{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T07:19:20Z","timestamp":1696231160118},"reference-count":30,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2016,6,22]],"date-time":"2016-06-22T00:00:00Z","timestamp":1466553600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Nephrology"],"published-print":{"date-parts":[[2016,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Aim<\/jats:title><jats:p>Involvement of pro\u2010inflammatory genes has been correlated with basic kidney diseases and end stage renal disease (ESRD). However, results at odds were often noted from such independent association studies. This study proposes a genome wide analysis approach to predict ESRD risk associated genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We included 42 single nucleotide polymorphisms (SNPs) showing association among north Indian ESRD cases and controls. ESRD cases comprised chronic glomerulonephritis (CGN), chronic interstitial nephritis (CIN), hypertension (HTN) and autosomal dominant polycystic kidney disease (ADPKD). Genotyping data obtained from our prior published reports were compared with Genome\u2010Wide Association Studies (GWAS) SNPs retrieved from HapMap and GWASCentral databases using R\u2010statistical package SNPAssoc. Linkage disequilibrium (LD), gene\u2013gene interaction, classification and regression tree (CART) and pathway analysis were carried out in the present study supplemented with IL\u20106 and TNF\u2010\u03b1 levels estimation using enzyme linked immunosorbent assay (ELISA).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Comparison of genotyping data with GWAS SNPs revealed significant associations for interleukin (IL)1\u2010RN, IL\u20106, MTHFR, tumour necrosis factor\u2010\u03b1 (TNF\u2010\u03b1) and CCR3 genes with ESRD. Nine SNPs were commonly associated with CGN, CIN, HTN, ADPKD and ESRD. LD (D\u2009=\u20090.9) and gene\u2010gene interaction (<jats:italic>P\u2009=<\/jats:italic>\u20090.0002) analyses revealed significant associations for IL\u20106 and TNF\u2010\u03b1 genes. In a consistent manner, CART analysis and functional analysis servers predict predisposing effects for TNF\u2010\u03b1 and IL\u20106 with ESRD. Finally, higher body circulating levels were observed for mutant TNF\u2010\u03b1 and IL\u20106 alleles among ESRD.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The study indicates significance for IL\u20106 and TNF\u2010\u03b1 gene with basic kidney diseases and ESRD. Extensive statistical tests, pathway analysis and functional assays also reflect attenuated level of significance for these SNPs. In future these may be brought from bench side to clinical practice as diagnostic biomarkers upon external and prospective replication and confirmation among other cohorts.<\/jats:p><\/jats:sec>","DOI":"10.1111\/nep.12635","type":"journal-article","created":{"date-parts":[[2015,9,30]],"date-time":"2015-09-30T13:53:15Z","timestamp":1443621195000},"page":"592-600","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Prediction of susceptible biomarkers for end stage renal disease among North Indians"],"prefix":"10.1111","volume":"21","author":[{"given":"Swayam","family":"Prakash","sequence":"first","affiliation":[{"name":"Department of Nephrology Sanjay Gandhi Postgraduate Institute of Medical Sciences  Raebareli Road Lucknow India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aditya Narayan","family":"Sarangi","sequence":"additional","affiliation":[{"name":"Biomedical Informatics Centre School of Telemedicine and Biomedical Informatics, Sanjay Gandhi Postgraduate Institute of Medical Sciences  Raebareli Road Lucknow India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gaurav","family":"Tripathi","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Faculty of Medicine University of Calgary  Calgary Alberta Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raj Kumar","family":"Sharma","sequence":"additional","affiliation":[{"name":"Department of Nephrology Sanjay Gandhi Postgraduate Institute of Medical Sciences  Raebareli Road Lucknow India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suraksha","family":"Agrawal","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics Sanjay Gandhi Postgraduate Institute of Medical Sciences  Raebareli Road Lucknow India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2016,6,22]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(14)60384-6"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11886-014-0476-5"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.2337\/dc06-0062"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11632"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature06258"},{"key":"e_1_2_6_7_1","first-page":"1","article-title":"Promise and pitfalls of the Immunochip","volume":"13","author":"Cortes A","year":"2011","journal-title":"Arthritis Res. 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