Common and Rare Variants Associated with Kidney Stones and Biochemical Traits
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ARTICLE Received 26 Jan 2015 | Accepted 2 Jul 2015 | Published 14 Aug 2015 DOI: 10.1038/ncomms8975 OPEN Common and rare variants associated with kidney stones and biochemical traits Asmundur Oddsson1,*, Patrick Sulem1,*, Hannes Helgason1,2, Vidar O. Edvardsson3,4,5, Gudmar Thorleifsson1, Gardar Sveinbjo¨rnsson1, Eik Haraldsdottir1, Gudmundur I. Eyjolfsson6, Olof Sigurdardottir7, Isleifur Olafsson8, Gisli Masson1, Hilma Holm1, Daniel F. Gudbjartsson1,2, Unnur Thorsteinsdottir1,4, Olafur S. Indridason9, Runolfur Palsson4,5,9 & Kari Stefansson1,4 Kidney stone disease is a complex disorder with a strong genetic component. We conducted a genome-wide association study of 28.3 million sequence variants detected through whole-genome sequencing of 2,636 Icelanders that were imputed into 5,419 kidney stone cases, including 2,172 cases with a history of recurrent kidney stones, and 279,870 controls. We identify sequence variants associating with kidney stones at ALPL (rs1256328[T], odds ratio (OR) ¼ 1.21, P ¼ 5.8  10 À 10) and a suggestive association at CASR (rs7627468[A], OR ¼ 1.16, P ¼ 2.0  10 À 8). Focusing our analysis on coding sequence variants in 63 genes with preferential kidney expression we identify two rare missense variants SLC34A1 p.Tyr489Cys (OR ¼ 2.38, P ¼ 2.8  10 À 5) and TRPV5 p.Leu530Arg (OR ¼ 3.62, P ¼ 4.1  10 À 5) associating with recurrent kidney stones. We also observe associations of the identified kidney stone variants with biochemical traits in a large population set, indicating potential biological mechanism. 1 deCODE genetics/Amgen, Inc., Reykjavik 101, Iceland. 2 School of Engineering and Natural Sciences, University of Iceland, Reykjavik 101, Iceland. 3 Children’s Medical Center, Landspitali—The National University Hospital of Iceland, Reykjavik 101, Iceland. 4 Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland. 5 The Rare Kidney Stone Consortium, Mayo Clinic, Rochester, Minnesota, USA. 6 Icelandic Medical Center (Laeknasetrid), Laboratory in Mjodd (RAM), Reykjavik 109, Iceland. 7 Department of Clinical Biochemistry, Akureyri Hospital, Akureyri, 600, Iceland. 8 Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik 101, Iceland. 9 Division of Nephrology, Internal Medicine Services, Landspitali—The National University Hospital of Iceland, Reykjavik Iceland. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to A.O. (email: [email protected]) or to K.S. (email: [email protected]). NATURE COMMUNICATIONS | 6:7975 | DOI: 10.1038/ncomms8975 | www.nature.com/naturecommunications 1 & 2015 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms8975 he lifetime risk of kidney stones is 8.8% in the United degree relatives) including 2,172 recurrent kidney stone formers States1 with an estimated recurrence rate of 14% after 1 (see Methods for definition) and 279,870 controls (88,266 chip- Tyear and 35% after 5 years2, placing a significant burden typed and 191,604 chip-typed first- or second-degree relatives). on the health care system1. In Iceland, the prevalence in We assessed the association of kidney stone associated individuals older than 70 years is 10.1% for men and 4.2% sequence variants with biochemical parameters involved in for women3. Kidney stones form when urine becomes calcium–phosphate metabolism (serum calcium, N ¼ 114,489; supersaturated with salts such as calcium oxalate or calcium serum ionized calcium, N ¼ 18,516; serum phosphate, N ¼ 51,056; phosphate and when urine concentrations of natural inhibitors of parathyroid hormone (PTH), N ¼ 15,541; 25-hydroxy vitamin D, stone formation such as citrate, magnesium, pyrophosphate, N ¼ 7,544; alkaline phosphatase (ALP), N ¼ 126,060), purine uromodulin and osteopontin are low4,5. Calcium oxalate and metabolism (serum uric acid, N ¼ 56,025), acid–base homeostasis calcium phosphate are the most common (B80%) constituents (serum bicarbonate (N ¼ 44,511), kidney function (serum of kidney stones5. The mechanism of stone formation involves creatinine, N ¼ 195,933) and ion homeostasis (serum chloride, both environmental factors such as diet6 and genetic traits. N ¼ 92,938; serum magnesium, N ¼ 37,188; serum potassium, Individuals with a family history of kidney stones are at a greater N ¼ 201,720; serum sodium, N ¼ 198,119). risk than others of developing the condition. Recent studies In this study, we found variants at three loci associated with estimate that up to 65% of kidney stone formers have a family kidney stones at a genome-wide significance level (0.05/28.3 history of kidney stones7–9 and both twin10 and genealogy11 million ¼ 1.8  10 À 9) and one additional locus with suggestive studies have reported strong heritability of kidney stone disease. association (Fig. 1; Table 1). At these loci, we also observed Candidate gene association studies have attempted to assess the genome-wide significant associations with serum calcium, role of several genes involved in calcium homeostasis on kidney phosphate, PTH and ALP that do not in all cases correlate with stone formation12. These studies have been limited by sample the corresponding kidney stone association signal. Focusing on size, the results are conflicting and they do not consider a broad coding variants in genes with preferential renal expression, we spectrum of sequence variants. also found two rare coding variants associating with kidney We previously published a genome-wide association study stones and recurrent stone formation. (GWAS) of kidney stone disease, testing a total of 303,120 variants in 1,507 cases and 34,033 controls from Iceland13. Following replication in additional cases and controls from Variants at ALPL. We observe a genome-wide significant signal Iceland and the Netherlands, we reported a genome-wide with two fully correlated markers associating with kidney significant association of the CLDN14 locus, encoding the tight stones in ALPL at 1p36.12, represented by rs1256328 [T] (minor junction protein Claudin-14, on 21q22.13 with kidney stones allele frequency (MAF) ¼ 17.79%, OR ¼ 1.21, P ¼ 5.8  10 À 10) (rs219780[C], allele frequency ¼ 79.20%, odds ratio (OR) ¼ 1.25, (Fig. 2; Table 1; Supplementary Table 1). A missense variant in P ¼ 4.0  10 À 12). A GWAS in the Japanese population ALPL (rs34605986 [A], MAF ¼ 15.21%, NP_000469.3:p. involving 904 cases and 7,471 controls reported three loci Val522Ala) that correlates with rs1256328 (r2 ¼ 0.73) also associated with kidney stones following replication in additional associates with kidney stones (OR ¼ 1.19, P ¼ 8.9  10 À 8) cases and controls, RGS14-SLC34A1, encoding regulator of (Supplementary Table 1). When considering the 3,119 variants G-protein signalling 14 and the Na/Pi co-transporter solute located within the linkage disequilibrium (LD) block containing carrier family 34 member 1, on 5q35.3 (rs11746443[A], rs1256328 no variants remained significant after adjusting for it OR ¼ 1.19, P ¼ 8.5  10 À 2), INMT-FAM188B-AQP1, a locus (P40.05/1,625 ¼ 3.1  10 À 5) (Fig. 2; Supplementary Table 1). including the gene encoding aquaporin 1, on 7p14.3 ALPL encodes a tissue nonspecific ALP. The sequence variant (rs1000597[C], OR ¼ 1.22, P ¼ 2.2  10 À 14), and DGKH, rs1256328 [T] and the correlated missense variant ALPL encoding diacylglycerol kinase eta, on 13q14.1 (rs4142110[C], p.Val522Ala have a significant association with increased serum OR ¼ 1.14, P ¼ 4.6  10 À 9)14. ALP levels in the general population (effect 47.8 s.d.%, In the current study, we have substantially increased the Po2.2  10 À 32) (Table 2). To attempt replication, we directly sample size from our previous study13 (N cases ¼ 5,419; genotyped the missense variant ALPL p.Val522Ala in a Danish N controls ¼ 279,870). We were also able to increase the population set (N ¼ 5,822, MAFDenmark ¼ 17.53%). We replicated number of sequence variants tested by performing GWAS on the association (P ¼ 3.0  10 À 4) with an effect ¼ 10.73 s.d.%. imputed genotypes of sequence variants identified through Combined analysis of discovery and replication sets yielded a whole-genome sequencing of 2,636 Icelanders, yielding a more P ¼ 3.5  10 À 35 and an effect ¼ 8.00 s.d.% with no heterogeneity extensive coverage of the genome. In addition to discovering between the populations (P ¼ 0.38). This is consistent with a associations with kidney stones, we assessed the association previous functional study where a mutated version of ALPL of these variants to 13 biochemical traits involved in carrying p.Val522Ala showed increased enzyme activity in a calcium–phosphate metabolism, purine metabolism, kidney cell-based assay20. Within ALPL, we also detect a low-frequency function, acid–base and ion homeostasis in a large population set. missense variant (rs149344982[A], MAF ¼ 1.42%, NP_000469.3: p.Arg152His), which associates strongly with reduced serum ALP levels (effect ¼À45.9 s.d.%, P ¼ 9.84  10 À 105) and suggestively Results with reduced risk of kidney stones (OR ¼ 0.742, P ¼ 8.1  10 À 3) Main findings. In our previous work, we sequenced the whole (Supplementary Table 2). ALPL p.Arg152His has little genomes of 2,636 Icelanders15,16 (median sequencing depth of correlation with the more common ALPL variants rs1256328 23  ) yielding 28.3 million sequence variants. Subsequently, we and p.Val522Ala (r2o0.0040) (Supplementary Table 3). This imputed these variants assisted by long-range haplotype phasing finding is in line with the effect of several rare loss-of-function into 98,721 Icelanders genotyped with Illumina SNP chips17,18. variants in ALPL that have been reported in patients with Using Icelandic genealogy data, we also calculated genotype hypophosphatasia (OMIM:146300), a syndrome characterized probabilities of untyped close relatives of chip-typed by decreased levels of ALP and elevated urine pyrophosphate 21, individuals19.