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We describe a method based on a latent Dirichlet allocation model for predicting functional effects of noncoding genetic variants in a cell-type- and/or tissue-specific way (FUN-LDA). Using this unsupervised approach, we predict tissue-specific functional effects for every position in the human genome in 127 different tissues and cell types. We demonstrate the usefulness of our predictions by using several validation experiments. Using eQTL data from several sources, including the GTEx project, Geuvadis project, and TwinsUK cohort, we show that eQTLs in specific tissues tend to be most enriched among the predicted functional variants in relevant tissues in Roadmap. We further show how these integrated functional scores can be used for (1) deriving the most likely cell or tissue type causally implicated for a complex trait by using summary statistics from genome-wide association studies and (2) estimating a tissue-based correlation matrix of various complex traits. We found large enrichment of heritability in functional components of relevant tissues for various complex traits, and FUN-LDA yielded higher enrichment estimates than existing methods. Finally, using experimentally validated functional variants from the literature and variants possibly implicated in disease by previous studies, we rigorously compare FUN-LDA with state-of-the-art functional annotation methods and show that FUN-LDA has better prediction accuracy and higher resolution than these methods. In particular, our results suggest that tissue- and cell-type-specific functional prediction methods tend to have substantially better prediction accuracy than organism-level prediction methods. Scores for each position in the human genome and for each ENCODE and Roadmap tissue are available online (see Web Resources).

Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and are highly genetically heterogeneous. We conducted whole-exome sequencing in 202 case subjects with RHD and identified diagnostic mutations in genes known to be associated with RHD in 7/202 case subjects. In an additional affected individual with RHD and a congenital heart defect, we found a homozygous loss-of-function (LOF) variant in SLIT3, recapitulating phenotypes reported with Slit3 inactivation in the mouse. To identify genes associated with RHD, we performed an exome-wide association study with 195 unresolved case subjects and 6,905 control subjects. The top signal resided in GREB1L, a gene implicated previously in Hoxb1 and Shha signaling in zebrafish. The significance of the association, which was p = 2.0 × 10-5 for novel LOF, increased to p = 4.1 × 10-6 for LOF and deleterious missense variants combined, and augmented further after accounting for segregation and de novo inheritance of rare variants (joint p = 2.3 × 10-7). Finally, CRISPR/Cas9 disruption or knockdown of greb1l in zebrafish caused specific pronephric defects, which were rescued by wild-type human GREB1L mRNA, but not mRNA containing alleles identified in case subjects. Together, our study provides insight into the genetic landscape of kidney malformations in humans, presents multiple candidates, and identifies SLIT3 and GREB1L as genes implicated in the pathogenesis of RHD.

Aberrant O-glycosylation of serum immunoglobulin A1 (IgA1) represents a heritable pathogenic defect in IgA nephropathy, the most common form of glomerulonephritis worldwide, but specific genetic factors involved in its determination are not known. We performed a quantitative GWAS for serum levels of galactose-deficient IgA1 (Gd-IgA1) in 2,633 subjects of European and East Asian ancestry and discovered two genome-wide significant loci, in C1GALT1 (rs13226913, P = 3.2 x 10−11) and C1GALT1C1 (rs5910940, P = 2.7 x 10−8). These genes encode molecular partners essential for enzymatic O-glycosylation of IgA1. We demonstrated that these two loci explain approximately 7% of variability in circulating Gd-IgA1 in Europeans, but only 2% in East Asians. Notably, the Gd-IgA1-increasing allele of rs13226913 is common in Europeans, but rare in East Asians. Moreover, rs13226913 represents a strong cis-eQTL for C1GALT1 that encodes the key enzyme responsible for the transfer of galactose to O-linked glycans on IgA1. By in vitro siRNA knock-down studies, we confirmed that mRNA levels of both C1GALT1 and C1GALT1C1 determine the rate of secretion of Gd-IgA1 in IgA1-producing cells. Our findings provide novel insights into the genetic regulation of O-glycosylation and are relevant not only to IgA nephropathy, but also to other complex traits associated with O-glycosylation defects, including inflammatory bowel disease, hematologic disease, and cancer., Author summary O-glycosylation is a common type of post-translational modification of proteins; specific abnormalities in the mechanism of O-glycosylation have been implicated in cancer, inflammatory and blood diseases. However, the molecular basis of abnormal O-glycosylation in these complex disorders is not known. We studied the genetic basis of defective O-glycosylation of serum immunoglobulin A1 (IgA1), that represents the key pathogenic defect in IgA nephropathy, the most common form of primary glomerulonephritis worldwide. We report our results of the first genome-wide association study for this trait using serum assays in 2,633 individuals of European and East-Asian ancestry. In our genome scan, we observed two significant signals with large effects, on chromosomes 7p21.3 and Xq24, jointly explaining about 7% of trait variability. These signals implicate two genes that encode molecular partners essential for enzymatic O-glycosylation of IgA1 and mucins, and represent potential new targets for therapy.

International audience; Background: The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown.Methods: We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies. We also carried out functional studies using zebrafish and mice.Results: We identified heterozygous deletions of 22q11.2 in 1.1% of the patients with congenital kidney anomalies and in 0.01% of population controls (odds ratio, 81.5; P=4.5×10-14). We localized the main drivers of renal disease in the DiGeorge syndrome to a 370-kb region containing nine genes. In zebrafish embryos, an induced loss of function in snap29, aifm3, and crkl resulted in renal defects; the loss of crkl alone was sufficient to induce defects. Five of 586 patients with congenital urinary anomalies had newly identified, heterozygous protein-altering variants, including a premature termination codon, in CRKL. The inactivation of Crkl in the mouse model induced developmental defects similar to those observed in patients with congenital urinary anomalies.Conclusions: We identified a recurrent 370-kb deletion at the 22q11.2 locus as a driver of kidney defects in the DiGeorge syndrome and in sporadic congenital kidney and urinary tract anomalies. Of the nine genes at this locus, SNAP29, AIFM3, and CRKL appear to be critical to the phenotype, with haploinsufficiency of CRKL emerging as the main genetic driver. (Funded by the National Institutes of Health and others.).

IgA nephropathy (IgAN) represents the leading cause of kidney failure among East Asian populations and the most frequent form of primary glomerulonephritis among Europeans. Patients with IgAN develop characteristic IgA1-containing immune complexes that deposit in the glomerular mesangium, producing progressive kidney injury. Recent studies define IgAN as an autoimmune trait of complex architecture with a strong genetic determination. This Review summarizes new insights into the role of the O-glycosylation pathway, anti-glycan immune response, mucosal immunity, antigen processing and presentation, and the alternative complement pathway in the pathogenesis of IgAN.

Glomerular diseases are major contributors to the global burden of end-stage kidney disease. The clinical course and outcome of these disorders are extremely variable and difficult to predict. The clinical trajectories range from a benign and spontaneously remitting condition to a symptomatic and rapidly progressive disease. The diagnosis is based entirely on the evaluation of kidney biopsy, but this invasive procedure carries multiple risks and often fails to predict the clinical course or responsiveness to treatment. However, more recent advances in genetics and molecular biology have facilitated elucidation of novel pathogenic mechanisms of these disorders. These discoveries fuel the development of novel biomarkers and offer prospects of noninvasive diagnosis and improved prognostication. Our review focuses on the most promising novel biomarkers that have recently emerged for the major types of glomerular diseases, including immunoglobulin A nephropathy, membranous nephropathy, focal segmental glomerulosclerosis, and membranoproliferative glomerulonephritis.

The last decade has seen major progress in understanding the pathogenesis as well as the prognosis and treatment of patients with IgA nephropathy (IgAN). Although the diagnostic criterion of a kidney biopsy demonstrating dominant or codominant IgA deposition remains unchanged, much more is known about the genetic and environmental factors predisposing to disease development and progression. These advances have led to the identification of novel diagnostic and prognostic markers. Among the most promising clinically are genetic profiling, quantification of galactose-deficient IgA1 levels, and measurement of anti-IgA1 immunoglobulins. While targeted treatment for IgAN remains elusive, there is mounting evidence for therapeutic interventions that alter the disease course. The appropriate validation and integration of these discoveries into clinical care represent a major challenge, but one that holds tremendous promise for refining prognostication, guiding therapy, and improving the lives of patients with IgAN.

In the version of this article initially published, affiliation 38 incorrectly read “ICNU-Nephrology and Urology Department, Barcelona, Spain”; “Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain” is the correct affiliation. The error has been corrected in the HTML and PDF versions of the article.

Copy number variants (CNVs) are increasingly recognized as an important cause of congenital malformations and likely explain over 16% of cases of congenital anomalies of the kidney and urinary tract (CAKUT). Here, we illustrate how a molecular diagnosis of CNV can be beneficial to the clinical management of a pediatric patient presenting with CAKUT and other organ defects.We describe a 14-year-old girl with a large de novo deletion of chromosome 3q13.31-22.1 that disrupts 101 known genes. The patient presented with CAKUT, neurodevelopmental delay, agenesis of corpus callosum (ACC), cardiac malformations, electrolyte and endocrine disorders, skeletal abnormalities and dysmorphic features. We performed extensive annotation of the deleted region to prioritize genes for specific phenotypes and to predict future disease risk.Our case defined new minimal chromosomal candidate regions for both CAKUT and ACC. The presence of the CASR gene in the deleted interval predicted a diagnosis of hypocalciuric hypercalcemia, which was confirmed by the serum and urine chemistries. Our gene annotation explained clinical hypothyroidism and predicted that the index case is at increased risk of thoracic aortic aneurysm, renal cell carcinoma and myeloproliferative disorder.Extended annotation of CNV regions refines the diagnosis and uncovers previously unrecognized phenotypic features. This approach enables personalized treatment and prevention strategies in patients harboring genomic deletions.

Recent genome-wide association studies (GWAS) have identified multiple susceptibility loci for immunoglobulin A nephropathy (IgAN), the most common form of glomerulonephritis, implicating independent defects in adaptive immunity (three loci on chromosome 6p21 in the MHC region), innate immunity (8p23 DEFA locus, 17p23 TNFSF13 locus, 22q12 HORMAD2 locus), and the alternative complement pathway (1q32 CFH/CFHR locus). In geospatial analysis of 85 populations, a genetic risk score based on the replicated GWAS loci is highest in Asians, intermediate in Europeans, and lowest in Africans, capturing the known difference in prevalence among world populations. The genetic risk score also uncovered a previously unsuspected increased prevalence of IgAN-attributable kidney failure in Northern Europe. The IgAN risk alleles have opposing effects on many immune-mediated diseases, suggesting that selection has contributed to variation in risk allele frequencies among different populations. Incorporating genetic, immunologic, and biochemical data, we present a multistep pathogenesis model that provides testable hypotheses for dissecting the mechanisms of disease.

Heritability is essential for understanding the biological causes of disease, but requires laborious patient recruitment and phenotype ascertainment. Electronic health records (EHR) passively capture a wide range of clinically relevant data and provide a novel resource for studying the heritability of traits that are not typically accessible. EHRs contain next-of-kin information collected via patient emergency contact forms, but until now, these data have gone unused in research. We mined emergency contact data at three academic medical centers and identified millions of familial relationships while maintaining patient privacy. Identified relationships were consistent with genetically-derived relatedness. We used EHR data to compute heritability estimates for 500 disease phenotypes. Overall, estimates were consistent with literature and between sites. Inconsistencies were indicative of limitations and opportunities unique to EHR research. These analyses provide a novel validation of the use of EHRs for genetics and disease research.One Sentence SummaryWe demonstrate that next-of-kin information can be used to identify familial relationships in the EHR, providing unique opportunities for precision medicine studies.

An intronic variant at the complement factor H (CFH) gene on chromosome 1q32 (rs6677604) associates with risk of IgA nephropathy (IgAN), but the association signal has not been uniformly replicated in Han Chinese populations. We investigated whether the causal sequence variant resides in the CFH gene or the neighboring complement factor H-related 1 (CFHR1) gene and CFHR3, which harbor an 84-kb combined deletion (CFHR3,1Δ) in linkage disequilibrium with rs6677604. Imputation of 1000 Genomes Project data did not suggest new causal single-nucleotide variants within the CFH cluster. We next performed copy number analysis across the CFH locus in two independent Han Chinese case-control cohorts (combined n=3581). The CFHR3,1Δ and rs6677604-A alleles were rare (4.4% in patients and 7.1% in controls) and in strong linkage disequilibrium with each other (r2=0.95); of these alleles, CFHR3,1Δ associated more significantly with decreased risk of IgAN (odds ratio [OR], 0.56; 95% confidence interval [95% CI], 0.46 to 0.70; P=8.5 × 10-8 versus OR, 0.61; 95% CI, 0.50 to 0.75; P=1.6 × 10-6 for rs6677604-A). Moreover, CFHR3,1Δ explained all of the association signal at rs6677604 and remained significant after conditioning on rs6677604 genotype (P=0.01). Exploratory analyses of clinical and histopathologic parameters using the Oxford classification criteria revealed a suggestive association of CFHR3,1Δ with reduced tubulointerstitial injury (OR, 0.46; 95% CI, 0.25 to 0.79). These data indicate that dysregulated activity of the alternative complement pathway contributes to IgAN pathogenesis in both Asians and Europeans and implicate CFHR3,1Δ as the functional allele at this locus.

Variations in peritoneal dialysis catheter design include differences in numbers of cuffs, shapes of subcutaneous paths (swan neck vs Tenckhoff), and shapes of intra-abdominal segments (straight vs coiled). The relative benefits of these designs have not been studied adequately. The objective of this study is to compare the clinical outcomes of coiled- versus straight-end swan neck peritoneal dialysis catheters.Prospective randomized controlled trial (RCT); results were meta-analyzed with other RCTs of coiled versus straight catheters.80 consecutive continuous ambulatory peritoneal dialysis patients were enrolled in the RCT. The meta-analysis considers data for 242 patients with coiled and 251 patients with straight catheters.Patients were randomly assigned to a coiled-end swan neck catheter (n = 40) or a straight-end swan neck catheter (n = 40) group.Catheter tip migration with dysfunction (primary outcome) and catheter failure, catheter-related infection, technique failure, and all-cause mortality (secondary outcomes).The primary outcome occurred in 18 patients in the coiled group and 9 in the straight group. This difference was not statistically significant (HR, 1.96; 95% CI, 0.88-4.37; P = 0.09). Although rates of early (8 weeks) catheter tip migration were similar between the 2 groups, we detected a significant association of the coiled design with increased risk of late (8 weeks) catheter tip migration (HR, 6.43; 95% CI, 1.45-28.6; P = 0.005). The increased risk of overall catheter failure in the coiled group was not statistically significant (P = 0.06). In the meta-analysis, coiled catheters were associated significantly with increased risk of catheter tip migration (based on 4 trials: RR, 2.08; 95% CI, 1.30-3.33; P = 0.002).Single-center open-label experimental study powered to detect differences in only the most common complication of catheter tip migration with dysfunction. Our RCT examines only swan neck catheters, whereas the meta-analysis considers both swan neck and Tenckhoff designs.Although we were unable to show statistically significant differences in the primary outcome in our RCT, pooled meta-analysis results suggest that coiled catheters may be more prone to migration and resultant dysfunction.

A chromosome 22q13 locus strongly associates with increased risk for idiopathic focal segmental glomerulosclerosis (FSGS), HIV-1-associated nephropathy (HIVAN), and hypertensive ESRD among individuals of African descent. Although initial studies implicated MYH9, more recent analyses localized the strongest association within the neighboring APOL1 gene. In this replication study, we examined the six top-most associated variants in APOL1 and MYH9 in an independent cohort of African Americans with various nephropathies (44 with FSGS, 21 with HIVAN, 32 with IgA nephropathy, and 74 healthy controls). All six variants associated with FSGS and HIVAN (additive ORs, 1.8 to 3.0; P values 3 × 10−2 to 5 × 10−5) but not with IgA nephropathy. In conditional and haplotype analyses, two APOL1 haplotypes accounted for virtually all of the association with FSGS and HIVAN on chromosome 22q13 (haplotype P value = 5.6 × 10−8). To assess the role of MYH9 deficiency in nephropathy, we crossbred Myh9-haploinsufficient mice (Myh9+/−) with HIV-1 transgenic mice. Myh9+/− mice were healthy and did not demonstrate overt proteinuria or nephropathy, irrespective of the presence of the HIV-1 transgene. These data further support the strong association of genetic variants in APOL1 with susceptibility to FSGS and HIVAN among African Americans.

We carried out a genome-wide association study of IgA nephropathy, a major cause of kidney failure worldwide. We studied 1,194 cases and 902 controls of Chinese Han ancestry, with targeted follow up in Chinese and European cohorts comprising 1,950 cases and 1,920 controls. We identified three independent loci in the major histocompatibility complex, as well as a common deletion of CFHR1 and CFHR3 at chromosome 1q32 and a locus at chromosome 22q12 that each surpassed genome-wide significance (P values for association between 1.59 × 10⁻²⁶ and 4.84 × 10⁻⁹ and minor allele odds ratios of 0.63-0.80). These five loci explain 4-7% of the disease variance and up to a tenfold variation in interindividual risk. Many of the alleles that protect against IgA nephropathy impart increased risk for other autoimmune or infectious diseases, and IgA nephropathy risk allele frequencies closely parallel the variation in disease prevalence among Asian, European and African populations, suggesting complex selective pressures.

Heritability is essential for understanding the biological causes of disease but requires laborious patient recruitment and phenotype ascertainment. Electronic health records (EHRs) passively capture a wide range of clinically relevant data and provide a resource for studying the heritability of traits that are not typically accessible. EHRs contain next-of-kin information collected via patient emergency contact forms, but until now, these data have gone unused in research. We mined emergency contact data at three academic medical centers and identified 7.4 million familial relationships while maintaining patient privacy. Identified relationships were consistent with genetically derived relatedness. We used EHR data to compute heritability estimates for 500 disease phenotypes. Overall, estimates were consistent with the literature and between sites. Inconsistencies were indicative of limitations and opportunities unique to EHR research. These analyses provide a validation of the use of EHRs for genetics and disease research.

Immunoglobulin A nephropathy (IgAN) is the most common form of primary glomerulonephritis worldwide and an important cause of kidney disease in young adults. Highly variable clinical presentation and outcome of IgAN suggest that this diagnosis may encompass multiple subsets of disease that are not distinguishable by currently available clinical tools. Marked differences in disease prevalence between individuals of European, Asian, and African ancestry suggest the existence of susceptibility genes that are present at variable frequencies in these populations. Familial forms of IgAN have also been reported throughout the world but are probably underrecognized because associated urinary abnormalities are often intermittent in affected family members. Of the many pathogenic mechanisms reported, defects in IgA1 glycosylation that lead to formation of immune complexes have been consistently demonstrated. Recent data indicates that these IgA1 glycosylation defects are inherited and constitute a heritable risk factor for IgAN. Because of the complex genetic architecture of IgAN, the efforts to map disease susceptibility genes have been difficult, and no causative mutations have yet been identified. Linkage-based approaches have been hindered by disease heterogeneity and lack of a reliable noninvasive diagnostic test for screening family members at risk of IgAN. Many candidate-gene association studies have been published, but most suffer from small sample size and methodological problems, and none of the results have been convincingly validated. New genomic approaches, including genome-wide association studies currently under way, offer promising tools for elucidating the genetic basis of IgAN. Electronic supplementary material The online version of this article (doi:10.1007/s00467-010-1500-7) contains supplementary material, which is available to authorized users.

American Indians have a disproportionately high rate of kidney disease likely due to a combination of increased environmental and genetic risk factors. In an attempt to localize genes influencing kidney disease risk factors, we performed a genome wide scan of estimated glomerular filtration rate on participants of the Strong Heart Family Study. Over 3 600 men and women from 13 American Indian tribes were recruited from 3 centers (Arizona, North and South Dakota, Oklahoma). Using SOLAR 2.1.2, multipoint variance component linkage analysis was performed in each center as well as the entire cohort after controlling for center effects. Two modeling strategies were utilized: model 1 incorporated age, sex and interaction terms and model 2 additionally controlled for diabetic status, systolic and diastolic blood pressure, body mass index, low density lipoproteins, high density lipoproteins, triglycerides and smoking status. Significant evidence for linkage in Arizona lay on 12p12.2 at 39cM nearest marker D12S310 (LOD=3.5). Additional loci with suggestive evidence for linkage were detected at 1p36.31 (LOD=2.0–2.3), 2q33.3 (LOD=1.8) and 9q34.2 (LOD=2.4). No significant evidence for additive interaction with diabetes, hypertension or obesity was noted. In conclusion, we found evidence for linkage of a quantitative trait locus influencing estimated glomerular filtration rate to a region of chromosome 12p in a large cohort of American Indians.

CASE PRESENTATION A 67-year-old Caucasian woman was admitted to our hospital with progressive shortness of breath and swelling of all four extremities. Her past medical history included type 2 diabetes and hypertension of approximately 20 and 10 years of duration, respectively, hypothyroidism, morbid obesity, paroxysmal atrial fibrillation, and sciatica. She denied a history of diabetic nephropathy or retinopathy. On questioning, she noted that over the previous 4 months she had developed new onset of lower extremity edema, increasing abdominal girth, and approximately 60 lb weight gain. More recently over the 3 weeks before admission, she had developed new onset of orthopnea and dyspnea with minimal exertion. She denied any recent history of chest pain, fever, foamy urine, or leg pain. Medications at the time of admission included lopressor 50 mg daily, lisinopril 10 mg daily, hydrochlorothiazide 50 mg daily, furosemide 40 mg daily, repaglinide 2 mg daily, rosiglitazone 8 mg daily, gabapentin 200 mg twice daily, and levothyroxine 200mg daily. Except for the gabapentin, which had been added 3 weeks before admission for her sciatica, she had been on stable dosing of her other medications for the previous several months. Rosiglitazone had been added approximately 36 months before the current presentation. The prescribing physician had not recorded a baseline weight at that time. She had not been treated with insulin for her diabetes, and she had not taken any non-steroidal anti-inflammatory agents in the previous few months. Pulse oximetry revealed an oxygen saturation of 90% while breathing room air, which increased to 100% while breathing supplemental oxygen at a rate of 2 l/min. She was afebrile, and her blood pressure was 120/70 mm Hg. On examination, she was anxious, visibly short of breath, and unable to complete full sentences. She was markedly obese. She had crackles in both lung fields up to the apices. She had deep pitting edema of the arms, legs, anterior abdominal wall, and pre-sacral areas. Heart sounds were distant. Examination of the head and neck, skin, and joints and lymph nodes was unremarkable. Electrocardiogram showed sinus tachycardia at a rate of 100 bpm. Portable chest X-ray (CXR) showed cardiomegaly and perihilar edema consistent with congestive heart failure (Figure 1). Ultrasound of the lower extremities showed no evidence of deep venous thrombosis and a ventilation-perfusion (V/Q) scan showed no evidence of pulmonary embolism. Patient laboratory data are indicated in Table 1.

In recent years, the sequencing of mammalian and microbial genomes has provided the opportunity to study how genetic variation in the host and pathogen influence the course of infectious disease. In the case of HIV-1 infection, such studies have led to identification of key viral proteins that determine pathogenicity, immune evasion, or drug resistance. In addition, candidate gene association studies have uncovered a large number of host genetic variants that influence the outcome of infection and some organ-specific complications. HIV-associated nephropathy (HIVAN) is a pathologically distinct complication of HIV infection. Interindividual variability in incidence, skewed ethnic distribution, and familial aggregation of HIVAN with other forms of ESRD have suggested genetic susceptibility as a major contributing factor. This article reviews the host genetic factors that influence the course of HIV-1 infection and discusses murine models that have increased the understanding of HIVAN pathogenesis and demonstrated the role of genetic background on determination of disease.

Focal segmental glomerulosclerosis (FSGS) is a histologically identifiable glomerular injury often leading to proteinuria and renal failure. To identify its causal genes, whole-exome sequencing and Sanger sequencing were performed on a large Chinese cohort that comprised 40 FSGS families, 50 sporadic FSGS patients, 9 independent autosomal recessive Alport's syndrome (ARAS) patients, and 190 ethnically matched healthy controls. Patients with extrarenal manifestations, indicating systemic diseases or other known hereditary renal diseases, were excluded. Heterozygous COL4A3 mutations were identified in five (12.5%) FSGS families and one (2%) sporadic FSGS patient. All identified mutations disrupted highly conserved protein sequences and none of them was found in either public databases or the 190 healthy controls. Of the FSGS patients with heterozygous COL4A3 mutations, segmental thinning of the glomerular base membrane (GBM) was only detected in the patient with electronic microscopy examination results available. Five ARAS patients (55.6%) had homozygous or compound-heterozygous mutations in COL4A3 or COL4A4. Serious changes in the GBM, hearing loss, and ocular abnormalities were found in 100%, 80%, and 40% of the ARAS patients, respectively. Overall, a new subgroup of FSGS patients resulting from heterozygous COL4A3 mutations was identified. The mutations are relatively frequent in families diagnosed with inherited forms of FSGS. Thus, we suggest screening for COL4A3 mutations in familial FSGS patients.

BACKGROUND. There is frequent uncertainty in the identification of specific etiologies of chronic kidney disease (CKD) in children. Recent studies indicate that chromosomal microarrays can identify rare genomic imbalances that can clarify the etiology of neurodevelopmental and cardiac disorders in children; however, the contribution of unsuspected genomic imbalance to the incidence of pediatric CKD is unknown. METHODS. We performed chromosomal microarrays to detect genomic imbalances in children enrolled in the Chronic Kidney Disease in Children (CKiD) prospective cohort study, a longitudinal prospective multiethnic observational study of North American children with mild to moderate CKD. Patients with clinically detectable syndromic disease were excluded from evaluation. We compared 419 unrelated children enrolled in CKiD to multiethnic cohorts of 21,575 children and adults that had undergone microarray genotyping for studies unrelated to CKD. RESULTS. We identified diagnostic copy number disorders in 31 children with CKD (7.4% of the cohort). We detected 10 known pathogenic genomic disorders, including the 17q12 deletion HNF1 homeobox B (HNF1B) and triple X syndromes in 19 of 419 unrelated CKiD cases as compared with 98 of 21,575 control individuals (OR 10.8, P = 6.1 × 10–20). In an additional 12 CKiD cases, we identified 12 likely pathogenic genomic imbalances that would be considered reportable in a clinical setting. These genomic imbalances were evenly distributed among patients diagnosed with congenital and noncongenital forms of CKD. In the vast majority of these cases, the genomic lesion was unsuspected based on the clinical assessment and either reclassified the disease or provided information that might have triggered additional clinical care, such as evaluation for metabolic or neuropsychiatric disease. CONCLUSION. A substantial proportion of children with CKD have an unsuspected genomic imbalance, suggesting genomic disorders as a risk factor for common forms of pediatric nephropathy. Detection of pathogenic imbalances has practical implications for personalized diagnosis and health monitoring in this population. TRIAL REGISTRATION. ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00327860","term_id":"NCT00327860"}}NCT00327860. FUNDING. This work was supported by the NIH, the National Institutes of Diabetes and Digestive and Kidney Diseases (NIDDK), the National Institute of Child Health and Human Development, and the National Heart, Lung, and Blood Institute.

Here, we report a genetic study of an extended family of Chinese ancestry with focal segmental glomerulosclerosis (FSGS), with one of the affected members also concurrently diagnosed with IgA nephropathy (IgAN). By genome-wide linkage analysis and subsequent sequencing, we identified an S85W mutation in the inverted formin 2 (INF2) gene that perfectly cosegregated with the kidney disease phenotype. The entire INF2 coding region was sequenced in 200 healthy controls, 55 families with FSGS, and 34 families with IgAN. This analysis identified a novel insertion, S129_Q130insVRQLS, in another FSGS pedigree. In vitro studies found that α-actinin 4 expression was decreased and INF2 showed perinuclear localization in S85W-transfected podocytes. Phosphorylation of serum response factor, and that its nuclear translation was decreased in S85W podocytes, indicated decreased activation in mutants. Abnormal actin organization was also found in S85W podocytes, while no change of microtubule structure was observed. Co-immunoprecipitation and immunofluorescence found decreased interaction between INF2 and Cdc42 in S85W podocytes. However, all these changes were not found in S129_Q130insVRQLS podocytes. The overall frequency of INF2 mutations was ~3.6% among Chinese familial FSGS, which was considerably lower than that from studies of European FSGS families. Thus, S85W but not the S129_Q130insVRQLS variant leads to podocyte cytoskeletal abnormalities, probably by impaired serum response factor phosphorylation.

IgA nephropathy is the most common form of primary glomerulonephritis worldwide. Mucosal infections and food antigens, including wheat gluten, have been proposed as potential contributing environmental factors. Increased immune reactivity to gluten and/or association with celiac disease, an autoimmune disorder triggered by ingestion of gluten, have been reported in IgA nephropathy. However, studies are inconsistent about this association. We aimed to evaluate the proposed link between IgA nephropathy and celiac disease or immune reactivity to gluten by conducting a comprehensive analysis of associated serologic markers in cohorts of well-characterized patients and controls. Study participants included patients with biopsy-proven IgA nephropathy (n = 99), unaffected controls of similar age, gender, and race (n = 96), and patients with biopsy-proven celiac disease (n = 30). All serum specimens were tested for IgG and IgA antibodies to native gliadin and deamidated gliadin, as well as IgA antibody to transglutaminase 2 (TG2). Anti-TG2 antibody-positive nephropathy patients and unaffected controls were subsequently tested for IgA anti-endomysial antibody and genotyped for celiac disease-associated HLA-DQ2 and -DQ8 alleles. In comparison to unaffected controls, there was not a statistically significant increase in IgA or IgG antibody reactivity to gliadin in individuals with IgA nephropathy. In addition, the levels of celiac disease-specific serologic markers, i.e., antibodies to deamidated gliadin and TG2, did not differ between IgA nephropathy patients and unaffected controls. Results of the additional anti-endomysial antibody testing and HLA genotyping were corroborative. The data from this case-control study do not reveal any evidence to suggest a significant role for celiac disease or immune reactivity to gluten in IgA nephropathy.

We performed a genome-wide association study (GWAS) of IgA nephropathy (IgAN), the most common form of glomerulonephritis, with discovery and follow-up in 20,612 individuals of European and East Asian ancestry. We identified six novel genome-wide significant associations, four in ITGAM-ITGAX, VAV3 and CARD9 and two new independent signals at HLA-DQB1 and DEFA. We replicated the nine previously reported signals, including known SNPs in the HLA-DQB1 and DEFA loci. The cumulative burden of risk alleles is strongly associated with age at disease onset. Most loci are either directly associated with risk of inflammatory bowel disease (IBD) or maintenance of the intestinal epithelial barrier and response to mucosal pathogens. The geo-spatial distribution of risk alleles is highly suggestive of multi-locus adaptation and the genetic risk correlates strongly with variation in local pathogens, particularly helminth diversity, suggesting a possible role for host-intestinal pathogen interactions in shaping the genetic landscape of IgAN.

Acute renal failure (ARF) in hospitalized patients remains associated with significant morbidity and mortality. Most reports have detailed the in-hospital outcomes in ARF patients. This commentary focuses on the outcomes (including quality of life) of ARF patients, both adults and children, after discharge from the hospital.

IgA nephropathy (IgAN), major cause of kidney failure worldwide, is common in Asians, moderately prevalent in Europeans, and rare in Africans. It is not known if these differences represent variation in genes, environment, or ascertainment. In a recent GWAS, we localized five IgAN susceptibility loci on Chr.6p21 (HLA-DQB1/DRB1, PSMB9/TAP1, and DPA1/DPB2 loci), Chr.1q32 (CFHR3/R1 locus), and Chr.22q12 (HORMAD2 locus). These IgAN loci are associated with risk of other immune-mediated disorders such as type I diabetes, multiple sclerosis, or inflammatory bowel disease. We tested association of these loci in eight new independent cohorts of Asian, European, and African-American ancestry (N = 4,789), followed by meta-analysis with risk-score modeling in 12 cohorts (N = 10,755) and geospatial analysis in 85 world populations. Four susceptibility loci robustly replicated and all five loci were genome-wide significant in the combined cohort (P = 5×10−32–3×10−10), with heterogeneity detected only at the PSMB9/TAP1 locus (I2 = 0.60). Conditional analyses identified two new independent risk alleles within the HLA-DQB1/DRB1 locus, defining multiple risk and protective haplotypes within this interval. We also detected a significant genetic interaction, whereby the odds ratio for the HORMAD2 protective allele was reversed in homozygotes for a CFHR3/R1 deletion (P = 2.5×10−4). A seven–SNP genetic risk score, which explained 4.7% of overall IgAN risk, increased sharply with Eastward and Northward distance from Africa (r = 0.30, P = 3×10−128). This model paralleled the known East–West gradient in disease risk. Moreover, the prediction of a South–North axis was confirmed by registry data showing that the prevalence of IgAN–attributable kidney failure is increased in Northern Europe, similar to multiple sclerosis and type I diabetes. Variation at IgAN susceptibility loci correlates with differences in disease prevalence among world populations. These findings inform genetic, biological, and epidemiological investigations of IgAN and permit cross-comparison with other complex traits that share genetic risk loci and geographic patterns with IgAN., Author Summary IgA nephropathy (IgAN) is the most common cause of kidney failure in Asia, has lower prevalence in Europe, and is very infrequent among populations of African ancestry. A long-standing question in the field is whether these differences represent variation in genes, environment, or ascertainment. In a recent genome-wide association study of 5,966 individuals, we identified five susceptibility loci for this trait. In this paper, we study the largest IgAN case-control cohort reported to date, composed of 10,775 individuals of European, Asian, and African-American ancestry. We confirm that all five loci are significant contributors to disease risk across this multi-ethnic cohort. In addition, we identify two novel independent susceptibility alleles within the HLA-DQB1/DRB1 locus and a new genetic interaction between loci on Chr.1p36 and Chr.22q22. We develop a seven–SNP genetic risk score that explains nearly 5% of variation in disease risk. In geospatial analysis of 85 world populations, the genetic risk score closely parallels worldwide patterns of disease prevalence. The genetic risk score also predicts an unsuspected Northward risk gradient in Europe. This genetic prediction is verified by examination of registry data demonstrating, similarly to other immune-mediated diseases such as multiple sclerosis and type I diabetes, a previously unrecognized increase in IgAN–attributable kidney failure in Northern European countries.

Here we discuss recent advances in understanding the biochemical, immunologic, and genetic pathogenesis of IgA nephropathy, the most common primary glomerulonephritis. Current data indicate that at least four processes contribute to development of IgA nephropathy. Patients with IgA nephropathy often have a genetically determined increase in circulating levels of IgA1 with galactose-deficient O-glycans in the hinge-region (Hit 1). This glycosylation aberrancy is, however, not sufficient to induce renal injury. Synthesis and binding of antibodies directed against galactose-deficient IgA1 are required for formation of immune complexes that accumulate in the glomerular mesangium (Hits 2 and 3). These immune complexes activate mesangial cells, inducing proliferation and secretion of extracellular matrix, cytokines, and chemokines, which result in renal injury (Hit 4). Recent genome-wide association studies identify five distinct susceptibility loci--in the MHC on chromosome 6p21, the complement factor H locus on chromosome 1q32, and in a cluster of genes on chromosome 22q22--that potentially influence these processes and contain candidate mediators of disease. The significant variation in prevalence of risk alleles among different populations may also explain some of the sizable geographic variation in disease prevalence. Elucidation of the pathogenesis of IgA nephropathy provides an opportunity to develop disease-specific therapies.

Serum galactose-deficient IgA1 (Gd-IgA1) is an inherited risk factor for adult IgA nephropathy (IgAN). The goal of this study is to determine the heritability of serum Gd-IgA1 levels in children with IgAN and Henoch-Schönlein nephritis (HSPN). For this purpose, we obtained serum from 34 Caucasian families (20 pediatric cases of HSPN, 14 pediatric cases of IgAN, and 54 of their first-degree relatives), as well as from 51 age- and ethnicity-matched pediatric controls and 141 healthy adult controls. Serum Gd-IgA1 levels were quantified using an HAA-lectin-based ELISA. Children with either IgAN or HSPN had significantly higher Gd-IgA1 levels compared with pediatric controls (p = 1.7 × 10−7 and p = 6.5 × 10−9, respectively). Serum levels of Gd-IgA1 were also elevated in a large fraction of the first-degree relatives of pediatric IgAN and HSPN patients compared with unrelated adult controls (p = 3.2 × 10−6 and p = 5.1 × 10−4, respectively). The unilineal transmission of the trait was observed for 75% of families, bilineal transmission in 5%, and sporadic occurrence in 20%. The age-, gender-, and household-adjusted heritability of serum Gd-IgA1 level was estimated at 76% (p = 0.021) in pediatric IgAN patients and at 64% (p = 0.018) in HSPN patients. Our data demonstrate that serum Gd-IgA1 levels are highly inherited in pediatric IgAN and HSPN, providing support for yet another shared pathogenic link between these disorders.

Aging is a physiological process involving both genetic factors and environmental agents that can lead to function loss in organs. In the kidney, aging can cause leakage of proteins in urine, starting with albumin. Discovering molecular mechanisms responsible for albuminuria during aging could offer new perspectives on the etiology of this abnormality. Haplotype association mapping in the mouse is a novel approach which uses the haplotypes of the relatively closely related mouse inbred strains and the variation of the phenotypes among these strains to find associations between haplotypes and phenotype. Albumin-to-creatinine ratios, measures of urinary albumin excretion, were determined in 30 inbred mouse strains at 12, 18, and 24 months of age. To determine genetic loci that are involved in albuminuria, haplotype association mapping was performed for males and females separately at all 3 time points using a set of 63,222 SNPs. One significant and 8 suggestive loci were identified, some of which map to previously identified loci for traits associated with kidney damage in the mouse, but with a much higher resolution, which narrowed the mapped loci. These 9 loci were then investigated in the data of the genome-wide association scan for diabetic nephropathy in human type 1 diabetes. Two of the 9 mouse loci were found to be significantly associated with diabetic nephropathy, suggesting common underlying genes predisposing to kidney disease in mice and humans.

Badura-Stronka M, Jamsheer A, Materna-Kiryluk A, Sowinska A, Kiryluk K, Budny B, Latos-Bielenska A. A novel nonsense mutation in CUL4B gene in three brothers with X-linked mental retardation syndrome. Cabezas syndrome (MIM 300354) is a recently identified syndromic form of X-linked mental retardation (XLMR) caused by mutations in the CUL4B gene. In total, nine XLMR families carrying mutations in the CUL4B gene have been described to date. Here, we present a detailed clinical phenotype of three affected brothers of Polish descent. Based on the symptoms, we made a clinical diagnosis of Cabezas syndrome, which was subsequently confirmed by identification of a novel nonsense mutation (c.2107AT, p.703KX) in exon 18 of the CUL4B gene. The mutation was inherited from an asymptomatic mother and was present in all three affected brothers. The patients presented with typical features of Cabezas syndrome, such as severe mental retardation, speech impairment, hyperactivity, seizures, intention tremor, inguinal hernia, small feet, and craniofacial dysmorphism. In addition to previously described symptoms, syndactyly of the second and third toes and skin manifestations (hyperhydrosis and keratosis pilaris) were present in our cases. Our report provides further support that Cabezas syndrome is a recognizable syndromic form of XLMR. We conclude that the CUL4B gene should be screened in males with severe speech impairment and primary intention tremor, especially if characteristic facial dysmorphism is also present.

Peritoneal dialysis outflow failure caused by omental wrapping is a serious complication that is difficult to diagnose noninvasively. We report a case of outflow failure in which catheterography showed several characteristics of omental wrapping: "pseudocele" formation, delayed catheter emptying, and uneven distribution of contrast in the abdominal cavity. A laparoscopic procedure was performed with identification of peritoneal adhesion and greater omental wrapping. The catheter was stripped from the omentum and repositioned in the Douglas peritoneal sac. Catheterography is a reliable, safe, noninvasive, and inexpensive alternative procedure to diagnose outflow failure caused by omental wrapping.

Because dopamine D1 receptors (DRD1) influence renal sodium transport and vascular hemodynamics, we examined whether genetic polymorphisms play a role in renal function. We conducted polymorphism discovery across the DRD1 open reading frame and its 5′-UTR and then performed association studies with estimated glomerular filtration rate (eGFR), plasma creatinine (pCr), and fractional excretion of uric acid (FeUA). We used a twin/family group of 428 subjects from 195 families and a replication cohort of 677 patients from the Kaiser health-care organization sampled from the lower percentiles of diastolic blood pressures. Although the coding region lacked common non-synonymous variants, we identified two polymorphisms in the DRD1 5′-UTR (G-94A, A-48G) that occurred with frequencies of 15 and 30%, respectively. In the twin/family study, renal traits were highly heritable, such that DRD1 G-94A significantly associated with eGFR, pCr, and FeUA. Homozygotes for the G-94A minor allele (A/A) exhibited lower eGFR, higher pCr, and lower FeUA. No effects were noted for DRD1 A-48G. Patients in the Kaiser group had similar effects of G-94A on eGFR and pCr. Kidney cells transfected with the -94A variant but not the wild type vectors had increased receptor density. Because the -94A allele is common and may reduce glomerular capillary hydrostatic pressure, G-94A profiling may aid in predicting survival of renal function in patients with progressive renal disease.

Multiple studies have linked podocyte gene variants to diverse sporadic nephropathies, including HIV-1–associated nephropathy (HIVAN). We previously used linkage analysis to identify a major HIVAN susceptibility locus in mouse, HIVAN1. We performed expression quantitative trait locus (eQTL) analysis of podocyte genes in HIV-1 transgenic mice to gain further insight into genetic susceptibility to HIVAN. In 2 independent crosses, we found that transcript levels of the podocyte gene nephrosis 2 homolog (Nphs2), were heritable and controlled by an ancestral cis-eQTL that conferred a 3-fold variation in expression and produced reactive changes in other podocyte genes. In addition, Nphs2 expression was controlled by 2 trans-eQTLs that localized to the nephropathy susceptibility intervals HIVAN1 and HIVAN2. Transregulation of podocyte genes was observed in the absence of HIV-1 or glomerulosclerosis, indicating that nephropathy susceptibility alleles induce latent perturbations in the podocyte expression network. Presence of the HIV-1 transgene interfered with transregulation, demonstrating effects of gene-environment interactions on disease. These data demonstrate that transcript levels of Nphs2 and related podocyte-expressed genes are networked and suggest that the genetic lesions introduced by HIVAN susceptibility alleles perturb this regulatory pathway and transcriptional responses to HIV-1, increasing susceptibility to nephropathy.

Background and Purpose— The objective of this study was to determine the relationship between chronic kidney disease (CKD), race–ethnicity, and vascular outcomes. Methods— A prospective, multiracial cohort of 3298 stroke-free subjects with 6.5 years of mean follow-up time for vascular outcomes (stroke, myocardial infarction, vascular death) was used. Kidney function was estimated using serum creatinine and Cockcroft-Gault formula. Cox proportional hazards models were fitted to evaluate the relationship between kidney function and vascular outcomes. Results— In multivariate analysis, Cockcroft-Gault formula between 15 and 59 mL/min was associated with a significant 43% increased stroke risk in the overall cohort. Blacks with Cockcroft-Gault formula between 15 and 59 mL/min had significantly increased risk of both stroke (hazard ratio, 2.65; 95% CI, 1.47 to 4.77) and combined vascular outcomes (hazard ratio, 1.59; 95% CI, 1.10–2.92). Conclusion— Chronic kidney disease is a significant risk factor for stroke and combined vascular events, especially in blacks.

SUMMARY This case illustrates in a striking manner the potential renalcomplications associated with chronic, unrecognized VAshunt infection. The diagnosis of shunt nephritis is challen-ging and, as exemplified by this case, may be overlooked forseveral years, resulting in significant morbidity in the form ofongoing renal injury with proteinuria and renal failure. Thefinding of hematuria, proteinuria and even mild renalinsufficiency in a patient with a VA shunt should promptan aggressive microbiologic diagnostic evaluation to excludesubacute infection. Renal biopsy should be considered todocument the pathognomonic membranoproliferative lesionand to assess the relative degrees of acute versus chronicinjury. Further, this case highlights the critical importance ofexcluding secondary forms of disease in any patient with anephritic presentation and biopsy findings demonstratingmembranoproliferative features, as identification and treat-ment of the underlying condition may lead to remission ofproteinuria and normalization of renal excretory function,even in patients with a baseline biopsy finding of significantsclerosis alongside ongoing active inflammation, as was thecase in this patient. Finally, in this exciting era where theelucidation of entire microbial genome sequences has becomepossible, future studies correlating bacterial genomes andproteomes with specific mechanisms of disease may holdpromise for identifying specific antigens involved in thepathogenesis of immune-mediated conditions, such as shuntnephritis.

CASE PRESENTATION A 71-year-old Hispanic woman presented to our medical center with a general sense of feeling ‘unwell.’ She suffered from multiple medical conditions, including long-standing history of diabetes, hypertension, hypercholesterolemia, depression, and end-stage renal disease (ESRD) for which she has been on dialysis for the last 3 years. Seven years prior to her current admission, the patient presented with an acute onset of left seventh nerve palsy associated with hypercalcemia and submandibular and perihilar lymphadenopathy. Submandibular lymph node biopsy showed infiltration with a polymorphous population of lymphocytes and granulomas, findings consistent with sarcoidosis. She was treated with a course of corticosteroids and methotrexate, with complete resolution of symptoms within 2 years of the diagnosis. Steroids were discontinued 6 years and methotrexate 4 years before her current admission. Her sarcoidosis remained in complete remission. Her past medical history was also significant for primary hyperparathyroidism; she underwent partial parathyroidectomy in the early 1980s. The patient’s kidney disease had been diagnosed 4 years prior, when she presented with a nephrotic syndrome and creatinine (Cr) of 1.5 mg per 100 ml (ref. 0.5–0.9 mg per 100 ml). The kidney biopsy performed at that time revealed advanced focal segmental glomerulosclerosis and she progressed to ESRD within 1 year of the diagnosis. Over the last 3 years, the patient has been maintained on regular thrice-weekly hemodialysis through a radial arteriovenous fistula with adequate clearance (urea reduction ratio ranging from 77 to 84%) and no major complications. The patient was brought to the emergency room by her family for unstable gait with ‘dance-like’ quality. The symptoms developed gradually over the period of 2 days. The patient neither missed dialysis nor had been ill, and had no sick contacts. Her medication regimen included aspirin, diltiazem, paroxetine, statin, glipizide, sevelamer, multivitamins, and stool softeners. She denied any exposure to antipsychotics or antiemetics. There was no family history of movement disorders, psychiatric disease, or renal disease. The patient used to work as a seamstress and retired several years ago. She did not smoke or drink and denied any illicit substance use. The patient’s pulse was 82–88 per min and the blood

Background and Objectives There is increasing evidence that galactose-deficient IgA1 (Gd-IgA1) and Gd-IgA1-containing immune complexes are important for the pathogenesis of IgA nephropathy (IgAN). In the present study, we assessed a novel noninvasive multi-biomarker approach in the diagnostic test for IgAN. Materials and Methods We compared serum levels of IgA, IgG, Gd-IgA1, Gd-IgA1-specific IgG and Gd-IgA1-specific IgA in 135 IgAN patients, 79 patients with non-IgAN chronic kidney disease (CKD) controls and 106 healthy controls. Serum was collected at the time of kidney biopsy from all IgAN and CKD patients. Results Each serum marker was significantly elevated in IgAN patients compared to CKD (P

in the prevalence of esophageal dysplasia in patients with and without gluten-related disorders, the patients with Celiac Disease seem to develop dysplasia earlier (Long Rank p=0.01). Conclusions: Our results show an increased prevalence of gluten-related disorders in a cohort of patients with BE compared to the population referred to our center. Patients with gluten-related disorders may have a higher risk of accelerated development of dysplasia. Future studies are needed to confirm these findings in a larger group of patients.