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Colvin A, Dabela E, Khan A, Hayes M, Connolly J, Mentch F, Almoguera B, Hakonarson H, Mukherjee E, Hripcsak G, Weng C, Kiryluk K, Wheless L, Petukhova L. 366 Adverse reproductive outcomes among women with hidradenitis suppurativa. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.02.388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Khan A, McGovern J, Yang Z, Wang C, Hughes T, Dabela E, Garzon M, Lauren C, Levin L, Dai Z, Hayes M, Connolly J, Mentch F, Almoguera B, Sleiman P, Hakonarson H, Denny J, Love J, Shalek A, Hripcsak G, Weng C, Ionita-Laza I, Kiryluk K, Petukhova L. 570 A genome-wide association study in an African American cohort implicates IL-12A in acne. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.02.597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Caliskan Y, Karahan G, Akgul SU, Mirioglu S, Ozluk Y, Yazici H, Demir E, Dirim AB, Turkmen A, Edwards J, Savran FO, Sever MS, Kiryluk K, Gharavi A, Lentine KL. LIMS1 Risk Genotype and T-Cell Mediated Rejection in Kidney Transplant Recipients. Nephrol Dial Transplant 2021; 36:2120-2129. [PMID: 33909908 DOI: 10.1093/ndt/gfab168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND This study aims to examine the association of LIM Zinc Finger Domain Containing 1 (LIMS1) genotype with allograft rejection in an independent kidney transplant cohort. METHODS We genotyped 841 kidney transplant recipients for LIMS1 rs893403 variant by Sanger sequencing followed by PCR confirmation of the deletion. Recipients who were homozygous for LIMS1 rs893403 genotype GG were compared to AA/AG genotypes. The primary outcome was T-cell mediated (TCMR) or antibody mediated rejection (ABMR) and secondary outcome was allograft loss. RESULTS After a median follow-up of 11.4 years, the rate of TCMR was higher in recipients with the GG (n = 200) compared to AA/AG (n = 641) genotypes [25 (12.5%) vs 35 (5.5%); p = 0.001] while ABMR did not differ by genotype [18 (9.0%) vs 62 (9.7%)]. Recipients with GG genotype had 2.4-times higher risk of TCMR than those who did not have this genotype (adjusted hazard ratio (aHR), 1.442.434.12, p = 0.001). A total of 189 (22.5%) recipients lost their allografts during follow up. Kaplan-Meier estimates of 5-year (94.3% vs. 94.4%, p = 0.99) and 10-year graft survival rates (86.9% vs. 83.4%, p = 0.31) did not differ significantly in those with GG compared to AA/AG groups. CONCLUSIONS Our study demonstrates that recipient LIMS1 risk genotype is associated with increased risk of TCMR after kidney transplantation, confirming the role of LIMS1 locus in allograft rejection. These findings may have clinical implications for the prediction and clinical management of kidney transplant rejection by pretransplant genetic testing of recipients and donors for LIMS1 risk genotype.
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Shang N, Khan A, Polubriaginof F, Zanoni F, Mehl K, Fasel D, Drawz PE, Carrol RJ, Denny JC, Hathcock MA, Arruda-Olson AM, Peissig PL, Dart RA, Brilliant MH, Larson EB, Carrell DS, Pendergrass S, Verma SS, Ritchie MD, Benoit B, Gainer VS, Karlson EW, Gordon AS, Jarvik GP, Stanaway IB, Crosslin DR, Mohan S, Ionita-Laza I, Tatonetti NP, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. NPJ Digit Med 2021; 4:70. [PMID: 33850243 PMCID: PMC8044136 DOI: 10.1038/s41746-021-00428-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
Chronic Kidney Disease (CKD) represents a slowly progressive disorder that is typically silent until late stages, but early intervention can significantly delay its progression. We designed a portable and scalable electronic CKD phenotype to facilitate early disease recognition and empower large-scale observational and genetic studies of kidney traits. The algorithm uses a combination of rule-based and machine-learning methods to automatically place patients on the staging grid of albuminuria by glomerular filtration rate ("A-by-G" grid). We manually validated the algorithm by 451 chart reviews across three medical systems, demonstrating overall positive predictive value of 95% for CKD cases and 97% for healthy controls. Independent case-control validation using 2350 patient records demonstrated diagnostic specificity of 97% and sensitivity of 87%. Application of the phenotype to 1.3 million patients demonstrated that over 80% of CKD cases are undetected using ICD codes alone. We also demonstrated several large-scale applications of the phenotype, including identifying stage-specific kidney disease comorbidities, in silico estimation of kidney trait heritability in thousands of pedigrees reconstructed from medical records, and biobank-based multicenter genome-wide and phenome-wide association studies.
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Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, Marasà M, Kim H, Lim TY, Weng PL, Sánchez-Rodríguez E, Mitrotti A, Ahram DF, Zanoni F, Fasel DA, Westland R, Sampson MG, Zhang JY, Bodria M, Kil BH, Shril S, Gesualdo L, Torri F, Scolari F, Izzi C, van Wijk JA, Saraga M, Santoro D, Conti G, Barton DE, Dobson MG, Puri P, Furth SL, Warady BA, Pisani I, Fiaccadori E, Allegri L, Degl'Innocenti ML, Piaggio G, Alam S, Gigante M, Zaza G, Esposito P, Lin F, Simões-e-Silva AC, Brodkiewicz A, Drozdz D, Zachwieja K, Miklaszewska M, Szczepanska M, Adamczyk P, Tkaczyk M, Tomczyk D, Sikora P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Lozanovski VJ, Gucev Z, Ionita-Laza I, Stanaway IB, Crosslin DR, Wong CS, Hildebrandt F, Barasch J, Kenny EE, Loos RJ, Levy B, Ghiggeri GM, Hakonarson H, Latos-Bieleńska A, Materna-Kiryluk A, Darlow JM, Tasic V, Willer C, Kiryluk K, Sanna-Cherchi S, Mendelsohn CL, Gharavi AG. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. J Am Soc Nephrol 2021; 32:805-820. [PMID: 33597122 PMCID: PMC8017540 DOI: 10.1681/asn.2020050681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Vesicoureteral reflux (VUR) is a common, familial genitourinary disorder, and a major cause of pediatric urinary tract infection (UTI) and kidney failure. The genetic basis of VUR is not well understood. METHODS A diagnostic analysis sought rare, pathogenic copy number variant (CNV) disorders among 1737 patients with VUR. A GWAS was performed in 1395 patients and 5366 controls, of European ancestry. RESULTS Altogether, 3% of VUR patients harbored an undiagnosed rare CNV disorder, such as the 1q21.1, 16p11.2, 22q11.21, and triple X syndromes ((OR, 3.12; 95% CI, 2.10 to 4.54; P=6.35×10-8) The GWAS identified three study-wide significant and five suggestive loci with large effects (ORs, 1.41-6.9), containing canonical developmental genes expressed in the developing urinary tract (WDPCP, OTX1, BMP5, VANGL1, and WNT5A). In particular, 3.3% of VUR patients were homozygous for an intronic variant in WDPCP (rs13013890; OR, 3.65; 95% CI, 2.39 to 5.56; P=1.86×10-9). This locus was associated with multiple genitourinary phenotypes in the UK Biobank and eMERGE studies. Analysis of Wnt5a mutant mice confirmed the role of Wnt5a signaling in bladder and ureteric morphogenesis. CONCLUSIONS These data demonstrate the genetic heterogeneity of VUR. Altogether, 6% of patients with VUR harbored a rare CNV or a common variant genotype conferring an OR >3. Identification of these genetic risk factors has multiple implications for clinical care and for analysis of outcomes in VUR.
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Huffman J, Butler-Laporte G, Khan A, Drivas TG, Peloso GM, Nakanishi T, Verma A, Kiryluk K, Richards JB, Zeberg H. Alternative splicing of OAS1 alters the risk for severe COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.20.21254005. [PMID: 33791713 PMCID: PMC8010745 DOI: 10.1101/2021.03.20.21254005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A locus containing OAS1/2/3 has been identified as a risk locus for severe COVID-19 among Europeans ancestry individuals, with a protective haplotype of ∼75 kilobases derived from Neanderthals. Here, we show that among several potentially causal variants at this locus, a splice variant of OAS1 occurs in people of African ancestry independently of the Neanderthal haplotype and confers protection against COVID-19 of a magnitude similar to that seen in individuals without African ancestry.
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Moszczuk B, Kiryluk K, Pączek L, Mucha K. Membranous Nephropathy: From Research Bench to Personalized Care. J Clin Med 2021; 10:jcm10061205. [PMID: 33799372 PMCID: PMC7998937 DOI: 10.3390/jcm10061205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/15/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
Membranous nephropathy is a glomerulopathy that causes nephrotic syndrome and, in at least a third of cases, lasting end-stage kidney disease (ESKD). It is also a rare case of revolutionary changes in our understanding of the disease, that translates from scientific findings to real diagnosis and treatment recommendations in less than ten years. In this review we present: (1) a short history and traditional approach to patients with membranous nephropathy, (2) current recommendations and treatment options that have emerged in recent years, (3) findings of new studies, with a particular focus on serological/immunological methods, genomic and proteomic studies, still requiring validation. With further development in this field, membranous nephropathy may become one of the first nephrological conditions that apply a truly personalized approach with the omission of invasive measures such as kidney biopsy.
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Nakanishi T, Pigazzini S, Degenhardt F, Cordioli M, Butler-Laporte G, Maya-Miles D, Nafría-Jiménez B, Bouysran Y, Niemi M, Palom A, Ellinghaus D, Khan A, Martínez-Bueno M, Rolker S, Amitano S, Tato LR, Fava F, Spinner CD, Prati D, Bernardo D, Garcia F, Darcis G, Fernández-Cadenas I, Holter JC, Banales J, Frithiof R, Kiryluk K, Duga S, Asselta R, Pereira AC, Romero-Gómez M, Bujanda L, Hov JR, Migeotte I, Renieri A, Planas AM, Ludwig KU, Buti M, Rahmouni S, Alarcón-Riquelme ME, Schulte EC, Franke A, Karlsen TH, Valenti L, Zeberg H, Richards JB, Ganna A. Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.07.21252875. [PMID: 33758887 PMCID: PMC7987046 DOI: 10.1101/2021.03.07.21252875] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND There is considerable variability in COVID-19 outcomes amongst younger adults-and some of this variation may be due to genetic predisposition. We characterized the clinical implications of the major genetic risk factor for COVID-19 severity, and its age-dependent effect, using individual-level data in a large international multi-centre consortium. METHOD The major common COVID-19 genetic risk factor is a chromosome 3 locus, tagged by the marker rs10490770. We combined individual level data for 13,424 COVID-19 positive patients (N=6,689 hospitalized) from 17 cohorts in nine countries to assess the association of this genetic marker with mortality, COVID-19-related complications and laboratory values. We next examined if the magnitude of these associations varied by age and were independent from known clinical COVID-19 risk factors. FINDINGS We found that rs10490770 risk allele carriers experienced an increased risk of all-cause mortality (hazard ratio [HR] 1·4, 95% confidence interval [CI] 1·2-1·6) and COVID-19 related mortality (HR 1·5, 95%CI 1·3-1·8). Risk allele carriers had increased odds of several COVID-19 complications: severe respiratory failure (odds ratio [OR] 2·0, 95%CI 1·6-2·6), venous thromboembolism (OR 1·7, 95%CI 1·2-2·4), and hepatic injury (OR 1·6, 95%CI 1·2-2·0). Risk allele carriers ≤ 60 years had higher odds of death or severe respiratory failure (OR 2·6, 95%CI 1·8-3·9) compared to those > 60 years OR 1·5 (95%CI 1·3-1·9, interaction p-value=0·04). Amongst individuals ≤ 60 years who died or experienced severe respiratory COVID-19 outcome, we found that 31·8% (95%CI 27·6-36·2) were risk variant carriers, compared to 13·9% (95%CI 12·6-15·2%) of those not experiencing these outcomes. Prediction of death or severe respiratory failure among those ≤ 60 years improved when including the risk allele (AUC 0·82 vs 0·84, p=0·016) and the prediction ability of rs10490770 risk allele was similar to, or better than, most established clinical risk factors. INTERPRETATION The major common COVID-19 risk locus on chromosome 3 is associated with increased risks of morbidity and mortality-and these are more pronounced amongst individuals ≤ 60 years. The effect on COVID-19 severity was similar to, or larger than most established risk factors, suggesting potential implications for clinical risk management. FUNDING Funding was obtained by each of the participating cohorts individually.
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Sanchez-Rodriguez E, Southard CT, Kiryluk K. GWAS-Based Discoveries in IgA Nephropathy, Membranous Nephropathy, and Steroid-Sensitive Nephrotic Syndrome. Clin J Am Soc Nephrol 2021; 16:458-466. [PMID: 32680915 PMCID: PMC8011010 DOI: 10.2215/cjn.14031119] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Over the past decade, genome-wide association studies (GWAS) have emerged as a powerful tool to understand the genetic basis of complex traits in humans. The GWAS approach has been successfully applied to primary glomerular disorders, providing numerous novel insights into the genetic architecture of IgA nephropathy, membranous nephropathy, and steroid-sensitive nephrotic syndrome. IgA nephropathy appears to have a highly complex polygenic architecture, with nearly 20 genome-wide significant loci of small-to-moderate effects discovered to date. In contrast, the genetic susceptibility to membranous nephropathy and steroid-sensitive nephrotic syndrome appears to be driven by a small number of large-effect loci. The MHC locus on chromosome 6p21 is strongly associated with genetic susceptibility to all major types of immune-mediated glomerulopathies. However, a distinct set of classical HLA alleles is associated with each individual disease type, pinpointing to specific immune mechanisms underlying each of these conditions. Additional insights from the discovery of non-HLA risk loci reinforced the role of innate and adaptive immunity in the pathogenesis of these disorders, and highlighted important susceptibility overlaps between glomerular and other autoimmune and inflammatory conditions. Despite these initial successes, much larger GWAS and sequencing studies are still needed for each individual glomerular disease type. Increased power will be critical to comprehensively test for genetic effects across the full spectrum of allelic frequencies, to detect gene-gene and gene-environment interactions, and to potentially improve the performance of polygenic risk predictors. Moreover, the existing studies are limited mostly to European and East Asian populations, stressing the urgency to expand genetic discovery efforts to more diverse populations worldwide.
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Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, Kang HM, O'Dushlaine C, Yadav A, Mansfield AJ, Li AH, Watanabe K, Gurski L, McCarthy SE, Locke AE, Khalid S, O'Keeffe S, Mbatchou J, Chazara O, Huang Y, Kvikstad E, O'Neill A, Nioi P, Parker MM, Petrovski S, Runz H, Szustakowski JD, Wang Q, Wong E, Cordova-Palomera A, Smith EN, Szalma S, Zheng X, Esmaeeli S, Davis JW, Lai YP, Chen X, Justice AE, Leader JB, Mirshahi T, Carey DJ, Verma A, Sirugo G, Ritchie MD, Rader DJ, Povysil G, Goldstein DB, Kiryluk K, Pairo-Castineira E, Rawlik K, Pasko D, Walker S, Meynert A, Kousathanas A, Moutsianas L, Tenesa A, Caulfield M, Scott R, Wilson JF, Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MA. A catalog of associations between rare coding variants and COVID-19 outcomes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.10.28.20221804. [PMID: 33655273 PMCID: PMC7924298 DOI: 10.1101/2020.10.28.20221804] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.
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Guo J, Yuan C, Shang N, Zheng T, Bello NA, Kiryluk K, Weng C, Wang S. Similarity-based health risk prediction using Domain Fusion and electronic health records data. J Biomed Inform 2021; 116:103711. [PMID: 33610881 DOI: 10.1016/j.jbi.2021.103711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/01/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
Electronic Health Record (EHR) data represents a valuable resource for individualized prospective prediction of health conditions. Statistical methods have been developed to measure patient similarity using EHR data, mostly using clinical attributes. Only a handful of recent methods have combined clinical analytics with other forms of similarity analytics, and no unified framework exists yet to measure comprehensive patient similarity. Here, we developed a generic framework named Patient similarity based on Domain Fusion (PsDF). PsDF performs patient similarity assessment on each available domain data separately, and then integrate the affinity information over various domains into a comprehensive similarity metric. We used the integrated patient similarity to support outcome prediction by assigning a risk score to each patient. With extensive simulations, we demonstrated that PsDF outperformed existing risk prediction methods including a random forest classifier, a regression-based model, and a naïve similarity method, especially when heterogeneous signals exist across different domains. Using PsDF and EHR data extracted from the data warehouse of Columbia University Irving Medical Center, we developed two different clinical prediction tools for two different clinical outcomes: incident cases of end stage kidney disease (ESKD) and severe aortic stenosis (AS) requiring valve replacement. We demonstrated that our new prediction method is scalable to large datasets, robust to random missingness, and generalizable to diverse clinical outcomes.
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Moldoveanu Z, Suzuki H, Reily C, Satake K, Novak L, Xu N, Huang ZQ, Knoppova B, Khan A, Hall S, Yanagawa H, Brown R, Winstead CJ, O'Quinn DB, Weinmann A, Gharavi AG, Kiryluk K, Julian BA, Weaver CT, Suzuki Y, Novak J. Experimental evidence of pathogenic role of IgG autoantibodies in IgA nephropathy. J Autoimmun 2021; 118:102593. [PMID: 33508637 DOI: 10.1016/j.jaut.2021.102593] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 01/13/2023]
Abstract
BACKGROUND IgA nephropathy is thought to be an autoimmune disease wherein galactose-deficient IgA1 (Gd-IgA1) is recognized by IgG autoantibodies, resulting in formation and renal accumulation of nephritogenic immune complexes. Although this hypothesis is supported by recent findings that, in renal immunodeposits of IgA nephropathy patients, IgG is enriched for Gd-IgA1-specific autoantibodies, experimental proof is still lacking. METHODS IgG isolated from sera of IgA nephropathy patients or produced as a recombinant IgG (rIgG) was mixed with human Gd-IgA1 to form immune complexes. IgG from healthy individuals served as a control. Nude and SCID mice were injected with human IgG and Gd-IgA1, in immune complexes or individually, and their presence in kidneys was ascertained by immunofluorescence. Pathologic changes in the glomeruli were evaluated by quantitative morphometry and exploratory transcriptomic profiling was performed by RNA-Seq. RESULTS Immunodeficient mice injected with Gd-IgA1 mixed with IgG autoantibodies from patients with IgA nephropathy, but not Gd-IgA1 mixed with IgG from healthy individuals, displayed IgA, IgG, and mouse complement C3 glomerular deposits and mesangioproliferative glomerular injury with hematuria and proteinuria. Un-complexed Gd-IgA1 or IgG did not induce pathological changes. Moreover, Gd-IgA1-rIgG immune complexes injected into immunodeficient mice induced histopathological changes characteristic of human disease. Exploratory transcriptome profiling of mouse kidney tissues indicated that these immune complexes altered gene expression of multiple pathways, in concordance with the changes observed in kidney biopsies of patients with IgA nephropathy. CONCLUSIONS This study provides the first in vivo evidence for a pathogenic role of IgG autoantibodies specific for Gd-IgA1 in the pathogenesis of IgA nephropathy.
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Povysil G, Butler-Laporte G, Shang N, Weng C, Khan A, Alaamery M, Nakanishi T, Zhou S, Forgetta V, Eveleigh R, Bourgey M, Aziz N, Jones S, Knoppers B, Scherer S, Strug L, Lepage P, Ragoussis J, Bourque G, Alghamdi J, Aljawini N, Albes N, Al-Afghani HM, Alghamdi B, Almutair M, Mahmoud ES, Safie LA, Bardisy HE, Al Harthi FS, Alshareef A, Suliman BA, Alqahtani S, AlMalik A, Alrashed MM, Massadeh S, Mooser V, Lathrop M, Arabi Y, Mbarek H, Saad C, Al-Muftah W, Badji R, Al Thani A, Ismail SI, Gharavi AG, Abedalthagafi MS, Richards JB, Goldstein DB, Kiryluk K. Failure to replicate the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.12.18.20248226. [PMID: 33398295 PMCID: PMC7781338 DOI: 10.1101/2020.12.18.20248226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,934 COVID-19 cases (713 with severe and 1,221 with mild disease) and 15,251 ancestry-matched population controls across four independent COVID-19 biobanks. We then tested if rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only one rare pLOF mutation across these genes amongst 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We find no evidence of association of rare loss-of-function variants in the proposed 13 candidate genes with severe COVID-19 outcomes.
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Poggio ED, McClelland RL, Blank KN, Hansen S, Bansal S, Bomback AS, Canetta PA, Khairallah P, Kiryluk K, Lecker SH, McMahon GM, Palevsky PM, Parikh S, Rosas SE, Tuttle K, Vazquez MA, Vijayan A, Rovin BH. Systematic Review and Meta-Analysis of Native Kidney Biopsy Complications. Clin J Am Soc Nephrol 2020; 15:1595-1602. [PMID: 33060160 PMCID: PMC7646247 DOI: 10.2215/cjn.04710420] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/21/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND AND OBJECTIVES Native kidney biopsies are commonly performed in the diagnosis of acute kidney diseases and CKD. Because of the invasive nature of the procedure, bleeding-related complications are not uncommon. The National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases-sponsored Kidney Precision Medicine Project requires that all participants undergo a kidney biopsy; therefore, the objective of this analysis was to study complication rates of native kidney biopsies performed using automated devices under kidney imaging. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS This is a systematic review and meta-analysis of the literature published from January 1983 to March 2018. The initial PubMed search yielded 1139 manuscripts. Using predetermined selection criteria, 87 manuscripts were included in the final analysis. A random effects meta-analysis for proportions was used to obtain combined estimates of complication rates. Freeman-Tukey double-arcsine transformations were used to stabilize variance as complications were rare. RESULTS A total of 118,064 biopsies were included in this study. Patient age ranged from 30 to 79 years, and 45% of patients were women. On the basis of our meta-analysis, pain at the site of biopsy is estimated to occur in 4.3% of biopsied patients, hematomas are estimated to occur in 11%, macroscopic hematuria is estimated to occur in 3.5%, bleeding requiring blood transfusions is estimated to occur in 1.6%, and interventions to stop bleeding are estimated to occur in only 0.3%. Death attributed to native kidney biopsy was a rare event, occurring only in an estimated 0.06% of all biopsies but only 0.03% of outpatient biopsies. Complication rates were higher in hospitalized patients and in those with acute kidney disease. The reported complications varied on the basis of study type and geographic location. CONCLUSIONS Although the native kidney biopsy is an invasive diagnostic procedure, the rates of bleeding complications are low. Albeit rare, death can occur postbiopsy. Complications are more frequently seen after kidney biopsies of hospitalized patients with AKI.
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Khan A, Hayes M, Connolly J, Mentch F, Sleiman P, Hakonarson H, Wang C, Hripcsak G, Kiryluk K, Petukhova L. 265 Genome-wide association study of hidradenitis suppurativa in a multi-ethnic cohort. J Invest Dermatol 2020. [DOI: 10.1016/j.jid.2020.03.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zanoni F, Verbitsky M, Carlassara L, Marasa M, Kiryluk K, Gharavi A. P0355FAMILY HISTORY OF COMPLEX TRAITS IN THE CUREGN COHORT: ASSOCIATIONS WITH RENAL FUNCTION, COMORBIDITY BURDEN AND DISEASE PROGRESSION. Nephrol Dial Transplant 2020. [DOI: 10.1093/ndt/gfaa142.p0355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background and Aims
Family history (FHx) of complex traits may reflect shared genetic/environmental risk. Few studies suggest associations with increased risk of comorbidities and worsening renal function, but this has not been examined in primary glomerulopathies (GNs). Herein, we studied the association of FHx of complex traits with presentation patterns, comorbidities and disease progression in a prospective cohort of patients with primary GN.
Method
The Cure Glomerulopathy Networ (CureGN) is a prospective multi-center observational study of GN patients (N=2474) affected by biopsy-proven Focal Segmental Glomerulosclerosis (FSGS), Minimal Change Disease (MCD), Membranous Nephropathy (MN) and IgA Nephropathy/Vasculitis (IgAN/V). Associations of self-reported FHx of diabetes (DM), coronary artery disease (CAD), cancer (C), clotting disorders (CD), and autoimmune diseases (AD) with eGFR, UPCR at diagnosis, and comorbidities prevalence were studied using linear and logistic regression models adjusted for age, sex, ethnicity, race, BMI and other relevant clinical covariates. Associations between FHx and ESRD/40%eGFR reduction were investigated with multivariate Cox models.
Results
FHx of DM was associated with lower eGFR and higher UPCR at diagnosis in the entire cohort (p=0.006 and p=0.03), lower eGFR in FSGS (p=0.02) and higher UPCR in IgAN/V (p=0.01). Regarding comorbidity burden (Table 1), FHx of DM was associated with higher prevalence of DM, heart failure and infections requiring hospitalization, FHx of C with cancer, FHx of CD with higher prevalence of thrombosis and FHx of AD with inflammatory bowel, celiac diseases, asthma and drug allergies. At the survival analysis adjusted for age, sex, ethnicity, race, BMI, diagnosis group, eGFR and UPCR at diagnosis, DM, hypertension, use of immunosuppressants and RAAS-inhibitors, FHx of DM was associated with higher risk of the composite outcome of ESRD/40%eGFR reduction in the entire cohort (HR 1.39, 95%CI 1.07-1.81, p=0.01), and specifically in FSGS (HR 1.76, 95%CI 1.08-2.85, p=0.02) and in the paediatric subgroup (HR 1.98, 95%CI 1.04-3.80, p=0.04).
Conclusion
FHx of complex traits are associated with higher prevalence of specific comorbidities. FHx of DM identifies patients with lower eGFR at diagnosis, higher prevalence of infections and higher risk of renal disease progression. These findings, which need to be confirmed in other cohorts, suggest that FHx could be an additional useful parameter for risk stratification and management of primary GN.
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Delbarba E, Marasa M, Canetta PA, Piva SE, Chatterjee D, Kil BH, Mu X, Gibson KL, Hladunewich MA, Hogan JJ, Julian BA, Kidd JM, Laurin LP, Nachman PH, Rheault MN, Rizk DV, Sanghani NS, Trachtman H, Wenderfer SE, Gharavi AG, Bomback AS, Ahn W, Appel GB, Babayev R, Batal I, Bomback AS, Brown E, Campenot ES, Canetta P, Chan B, Chatterjee D, D’Agati VD, Delbarba E, Fernandez H, Foroncewicz B, Gharavi AG, Ghiggeri GM, Hines WH, Jain NG, Kil BH, Kiryluk K, Lau WL, Lin F, Lugani F, Marasa M, Markowitz G, Mohan S, Mu X, Mucha K, Nickolas TL, Piva S, Radhakrishnan J, Rao MK, Sanna-Cherchi S, Santoriello D, Stokes MB, Yu N, Valeri AM, Zviti R, Greenbaum LA, Smoyer WE, Al-Uzri A, Ashoor I, Aviles D, Baracco R, Barcia J, Bartosh S, Belsha C, Bowers C, Braun MC, Chishti A, Claes D, Cramer C, Davis K, Erkan E, Feig D, Freundlich M, Gbadegesin R, Hanna M, Hidalgo G, Hunley TE, Jain A, Kallash M, Khalid M, Klein JB, Lane JC, Mahan J, Mathews N, Nester C, Pan C, Patterson L, Patel H, Revell A, Rheault MN, Silva C, Sreedharan R, Srivastava T, Steinke J, Twombley K, Wenderfer SE, Vasylyeva TL, Weaver DJ, Wong CS, Almaani S, Ayoub I, Budisavljevic M, Derebail V, Fatima H, Falk R, Fogo A, Gehr T, Gibson K, Glenn D, Harris R, Hogan S, Jain K, Jennette JC, Julian B, Kidd J, Laurin LP, Massey HD, Mottl A, Nachman P, Nadasdy T, Novak J, Parikh S, Pichette V, Poulton C, Powell TB, Renfrow M, Rizk D, Rovin B, Royal V, Saha M, Sanghani N, Self S, Adler S, Alpers C, Matar RB, Brown E, Cattran D, Choi M, Dell KM, Dukkipati R, Fervenza FC, Fornoni A, Gadegbeku C, Gipson P, Hasely L, Hingorani S, Hladunewich M, Hogan J, Holzman LB, Jefferson JA, Jhaveri K, Johnstone DB, Kaskel F, Kogan A, Kopp J, Lafayette R, Lemley KV, Malaga-Dieguez L, Meyers K, Neu A, O’Shaughnessy MM, O’Toole JF, Parekh R, Reich H, Reidy K, Rondon H, Sambandam KK, Sedor JR, Selewski DT, Sethna CB, Schelling J, Sperati JC, Swiatecka-Urban A, Trachtman H, Tuttle KR, Weisstuch J, Vento S, Zhdanova O, Gillespie B, Gipson DS, Hill-Callahan P, Helmuth M, Herreshoff E, Kretzler M, Lienczewski C, Mansfield S, Mariani L, Nast CC, Robinson BM, Troost J, Wladkowski M, Zee J, Zinsser D, Guay-Woodford LM. Persistent Disease Activity in Patients With Long-Standing Glomerular Disease. Kidney Int Rep 2020; 5:860-871. [PMID: 32518868 PMCID: PMC7270998 DOI: 10.1016/j.ekir.2020.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/11/2020] [Accepted: 03/09/2020] [Indexed: 11/03/2022] Open
Abstract
Introduction Methods Results Conclusion
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Batal I, Vasilescu ER, Dadhania DM, Adel AA, Husain SA, Avasare R, Serban G, Santoriello D, Khairallah P, Patel A, Moritz MJ, Latulippe E, Riopel J, Khallout K, Swanson SJ, Bomback AS, Mohan S, Ratner L, Radhakrishnan J, Cohen DJ, Appel GB, Stokes MB, Markowitz GS, Seshan SV, De Serres SA, Andeen N, Loupy A, Kiryluk K, D'Agati VD. Association of HLA Typing and Alloimmunity With Posttransplantation Membranous Nephropathy: A Multicenter Case Series. Am J Kidney Dis 2020; 76:374-383. [PMID: 32359820 PMCID: PMC7483441 DOI: 10.1053/j.ajkd.2020.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022]
Abstract
RATIONALE & OBJECTIVES Posttransplantation membranous nephropathy (MN) represents a rare complication of kidney transplantation that can be classified as recurrent or de novo. The clinical, pathologic, and immunogenetic characteristics of posttransplantation MN and the differences between de novo and recurrent MN are not well understood. STUDY DESIGN Multicenter case series. SETTING & PARTICIPANTS We included 77 patients from 5 North American and European medical centers with post-kidney transplantation MN (27 de novo and 50 recurrent). Patients with MN in the native kidney who received kidney allografts but did not develop recurrent MN were used as nonrecurrent controls (n = 43). To improve understanding of posttransplantation MN, we compared de novo MN with recurrent MN and then contrasted recurrent MN with nonrecurrent controls. FINDINGS Compared with recurrent MN, de novo MN was less likely to be classified as primary MN (OR, 0.04; P < 0.001) and had more concurrent antibody-mediated rejection (OR, 12.0; P < 0.001) and inferior allograft survival (HR for allograft failure, 3.2; P = 0.007). HLA-DQ2 and HLA-DR17 antigens were more common in recipients with recurrent MN compared with those with de novo MN; however, the frequency of these recipient antigens in recurrent MN was similar to that in nonrecurrent MN controls. Among the 93 kidney transplant recipients with native kidney failure attributed to MN, older recipient age (HR per each year older, 1.03; P = 0.02), recipient HLA-A3 antigen (HR, 2.5; P = 0.003), steroid-free immunosuppressive regimens (HR, 2.84; P < 0.001), and living related allograft (HR, 1.94; P = 0.03) were predictors of MN recurrence. LIMITATIONS Retrospective case series, limited sample size due to rarity of the disease, nonstandardized nature of data collection and biopsies. CONCLUSIONS De novo and recurrent MN likely represent separate diseases. De novo MN is associated with humoral alloimmunity and guarded outcome. Potential predisposing factors for recurrent MN include recipients who are older, recipient HLA-A3 antigen, steroid-free immunosuppressive regimen, and living related donor kidney.
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Li Y, Groopman EE, D'Agati V, Prakash S, Zhang J, Mizerska-Wasiak M, Caliskan Y, Fasel D, Karnib HH, Bono L, Omran SA, Sabban EA, Kiryluk K, Caridi G, Ghiggeri GM, Sanna-Cherchi S, Scolari F, Gharavi AG. Type IV Collagen Mutations in Familial IgA Nephropathy. Kidney Int Rep 2020; 5:1075-1078. [PMID: 32647767 PMCID: PMC7335950 DOI: 10.1016/j.ekir.2020.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/23/2020] [Accepted: 04/10/2020] [Indexed: 01/15/2023] Open
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Nestor JG, Marasa M, Milo-Rasouly H, Groopman EE, Husain SA, Mohan S, Fernandez H, Aggarwal VS, Ahram DF, Vena N, Bogyo K, Bomback AS, Radhakrishnan J, Appel GB, Ahn W, Cohen DJ, Canetta PA, Dube GK, Rao MK, Morris HK, Crew RJ, Sanna-Cherchi S, Kiryluk K, Gharavi AG. Pilot Study of Return of Genetic Results to Patients in Adult Nephrology. Clin J Am Soc Nephrol 2020; 15:651-664. [PMID: 32299846 PMCID: PMC7269209 DOI: 10.2215/cjn.12481019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/12/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND OBJECTIVES Actionable genetic findings have implications for care of patients with kidney disease, and genetic testing is an emerging tool in nephrology practice. However, there are scarce data regarding best practices for return of results and clinical application of actionable genetic findings for kidney patients. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We developed a return of results workflow in collaborations with clinicians for the retrospective recontact of adult nephrology patients who had been recruited into a biobank research study for exome sequencing and were identified to have medically actionable genetic findings. RESULTS Using this workflow, we attempted to recontact a diverse pilot cohort of 104 nephrology research participants with actionable genetic findings, encompassing 34 different monogenic etiologies of nephropathy and five single-gene disorders recommended by the American College of Medical Genetics and Genomics for return as medically actionable secondary findings. We successfully recontacted 64 (62%) participants and returned results to 41 (39%) individuals. In each case, the genetic diagnosis had meaningful implications for the patients' nephrology care. Through implementation efforts and qualitative interviews with providers, we identified over 20 key challenges associated with returning results to study participants, and found that physician knowledge gaps in genomics was a recurrent theme. We iteratively addressed these challenges to yield an optimized workflow, which included standardized consultation notes with tailored management recommendations, monthly educational conferences on core topics in genomics, and a curated list of expert clinicians for patients requiring extranephrologic referrals. CONCLUSIONS Developing the infrastructure to support return of genetic results in nephrology was resource-intensive, but presented potential opportunities for improving patient care. PODCAST This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2020_04_16_12481019.mp3.
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Yamada K, Huang ZQ, Raska M, Reily C, Anderson JC, Suzuki H, Kiryluk K, Gharavi AG, Julian BA, Willey CD, Novak J. Leukemia Inhibitory Factor Signaling Enhances Production of Galactose-Deficient IgA1 in IgA Nephropathy. KIDNEY DISEASES 2020; 6:168-180. [PMID: 32523959 DOI: 10.1159/000505748] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022]
Abstract
Objectives IgA nephropathy (IgAN) is thought to involve an autoimmune process wherein galactose-deficient IgA1 (Gd-IgA1), recognized as autoantigen by autoantibodies, forms pathogenic immune complexes. Mounting evidence has implicated abnormal activation of some protein-tyrosine kinases (PTKs) in IgAN. Furthermore, genome-wide association studies (GWAS) of IgAN provided insight into disease pathobiology and genetics. A GWAS locus on chromosome 22q12 contains genes encoding leukemia inhibitory factor (LIF) and oncostatin M, interleukin (IL)-6-related cytokines implicated in mucosal immunity and inflammation. We have previously shown that IL-6 mediates overproduction of Gd-IgA1 through aberrant STAT3 activation. Here, we show that LIF enhanced production of Gd-IgA1 in IgA1-secreting cells of patients with IgAN and provide initial analyses of LIF signaling. Methods We characterized LIF signaling that is involved in the overproduction of Gd-IgA1, using IgA1-secreting cell lines derived from peripheral blood of patients with IgAN and healthy controls (HC). We used global PTK activity profiling, immunoblotting, lectin ELISA, and siRNA knock-down. Results LIF stimulation did not significantly affect production of total IgA1 in IgA1-secreting cells from patients with IgAN or HC. However, LIF increased production of Gd-IgA1, but only in the cells from patients with IgAN. LIF stimulation enhanced phosphorylation of STAT1 in IgA1-secreting cells from patients with IgAN to a higher degree than in the cells from HC. siRNA knock-down of STAT1 blocked LIF-mediated overproduction of Gd-IgA1. Unexpectedly, this abnormal phosphorylation of STAT1 in IgA1-secreting cells from patients with IgAN was not mediated by JAK, but rather involved activation of Src-family PTKs (SFKs). Conclusion Abnormal LIF/STAT1 signaling represents another pathway potentially leading to overproduction of Gd-IgA1 in IgAN, providing possible explanation for the phenotype associated with chromosome 22q12 GWAS locus. Abnormal LIF/STAT1 signaling and the associated SFKs may represent potential diagnostic and/or therapeutic targets in IgAN.
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Xu D, Wang C, Kiryluk K, Buxbaum JD, Ionita-Laza I. Co-localization between Sequence Constraint and Epigenomic Information Improves Interpretation of Whole-Genome Sequencing Data. Am J Hum Genet 2020; 106:513-524. [PMID: 32243819 PMCID: PMC7118583 DOI: 10.1016/j.ajhg.2020.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/09/2020] [Indexed: 10/24/2022] Open
Abstract
The identification of functional regions in the noncoding human genome is difficult but critical in order to gain understanding of the role noncoding variation plays in gene regulation in human health and disease. We describe here a co-localization approach that aims to identify constrained sequences that co-localize with tissue- or cell-type-specific regulatory regions, and we show that the resulting score is particularly well suited for the identification of rare regulatory variants. For 127 tissues and cell types in the ENCODE/Roadmap Epigenomics Project, we provide catalogs of putative tissue- or cell-type-specific regulatory regions under sequence constraint. We use the newly developed co-localization score for brain tissues to score de novo mutations in whole genomes from 1,902 individuals affected with autism spectrum disorder (ASD) and their unaffected siblings in the Simons Simplex Collection. We show that noncoding de novo mutations near genes co-expressed in midfetal brain with high confidence ASD risk genes, and near FMRP gene targets are more likely to be in co-localized regions if they occur in ASD probands versus in their unaffected siblings. We also observed a similar enrichment for mutations near lincRNAs, previously shown to co-express with ASD risk genes. Additionally, we provide strong evidence that prioritized de novo mutations in autism probands point to a small set of well-known ASD genes, the disruption of which produces relevant mouse phenotypes such as abnormal social investigation and abnormal discrimination/associative learning, unlike the de novo mutations in unaffected siblings. The genome-wide co-localization results are available online.
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Fishman CE, Mohebnasab M, van Setten J, Zanoni F, Wang C, Deaglio S, Amoroso A, Callans L, van Gelder T, Lee S, Kiryluk K, Lanktree MB, Keating BJ. Genome-Wide Study Updates in the International Genetics and Translational Research in Transplantation Network (iGeneTRAiN). Front Genet 2019; 10:1084. [PMID: 31803228 PMCID: PMC6873800 DOI: 10.3389/fgene.2019.01084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
The prevalence of end-stage renal disease (ESRD) and the number of kidney transplants performed continues to rise every year, straining the procurement of deceased and living kidney allografts and health systems. Genome-wide genotyping and sequencing of diseased populations have uncovered genetic contributors in substantial proportions of ESRD patients. A number of these discoveries are beginning to be utilized in risk stratification and clinical management of patients. Specifically, genetics can provide insight into the primary cause of chronic kidney disease (CKD), the risk of progression to ESRD, and post-transplant outcomes, including various forms of allograft rejection. The International Genetics & Translational Research in Transplantation Network (iGeneTRAiN), is a multi-site consortium that encompasses >45 genetic studies with genome-wide genotyping from over 51,000 transplant samples, including genome-wide data from >30 kidney transplant cohorts (n = 28,015). iGeneTRAiN is statistically powered to capture both rare and common genetic contributions to ESRD and post-transplant outcomes. The primary cause of ESRD is often difficult to ascertain, especially where formal biopsy diagnosis is not performed, and is unavailable in ∼2% to >20% of kidney transplant recipients in iGeneTRAiN studies. We overview our current copy number variant (CNV) screening approaches from genome-wide genotyping datasets in iGeneTRAiN, in attempts to discover and validate genetic contributors to CKD and ESRD. Greater aggregation and analyses of well phenotyped patients with genome-wide datasets will undoubtedly yield insights into the underlying pathophysiological mechanisms of CKD, leading the way to improved diagnostic precision in nephrology.
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Neugut YD, Mohan S, Gharavi AG, Kiryluk K. Cases in Precision Medicine: APOL1 and Genetic Testing in the Evaluation of Chronic Kidney Disease and Potential Transplant. Ann Intern Med 2019; 171:659-664. [PMID: 31590185 PMCID: PMC7441647 DOI: 10.7326/m19-1389] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
This article discusses potential indications for genetic testing in an African American patient with chronic kidney disease who is being evaluated for a kidney transplant. Two known risk variants in the APOL1 (apolipoprotein L1) gene predispose to kidney disease and are found almost exclusively in persons of African ancestry. APOL1 risk variants are considered, including whether clinicians should incorporate genetic testing in the screening process for living kidney donors. In addition to APOL1 testing, the role of diagnostic exome sequencing in evaluating potential transplant recipients and donors with a positive family history of kidney disease is discussed.
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