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1.
The quest for genetic risk factors for Crohn's disease in the post-GWAS era
Karin Fransen, Mitja Mitrovič, Cleo C van Diemen, Rinse K. Weersma, 2011, pregledni znanstveni članek

Opis: Multiple genome-wide association studies (GWASs) and two large scale meta-analyses have been performed for Crohn's disease and have identified 71 susceptibility loci. These findings have contributed greatly to our current understanding of the disease pathogenesis. Yet, these loci only explain approximately 23% of the disease heritability. One of the future challenges inthis post-GWAS era is to identify potential sources of the remaining heritability. Such sources may include common variants with limited effect size, rare variants with higher effect sizes, structural variations, or even more complicated mechanisms such as epistatic, gene-environment and epigeneticinteractions. Here, we outline potential sources of this hidden heritability, focusing on Crohn's disease and the currently available data. Wealso discuss future strategies to determine more about the heritability; these strategies include expanding current GWAS, fine-mapping, whole genome sequencing or exome sequencing, and using family-based approaches. Despite thecurrent limitations, such strategies may help to transfer research achievements into clinical practice and guide the improvement of preventive and therapeutic measures.
Ključne besede: genetic risk factors, Crohn’s disease
Objavljeno: 05.06.2012; Ogledov: 747; Prenosov: 6
.pdf Polno besedilo (477,79 KB)
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2.
Asociacijska analiza na celotnem genomu pri slovenskih bolnikih s kronično vnetno črevesno boleznijo
Mitja Mitrovič, 2013, doktorska disertacija

Opis: V preteklih desetletjih je bil v raziskave in razumevanje patogeneze KVČB vložen precejšen napor, vendar natančni vzroki nastanka bolezni še niso povsem pojasnjeni. Po zdaj najbolj uveljavljeni hipotezi se bolezen pojavi zaradi pretiranega imunskega odziva na normalno črevesno mikrofloro pri gensko dovzetnih posameznikih. Bolniki s KVČB zbolijo za eno od dveh precej podobnih oblik kroničnega vnetja črevesja: ulceroznim kolitisom (UK) ali Crohnovo boleznijo (CB). V 10−15 odstotkih primerov pa bolniki ne kažejo jasnih kliničnih, endoskopskih in histoloških značilnosti CB ali UK, in govorimo o intermediarnem kolitisu (IK). Največjo pogostost bolezni so ugotovili v Kanadi in Severni Evropi, najmanjšo pa v deželah v razvoju in v Aziji, pri čemer je UK pogostejši kot CB. Za slovensko populacijo sicer ni konkretnih epidemioloških podatkov, vendar je bilo ob koncu 90. let v Sloveniji 1150 bolnikov s KVČB, kar nas uvršča na dno evropske lestvice. Na nastanek bolezni vplivajo različni dejavniki okolja, iz epidemioloških raziskav družin in dvojčkov pa nedvomno izhaja, da k tveganju za KVČB prispevajo tudi genski dejavniki. Kljub številnim dokazom o genskem ozadju bolezni se je natančno določanje genskih determinant začelo šele v zadnjih petnajstih letih. Temeljilo je na številnih raziskovalnih pristopih. Asociacijske študije na celotnem genomu (GWAS) so z odkritjem povezav med KVČB in 99 lokusi največ prispevale k razumevanju genskega ozadja bolezni. Med pomembnejše izzive v obdobju po GWAS spadata odkrivanje vzročnih variant in analiza njihovih funkcionalnih posledic, s tem pa posledično tudi rešitev problema manjkajočega dednostnega deleža pri kompleksnih boleznih. Zaradi tega so bili predlagani številni pristopi, kot so npr. fino kartiranje, analiza eQTL-ov in GWAS pri družinah obolelih, vključno s preučevanjem učinkov starševskega izvora (angl. parent of origin − POO) na izražanje genov. Ob tem pa so številne raziskovalne skupine, ki se ukvarjajo z genetiko KVČB, pod okriljem konzorcija International Inflammatory Bowel Disease Consortium (IIBDGC) združile moči v projektu ImmunoChip (iCHIP), ki predstavlja tarčno mikromrežo DNK za analiziranje imunsko posredovanih bolezni. V raziskavi smo izvedli z iCHIP-om prvo tarčno študijo GWAS pri 227 bolnikih s KVČB in 210 zdravih posameznikih. Zaradi razmeroma omejenega števila preiskovancev sicer nismo imeli zadostne statistične moči za odkrivanje statistično značilnih povezav, vendar smo nakazali na nominalne povezave z boleznijo na kromosomih 1, 5, 8, 13 in 16. V sodelovanju z drugimi člani projekta iCHIP, ki je v metaanalizi vključeval približno 75.000 bolnikov s KVČB in zdravih posameznikov, smo prispevali k odkritju 71 novih statistično značilnih povezav z boleznijo, tako da se je skupno število bolezenskih lokusov z 99 povzpelo na 163. Glede odkrivanja skupnih mehanizmov kompleksnih bolezni je pomembna tudi ugotovitev, da je več kot dve tretjini lokusov KVČB impliciranih v patogenezi drugih imunsko posredovanih bolezni, kot so ankilizirajoči spondilitis, psoriaza in mikobakterijske okužbe. V raziskavi smo ločeno izvedli tudi asociacijsko analizo SNP-jev genov NOD2 in IL23R ter prvič povezali omenjena gena s patogenezo KVČB pri slovenskih bolnikih. Genotipske podatke smo pridobili z optimizacijo metode analize DNK s talilnimi krivuljami visoke ločljivosti (HRMA), ki se je izkazala kot hitra, preprosta, natančna in cenovno ugodna metoda za odkrivanje redkih mutacij in za gensko tipizacijo. V študiji smo s kartiranjem cis-eQTL-ov v regiji s tremi kandidatnimi geni ( ) ugotovili, da polimorfizma rs10178214, rs1041973 in redka varianta ccc-2-102248784-A-G statistično značilno vplivajo na izražanje gena IL1RL1 v periferni venski krvi. Nismo pa opazili statistično značilnega izražanja tarčnih genov v črevesnih biopsijah bolnikov s CB. V raziskavi smo pri nizozemskih bolnikih s KVČB odkrili omejen učinek POO genov IL12B, PRDM1 in NOD2, ki pa nam ga v večji neodvisni kohorti ni uspelo replicirati.
Ključne besede: kronična vnetna črevesna bolezen, asociacijska analiza na celotnem genomu, ImmunoChip
Objavljeno: 08.05.2013; Ogledov: 1812; Prenosov: 163
.pdf Polno besedilo (74,81 MB)

3.
Limited evidence for parent-of-origin effects in inflammatory bowel disease associated loci
Mitja Mitrovič, Karin Fransen, Uroš Potočnik, 2012, izvirni znanstveni članek

Opis: Background Genome-wide association studies of two main forms of inflammatory bowel diseases (IBD), Crohnʼs disease (CD) and ulcerative colitis (UC), have identified 99 susceptibility loci, but these explain only ~23% of the genetic risk. Part of the Žhidden heritabilityʼ could be in transmissible genetic effects in which mRNA expression in the offspring depends on the parental origin of the allele (genomic imprinting), since children whose mothers have CD are more often affected than children with affected fathers. We analyzed parent-of-origin (POO) effects in Dutch and Indian cohorts of IBD patients. Methods We selected 28 genetic loci associated with both CD and UC, and testedthem for POO effects in 181 Dutch IBD case-parent trios. Three susceptibility variants in NOD2 were tested in 111 CD trios and a significant finding was re-evaluated in 598 German trios. The UC-associated gene, BTNL2, reportedly imprinted, was tested in 70 Dutch UC trios. Finally, we used 62 independent Indian UC trios to test POO effects of five established Indian UC risk loci. Results We identified POO effects for NOD2 (L1007fs; OR = 21.0, P-value = 0.013) for CD; these results could not be replicated in an independent cohort (OR = 0.97, P-value = 0.95). A POO effect in IBD was observed for IL12B (OR = 3.2, P-value = 0.019) and PRDM1 (OR = 5.6, P-value = 0.04). In the Indian trios the IL10 locus showed a POO effect (OR = 0.2, P-value = 0.03). Conclusions Little is known about the effect of genomic imprinting in complex diseases such as IBD. We present limited evidence for POO effects for the tested IBD loci. POO effects explain part of the hidden heritability for complex genetic diseases but need to be investigated further.
Ključne besede: inflammatory bowel diseases, IBD, genetic locus, genetics
Objavljeno: 10.07.2015; Ogledov: 279; Prenosov: 1
.pdf Polno besedilo (495,25 KB)

4.
Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
Jimmy Z Liu, Mitja Mitrovič, 2013, izvirni znanstveni članek

Opis: Primary sclerosing cholangitis (PSC) is a severe liver disease of unknown etiology leading to fibrotic destruction of the bile ducts and ultimately to the need for liver transplantation1, 2, 3. We compared 3,789 PSC cases of European ancestry to 25,079 population controls across 130,422 SNPs genotyped using the Immunochip4. We identified 12 genome-wide significant associations outside the human leukocyte antigen (HLA) complex, 9 of which were new, increasing the number of known PSC risk loci to 16. Despite comorbidity with inflammatory bowel disease (IBD) in 72% of the cases, 6 of the 12 loci showed significantly stronger association with PSC than with IBD, suggesting overlapping yet distinct genetic architectures for these two diseases. We incorporated association statistics from 7 diseases clinically occurring with PSC in the analysis and found suggestive evidence for 33 additional pleiotropic PSC risk loci. Together with network analyses, these findings add to the genetic risk map of PSC and expand on the relationship between PSC and other immune-mediated diseases.
Objavljeno: 10.07.2015; Ogledov: 252; Prenosov: 0
URL Polno besedilo (0,00 KB)

5.
High-resolution melting curve analysis for high-throughput genotyping of NOD2/CARD15 mutations and distribution of these mutations in Slovenian inflammatory bowel diseases patients
Mitja Mitrovič, Uroš Potočnik, 2011, izvirni znanstveni članek

Opis: Inflammatory bowel diseases (IBD) are usually classified into Crohn's disease (CD) and ulcerative colitis (UC). NOD2/CARD15 was the first identified CD-susceptibility gene and was confirmed as the most potent disease gene in CD pathogenesis. Three NOD2/CARD15 variants, namely two missense polymorphisms R702W (rs2066844) and G908R (rs2066845), and a frame shift polymorphism L1007fs (rs2066847), were associated with CD in Caucasian populations. High resolution melting analysis (HRMA) with saturation LCGreen dyes was previously reported as a simple, inexpensive, accurate and sensitive method for genotyping and/or scanning of rare variants. For this reasons we used qPCR-HRMA for genotyping NOD2/CARD15 variants in 588 Slovenian IBD patients and 256 healthy controls. PCR-RFLP was used as a reference method for genotyping of clinical samples. The optimization of an HRM experiment required careful design and adjustment of main parameters, such as primer concentration, MgCl_{2} concentration, probe design and template DNA concentration. Different HRMA approaches were tested and used to develop a reliable and low-cost SNP genotyping assays for polymorphisms in NOD2/CARD15 gene. Direct HRMA was the fastest and cheapest HRMA approach for L1007fs and R702W polymorphisms, yet for G908R polymorphism sufficient reliability was achieved after introduction of unlabeled probe. In association analysis, we found statistically significant association of L1007fs (p =0.001, OR=3.011, CI95%=1.494-6.071) and G908R (p=2.62 * 10^{-4}, OR=14.117, CI95%= 1.884-105.799) polymorphisms with CD patients. At least one of NOD2/CARD15 polymorphisms was found in 78/354 (22.03% (12.69%) in UC patients and in 26/256 (10.15%) in healthy controls. We have successfully implemented NOD2/CARD15 HRMA assays, which may contribute to the development of genetic profiles for risk prediction of developing CD and for differential diagnosis of CD vs. UC.
Ključne besede: high-resolution melting analysis, NOD2/CARD15, inflammatory bowel diseases
Objavljeno: 14.06.2017; Ogledov: 118; Prenosov: 0
.pdf Polno besedilo (1,72 MB)

6.
High resolution melting curve analysis for high-throughput SNP genotyping in IL23R gene and association of IL23R with Slovenian inflammatory bowel diseases patients
Mitja Mitrovič, Uroš Potočnik, 2010, izvirni znanstveni članek

Opis: Single nucleotide polymorphism (SNP) analysis is important tool in the studies of genetic factors associated with complex diseases and with genetically influenced response to drug therapy (pharmacogenetics). Recently, a new generation of generic dsDNA binding dyes (LCGreen$^{TM}$) contributed to the development of fast and low-cost method for SNP detection and/or genotyping based on high resolution melting (HRM) analysis. The aim of our study was to develop HRM assay for IL23R gene (rs7517847) and to perform association study in Slovenian inflammatory bowel diseases (IBD) patients. We genotyped 345 Slovenian healthy controls and 295 IBD patients including 159 with Crohn's disease (CD) and 136 with ulcerative colitis (UC) for rs7517847 polymorphism in IL23R gene using standard RFLP and optimized HRM methods. In this study, we showed, that HRM is a simple, fast and reliable method for genotyping of clinical samples where homozygotes (GG and TT) were determined by Tm calling method and difference between homozygotes and heterozygotes was determined by different melting curve shape using gene scanning method. With combination of results from Tm calling and gene scanning methods, we achieved 98,6% concordance between PCR-RFLP and PCRHRM results, based on the analysis of 640 samples. We found statistically significant association of IL23R polymorphism with Slovenian Crohn's disease patients when comparing genotype and allele frequencies between CD patients and controls. Allele frequency of minor allele G was 0,46 in controls and was reduced to 0,33 in CD patients (p < 0,001, OR = 0,588). The frequency of T/T genotype carriers was higher in CD patients (50,3%) than in controls (26,7%, p = 0,002, OR = 2,558). We found weak association between IL23R polymorphism and Slovenian UC patients. Carriers of T/T genotype have higher risk for UC (p = 0,035, OR = 1,599). These results suggest IL23R plays important role in CD and UC development in Slovenian patients.
Ključne besede: SNP genotyping, high resolution melting, DNA dyes, inflammatory bowel diseases, LC Green Plus
Objavljeno: 18.08.2017; Ogledov: 84; Prenosov: 0
.pdf Polno besedilo (232,19 KB)

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