Introduction: Older adults with diabetes have variable prognosis. There is critical need to impro... more Introduction: Older adults with diabetes have variable prognosis. There is critical need to improve risk stratification among this population to understand who is most likely to experience adverse outcomes. Low 1,5-anhydroglucitol (1,5-AG) is a biomarker of glycemic variability and has demonstrated value for identification of middle-aged adults with diabetes at risk for major clinical outcomes. Total hospitalizations are a useful summary measure of poor health outcomes. It is unknown whether 1,5-AG can identify older adults at risk for hospitalizations and all-cause mortality. Methods: We included 2,061 participants from the Atherosclerosis Risk in Communities (ARIC) Study with diagnosed diabetes who attended the 2011-2013 visit. We dichotomized 1,5-AG (≥6μg/mL; <6μg/mL) and followed participants until December 31, 2015. We examined the associations of 1,5-AG with total and diabetes-related hospitalizations using negative binomial regression and all-cause mortality using Cox regr...
Horia C. Stanescu, M.D., Mauricio Arcos-Burgos, M.D., Ph.D., Alan Medlar, M.Sc., Detlef Bockenhau... more Horia C. Stanescu, M.D., Mauricio Arcos-Burgos, M.D., Ph.D., Alan Medlar, M.Sc., Detlef Bockenhauer, M.D., Ph.D., Anna Kottgen, M.D., M.P.H., Liviu Dragomirescu, Ph.D., Catalin Voinescu, B.Sc., Naina Patel, B.Sc., Kerra Pearce, M.Sc., Mike Hubank, Ph.D., Henry A.F. Stephens, Ph.D., Valerie Laundy, F.I.M.L.S., Sandosh Padmanabhan, M.D., Ph.D., Anna Zawadzka, Julia M. Hofstra, M.D., Marieke J.H. Coenen, Ph.D., Martin den Heijer, M.D., Ph.D., Lambertus A.L.M. Kiemeney, Ph.D., Delphine Bacq-Daian, M.Sc., Benedicte Stengel, M.D., Ph.D., Stephen H. Powis, Ph.D., F.R.C.P., Paul Brenchley, Ph.D., John Feehally, D.M., F.R.C.P., Andrew J. Rees, F.R.C.P., F.Med.Sci., Hanna Debiec, Ph.D., Jack F.M. Wetzels, M.D., Ph.D., Pierre Ronco, M.D., Ph.D., Peter W. Mathieson, Ph.D., F.R.C.P., and Robert Kleta, M.D., Ph.D.
Omics data facilitate the gain of novel insights into the pathophysiology of diseases and, conseq... more Omics data facilitate the gain of novel insights into the pathophysiology of diseases and, consequently, their diagnosis, treatment, and prevention. To that end, it is necessary to integrate omics data with other data types such as clinical, phenotypic, and demographic parameters of categorical or continuous nature. Here, we exemplify this data integration issue for a study on chronic kidney disease (CKD), where complex clinical and demographic parameters were assessed together with one-dimensional (1D) 1H NMR metabolic fingerprints. Routine analysis screens for associations of single metabolic features with clinical parameters, which requires confounding variables typically chosen by expert knowledge to be taken into account. This knowledge can be incomplete or unavailable. The results of this article are manifold. We introduce a framework for data integration that intrinsically adjusts for confounding variables. We give its mathematical and algorithmic foundation, provide a state-...
Improved understanding of the proteome can facilitate the identification of causal mechanisms for... more Improved understanding of the proteome can facilitate the identification of causal mechanisms for complex traits. We conducted a comprehensive analysis of the common variant cis-regulatory genetic architecture of 4,665 plasma proteins from 7,213 European Americans (EA) and 1,871 African Americans (AA) from the Atherosclerosis Risk in Communities (ARIC) cohort study. We identified and fine-mapped 1,992 plasma proteins in EA and 1,605 in AA, which had significant cis- single-nucleotide polymorphism (SNP) associations. Estimates of cis-heritability (cis-h2) for plasma proteins were similar across EA and AA (median cis-h2 = 0.09 for EA and 0.10 for AA). Elastic-net-based models for cis-SNP-based protein prediction produced high accuracy (median R2/cis-h2 = 0.79 for EA and 0.69 for AA). We illustrate the application of these models to conduct proteome-wide association studies (PWAS) for two related complex traits, serum urate and gout, and further conduct conditional analyses to interpre...
Background: Evidence is mounting that intraprostatic inflammation influences prostate cancer deve... more Background: Evidence is mounting that intraprostatic inflammation influences prostate cancer development. Uric acid crystals depositing in the prostate could result in injury and inflammation, increasing prostate cancer risk. Methods: Included were 6,574 men ages 45–64 years who enrolled in the Atherosclerosis Risk in Communities study in 1987 to 1989. We used Cox proportional hazards regression to estimate the association of serum urate concentration alone and to improve accuracy, jointly with a genetic risk score (GRS, N = 4,983) derived from variants predictive of urate concentration, with prostate cancer (N = 813) risk. Results: Serum urate concentration or joint categories of urate concentration and GRS were not associated with prostate cancer risk (Ptrend for quartiles = 0.3). Results were generally similar by race and after excluding users of medications that influence uric acid. Conclusions: Serum urate alone and with a urate-associated GRS were not associated with prostate cancer risk. Impact: It is unlikely that circulating urate concentration influences prostate cancer development.
Patients with chronic kidney disease and severely decreased glomerular filtration rate (GFR) are ... more Patients with chronic kidney disease and severely decreased glomerular filtration rate (GFR) are at high risk for kidney failure, cardiovascular disease (CVD) and death. Accurate estimates of risk and timing of these clinical outcomes could guide patient counseling and therapy. Therefore, we developed models using data of 264,296 individuals in 30 countries participating in the international Chronic Kidney Disease Prognosis Consortium with estimated GFR (eGFR)s under 30 ml/min/1.73m. Median participant eGFR and urine albumin-to-creatinine ratio were 24 ml/min/1.73m and 168 mg/g, respectively. Using competing-risk regression, random-effect meta-analysis, and Markov processes with Monte Carlo simulations, we developed two- and four-year models of the probability and timing of kidney failure requiring kidney replacement therapy (KRT), a non-fatal CVD event, and death according to age, sex, race, eGFR, albumin-to-creatinine ratio, systolic blood pressure, smoking status, diabetes mellit...
Chronic kidney disease (CKD) is defined by reduced estimated glomerular filtration rate (eGFR). P... more Chronic kidney disease (CKD) is defined by reduced estimated glomerular filtration rate (eGFR). Previous genetic studies have implicated regulatory mechanisms contributing to CKD. Here we present epigenome-wide association studies of eGFR and CKD using whole-blood DNA methylation of 2264 ARIC Study and 2595 Framingham Heart Study participants to identify epigenetic signatures of kidney function. Of 19 CpG sites significantly associated (P < 1e-07) with eGFR/CKD and replicated, five also associate with renal fibrosis in biopsies from CKD patients and show concordant DNA methylation changes in kidney cortex. Lead CpGs at PTPN6/PHB2, ANKRD11, and TNRC18 map to active enhancers in kidney cortex. At PTPN6/PHB2 cg19942083, methylation in kidney cortex associates with lower renal PTPN6 expression, higher eGFR, and less renal fibrosis. The regions containing the 243 eGFR-associated (P < 1e-05) CpGs are significantly enriched for transcription factor binding sites of EBF1, EP300, and C...
Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of th... more Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question. Expression quantitative trait loci (eQTL) analysis is a method to identify genetic variation associated with gene expression changes in specific tissue types. We hypothesized that an integrative analysis combining CKD GWAS and kidney eQTL results can identify candidate genes for CKD. We performed eQTL analysis by correlating genotype with RNA-seq-based gene expression levels in 96 human kidney samples. Applying stringent statistical criteria, we detected 1,886 genes whose expression differs with the sequence variants. Using direct overlap and Bayesian methods, we identified new potential target genes for CKD...
Lp(a) concentrations represent a major cardiovascular risk factor and are almost entirely control... more Lp(a) concentrations represent a major cardiovascular risk factor and are almost entirely controlled by one single locus (LPA). However, many genetic factors in LPA governing the enormous variance of Lp(a) levels are still unknown. Since up to 70% of the LPA coding sequence are located in a difficult to access hypervariable copy number variation named KIV-2, we hypothesized that it may contain novel functional variants with pronounced effects on Lp(a) concentrations. We performed a large scale mutation analysis in the KIV-2 using an extreme phenotype approach. We compiled an discovery set of 123 samples showing discordance between LPA isoform phenotype and Lp(a) concentrations and controls. Using ultra-deep sequencing, we identified a splice site variant (G4925A) in preferential association with the smaller LPA isoforms. Follow-up in a European general population (n = 2892) revealed an exceptionally high carrier frequency of 22.1% in the general population. The variant explains 20.6...
The global nephrology community recognises the need for a cohesive plan to address the problem of... more The global nephrology community recognises the need for a cohesive plan to address the problem of chronic kidney disease (CKD). In July, 2016, the International Society of Nephrology hosted a CKD summit of more than 85 people with diverse expertise and professional backgrounds from around the globe. The purpose was to identify and prioritise key activities for the next 5-10 years in the domains of clinical care, research, and advocacy and to create an action plan and performance framework based on ten themes: strengthen CKD surveillance; tackle major risk factors for CKD; reduce acute kidney injury-a special risk factor for CKD; enhance understanding of the genetic causes of CKD; establish better diagnostic methods in CKD; improve understanding of the natural course of CKD; assess and implement established treatment options in patients with CKD; improve management of symptoms and complications of CKD; develop novel therapeutic interventions to slow CKD progression and reduce CKD com...
Genome-wide association studies (GWAS) evaluate associations between genetic variants and a trait... more Genome-wide association studies (GWAS) evaluate associations between genetic variants and a trait or disease of interest free of prior biological hypotheses. GWAS require stringent correction for multiple testing, with genome-wide significance typically defined as association p-value <5*10-8. This study presents a new tool that uses external information about genes to prioritize SNP associations (GenToS). For a given list of candidate genes, GenToS calculates an appropriate statistical significance threshold and then searches for trait-associated variants in summary statistics from human GWAS. It thereby allows for identifying trait-associated genetic variants that do not meet genome-wide significance. The program additionally tests for enrichment of significant candidate gene associations in the human GWAS data compared to the number expected by chance. As proof of principle, this report used external information from a comprehensive resource of genetically manipulated and syste...
Journal of the American Society of Nephrology : JASN, Jan 5, 2016
Genome-wide association studies have identified >50 common variants associated with kidney fun... more Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L;…
American Journal of Kidney Diseases the Official Journal of the National Kidney Foundation, Apr 27, 2012
BackgroundIdentifying individuals at risk for chronic kidney disease (CKD) is critical for timely... more BackgroundIdentifying individuals at risk for chronic kidney disease (CKD) is critical for timely treatment initiation to slow progression of the disease. Neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule 1 (KIM-1) are known biomarkers of acute kidney injury, but it is unknown whether these markers are associated with incident CKD stage 3 in the general population.Study DesignMatched case-control studySetting and ParticipantsAfrican American and Caucasian participants from the Atherosclerosis Risk in Communities (ARIC) study who at baseline had an estimated glomerular filtration rate ≥ 60 ml/min/1.73 m2 and urinary albumin-creatinine ratio (UACR) ≤ 30 mg/g. A total of 143 controls were matched on age, sex and race to 143 cases of incident CKD stage 3 after 8.6 years of follow-up.PredictorsQuartile of NGAL and KIM-1.Outcomes & MeasurementsIncident CKD stage 3 (eGFR < 60 ml/min/1.73 m2 at follow-up and a decrease in eGFR from baseline to follow-up of ≥25%)ResultsBoth NGAL (p=0.05) and KIM-1 (p<0.001) were positively correlated with baseline UACR; neither was associated with baseline eGFR. Participants with NGAL concentrations in the fourth quartile had more than 2-fold higher odds (adjusted OR, 2.11, 95% CI, 0.96–4.64) of incident CKD stage 3 compared to participants in the first quartile after multivariable adjustment (p-trend=0.03). Adjustment for urinary creatinine and albumin resulted in a non-significant association (highest quartile adjusted OR. 1.52; 95% CI, 0.64–3.58; p=0.2). No significant association between KIM-1 levels and incident CKD was observed in crude or adjusted models.LimitationsThe relatively small sample size of the study limits precision and power to detect weak associations.ConclusionsHigher NGAL levels, but not KIM-1 levels, were associated with incident CKD stage 3. Adjustment for urinary creatinine and albumin concentration attenuated this association. Additional studies are needed to confirm these findings and assess the utility of urinary NGAL as a marker of CKD risk.
Diabetes mellitus (DM) is the leading cause of end-stage renal disease. Little is known about pra... more Diabetes mellitus (DM) is the leading cause of end-stage renal disease. Little is known about practice patterns of anti-diabetic therapy in the presence of chronic kidney disease (CKD) and correlates with glycaemic control. We therefore aimed to analyze current antidiabetic treatment and correlates of metabolic control in a large contemporary prospective cohort of patients with diabetes and CKD. The German Chronic Kidney Disease (GCKD) study enrolled 5217 patients aged 18-74 years with an estimated glomerular filtration rate (eGFR) between 30-60 mL/min/1.73 m(2) or proteinuria >0.5 g/d. The use of diet prescription, oral anti-diabetic medication, and insulin was assessed at baseline. HbA1c, measured centrally, was the main outcome measure. At baseline, DM was present in 1842 patients (35 %) and the median HbA1C was 7.0 % (25(th)-75(th) percentile: 6.8-7.9 %), equalling 53 mmol/mol (51, 63); 24.2 % of patients received dietary treatment only, 25.5 % oral antidiabetic drugs but not...
European journal of human genetics : EJHG, Aug 27, 2016
Whole-exome sequencing allows for an unbiased and comprehensive mutation screening. Although succ... more Whole-exome sequencing allows for an unbiased and comprehensive mutation screening. Although successfully used to facilitate the diagnosis of single-gene disorders, the genetic cause(s) of a substantial proportion of presumed monogenic diseases remain to be identified. We used whole-exome sequencing to examine offspring from a consanguineous marriage featuring a novel combination of congenital hypothyroidism, hypomagnesemia and hypercholesterolemia. Rather than identifying one causative variant, we report the first instance in which three independent autosomal-recessive single-gene disorders were identified in one patient. Together, the causal variants give rise to a blended and seemingly novel phenotype: we experimentally characterized a novel splice variant in the thyroglobulin gene (c.638+5G>A), resulting in skipping of exon 5, and detected a pathogenic splice variant in the magnesium transporter gene TRPM6 (c.2667+1G>A), causing familial hypomagnesemia. Based on the third ...
The journals of gerontology. Series A, Biological sciences and medical sciences, Jan 28, 2015
It is unclear whether traditional and genetic risk factors in middle age predict the onset of gou... more It is unclear whether traditional and genetic risk factors in middle age predict the onset of gout in older age. We studied the incidence of gout in older adults using the Atherosclerosis Risk in Communities study, a prospective U.S. population-based cohort of middle-aged adults enrolled between 1987 and 1989 with ongoing follow-up. A genetic urate score was formed from common urate-associated single nucleotide polymorphisms for eight genes. The adjusted hazard ratio and 95% confidence interval of incident gout by traditional and genetic risk factors in middle age were estimated using a Cox proportional hazards model. The cumulative incidence from middle age to age 65 was 8.6% in men and 2.5% in women; by age 75 the cumulative incidence was 11.8% and 5.0%. In middle age, increased adiposity, beer intake, protein intake, smoking status, hypertension, diuretic use, and kidney function (but not sex) were associated with an increased gout risk in older age. In addition, a 100 µmol/L inc...
Introduction: Older adults with diabetes have variable prognosis. There is critical need to impro... more Introduction: Older adults with diabetes have variable prognosis. There is critical need to improve risk stratification among this population to understand who is most likely to experience adverse outcomes. Low 1,5-anhydroglucitol (1,5-AG) is a biomarker of glycemic variability and has demonstrated value for identification of middle-aged adults with diabetes at risk for major clinical outcomes. Total hospitalizations are a useful summary measure of poor health outcomes. It is unknown whether 1,5-AG can identify older adults at risk for hospitalizations and all-cause mortality. Methods: We included 2,061 participants from the Atherosclerosis Risk in Communities (ARIC) Study with diagnosed diabetes who attended the 2011-2013 visit. We dichotomized 1,5-AG (≥6μg/mL; <6μg/mL) and followed participants until December 31, 2015. We examined the associations of 1,5-AG with total and diabetes-related hospitalizations using negative binomial regression and all-cause mortality using Cox regr...
Horia C. Stanescu, M.D., Mauricio Arcos-Burgos, M.D., Ph.D., Alan Medlar, M.Sc., Detlef Bockenhau... more Horia C. Stanescu, M.D., Mauricio Arcos-Burgos, M.D., Ph.D., Alan Medlar, M.Sc., Detlef Bockenhauer, M.D., Ph.D., Anna Kottgen, M.D., M.P.H., Liviu Dragomirescu, Ph.D., Catalin Voinescu, B.Sc., Naina Patel, B.Sc., Kerra Pearce, M.Sc., Mike Hubank, Ph.D., Henry A.F. Stephens, Ph.D., Valerie Laundy, F.I.M.L.S., Sandosh Padmanabhan, M.D., Ph.D., Anna Zawadzka, Julia M. Hofstra, M.D., Marieke J.H. Coenen, Ph.D., Martin den Heijer, M.D., Ph.D., Lambertus A.L.M. Kiemeney, Ph.D., Delphine Bacq-Daian, M.Sc., Benedicte Stengel, M.D., Ph.D., Stephen H. Powis, Ph.D., F.R.C.P., Paul Brenchley, Ph.D., John Feehally, D.M., F.R.C.P., Andrew J. Rees, F.R.C.P., F.Med.Sci., Hanna Debiec, Ph.D., Jack F.M. Wetzels, M.D., Ph.D., Pierre Ronco, M.D., Ph.D., Peter W. Mathieson, Ph.D., F.R.C.P., and Robert Kleta, M.D., Ph.D.
Omics data facilitate the gain of novel insights into the pathophysiology of diseases and, conseq... more Omics data facilitate the gain of novel insights into the pathophysiology of diseases and, consequently, their diagnosis, treatment, and prevention. To that end, it is necessary to integrate omics data with other data types such as clinical, phenotypic, and demographic parameters of categorical or continuous nature. Here, we exemplify this data integration issue for a study on chronic kidney disease (CKD), where complex clinical and demographic parameters were assessed together with one-dimensional (1D) 1H NMR metabolic fingerprints. Routine analysis screens for associations of single metabolic features with clinical parameters, which requires confounding variables typically chosen by expert knowledge to be taken into account. This knowledge can be incomplete or unavailable. The results of this article are manifold. We introduce a framework for data integration that intrinsically adjusts for confounding variables. We give its mathematical and algorithmic foundation, provide a state-...
Improved understanding of the proteome can facilitate the identification of causal mechanisms for... more Improved understanding of the proteome can facilitate the identification of causal mechanisms for complex traits. We conducted a comprehensive analysis of the common variant cis-regulatory genetic architecture of 4,665 plasma proteins from 7,213 European Americans (EA) and 1,871 African Americans (AA) from the Atherosclerosis Risk in Communities (ARIC) cohort study. We identified and fine-mapped 1,992 plasma proteins in EA and 1,605 in AA, which had significant cis- single-nucleotide polymorphism (SNP) associations. Estimates of cis-heritability (cis-h2) for plasma proteins were similar across EA and AA (median cis-h2 = 0.09 for EA and 0.10 for AA). Elastic-net-based models for cis-SNP-based protein prediction produced high accuracy (median R2/cis-h2 = 0.79 for EA and 0.69 for AA). We illustrate the application of these models to conduct proteome-wide association studies (PWAS) for two related complex traits, serum urate and gout, and further conduct conditional analyses to interpre...
Background: Evidence is mounting that intraprostatic inflammation influences prostate cancer deve... more Background: Evidence is mounting that intraprostatic inflammation influences prostate cancer development. Uric acid crystals depositing in the prostate could result in injury and inflammation, increasing prostate cancer risk. Methods: Included were 6,574 men ages 45–64 years who enrolled in the Atherosclerosis Risk in Communities study in 1987 to 1989. We used Cox proportional hazards regression to estimate the association of serum urate concentration alone and to improve accuracy, jointly with a genetic risk score (GRS, N = 4,983) derived from variants predictive of urate concentration, with prostate cancer (N = 813) risk. Results: Serum urate concentration or joint categories of urate concentration and GRS were not associated with prostate cancer risk (Ptrend for quartiles = 0.3). Results were generally similar by race and after excluding users of medications that influence uric acid. Conclusions: Serum urate alone and with a urate-associated GRS were not associated with prostate cancer risk. Impact: It is unlikely that circulating urate concentration influences prostate cancer development.
Patients with chronic kidney disease and severely decreased glomerular filtration rate (GFR) are ... more Patients with chronic kidney disease and severely decreased glomerular filtration rate (GFR) are at high risk for kidney failure, cardiovascular disease (CVD) and death. Accurate estimates of risk and timing of these clinical outcomes could guide patient counseling and therapy. Therefore, we developed models using data of 264,296 individuals in 30 countries participating in the international Chronic Kidney Disease Prognosis Consortium with estimated GFR (eGFR)s under 30 ml/min/1.73m. Median participant eGFR and urine albumin-to-creatinine ratio were 24 ml/min/1.73m and 168 mg/g, respectively. Using competing-risk regression, random-effect meta-analysis, and Markov processes with Monte Carlo simulations, we developed two- and four-year models of the probability and timing of kidney failure requiring kidney replacement therapy (KRT), a non-fatal CVD event, and death according to age, sex, race, eGFR, albumin-to-creatinine ratio, systolic blood pressure, smoking status, diabetes mellit...
Chronic kidney disease (CKD) is defined by reduced estimated glomerular filtration rate (eGFR). P... more Chronic kidney disease (CKD) is defined by reduced estimated glomerular filtration rate (eGFR). Previous genetic studies have implicated regulatory mechanisms contributing to CKD. Here we present epigenome-wide association studies of eGFR and CKD using whole-blood DNA methylation of 2264 ARIC Study and 2595 Framingham Heart Study participants to identify epigenetic signatures of kidney function. Of 19 CpG sites significantly associated (P < 1e-07) with eGFR/CKD and replicated, five also associate with renal fibrosis in biopsies from CKD patients and show concordant DNA methylation changes in kidney cortex. Lead CpGs at PTPN6/PHB2, ANKRD11, and TNRC18 map to active enhancers in kidney cortex. At PTPN6/PHB2 cg19942083, methylation in kidney cortex associates with lower renal PTPN6 expression, higher eGFR, and less renal fibrosis. The regions containing the 243 eGFR-associated (P < 1e-05) CpGs are significantly enriched for transcription factor binding sites of EBF1, EP300, and C...
Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of th... more Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question. Expression quantitative trait loci (eQTL) analysis is a method to identify genetic variation associated with gene expression changes in specific tissue types. We hypothesized that an integrative analysis combining CKD GWAS and kidney eQTL results can identify candidate genes for CKD. We performed eQTL analysis by correlating genotype with RNA-seq-based gene expression levels in 96 human kidney samples. Applying stringent statistical criteria, we detected 1,886 genes whose expression differs with the sequence variants. Using direct overlap and Bayesian methods, we identified new potential target genes for CKD...
Lp(a) concentrations represent a major cardiovascular risk factor and are almost entirely control... more Lp(a) concentrations represent a major cardiovascular risk factor and are almost entirely controlled by one single locus (LPA). However, many genetic factors in LPA governing the enormous variance of Lp(a) levels are still unknown. Since up to 70% of the LPA coding sequence are located in a difficult to access hypervariable copy number variation named KIV-2, we hypothesized that it may contain novel functional variants with pronounced effects on Lp(a) concentrations. We performed a large scale mutation analysis in the KIV-2 using an extreme phenotype approach. We compiled an discovery set of 123 samples showing discordance between LPA isoform phenotype and Lp(a) concentrations and controls. Using ultra-deep sequencing, we identified a splice site variant (G4925A) in preferential association with the smaller LPA isoforms. Follow-up in a European general population (n = 2892) revealed an exceptionally high carrier frequency of 22.1% in the general population. The variant explains 20.6...
The global nephrology community recognises the need for a cohesive plan to address the problem of... more The global nephrology community recognises the need for a cohesive plan to address the problem of chronic kidney disease (CKD). In July, 2016, the International Society of Nephrology hosted a CKD summit of more than 85 people with diverse expertise and professional backgrounds from around the globe. The purpose was to identify and prioritise key activities for the next 5-10 years in the domains of clinical care, research, and advocacy and to create an action plan and performance framework based on ten themes: strengthen CKD surveillance; tackle major risk factors for CKD; reduce acute kidney injury-a special risk factor for CKD; enhance understanding of the genetic causes of CKD; establish better diagnostic methods in CKD; improve understanding of the natural course of CKD; assess and implement established treatment options in patients with CKD; improve management of symptoms and complications of CKD; develop novel therapeutic interventions to slow CKD progression and reduce CKD com...
Genome-wide association studies (GWAS) evaluate associations between genetic variants and a trait... more Genome-wide association studies (GWAS) evaluate associations between genetic variants and a trait or disease of interest free of prior biological hypotheses. GWAS require stringent correction for multiple testing, with genome-wide significance typically defined as association p-value <5*10-8. This study presents a new tool that uses external information about genes to prioritize SNP associations (GenToS). For a given list of candidate genes, GenToS calculates an appropriate statistical significance threshold and then searches for trait-associated variants in summary statistics from human GWAS. It thereby allows for identifying trait-associated genetic variants that do not meet genome-wide significance. The program additionally tests for enrichment of significant candidate gene associations in the human GWAS data compared to the number expected by chance. As proof of principle, this report used external information from a comprehensive resource of genetically manipulated and syste...
Journal of the American Society of Nephrology : JASN, Jan 5, 2016
Genome-wide association studies have identified >50 common variants associated with kidney fun... more Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L;…
American Journal of Kidney Diseases the Official Journal of the National Kidney Foundation, Apr 27, 2012
BackgroundIdentifying individuals at risk for chronic kidney disease (CKD) is critical for timely... more BackgroundIdentifying individuals at risk for chronic kidney disease (CKD) is critical for timely treatment initiation to slow progression of the disease. Neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule 1 (KIM-1) are known biomarkers of acute kidney injury, but it is unknown whether these markers are associated with incident CKD stage 3 in the general population.Study DesignMatched case-control studySetting and ParticipantsAfrican American and Caucasian participants from the Atherosclerosis Risk in Communities (ARIC) study who at baseline had an estimated glomerular filtration rate ≥ 60 ml/min/1.73 m2 and urinary albumin-creatinine ratio (UACR) ≤ 30 mg/g. A total of 143 controls were matched on age, sex and race to 143 cases of incident CKD stage 3 after 8.6 years of follow-up.PredictorsQuartile of NGAL and KIM-1.Outcomes & MeasurementsIncident CKD stage 3 (eGFR < 60 ml/min/1.73 m2 at follow-up and a decrease in eGFR from baseline to follow-up of ≥25%)ResultsBoth NGAL (p=0.05) and KIM-1 (p<0.001) were positively correlated with baseline UACR; neither was associated with baseline eGFR. Participants with NGAL concentrations in the fourth quartile had more than 2-fold higher odds (adjusted OR, 2.11, 95% CI, 0.96–4.64) of incident CKD stage 3 compared to participants in the first quartile after multivariable adjustment (p-trend=0.03). Adjustment for urinary creatinine and albumin resulted in a non-significant association (highest quartile adjusted OR. 1.52; 95% CI, 0.64–3.58; p=0.2). No significant association between KIM-1 levels and incident CKD was observed in crude or adjusted models.LimitationsThe relatively small sample size of the study limits precision and power to detect weak associations.ConclusionsHigher NGAL levels, but not KIM-1 levels, were associated with incident CKD stage 3. Adjustment for urinary creatinine and albumin concentration attenuated this association. Additional studies are needed to confirm these findings and assess the utility of urinary NGAL as a marker of CKD risk.
Diabetes mellitus (DM) is the leading cause of end-stage renal disease. Little is known about pra... more Diabetes mellitus (DM) is the leading cause of end-stage renal disease. Little is known about practice patterns of anti-diabetic therapy in the presence of chronic kidney disease (CKD) and correlates with glycaemic control. We therefore aimed to analyze current antidiabetic treatment and correlates of metabolic control in a large contemporary prospective cohort of patients with diabetes and CKD. The German Chronic Kidney Disease (GCKD) study enrolled 5217 patients aged 18-74 years with an estimated glomerular filtration rate (eGFR) between 30-60 mL/min/1.73 m(2) or proteinuria >0.5 g/d. The use of diet prescription, oral anti-diabetic medication, and insulin was assessed at baseline. HbA1c, measured centrally, was the main outcome measure. At baseline, DM was present in 1842 patients (35 %) and the median HbA1C was 7.0 % (25(th)-75(th) percentile: 6.8-7.9 %), equalling 53 mmol/mol (51, 63); 24.2 % of patients received dietary treatment only, 25.5 % oral antidiabetic drugs but not...
European journal of human genetics : EJHG, Aug 27, 2016
Whole-exome sequencing allows for an unbiased and comprehensive mutation screening. Although succ... more Whole-exome sequencing allows for an unbiased and comprehensive mutation screening. Although successfully used to facilitate the diagnosis of single-gene disorders, the genetic cause(s) of a substantial proportion of presumed monogenic diseases remain to be identified. We used whole-exome sequencing to examine offspring from a consanguineous marriage featuring a novel combination of congenital hypothyroidism, hypomagnesemia and hypercholesterolemia. Rather than identifying one causative variant, we report the first instance in which three independent autosomal-recessive single-gene disorders were identified in one patient. Together, the causal variants give rise to a blended and seemingly novel phenotype: we experimentally characterized a novel splice variant in the thyroglobulin gene (c.638+5G>A), resulting in skipping of exon 5, and detected a pathogenic splice variant in the magnesium transporter gene TRPM6 (c.2667+1G>A), causing familial hypomagnesemia. Based on the third ...
The journals of gerontology. Series A, Biological sciences and medical sciences, Jan 28, 2015
It is unclear whether traditional and genetic risk factors in middle age predict the onset of gou... more It is unclear whether traditional and genetic risk factors in middle age predict the onset of gout in older age. We studied the incidence of gout in older adults using the Atherosclerosis Risk in Communities study, a prospective U.S. population-based cohort of middle-aged adults enrolled between 1987 and 1989 with ongoing follow-up. A genetic urate score was formed from common urate-associated single nucleotide polymorphisms for eight genes. The adjusted hazard ratio and 95% confidence interval of incident gout by traditional and genetic risk factors in middle age were estimated using a Cox proportional hazards model. The cumulative incidence from middle age to age 65 was 8.6% in men and 2.5% in women; by age 75 the cumulative incidence was 11.8% and 5.0%. In middle age, increased adiposity, beer intake, protein intake, smoking status, hypertension, diuretic use, and kidney function (but not sex) were associated with an increased gout risk in older age. In addition, a 100 µmol/L inc...
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Papers by Anna Kottgen