| Literature DB >> 31803228 |
Claire E Fishman1, Maede Mohebnasab1, Jessica van Setten2, Francesca Zanoni3, Chen Wang3, Silvia Deaglio4,5, Antonio Amoroso4,5, Lauren Callans1, Teun van Gelder6, Sangho Lee7, Krzysztof Kiryluk3, Matthew B Lanktree8, Brendan J Keating1.
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.Entities:
Keywords: GWAS; genomics; kidney disease; whole exome sequencing analyses; whole genome sequencing
Year: 2019 PMID: 31803228 PMCID: PMC6873800 DOI: 10.3389/fgene.2019.01084
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Figure 1Geographical Map of Current iGeneTRAiN Kidney Sites and Sub-sites.
Primary cause of ESRD in iGeneTRAiN kidney cohorts.
| Primary Cause of ESRD | University of Pennsylvania | Transplant-LINES | BioMARGIN‡ | Swiss Transplant Cohort Study† | WTCCC-3† | Go-CAR | Columbia Transplant Biobank | Torino Transplant Cohort‡ | Rotterdam‡ | DeKAF* | Gen03* | Scripps | Leiden* | Vienna | Vanderbilt | Seoul†,‡ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 310 (26.8%) | 51 (4.0%) | 115 (8.5%) | 116 (7.4%) | 186 (7.3%) | 219 (37.2%) | 176 (15.6%) | 22 (3.3%) | – (17.0%) | 553 (28.5%) | 178 (22.8%) | – | 22 (25.0%) | 113 (12.8%) | – | 240 (20.9%) | |
| 202 (17.5%) | 104 (8.2%) | 67 (4.9%) | 183 (11.6%) | 111 (4.4%) | 109 (18.5%) | 123 (10.9%) | 36 (5.4%) | – (13.0%) | 132 (6.8%) | 43 (5.5%) | – | – | 88 (10.0%) | – | 244 (21.3%) | |
| 340 (29.4%) | 401 (31.6%) | 329 (24.2%) | 433 (27.5%) | 482 (19.0%) | 111 (18.9%) | 431 (38.3%) | 198 (29.7%) | – (20.0%) | 446 (23.0%) | 226 (29.0%) | – | 14 (15.9%) | 296 (33.6%) | – | 251 (21.9%) | |
| 3 (0.3%) | 1 (0.1%) | 3 (0.2%) | 0 (0.0%) | 8 (0.3%) | 0 (0.0%) | 5 (0.4%) | 2 (0.3%) | – (4.0%) | – | – | – | – | 4 (0.5%) | – | 0 (0.0%) | |
| 31 (2.7%) | 107 (8.4%) | 79 (5.8%) | 85 (5.4%) | 203 (8.0%) | 22 (3.7%) | 17 (1.5%) | 87 (13.1%) | – (6.0%) | – | – | – | – | 56 (6.4%) | – | 6 (0.5%) | |
| 19 (1.6%) | 68 (5.4%) | 57 (4.2%) | 40 (2.5%) | 26 (1.0%) | 14 (2.4%) | 58 (5.2%) | 31 (4.7%) | – (3.0%) | – | – | – | – | 18 (2.1%) | – | 0 (0.0%) | |
| 143 (12.4%) | 235 (18.5%) | 245 (18.0%) | 327 (20.8%) | 361 (14.2%) | 67 (11.4%) | 145 (12.9%) | 110 (16.5%) | – (14.0%) | 308 (15.9%) | 123 (15.8%) | – | 52 (59.1%) | 147 (16.7%) | – | 25 (2.2%) | |
| 2 (1.7%) | 15 (1.2%) | 19 (1.4%) | 46 (2.9%) | 16 (0.6%) | 18 (3.1%) | 31 (2.8%) | 9 (1.4%) | – (1.0%) | – | – | – | – | 25 (2.8%) | – | 4 (0.4%) | |
| 5 (0.4%) | 6 (0.5%) | 21 (1.5%) | 0 (0.0%) | 20 (0.8%) | 2 (0.3%) | 6 (0.5%) | 5 (0.8%) | – (3.0%) | – | – | – | – | 14 (1.6%) | – | 0 (0.0%) | |
| 50 (4.3%) | 59 (4.6%) | 64 (4.7%) | 344 (21.9%) | 165 (6.5%) | 12 (2.0%) | 9 (0.8%) | 6 (0.9%) | – (10.0%) | 432 (22.3%) | 166 (21.3%) | – | – | 17 (1.9%) | – | 0 (0.0%) | |
| 29 (2.5%) | 168 (13.2%) | 161 (11.8%) | 0 (0.0%) | 0 (0.0%) | 14 (2.4%) | 125 (11.1%) | 160 (24.0%) | – (9.0%) | – | – | – | – | 100 (11.4%) | – | 185 (16.1%) | |
| 4 (0.4%) | 56 (4.4%) | 200 (14.7%) | 0 (0.0%) | 966 (38.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | – (0.0%) | 67 (3.5%) | 44 (5.6%) | – | – | 2 (0.2%) | – | 193 (16.8%) | |
*Data includes Caucasian only ancestry. ‡Recently added iGeneTRAiN kidney cohort.
†National level iGeneTRAiN kidney cohort. See for full breakdown of primary cause of ESRD.
Figure 2(A) Copy Number Variant Region Analyses of the NPHP1 locus using the Axiom Analysis Suite 4.0 to call diploid state (CN=2), one copy deletion state (CN=1), two copy deletion state (CN=0), and duplication state (CN=3). The x-axis shows the chromosomal location on Chromosome 2 while the y-axis shows the standard Log2Ratio intensity. (B) In depth illustration of the duplication (CN=3) state.