde se han reportado asociaciones con variantes hipofuncionales de genes de este metabolismo sumado a que el bajo consumo materno de esos micronutrientes es uno de los factores ambientales más importantes. Esta vitamina es crucial para la síntesis y metilación del ADN. En Chile, a pesar del aumento del consumo de folatos, no ha disminuido la tasa de FOFs. En el presente estudio se evaluó el riesgo de FOFNS en Chile asociado a niveles bajos de metilación global del ADN. Para ello se evaluaron 95 casos y 95 controles pareados por sexo y edad donde se cuantificó mediante pirosecuenciación los niveles de metilación de LINE-1 (marcador de metilación global del ADN) en células de la mucosa oral. Además, se evaluó la asociación de los niveles de metilación de LINE-1 con las variantes de los genes del metabolismo del folato MTHFR, SLC19A1 y TCN2. Los resultados muestran un aumento del riesgo de FOFNS asociado a hipometilación del ADN (p=0.008), pero este riesgo no se ve modificado por el genotipo de ninguna de las variantes de los tres genes analizados. En conclusión, nuestros hallazgos confirman la hipótesis sobre el aumento de la susceptibilidad a FOFNS cuando el DNA esta poco metilado, lo que podría afectar la expresión génica. Los resultados de interacción gen-metilación pueden ser efecto del modesto tamaño muestral utilizado.
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Discovering the associations between genetic variables and disease status can help reduce the burden of disease on society. This thesis focuses on the methods required to detect …
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Pemetrexed, one of the most commonly used drugs in advanced non–small cell lung cancer (NSCLC) therapies, often leads to various therapeutic responses in patients. These therapeutic responses to pemetrexed, including adverse drug reactions (ADRs) and its intended therapeutic effects, have been demonstrated to be highly individual-specific. Such difference in therapeutic responses across individuals may be caused by the unique genetic variations in each patient. However, only a few pemetrexed-based studies have been performed using Han Chinese patients. In this study, we aimed to identify genetic signatures of therapeutic responses of pemetrexed-based treatment using 203 Han Chinese patients with advanced NSCLC. All the participants received two different types of therapies: 1) treatment with only pemetrexed and 2) treatment with both pemetrexed and platinum (mainly cisplatin and carboplatin). We then performed a genetic association analysis on 16 selected single-nucleotide polymorphisms (SNPs) in 7 genes using these 2 groups. The analysis of patients receiving only pemetrexed suggests that the SNP rs1051298 on the SLC19A1 gene (c.*746C > T) increased the risk of all ADRs (collected all types of ADRs) in different cycles of pemetrexed therapy [1-2 cycles: P = 0.0059, odds ratio (OR) = 3.143; 1-4 cycles: P = 0.0072, OR = 2.340; 1-6 cycles: P = 0.0071, OR = 2.243]. This influence of rs1051298 is particularly significant in terms of liver injury (1-4 cycles: P = 0.0056, OR = 3.863; 1-6 cycles: P = 0.0071, OR = 3.466). In all the patients, including patients who received both pemetrexed and platinum, SNP rs1801133 on the MTHFR gene (665C > T) was found to be significantly associated with hematological ADRs in 1 to 2 cycles (P = 0.0079, OR = 3.566). Additionally, we discovered that SNP rs12995526 (c.815-102T > C) in the ATIC gene and SNP rs11545077 (c.91G > T) in the GGH gene were associated with both ADRs and therapeutic effects. In summary, our study identified several potential biomarkers that were significantly associated with ADRs and therapeutic effects of pemetrexed-related treatments using Han Chinese patients. Our discoveries will provide important clues for personalized pemetrexed-based treatment design for Han Chinese NSCLC patients in the future.
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Readmissions following transcatheter aortic valve replacement (TAVR) are common but detailed analysis of 1-year ICU and non-ICU readmissions for cardiac and noncardiac causes are limited. Methods: Our study population was 1,037 patients who underwent TAVR between 2011–2017 at a tertiary center. Patients who died during their index hospitalization (n=20) were excluded. Readmissions were adjudicated and classified based on primary readmission diagnosis (cardiac versus noncardiac) and ICU versus Non-ICU designations. Incidence, causes, and outcomes of 1-year readmissions were evaluated. Results: Of the 1,017 patients, there were readmissions due to noncardiac causes in 350 (34.4%) and cardiac causes in 208 (20.5%) during a mean 1.96 years of follow-up. The most common noncardiac causes of readmission were sepsis/infection (14.3%), gastrointestinal (8.3%), and respiratory (4.8%), whereas heart failure (14.0%) and arrhythmias (4.6%) were the most common cardiac causes of readmission. The risk of a noncardiac readmission was highest in the period immediately following TAVR (~ 4.5% per month) with an early high hazard phase that gradually declined over months (Figure 1). However, the risk of cardiac readmission remained stable at ~ 1% per month throughout. TAVR patients that were readmitted for any cause had significantly increased mortality; this was especially true for patients readmitted to an ICU. Conclusions: In TAVR patients who survived their index hospitalization, non-cardiac readmissions were more prevalent than cardiac. The risk of readmission and/or mortality is highest immediately post-procedure and declines thereafter. Readmission to ICU portends the highest risk of subsequent death in this cohort. CCMCritical Care MedicineCrit Care Med0090-3493Lippincott Williams & WilkinsHagerstown, MDCCM
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Carboplatin/taxane-induced gastrointestinal toxicity: a pharmacogenomics study on the SCOTROC1 trial
Carboplatin/taxane combination is first-line therapy for ovarian cancer. However, patients can encounter treatment delays, impaired quality of life, even death because of chemotherapy-induced gastrointestinal (GI) toxicity. A candidate gene study was conducted to assess potential association of genetic variants with GI toxicity in 808 patients who received carboplatin/taxane in the Scottish Randomized Trial in Ovarian Cancer 1 (SCOTROC1). Patients were randomized into discovery and validation cohorts consisting of 404 patients each. Clinical covariates and genetic variants associated with grade III/IV GI toxicity in discovery cohort were evaluated in replication cohort. Chemotherapy-induced GI toxicity was significantly associated with seven single-nucleotide polymorphisms in the ATP7B, GSR, VEGFA and SCN10A genes. Patients with risk genotypes were at 1.53 to 18.01 higher odds to develop carboplatin/taxane-induced GI toxicity (P<0.01). Variants in the VEGF gene were marginally associated with survival time. Our data provide potential targets for modulation/inhibition of GI toxicity in ovarian cancer patients.
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Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders with complex genetic etiology. Recent studies have indicated that children with ASD may have altered folate or methionine metabolism, suggesting that the folate-methionine cycle may play a key role in the etiology of ASD. SLC19A1, also referred to as reduced folate carrier 1 (RFC1), is a member of the solute carrier group of transporters and is one of the key enzymes in the folate metabolism pathway. Findings from multiple genomic screens suggest the presence of an autism susceptibility locus on chromosome 21q22.3, which includes SLC19A1. Therefore, we performed a case-control study in a Japanese population. In this study, DNA samples obtained from 147 ASD patients at the Kanazawa University Hospital in Japan and 150 unrelated healthy Japanese volunteers were examined by the sequence-specific primer-polymerase chain reaction method pooled with fluorescence correlation spectroscopy. p < 0.05 was considered to represent a statistically significant outcome. Of 13 single nucleotide polymorphisms (SNPs) examined, a significant p-value was obtained for AA genotype of one SNP (rs1023159, OR = 0.39, 95% CI = 0.16-0.91, p = 0.0394; Fisher's exact test). Despite some conflicting results, our findings supported a role for the polymorphism rs1023159 of the SLC19A1 gene, alone or in combination, as a risk factor for ASD. However, the findings were not consistent after multiple testing corrections. In conclusion, although our results supported a role of the SLC19A1 gene in the etiology of ASD, it was not a significant risk factor for the ASD samples analyzed in this study.
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La labioschisi con o senza palatoschisi non-sindromica (NSCL/P) è tra le più frequenti alterazioni dello sviluppo embrionale, causata dall’interazione di fattori genetici e ambientali, moti dei quali ancora ignoti. L'obiettivo del mio progetto di Dottorato consiste nell’identificazione di fattori di rischio genetico in un processo a due stadi che prevede la selezione di geni candidati e la verifica del loro coinvolgimento nella determinazione della malformazione mediante studi di associazione. Ho analizzato alcuni polimorfismi a singolo nucleotide (SNPs) dei geni RFC1 e DHFR, appartenenti alla via metabolica dell’acido folico, evidenziando una debole associazione tra alcuni degli SNPs indagati e la NSCL/P nella popolazione italiana. Presso il laboratorio della Dott.ssa Mangold dell’Università di Bonn, ho valutato il ruolo di 15 diverse regioni cromosomiche nel determinare la suscettibilità alla malattia, evidenziando una significativa associazione per i marcatori localizzati in 8q24 e 1p22. Ho quindi rivolto la mia attenzione al ruolo del complesso Polycomb nell’insorgenza della schisi. Nell’uomo i due complessi Polycomb, PRC1 e PRC2, rimodellano la cromatina agendo da regolatori dei meccanismi trascrizionali alla base della differenziazione cellulare e dello sviluppo embrionale. Ho ipotizzato che mutazioni a carico di geni appartenenti a PRC2 possano essere considerati potenziali fattori di rischio genetico nel determinare la NSCL/P. Il razionale consiste nel fatto che JARID2, una proteina che interagisce con PRC2, è associata all’insorgenza della NSCL/P ed espressa a livello delle cellule epiteliali delle lamine palatine che si approssimano alla fusione. L’indagine condotta analizzando i geni di elementi o partner dei due complessi Polycomb, ha evidenziato un’associazione significativa con alcuni polimorfismi dei geni indagati, associazione ulteriormente confermata dall’analisi degli aplotipi. Le analisi condotte sui geni candidati mi hanno permesso di raccogliere dati interessanti sull’eziologia della malformazione. Studi indipendenti saranno necessari per poter validare l'associazione tra le varianti genetiche di questi geni candidati e la NSCL/P.
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A Fissura Oral (FO) é uma malformação craniofacial comum na espécie humana e sua etiologia é complexa com aspectos genéticos e ambientais envolvidos na sua formação. Por ser uma malformação de prevalência variável, estudos de associação em populações distintas são necessários, principalmente em populações heterogêneas como no Brasil. A suplementação com ácido fólico está envolvida na redução do risco de recorrência para algumas malformações, mas a natureza da reação entre a ingestão do ácido fólico, a interação entre os genes da rota metabólica e o seu efeito nas concentrações de folato é pouco caracterizada. Além disso, existem poucos estudos envolvendo um grande número de genes e a suplementação com ácido fólico a longo prazo. O objetivo desse trabalho foi estudar o papel dos genes MSX1 e IRF6 e região 8q24 em indivíduos com fissuras orais não sindrômicas de diferentes regiões do Brasil e analisar o efeito da suplementação com ácido fólico e dos polimorfismos nos genes da rota metabólica do folato nos níveis de folato séricos e eritrocitários. Nossos resultados mostram associação positiva entre o alelo 4 do polimorfismo de repetição CA (MSX1) e FO, alelo A da variante rs987525 (8q24) foi associado com FL/P e o haplótipo G/A (rs2235371/rs642961) do gene IRF6 associado com o aumento do risco para FL/P. Dos 23 genes da rota metabólica do ácido fólico estudados, 5 (FPGS, FOLR1, FOLR2, SHMTI e MTHFR) foram relacionados com os níveis de folato sérico e eritrocitário. As variantes rs7033913 (FPGS), rs11235462 (FOLR1) e rs2276048 (FOLR2) foram associadas com os níveis de folato sérico após suplementação. Os polimorfismos rs2168781 e rs2461837 (SHMT1) foram relacionados com os níveis de folato eritrocitário basal e o rs1801131(MTHFR) com os níveis de folato eritrocitário durante a suplementação. Conhecer a etiologia das fissuras orais e entender os efeitos da suplementação e de variantes dos genes da rota do folato nos níveis basais de folato é essencial tanto para auxiliar no manejo clínico através de uma medicina personalizada quanto para aconselhamento genético.
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The molecular basis of orofacial development is largely unknown and needs to be unravelled. Non-syndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial malformation, with an incidence of about 1/700 live births, although variable according to ethnicity. Being a multifactorial disease, it arises as a result of an interplay between genetic and environmental factors. Several approaches have been developed to identify susceptibility genes. Genes belonging to the folate/homocysteine pathway are attracting increasing interest because folate supplementation before and during early pregnancy can reduce the risk of NSCL/P. We performed a family based association study in order to assess if a genetic variant of RFC1 could be involved in NSCL/P onset. We genotyped 404 unrelated probands and their relatives for three biallelic polymorphic variants (rs1051266, rs4818789 and rs3788205), that were selected because they produced conflicting results on previous investigations. Evidence of association was found between the investigated polymorphisms and NSCL/P in our sample of the Italian population, albeit with weak significance levels. Results from this investigation provided a support of previous studies suggesting a role of RFC1 in NSCL/P aetiology, reinforcing the concept that genetic predisposition to NSCL/P varies enormously within different ethnic groups.
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Clinical results of a randomized phase III trial comparing pemetrexed–carboplatin (PC) with etoposide–carboplatin (EC) in chemonaive patients with extensive-stage disease small-cell lung cancer (ED-SCLC) resulted in trial closure for futility; biomarker analyses using immunohistochemistry (IHC) and single-nucleotide polymorphisms (SNPs) are described herein.
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Using linear regression models, we studied the main and 2-way interaction effects of the predictor variables gender, age, BMI, and 64 folate/vitamin B-12/homocysteine (Hcy)/lipid/cholesterol-related single nucleotide polymorphisms (SNP) on log-transformed plasma Hcy normalized by RBC folate measurements (nHcy) in 373 healthy Caucasian adults (50% women). Variable selection was conducted by stepwise Akaike information criterion or least angle regression and both methods led to the same final model. Significant predictors (where P values were adjusted for false discovery rate) included type of blood sample [whole blood (WB) vs. plasma-depleted WB; P < 0.001] used for folate analysis, gender (P < 0.001), and SNP in genes SPTLC1 (rs11790991; P = 0.040), CRBP2 (rs2118981; P < 0.001), BHMT (rs3733890; P = 0.019), and CETP (rs5882; P = 0.017). Significant 2-way interaction effects included gender × MTHFR (rs1801131; P = 0.012), gender × CRBP2 (rs2118981; P = 0.011), and gender × SCARB1 (rs83882; P = 0.003). The relation of nHcy concentrations with the significant SNP (SPTLC1, BHMT, CETP, CRBP2, MTHFR, and SCARB1) is of interest, especially because we surveyed the main and interaction effects in healthy adults, but it is an important area for future study. As discussed, understanding Hcy and genetic regulation is important, because Hcy may be related to inflammation, obesity, cardiovascular disease, and diabetes mellitus. We conclude that gender and SNP significantly affect nHcy.
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Folate-associated one-carbon metabolism (FOCM) is an important pathway in colorectal neoplasia risk but data on genetic variation in this pathway are largely limited to studies of single SNPs in selected genes.
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Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect that has a multifactorial etiology. Despite having substantial genetic liability, less than 15% of the genetic contribution to NSCLP has been delineated. In our efforts to dissect the genetics of NSCLP, we found that variation in the CRISPLD2 (cysteine rich secretory protein LCCL domain containing 2) gene is associated with NSCLP and that the protein is expressed in the developing murine craniofacies. In addition, we found suggestive linkage of NSCLP (LOD>1.0) to the chromosomal region on 8q13.2-21.13 that contains the CRISPLD1 gene. The protein products of both CRISPLD1 and CRISPLD2 contain more cysteine residues than comparably sized proteins. Interestingly, the folic acid pathway produces endogenous cysteines, and variation in genes in this pathway is associated with NSCLP. Based on these observations, we hypothesized that variation in CRISPLD1 contributes to NSCLP and that both CRISPLD genes interact with each other and genes in the folic acid pathway. SNPs in CRISPLD1 were genotyped in our nonHispanic white and Hispanic multiplex and simplex NSCLP families. There was little evidence for a role of variation for CRISPLD1 alone in NSCLP. However, interactions were detected between CRISPLD1/CRISPLD2 SNPs and variation in folate pathway genes. Altered transmission of one CRISPLD1 SNP was detected in the nonHispanic white simplex families. Importantly, interactions were detected between SNPs in CRISPLD1 and CRISPLD2 (15 interactions, 0.0031≤p<0.05). These novel findings suggest that CRISPLD1 plays a role in NSCLP through the interaction with CRISPLD2 and folate pathway genes.
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Genetic susceptibility is an important risk factor for aortic aneurysm and dissection. Recent case-control association studies have identified six single nucleotide polymorphisms (SNPs) associated with abdominal aortic aneurysm (AAA) in a Caucasian population. We aimed to determine whether these loci confer susceptibility to thoracic aortic dissection (TAD) in a Chinese Han population and thus to establish cross-race susceptibility to TAD.
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Previous studies suggested an association between abdominal aortic aneurysm (AAA) and hyperhomocysteinaemia, a complex trait determined by genetic and environmental factors. Our hypothesis was that polymorphisms in genes directly or indirectly involved in methionine metabolism may contribute to AAA susceptibility. Method: We studied 56 polymorphisms in MTHFR, MTR, MTRR, CBS, MTHFD1, SLC19A1, NNMT, TCN2, AHCY, BHMT, BHMT2, FOLH1, TYMS, ENOSF1, SHMT1, PON1, PON2 genes according to their demonstrated/putative function, localisation in promoter or regulatory and coding regions and/or heterozygosity values .0.300. Polymorphisms were evaluated by using a primer extension based microarray technology in 423 AAA patients and 423 matched controls. Results: All polymorphisms resulted in Hardy–Weinberg equilibrium in patients and controls. At the multiple logistic regression analysis adjusted for traditional cardiovascular risk factors (sex, age, hypertension, smoking habit, dyslipidaemia, diabetes) and chronic obstructive pulmonary disease (COPD), rs8003379 MTHFD1 (odds ratio (OR) 0.41, 95% confidence interval (CI) 0.26 to 0.65) and rs326118 MTRR (OR 0.47, 95% CI 0.29 to 0.77) polymorphisms resulted in independent susceptibility factor for AAA. Conclusions: After haplotype reconstruction, logistic regression analyses adjusted for traditional risk factors and COPD showed a significant association among AAA and AHCY, FOLH1, MTHFD1, MTR, NNMT, PON1 and TYMS haplotypes. Our findings offer new insights into the pathogenesis of AAA.
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The International Adjuvant Lung Cancer Trial (IALT) demonstrated an absolute survival rate benefice of cisplatin based chemotherapy of 4% in surgically treated patients with non small cell lung carcinoma (NSCLC). To identify immunohistochemical biomarkers which correlate differently with survival in the chemotherapy and observation group (predictive analysis) we collected 867 paraffin blocks from 28 centers and made a histopathological review allowing selection of 783 tumors recorded as NSCLC with …
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Carboplatin/taxane combination is first-line therapy for ovarian cancer. However, patients can encounter treatment delays, impaired quality of life, even death because of chemotherapy-…
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