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1.
Genet Epidemiol ; 47(5): 365-378, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37060326

RESUMO

Many diseases recur after recovery, for example, recurrences in cancer and infections. However, research is often focused on analysing only time-to-first recurrence, thereby ignoring any subsequent recurrences that may occur after the first. Statistical models for the analysis of recurrent events are available, of which the extended Cox proportional hazards frailty model is the current state-of-the-art. However, this model is too statistically complex for computationally efficient application in high-dimensional data sets, including genome-wide association studies (GWAS). Here, we develop an application for fast and accurate recurrent event analysis in GWAS, called SPARE (SaddlePoint Approximation for Recurrent Event analysis). In SPARE, every DNA variant is tested for association with recurrence risk using a modified score statistic. A saddlepoint approximation is implemented to achieve statistical accuracy. SPARE controls the Type I error, and its statistical power is similar to existing recurrent event models, yet SPARE is significantly faster. An application of SPARE in a recurrent event GWAS on bladder cancer for 6.2 million DNA variants in 1,443 individuals required less than 15 min, whereas existing recurrent event methods would require several weeks.


Assuntos
Estudo de Associação Genômica Ampla , Recidiva Local de Neoplasia , Humanos , Modelos Genéticos , Modelos Estatísticos , Modelos de Riscos Proporcionais
2.
Br J Clin Pharmacol ; 2024 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-39107874

RESUMO

AIMS: Sunitinib exhibits considerable interindividual variability in exposure. While the target total plasma concentration of sunitinib and its active metabolite is 50-87.5 ng/mL for the intermittent dosing schedule, ~10-21% of patients experience higher exposures (>87.5 ng/mL), correlated with an increased risk for toxicity. Previous research identified single nucleotide variants (SNVs) in genes from the sunitinib pharmacokinetic pathway to be associated with efficacy and toxicity. However, significant interindividual variability in exposure remains unexplained. Our aim was to identify genetic variants associated with supratherapeutic exposure of sunitinib. METHODS: This was a genome-wide association study. Cases were identified during routine therapeutic drug monitoring and consisted of patients with dose-normalized sunitinib plasma concentrations >87.5 ng/mL (intermittent dosing) or >75 ng/mL (continuous dosing). Controls were sampled from the historical cohort EuroTARGET who tolerated the standard dose of 50 mg in an intermittent schedule. SNVs were tested for an association with sunitinib exposure. A P-value ≤5 × 10-8 was considered significant and a P-value between 5 × 10-8 and 5 × 10-6 was considered suggestive. RESULTS: Sixty-nine cases and 345 controls were included for association analysis. One SNV (rs6923761), located on the gene glucagon-like peptide 1 receptor, was significantly associated with increased sunitinib exposure (P = 7.86 × 10-19). Twelve SNVs were suggestive for an association with sunitinib exposure (P ≤ 5 × 10-6). CONCLUSIONS: While rs6923671 is associated with high sunitinib exposure, the underlying mechanism is not yet clarified and warrants further investigation. We could not confirm the earlier found associations between SNVs in candidate genes involved in the pharmacokinetic pathway of sunitinib and its efficacy and toxicity.

3.
Int J Mol Sci ; 24(7)2023 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-37047060

RESUMO

Pelvic organ prolapse (POP) represents a major health care burden in women, but its underlying pathophysiological mechanisms have not been elucidated. We first used a case-control design to perform an exome chip study in 526 women with POP and 960 control women to identify single nucleotide variants (SNVs) associated with the disease. We then integrated the functional interactions between the POP candidate proteins derived from the exome chip study and other POP candidate molecules into a molecular landscape. We found significant associations between POP and SNVs in 54 genes. The proteins encoded by 26 of these genes fit into the molecular landscape, together with 43 other POP candidate molecules. The POP landscape is located in and around epithelial cells and fibroblasts of the urogenital tract and harbors four interacting biological processes-epithelial-mesenchymal transition, immune response, modulation of the extracellular matrix, and fibroblast function-that are regulated by sex hormones and TGFB1. Our findings were corroborated by enrichment analyses of differential gene expression data from an independent POP cohort. Lastly, based on the landscape and using vaginal fibroblasts from women with POP, we predicted and showed that metformin alters gene expression in these fibroblasts in a beneficial direction. In conclusion, our integrated molecular landscape of POP provides insights into the biological processes underlying the disease and clues towards novel treatments.


Assuntos
Prolapso de Órgão Pélvico , Feminino , Humanos , Prolapso de Órgão Pélvico/genética , Prolapso de Órgão Pélvico/metabolismo , Vagina/metabolismo , Causalidade
4.
Am J Hum Genet ; 101(1): 50-64, 2017 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-28669404

RESUMO

Clonal hematopoiesis results from somatic mutations in hematopoietic stem cells, which give an advantage to mutant cells, driving their clonal expansion and potentially leading to leukemia. The acquisition of clonal hematopoiesis-driver mutations (CHDMs) occurs with normal aging and these mutations have been detected in more than 10% of individuals ≥65 years. We aimed to examine the prevalence and characteristics of CHDMs throughout adult life. We developed a targeted re-sequencing assay combining high-throughput with ultra-high sensitivity based on single-molecule molecular inversion probes (smMIPs). Using smMIPs, we screened more than 100 loci for CHDMs in more than 2,000 blood DNA samples from population controls between 20 and 69 years of age. Loci screened included 40 regions known to drive clonal hematopoiesis when mutated and 64 novel candidate loci. We identified 224 somatic mutations throughout our cohort, of which 216 were coding mutations in known driver genes (DNMT3A, JAK2, GNAS, TET2, and ASXL1), including 196 point mutations and 20 indels. Our assay's improved sensitivity allowed us to detect mutations with variant allele frequencies as low as 0.001. CHDMs were identified in more than 20% of individuals 60 to 69 years of age and in 3% of individuals 20 to 29 years of age, approximately double the previously reported prevalence despite screening a limited set of loci. Our findings support the occurrence of clonal hematopoiesis-associated mutations as a widespread mechanism linked with aging, suggesting that mosaicism as a result of clonal evolution of cells harboring somatic mutations is a universal mechanism occurring at all ages in healthy humans.


Assuntos
Análise Mutacional de DNA/métodos , Hematopoese/genética , Mutação/genética , Adulto , Idoso , Sequência de Bases , Células Clonais , Loci Gênicos , Humanos , Pessoa de Meia-Idade , Sondas Moleculares/metabolismo , Fases de Leitura Aberta/genética , Reprodutibilidade dos Testes , Mapeamento por Restrição , Adulto Jovem
5.
Hum Mol Genet ; 25(6): 1203-14, 2016 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-26732427

RESUMO

Candidate gene and genome-wide association studies (GWAS) have identified 15 independent genomic regions associated with bladder cancer risk. In search for additional susceptibility variants, we followed up on four promising single-nucleotide polymorphisms (SNPs) that had not achieved genome-wide significance in 6911 cases and 11 814 controls (rs6104690, rs4510656, rs5003154 and rs4907479, P < 1 × 10(-6)), using additional data from existing GWAS datasets and targeted genotyping for studies that did not have GWAS data. In a combined analysis, which included data on up to 15 058 cases and 286 270 controls, two SNPs achieved genome-wide statistical significance: rs6104690 in a gene desert at 20p12.2 (P = 2.19 × 10(-11)) and rs4907479 within the MCF2L gene at 13q34 (P = 3.3 × 10(-10)). Imputation and fine-mapping analyses were performed in these two regions for a subset of 5551 bladder cancer cases and 10 242 controls. Analyses at the 13q34 region suggest a single signal marked by rs4907479. In contrast, we detected two signals in the 20p12.2 region-the first signal is marked by rs6104690, and the second signal is marked by two moderately correlated SNPs (r(2) = 0.53), rs6108803 and the previously reported rs62185668. The second 20p12.2 signal is more strongly associated with the risk of muscle-invasive (T2-T4 stage) compared with non-muscle-invasive (Ta, T1 stage) bladder cancer (case-case P ≤ 0.02 for both rs62185668 and rs6108803). Functional analyses are needed to explore the biological mechanisms underlying these novel genetic associations with risk for bladder cancer.


Assuntos
Cromossomos Humanos Par 13 , Cromossomos Humanos Par 20 , Neoplasias da Bexiga Urinária/genética , População Branca/genética , Biomarcadores Tumorais/genética , Estudos de Casos e Controles , Feminino , Estudos de Associação Genética , Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla , Humanos , Desequilíbrio de Ligação , Masculino , Polimorfismo de Nucleotídeo Único , Fatores de Risco , Neoplasias da Bexiga Urinária/etnologia
6.
Hum Mol Genet ; 25(5): 1008-18, 2016 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-26740556

RESUMO

Transcriptional and splicing anomalies have been observed in intron 8 of the CASP8 gene (encoding procaspase-8) in association with cutaneous basal-cell carcinoma (BCC) and linked to a germline SNP rs700635. Here, we show that the rs700635[C] allele, which is associated with increased risk of BCC and breast cancer, is protective against prostate cancer [odds ratio (OR) = 0.91, P = 1.0 × 10(-6)]. rs700635[C] is also associated with failures to correctly splice out CASP8 intron 8 in breast and prostate tumours and in corresponding normal tissues. Investigation of rs700635[C] carriers revealed that they have a human-specific short interspersed element-variable number of tandem repeat-Alu (SINE-VNTR-Alu), subfamily-E retrotransposon (SVA-E) inserted into CASP8 intron 8. The SVA-E shows evidence of prior activity, because it has transduced some CASP8 sequences during subsequent retrotransposition events. Whole-genome sequence (WGS) data were used to tag the SVA-E with a surrogate SNP rs1035142[T] (r(2) = 0.999), which showed associations with both the splicing anomalies (P = 6.5 × 10(-32)) and with protection against prostate cancer (OR = 0.91, P = 3.8 × 10(-7)).


Assuntos
Neoplasias da Mama/genética , Carcinoma Basocelular/genética , Caspase 8/genética , Neoplasias da Próstata/genética , Splicing de RNA , Retroelementos , Neoplasias Cutâneas/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Alelos , Sequência de Bases , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Carcinoma Basocelular/metabolismo , Carcinoma Basocelular/patologia , Caspase 8/metabolismo , Feminino , Estudo de Associação Genômica Ampla , Humanos , Íntrons , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Razão de Chances , Polimorfismo de Nucleotídeo Único , Neoplasias da Próstata/metabolismo , Neoplasias da Próstata/patologia , Neoplasias da Próstata/prevenção & controle , Fatores de Proteção , Neoplasias Cutâneas/metabolismo , Neoplasias Cutâneas/patologia
7.
Carcinogenesis ; 38(12): 1167-1179, 2017 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-29028944

RESUMO

Little is known whether genetic variants identified in genome-wide association studies interact to increase bladder cancer risk. Recently, we identified two- and three-variant combinations associated with a particular increase of bladder cancer risk in a urinary bladder cancer case-control series (Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), 1501 cases, 1565 controls). In an independent case-control series (Nijmegen Bladder Cancer Study, NBCS, 1468 cases, 1720 controls) we confirmed these two- and three-variant combinations. Pooled analysis of the two studies as discovery group (IfADo-NBCS) resulted in sufficient statistical power to test up to four-variant combinations by a logistic regression approach. The New England and Spanish Bladder Cancer Studies (2080 cases and 2167 controls) were used as a replication series. Twelve previously identified risk variants were considered. The strongest four-variant combination was obtained in never smokers. The combination of rs1014971[AA] near apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A (APOBEC3A) and chromobox homolog 6 (CBX6), solute carrier family 1s4 (urea transporter), member 1 (Kidd blood group) (SLC14A1) exon single nucleotide polymorphism (SNP) rs1058396[AG, GG], UDP glucuronosyltransferase 1 family, polypeptide A complex locus (UGT1A) intron SNP rs11892031[AA] and rs8102137[CC, CT] near cyclin E1 (CCNE1) resulted in an unadjusted odds ratio (OR) of 2.59 (95% CI = 1.93-3.47; P = 1.87 × 10-10), while the individual variant ORs ranged only between 1.11 and 1.30. The combination replicated in the New England and Spanish Bladder Cancer Studies (ORunadjusted = 1.60, 95% CI = 1.10-2.33; P = 0.013). The four-variant combination is relatively frequent, with 25% in never smoking cases and 11% in never smoking controls (total study group: 19% cases, 14% controls). In conclusion, we show that four high-risk variants can statistically interact to confer increased bladder cancer risk particularly in never smokers.


Assuntos
Predisposição Genética para Doença/genética , Neoplasias da Bexiga Urinária/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Estudos de Casos e Controles , Feminino , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Razão de Chances , Polimorfismo de Nucleotídeo Único , Fatores de Risco , Adulto Jovem
8.
PLoS Genet ; 10(1): e1004134, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24497844

RESUMO

3% of the population develops saccular intracranial aneurysms (sIAs), a complex trait, with a sporadic and a familial form. Subarachnoid hemorrhage from sIA (sIA-SAH) is a devastating form of stroke. Certain rare genetic variants are enriched in the Finns, a population isolate with a small founder population and bottleneck events. As the sIA-SAH incidence in Finland is >2× increased, such variants may associate with sIA in the Finnish population. We tested 9.4 million variants for association in 760 Finnish sIA patients (enriched for familial sIA), and in 2,513 matched controls with case-control status and with the number of sIAs. The most promising loci (p<5E-6) were replicated in 858 Finnish sIA patients and 4,048 controls. The frequencies and effect sizes of the replicated variants were compared to a continental European population using 717 Dutch cases and 3,004 controls. We discovered four new high-risk loci with low frequency lead variants. Three were associated with the case-control status: 2q23.3 (MAF 2.1%, OR 1.89, p 1.42×10-9); 5q31.3 (MAF 2.7%, OR 1.66, p 3.17×10-8); 6q24.2 (MAF 2.6%, OR 1.87, p 1.87×10-11) and one with the number of sIAs: 7p22.1 (MAF 3.3%, RR 1.59, p 6.08×-9). Two of the associations (5q31.3, 6q24.2) replicated in the Dutch sample. The 7p22.1 locus was strongly differentiated; the lead variant was more frequent in Finland (4.6%) than in the Netherlands (0.3%). Additionally, we replicated a previously inconclusive locus on 2q33.1 in all samples tested (OR 1.27, p 1.87×10-12). The five loci explain 2.1% of the sIA heritability in Finland, and may relate to, but not explain, the increased incidence of sIA-SAH in Finland. This study illustrates the utility of population isolates, familial enrichment, dense genotype imputation and alternate phenotyping in search for variants associated with complex diseases.


Assuntos
Estudo de Associação Genômica Ampla , Aneurisma Intracraniano/genética , Acidente Vascular Cerebral/genética , Hemorragia Subaracnóidea/genética , Cromossomos Humanos Par 2/genética , Europa (Continente) , Finlândia , Frequência do Gene , Predisposição Genética para Doença , Variação Genética , Genética Populacional , Humanos , Aneurisma Intracraniano/patologia , Fatores de Risco , Acidente Vascular Cerebral/patologia , Hemorragia Subaracnóidea/patologia
9.
PLoS Genet ; 10(2): e1004123, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24586183

RESUMO

Autoimmune thyroid diseases (AITD) are common, affecting 2-5% of the general population. Individuals with positive thyroid peroxidase antibodies (TPOAbs) have an increased risk of autoimmune hypothyroidism (Hashimoto's thyroiditis), as well as autoimmune hyperthyroidism (Graves' disease). As the possible causative genes of TPOAbs and AITD remain largely unknown, we performed GWAS meta-analyses in 18,297 individuals for TPOAb-positivity (1769 TPOAb-positives and 16,528 TPOAb-negatives) and in 12,353 individuals for TPOAb serum levels, with replication in 8,990 individuals. Significant associations (P<5×10(-8)) were detected at TPO-rs11675434, ATXN2-rs653178, and BACH2-rs10944479 for TPOAb-positivity, and at TPO-rs11675434, MAGI3-rs1230666, and KALRN-rs2010099 for TPOAb levels. Individual and combined effects (genetic risk scores) of these variants on (subclinical) hypo- and hyperthyroidism, goiter and thyroid cancer were studied. Individuals with a high genetic risk score had, besides an increased risk of TPOAb-positivity (OR: 2.18, 95% CI 1.68-2.81, P = 8.1×10(-8)), a higher risk of increased thyroid-stimulating hormone levels (OR: 1.51, 95% CI 1.26-1.82, P = 2.9×10(-6)), as well as a decreased risk of goiter (OR: 0.77, 95% CI 0.66-0.89, P = 6.5×10(-4)). The MAGI3 and BACH2 variants were associated with an increased risk of hyperthyroidism, which was replicated in an independent cohort of patients with Graves' disease (OR: 1.37, 95% CI 1.22-1.54, P = 1.2×10(-7) and OR: 1.25, 95% CI 1.12-1.39, P = 6.2×10(-5)). The MAGI3 variant was also associated with an increased risk of hypothyroidism (OR: 1.57, 95% CI 1.18-2.10, P = 1.9×10(-3)). This first GWAS meta-analysis for TPOAbs identified five newly associated loci, three of which were also associated with clinical thyroid disease. With these markers we identified a large subgroup in the general population with a substantially increased risk of TPOAbs. The results provide insight into why individuals with thyroid autoimmunity do or do not eventually develop thyroid disease, and these markers may therefore predict which TPOAb-positives are particularly at risk of developing clinical thyroid dysfunction.


Assuntos
Autoanticorpos/genética , Doença de Graves/genética , Doença de Hashimoto/genética , Iodeto Peroxidase/genética , Autoanticorpos/isolamento & purificação , Loci Gênicos , Estudo de Associação Genômica Ampla , Doença de Graves/patologia , Doença de Hashimoto/patologia , Humanos , Iodeto Peroxidase/imunologia , Fatores de Risco , Tireoidite Autoimune , Tireotropina/metabolismo
10.
Hum Mol Genet ; 23(20): 5545-57, 2014 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-24861552

RESUMO

Genome-wide association studies (GWAS) of urinary bladder cancer (UBC) have yielded common variants at 12 loci that associate with risk of the disease. We report here the results of a GWAS of UBC including 1670 UBC cases and 90 180 controls, followed by replication analysis in additional 5266 UBC cases and 10 456 controls. We tested a dataset containing 34.2 million variants, generated by imputation based on whole-genome sequencing of 2230 Icelanders. Several correlated variants at 20p12, represented by rs62185668, show genome-wide significant association with UBC after combining discovery and replication results (OR = 1.19, P = 1.5 × 10(-11) for rs62185668-A, minor allele frequency = 23.6%). The variants are located in a non-coding region approximately 300 kb upstream from the JAG1 gene, an important component of the Notch signaling pathways that may be oncogenic or tumor suppressive in several forms of cancer. Our results add to the growing number of UBC risk variants discovered through GWAS.


Assuntos
Proteínas de Ligação ao Cálcio/genética , Cromossomos Humanos Par 20/genética , Peptídeos e Proteínas de Sinalização Intercelular/genética , Proteínas de Membrana/genética , Neoplasias da Bexiga Urinária/genética , População Branca/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Estudos de Casos e Controles , Feminino , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Proteína Jagged-1 , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , Proteínas Serrate-Jagged
11.
Prostate ; 76(10): 897-904, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-26989049

RESUMO

BACKGROUND: The definition of hereditary prostate cancer (HPC) is based on family history and age at onset. Intuitively, HPC is a serious subtype of prostate cancer but there are only limited data on the clinical phenotype of HPC. Here, we aimed to compare the prognosis of HPC to the sporadic form of prostate cancer (SPC). METHODS: HPC patients were identified through a national registry of HPC families in the Netherlands, selecting patients diagnosed from the year 2000 onward (n = 324). SPC patients were identified from the Netherlands Cancer Registry (NCR) between 2003 and 2006 for a population-based study into the genetic susceptibility of PC (n = 1,664). Detailed clinical data were collected by NCR-registrars, using a standardized registration form. Follow-up extended up to the end of 2013. Differences between the groups were evaluated by cross-tabulations and tested for statistical significance while accounting for familial dependency of observations by GEE. Differences in progression-free and overall survival were evaluated using χ(2) testing with GEE in a proportional-hazards model. RESULTS: HPC patients were on average 3 years younger at diagnosis, had lower PSA values, lower Gleason scores, and more often locally confined disease. Of the HPC patients, 35% had high-risk disease (NICE-criteria) versus 51% of the SPC patients. HPC patients were less often treated with active surveillance. Kaplan-Meier 5-year progression-free survival after radical prostatectomy was comparable for HPC (78%) and SPC (74%; P = 0.30). The 5-year overall survival was 85% (95%CI 81-89%) for HPC versus 80% (95%CI 78-82%) for SPC (P = 0.03). CONCLUSIONS: HPC has a favorable clinical phenotype but patients more often underwent radical treatment. The major limitation of HPC is the absence of a genetics-based definition of HPC, which may lead to over-diagnosis of PC in men with a family history of prostate cancer. The HPC definition should, therefore, be re-evaluated, aiming at a reduction of over-diagnosis and overtreatment among men with multiple relatives diagnosed with PC. Prostate 76:897-904, 2016. © 2016 The Authors. The Prostate published by Wiley Periodicals, Inc.


Assuntos
Neoplasias da Próstata/genética , Fatores Etários , Idoso , Intervalo Livre de Doença , Predisposição Genética para Doença , Humanos , Masculino , Pessoa de Meia-Idade , Países Baixos , Fenótipo , Prognóstico , Modelos de Riscos Proporcionais , Antígeno Prostático Específico/sangue , Prostatectomia , Neoplasias da Próstata/diagnóstico , Neoplasias da Próstata/mortalidade , Neoplasias da Próstata/cirurgia , Sistema de Registros , Taxa de Sobrevida
12.
Gastroenterology ; 149(4): 907-17.e7, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26072396

RESUMO

BACKGROUND & AIMS: More than 20% of patients with inflammatory bowel disease (IBD) discontinue thiopurine therapy because of severe adverse drug reactions (ADRs); leukopenia is one of the most serious ADRs. Variants in the gene encoding thiopurine S-methyltransferase (TPMT) alter its enzymatic activity, resulting in higher levels of thiopurine metabolites, which can cause leukopenia. We performed a prospective study to determine whether genotype analysis of TPMT before thiopurine treatment, and dose selection based on the results, affects the outcomes of patients with IBD. METHODS: In a study performed at 30 Dutch hospitals, patients were assigned randomly to groups that received standard treatment (control) or pretreatment screening (intervention) for 3 common variants of TPMT (TPMT*2, TPMT*3A, and TPMT*3C). Patients in the intervention group found to be heterozygous carriers of a variant received 50% of the standard dose of thiopurine (azathioprine or 6-mercaptopurine), and patients homozygous for a variant received 0%-10% of the standard dose. We compared, in an intention-to-treat analysis, outcomes of the intervention (n = 405) and control groups (n = 378) after 20 weeks of treatment. Primary outcomes were the occurrence of hematologic ADRs (leukocyte count < 3.0*10(9)/L or reduced platelet count < 100*10(9)/L) and disease activity (based on the Harvey-Bradshaw Index for Crohn's disease [n = 356] or the partial Mayo score for ulcerative colitis [n = 253]). RESULTS: Similar proportions of patients in the intervention and control groups developed a hematologic ADR (7.4% vs 7.9%; relative risk, 0.93; 95% confidence interval, 0.57-1.52) in the 20 weeks of follow-up evaluation; the groups also had similar mean levels of disease activity (P = .18 for Crohn's disease and P = .14 for ulcerative colitis). However, a significantly smaller proportion of carriers of the TPMT variants in the intervention group (2.6%) developed hematologic ADRs compared with patients in the control group (22.9%) (relative risk, 0.11; 95% confidence interval, 0.01-0.85). CONCLUSIONS: Screening for variants in TPMT did not reduce the proportions of patients with hematologic ADRs during thiopurine treatment for IBD. However, there was a 10-fold reduction in hematologic ADRs among variant carriers who were identified and received a dose reduction, compared with variant carriers who did not, without differences in treatment efficacy. ClinicalTrials.gov number: NCT00521950.


Assuntos
Anti-Inflamatórios/administração & dosagem , Azatioprina/administração & dosagem , Colite Ulcerativa/tratamento farmacológico , Doença de Crohn/tratamento farmacológico , Fármacos Gastrointestinais/administração & dosagem , Variação Genética , Leucopenia/prevenção & controle , Mercaptopurina/administração & dosagem , Metiltransferases/genética , Trombocitopenia/prevenção & controle , Adulto , Anti-Inflamatórios/efeitos adversos , Anti-Inflamatórios/metabolismo , Azatioprina/efeitos adversos , Azatioprina/metabolismo , Colite Ulcerativa/diagnóstico , Colite Ulcerativa/enzimologia , Colite Ulcerativa/genética , Doença de Crohn/diagnóstico , Doença de Crohn/enzimologia , Doença de Crohn/genética , Cálculos da Dosagem de Medicamento , Feminino , Fármacos Gastrointestinais/efeitos adversos , Fármacos Gastrointestinais/metabolismo , Testes Genéticos , Heterozigoto , Homozigoto , Humanos , Leucopenia/induzido quimicamente , Masculino , Mercaptopurina/efeitos adversos , Mercaptopurina/metabolismo , Metiltransferases/metabolismo , Pessoa de Meia-Idade , Países Baixos , Farmacogenética , Fenótipo , Valor Preditivo dos Testes , Estudos Prospectivos , Fatores de Risco , Trombocitopenia/induzido quimicamente , Resultado do Tratamento , Adulto Jovem
13.
PLoS Pathog ; 10(10): e1004485, 2014 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-25356988

RESUMO

The anti-tuberculosis-vaccine Bacillus Calmette-Guérin (BCG) is the most widely used vaccine in the world. In addition to its effects against tuberculosis, BCG vaccination also induces non-specific beneficial effects against certain forms of malignancy and against infections with unrelated pathogens. It has been recently proposed that the non-specific effects of BCG are mediated through epigenetic reprogramming of monocytes, a process called trained immunity. In the present study we demonstrate that autophagy contributes to trained immunity induced by BCG. Pharmacologic inhibition of autophagy blocked trained immunity induced in vitro by stimuli such as ß-glucans or BCG. Single nucleotide polymorphisms (SNPs) in the autophagy genes ATG2B (rs3759601) and ATG5 (rs2245214) influenced both the in vitro and in vivo training effect of BCG upon restimulation with unrelated bacterial or fungal stimuli. Furthermore, pharmacologic or genetic inhibition of autophagy blocked epigenetic reprogramming of monocytes at the level of H3K4 trimethylation. Finally, we demonstrate that rs3759601 in ATG2B correlates with progression and recurrence of bladder cancer after BCG intravesical instillation therapy. These findings identify a key role of autophagy for the nonspecific protective effects of BCG.


Assuntos
Autofagia , Vacina BCG/uso terapêutico , Mycobacterium bovis/imunologia , Polimorfismo de Nucleotídeo Único , Neoplasias da Bexiga Urinária/tratamento farmacológico , Adjuvantes Imunológicos/administração & dosagem , Adjuvantes Imunológicos/uso terapêutico , Administração Intravesical , Antineoplásicos/administração & dosagem , Antineoplásicos/uso terapêutico , Autofagia/genética , Autofagia/imunologia , Proteína 5 Relacionada à Autofagia , Proteínas Relacionadas à Autofagia , Vacina BCG/administração & dosagem , Citocinas/metabolismo , Humanos , Estimativa de Kaplan-Meier , Proteínas Associadas aos Microtúbulos/genética , Monócitos/imunologia , Recidiva Local de Neoplasia , Neoplasias da Bexiga Urinária/imunologia , Neoplasias da Bexiga Urinária/virologia , Vacinação , Proteínas de Transporte Vesicular/genética , beta-Glucanas/metabolismo
14.
Int J Cancer ; 136(5): 1117-24, 2015 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-24978702

RESUMO

A history of urinary bladder cancer (UBC) in first-degree relatives increases UBC risk by twofold. The influence of positive family history on UBC prognosis is unknown. Here, we investigated association of first-degree UBC family history with clinicopathological characteristics and prognosis of UBC patients. Detailed clinical data of 1,465 non-muscle-invasive bladder cancer (NMIBC) and 250 muscle-invasive or metastatic bladder cancer (MIBC) patients, diagnosed from 1995 to 2010, were collected through medical file review. Competing risk analyses were used to compare recurrence-free survival (RFS) and progression-free survival (PFS) of NMIBC patients according to self-reported UBC family history. Overall survival in MIBC patients was estimated using Kaplan-Meier analysis. The added value of family history in prediction of NMIBC prognosis was quantified with Harrell's concordance-index. Hundred (6.8%) NMIBC and 14 (5.6%) MIBC patients reported UBC in first-degree relatives. Positive family history was statistically significantly associated with smaller tumor size and non-significantly with more favorable distribution of other tumor characteristics. In univariable analyses, positive family history correlated with longer RFS (p = 0.11) and PFS (p = 0.04). Hazard ratios for positive vs. negative family history after adjustment for clinicopathological characteristics were 0.75 (95% CI = 0.53-1.07) and 0.45 (95% CI = 0.18-1.12) for RFS and PFS, respectively. Five familial and 48 sporadic MIBC patients (Kaplan-Meier 10-year risk: 41% and 25%) died within 10 years. Family history did not improve the c-index of prediction models. This study shows that a first-degree family history of UBC is not clearly associated with NMIBC prognosis. Family history does not aid in prediction of NMIBC recurrence or progression.


Assuntos
Predisposição Genética para Doença , Recidiva Local de Neoplasia/genética , Neoplasias da Bexiga Urinária/genética , Idoso , Progressão da Doença , Família , Feminino , Seguimentos , Humanos , Masculino , Gradação de Tumores , Recidiva Local de Neoplasia/epidemiologia , Recidiva Local de Neoplasia/mortalidade , Estadiamento de Neoplasias , Países Baixos/epidemiologia , Prognóstico , Estudos Retrospectivos , Medição de Risco , Taxa de Sobrevida , Neoplasias da Bexiga Urinária/epidemiologia , Neoplasias da Bexiga Urinária/mortalidade
15.
Prostate ; 75(5): 474-83, 2015 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-25560306

RESUMO

BACKGROUND: More than 70 single nucleotide polymorphisms (SNPs) have been reported to be associated with prostate cancer (PC) risk; these were mainly identified in the general population with predominantly sporadic PC (SPC). Previous studies have suggested similar associations between a selection of these SNPs and hereditary PC (HPC). Our aim was to evaluate the effect of all known PC risk SNPs and their discriminative value for SPC and HPC. METHODS: Seventy-four PC susceptibility SNPs (reported in literature up to June 2014) were genotyped in a population-based series of 620 SPC patients, 312 HPC patients from the national Dutch registry and 1819 population-based referents. Association analyses were performed using logistic regression, focusing on directional consistency of the odds ratios (ORs) with those in the original reports, that is, whether the OR was in the same direction as in the original report. Discriminative performance was evaluated by a genetic risk score used in logistic regression and receiver operating characteristic (ROC) curve analyses. RESULTS: Directional consistency was seen for 62 SNPs in SPC and 64 SNPs in HPC, 56 of which overlapped. ORs were mostly higher for HPC with 22 ORs >1.25 versus 5 for SPC. Discriminative performance was better for HPC with an area under the ROC curve of 0.73 versus 0.64 for SPC. CONCLUSIONS: A large overlap was found for the associations between low-penetrance susceptibility SNPs and SPC and HPC, suggesting a similarity in genetic etiology. This warrants a reconsideration of "HPC" and a restrictive policy toward prostate-specific antigen testing in men with a positive family history. Genetic risk scores might be used for PC risk stratification on the population level.


Assuntos
Predisposição Genética para Doença , Polimorfismo de Nucleotídeo Único/genética , Neoplasias da Próstata/genética , Idoso , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Países Baixos , Curva ROC , Fatores de Risco
16.
Ann Rheum Dis ; 74(12): 2183-7, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25114059

RESUMO

OBJECTIVES: Pharmacogenetic studies of tumour necrosis factor inhibitors (TNFi) response in patients with rheumatoid arthritis (RA) have largely relied on the changes in complex disease scores, such as disease activity score 28 (DAS28), as a measure of treatment response. It is expected that genetic architecture of such complex score is heterogeneous and not very suitable for pharmacogenetic studies. We aimed to select the most optimal phenotype for TNFi response using heritability estimates. METHODS: Using two linear mixed-modelling approaches (Bayz and GCTA), we estimated heritability, together with genomic and environmental correlations for the TNFi drug-response phenotype ΔDAS28 and its separate components: Δ swollen joint count (SJC), Δ tender joint count (TJC), Δ erythrocyte sedimentation rate (ESR) and Δ visual-analogue scale of general health (VAS-GH). For this, we used genome-wide single nucleotide polymorphism (SNP) data from 878 TNFi-treated Dutch patients with RA. Furthermore, a multivariate genome-wide association study (GWAS) approach was implemented, analysing separate DAS28 components simultaneously. RESULTS: The highest heritability estimates were found for ΔSJC (h(2)gbayz=0.76 and h(2)gGCTA=0.87) and ΔTJC (h(2)gbayz=0.62 and h(2)gGCTA=0.82); lower heritability was found for ΔDAS28 (h(2)gbayz=0.59 and h(2)gGCTA=0.71) while estimates for ΔESR and ΔVASGH were near or equal to zero. The highest genomic correlations were observed for ΔSJC and ΔTJC (0.49), and the highest environmental correlation was seen between ΔTJC and ΔVASGH (0.62). The multivariate GWAS did not generate excess of low p values as compared with a univariate analysis of ΔDAS28. CONCLUSIONS: Our results indicate that multiple SNPs together explain a substantial portion of the variation in change in joint counts in TNFi-treated patients with RA. In conclusion, of the outcomes studied, the joint counts are most suitable for TNFi pharmacogenetics in RA.


Assuntos
Antirreumáticos/uso terapêutico , Artrite Reumatoide/genética , DNA/genética , Estudo de Associação Genômica Ampla , Polimorfismo Genético , Fator de Necrose Tumoral alfa/antagonistas & inibidores , Adulto , Idoso , Artrite Reumatoide/tratamento farmacológico , Artrite Reumatoide/metabolismo , Feminino , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Fenótipo , Índice de Gravidade de Doença
17.
BMC Genet ; 16: 79, 2015 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-26159428

RESUMO

BACKGROUND: Previous reports suggested a role for iron and hepcidin in atherosclerosis. Here, we evaluated the causality of these associations from a genetic perspective via (i) a Mendelian randomization (MR) approach, (ii) study of association of atherosclerosis-related single nucleotide polymorphisms (SNPs) with iron and hepcidin, and (iii) estimation of genomic correlations between hepcidin, iron and atherosclerosis. RESULTS: Analyses were performed in a general population sample. Iron parameters (serum iron, serum ferritin, total iron-binding capacity and transferrin saturation), serum hepcidin and genome-wide SNP data were available for N = 1,819; non-invasive measurements of atherosclerosis (NIMA), i.e., presence of plaque, intima media thickness and ankle-brachial index (ABI), for N = 549. For the MR, we used 12 iron-related SNPs that were previously identified in a genome-wide association meta-analysis on iron status, and assessed associations of individual SNPs and quartiles of a multi-SNP score with NIMA. Quartile 4 versus quartile 1 of the multi-SNP score showed directionally consistent associations with the hypothesized direction of effect for all NIMA in women, indicating that increased body iron status is a risk factor for atherosclerosis in women. We observed no single SNP associations that fit the hypothesized directions of effect between iron and NIMA, except for rs651007, associated with decreased ferritin concentration and decreased atherosclerosis risk. Two of six NIMA-related SNPs showed association with the ratio hepcidin/ferritin, suggesting that an increased hepcidin/ferritin ratio increases atherosclerosis risk. Genomic correlations were close to zero, except for hepcidin and ferritin with ABI at rest [-0.27 (SE 0.34) and -0.22 (SE 0.35), respectively] and ABI after exercise [-0.29 (SE 0.34) and -0.30 (0.35), respectively]. The negative sign indicates an increased atherosclerosis risk with increased hepcidin and ferritin concentrations. CONCLUSIONS: Our results suggest a potential causal role for hepcidin and ferritin in atherosclerosis, and may indicate that iron status is causally related to atherosclerosis in women.


Assuntos
Aterosclerose/sangue , Aterosclerose/etiologia , Hepcidinas/sangue , Ferro/sangue , Adulto , Idoso , Aterosclerose/patologia , Feminino , Ferritinas/sangue , Estudos de Associação Genética , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Placa Aterosclerótica , Polimorfismo de Nucleotídeo Único , Fatores de Risco
18.
Arterioscler Thromb Vasc Biol ; 34(2): 446-56, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24334869

RESUMO

OBJECTIVE: Iron and the iron regulatory hormone hepcidin, major determinant of body iron distribution, are hypothesized to play a role in cardiovascular disease. Here, we assess the associations of hepcidin as well as ferritin, iron, total iron-binding capacity, and transferrin saturation (ie, iron parameters) with noninvasive measurements of atherosclerosis in men and women of a population-based cohort. APPROACH AND RESULTS: We included 766 participants of the Nijmegen Biomedical Study aged 46 to 67 years for whom serum measurements of hepcidin, iron parameters, and noninvasive measurements of atherosclerosis were available. Noninvasive measurements of atherosclerosis were presence of plaque, ankle-brachial index, and intima-media thickness. We performed multivariable logistic and linear regression analyses using quartiles of hepcidin and iron parameters. Analyses were stratified by sex and adjusted for several demographic, clinical, and biochemical determinants, including traditional risk factors of cardiovascular disease based on the Framingham risk score. Hepcidin and the hepcidin/ferritin ratio, reflecting hepcidin expression relative to iron stores, were significantly associated with the presence of plaque in women (adjusted odds ratios for quartile 4 versus quartile 1 [95% confidence intervals] of 3.07 [1.36-6.90] and 2.31 [1.03-5.18], respectively). The hepcidin/ferritin ratio was significantly and negatively associated with ankle-brachial index at rest in men and women (adjusted ß for quartile 4 versus quartile 1 [95% confidence intervals] of -0.03 [-0.07 to 0.00] and -0.04 [-0.06 to -0.01], respectively). CONCLUSIONS: Our results suggest that the body iron distribution as determined by hepcidin affects the development of atherosclerosis in women.


Assuntos
Artérias Carótidas/patologia , Doenças das Artérias Carótidas/sangue , Hepcidinas/sangue , Placa Aterosclerótica , Pós-Menopausa/sangue , Fatores Etários , Idoso , Índice Tornozelo-Braço , Biomarcadores/sangue , Doenças das Artérias Carótidas/diagnóstico , Doenças das Artérias Carótidas/epidemiologia , Espessura Intima-Media Carotídea , Feminino , Ferritinas/sangue , Inquéritos Epidemiológicos , Humanos , Ferro/sangue , Modelos Lineares , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Análise Multivariada , Países Baixos/epidemiologia , Razão de Chances , Prognóstico , Fatores de Risco , Fatores Sexuais , Transferrina/análise
19.
PLoS Genet ; 8(5): e1002746, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-22693459

RESUMO

Androgenetic alopecia (AGA) is a highly heritable condition and the most common form of hair loss in humans. Susceptibility loci have been described on the X chromosome and chromosome 20, but these loci explain a minority of its heritable variance. We conducted a large-scale meta-analysis of seven genome-wide association studies for early-onset AGA in 12,806 individuals of European ancestry. While replicating the two AGA loci on the X chromosome and chromosome 20, six novel susceptibility loci reached genome-wide significance (p = 2.62×10⁻9-1.01×10⁻¹²). Unexpectedly, we identified a risk allele at 17q21.31 that was recently associated with Parkinson's disease (PD) at a genome-wide significant level. We then tested the association between early-onset AGA and the risk of PD in a cross-sectional analysis of 568 PD cases and 7,664 controls. Early-onset AGA cases had significantly increased odds of subsequent PD (OR = 1.28, 95% confidence interval: 1.06-1.55, p = 8.9×10⁻³). Further, the AGA susceptibility alleles at the 17q21.31 locus are on the H1 haplotype, which is under negative selection in Europeans and has been linked to decreased fertility. Combining the risk alleles of six novel and two established susceptibility loci, we created a genotype risk score and tested its association with AGA in an additional sample. Individuals in the highest risk quartile of a genotype score had an approximately six-fold increased risk of early-onset AGA [odds ratio (OR) = 5.78, p = 1.4×10⁻88]. Our results highlight unexpected associations between early-onset AGA, Parkinson's disease, and decreased fertility, providing important insights into the pathophysiology of these conditions.


Assuntos
Alopecia/genética , Estudo de Associação Genômica Ampla , Doença de Parkinson/genética , Adulto , Idoso , Alelos , Fertilidade/genética , Predisposição Genética para Doença , Genótipo , Haplótipos , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , Fatores de Risco
20.
Stroke ; 45(11): 3194-9, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25256182

RESUMO

BACKGROUND AND PURPOSE: Common variants have been identified using genome-wide association studies which contribute to intracranial aneurysms (IA) susceptibility. However, it is clear that the variants identified to date do not account for the estimated genetic contribution to disease risk. METHODS: Initial analysis was performed in a discovery sample of 2617 IA cases and 2548 controls of white ancestry. Novel chromosomal regions meeting genome-wide significance were further tested for association in 2 independent replication samples: Dutch (717 cases; 3004 controls) and Finnish (799 cases; 2317 controls). A meta-analysis was performed to combine the results from the 3 studies for key chromosomal regions of interest. RESULTS: Genome-wide evidence of association was detected in the discovery sample on chromosome 9 (CDKN2BAS; rs10733376: P<1.0×10(-11)), in a gene previously associated with IA. A novel region on chromosome 7, near HDAC9, was associated with IA (rs10230207; P=4.14×10(-8)). This association replicated in the Dutch sample (P=0.01) but failed to show association in the Finnish sample (P=0.25). Meta-analysis results of the 3 cohorts reached statistical significant (P=9.91×10(-10)). CONCLUSIONS: We detected a novel region associated with IA susceptibility that was replicated in an independent Dutch sample. This region on chromosome 7 has been previously associated with ischemic stroke and the large vessel stroke occlusive subtype (including HDAC9), suggesting a possible genetic link between this stroke subtype and IA.


Assuntos
Cromossomos Humanos Par 7/genética , Estudo de Associação Genômica Ampla/métodos , Aneurisma Intracraniano/genética , Polimorfismo de Nucleotídeo Único/genética , População Branca/genética , Adulto , Idoso , Estudos de Coortes , Feminino , Humanos , Aneurisma Intracraniano/diagnóstico , Masculino , Pessoa de Meia-Idade
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