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Clonal hematopoiesis of indeterminate potential (CHIP), defined by the age-related ontogenesis of expanded leukemogenic mutations indicative of a genetically distinct clonal leukocyte population, is associated with risk of hematologic malignancy and cardiovascular disease. In experimental models, recapitulation of CHIP promotes kidney interstitial fibrosis with direct tissue infiltration of donor macrophages. We tested the hypothesis that CHIP is associated with kidney function decline in the general population.Cohort Study: Setting and Participants: 12,004 individuals from three community-based cohorts in the TOPMed Consortium.CHIP status from blood DNA-derived whole genome sequences.Risk of 30% decline in estimated glomerular filtration rate (eGFR) and percent eGFR decline per year during follow-up.Cox proportional hazards models for 30% eGFR decline endpoint and generalized estimating equations for annualized relative change in eGFR with meta-analysis. Study-specific estimates were combined using fixed-effect meta-analysis.Median baseline eGFR was 84 ml/min/1.73mSmall number of participants with moderate-to-advanced kidney disease and restricted set of CHIP driver mutations.We report an association between CHIP and kidney function decline in three general population cohorts without known kidney disease. Further studies are needed to investigate this novel condition and its potential impact among individuals with overt kidney disease.

Age is a predominant risk factor for acute kidney injury (AKI), yet the biological mechanisms underlying this risk are largely unknown and to date no genetic mechanisms for AKI have been established. Clonal hematopoiesis of indeterminate potential (CHIP) is a recently recognized biological mechanism conferring risk of several chronic aging diseases including cardiovascular disease, pulmonary disease and liver disease. In CHIP, blood stem cells acquire mutations in myeloid cancer driver genes such asDNMT3A, TET2, ASXL1andJAK2and the myeloid progeny of these mutated cells contribute to end-organ damage through inflammatory dysregulation. We sought to establish whether CHIP causes acute kidney injury (AKI). To address this question, we first evaluated associations with incident AKI events in three population-based epidemiology cohorts (N = 442,153). We found that CHIP was associated with a greater risk of AKI (adjusted HR 1.26, 95% CI: 1.19–1.34, pDNMT3A(HR: 1.49, 95% CI: 1.37–1.61, pDNMT3ACHIP was more common among those with a non-resolving pattern of injury (HR 2.3, 95% CI: 1.14–4.64, p = 0.03). To gain mechanistic insight, we evaluated the role ofTet2-CHIP to AKI in ischemia-reperfusion injury (IRI) and unilateral ureteral obstruction (UUO) mouse models. In both models, we observed more severe AKI and greater post-AKI kidney fibrosis inTet2-CHIP mice. Kidney macrophage infiltration was markedly increased inTet2-CHIP mice andTet2-CHIP mutant renal macrophages displayed greater pro-inflammatory responses. In summary, this work establishes CHIP as a genetic mechanism conferring risk of AKI and impaired kidney function recovery following AKI via an aberrant inflammatory response in CHIP derived renal macrophages.

Adenosine triphosphate-citrate lyase (ACLY) inhibition is a therapeutic strategy under investigation for atherosclerotic cardiovascular disease, nonalcoholic steatohepatitis, and metabolic syndrome. Mouse models suggest that ACLY inhibition could reduce inflammation and kidney fibrosis. Genetic analysis of ACLY in chronic kidney disease (CKD) has not been performed.We constructed a genetic instrument by selecting variants associated withMendelian randomization analyses revealed that genetically reduced ACLY expression was associated with reduced risk of CKD but had no effect on either eGFR or ACR. Further evaluation of ACLY in kidney disease is warranted.

Using age- and height-adjusted total kidney volume, the Mayo Clinic Imaging Classification provides a validated approach to assess the risk of chronic kidney disease (CKD) progression in autosomal dominant polycystic kidney disease (ADPKD), but requires excluding patients with atypical imaging patterns, whose clinical characteristics have been poorly defined. We report an analysis of the prevalence, clinical and genetic characteristics of patients with atypical polycystic kidney disease by imaging. Patients from the extended Toronto Genetic Epidemiology Study of Polycystic Kidney Disease recruited between 2016 and 2018 completed a standardized clinical questionnaire, kidney function assessment, genetic testing, and kidney imaging by magnetic resonance or computed tomography. We compared the prevalence, clinical features, genetics, and renal prognosis of atypical versus typical polycystic kidney disease by imaging. Forty-six of the 523 (8.8%) patients displayed atypical polycystic kidney disease by imaging; they were older (55 vs. 43 years; P P PKD1 or PKD2 mutation (9.2% vs. 80.4%; P P

Clonal hematopoiesis of indeterminate potential (CHIP) is a common form of age-related somatic mosaicism that is associated with significant morbidity and mortality. CHIP mutations can be identified in peripheral blood samples sequenced using approaches that cover the whole genome, whole exome or targeted genetic regions; however, differentiating true CHIP mutations from sequencing artifacts and germline variants is a considerable bioinformatic challenge. We present a stepwise method that combines filtering based on sequencing metrics, variant annotation, and novel population-based associations to increase the accuracy of CHIP calls. We apply this approach to ascertain CHIP in ∼550,000 individuals in the UK Biobank complete whole exome cohort and the All of Us Research Program initial whole genome release cohort. CHIP ascertainment on this scale unmasks recurrent artifactual variants and highlights the importance of specialized filtering approaches for several genes includingTET2andASXL1. We show how small changes in filtering parameters can considerably increase CHIP misclassification and reduce the effect size of epidemiological associations. Our high-fidelity call set refines prior population-based associations of CHIP with incident outcomes. For example, the annualized incidence of myeloid malignancy in individuals with small CHIP clones is 0.03%/year, which increases to 0.5%/year amongst individuals with very large CHIP clones. We also find a significantly lower prevalence of CHIP in individuals of self-reported Latino or Hispanic ethnicity in All of Us, highlighting the importance of including diverse populations. The standardization of CHIP calling will increase the fidelity of CHIP epidemiological work and is required for clinical CHIP diagnostic assays.

Autosomal dominant polycystic kidney disease is the most common monogenic cause of ESKD. Genetic studies from patients and animal models have informed disease pathobiology and strongly support a "threshold model" in which cyst formation is triggered by reduced functional polycystin dosage below a critical threshold within individual tubular epithelial cells due to (1) germline and somatic PKD1 and/or PKD2 mutations, (2) mutations of genes (e.g., SEC63, SEC61B, GANAB, PRKCSH, DNAJB11, ALG8, and ALG9) in the endoplasmic reticulum protein biosynthetic pathway, or (3) somatic mosaicism. Genetic testing has the potential to provide diagnostic and prognostic information in cystic kidney disease. However, mutation screening of PKD1 is challenging due to its large size and complexity, making it both costly and labor intensive. Moreover, conventional Sanger sequencing-based genetic testing is currently limited in elucidating the causes of atypical polycystic kidney disease, such as within-family disease discordance, atypical kidney imaging patterns, and discordant disease severity between total kidney volume and rate of eGFR decline. In addition, environmental factors, genetic modifiers, and somatic mosaicism also contribute to disease variability, further limiting prognostication by mutation class in individual patients. Recent innovations in next-generation sequencing are poised to transform and extend molecular diagnostics at reasonable costs. By comprehensive screening of multiple cystic disease and modifier genes, targeted gene panel, whole-exome, or whole-genome sequencing is expected to improve both diagnostic and prognostic accuracy to advance personalized medicine in autosomal dominant polycystic kidney disease.

Background and objectives Progression of autosomal dominant polycystic kidney disease (ADPKD) is highly variable. On average, protein-truncating PKD1 mutations are associated with the most severe kidney disease among all mutation classes. Here, we report that patients with protein-truncating PKD1 mutations may also have mild kidney disease, a finding not previously well recognized. Design, setting, participants, & measurements From the extended Toronto Genetic Epidemiologic Study of Polycystic Kidney Disease, 487 patients had PKD1 and PKD2 sequencing and typical ADPKD imaging patterns by magnetic resonance imaging or computed tomography. Mayo Clinic Imaging Classification on the basis of age- and height-adjusted total kidney volume was used to assess their cystic disease severity; classes 1A or 1B were used as a proxy to define mild disease. Multivariable linear regression was performed to test the effects of age, sex, and mutation classes on log-transformed height-adjusted total kidney volume and eGFR. Results Among 174 study patients with typical imaging patterns and protein-truncating PKD1 mutations, 32 (18%) were found to have mild disease on the basis of imaging results (i.e., Mayo Clinic Imaging class 1A–1B), with their mutations spanning the entire gene. By multivariable analyses of age, sex, and mutation class, they displayed mild disease similar to patients with PKD2 mutations and Mayo Clinic Imaging class 1A–1B. Most of these mildly affected patients with protein-truncating PKD1 mutations reported a positive family history of ADPKD in preceding generations and displayed significant intrafamilial disease variability. Conclusions Despite having the most severe mutation class, 18% of patients with protein-truncating PKD1 mutations had mild disease on the basis of clinical and imaging assessment. Podcast This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2021_02_18_CJN11100720_final.mp3

Preprint servers, such as arXiv and bioRxiv, have disrupted the scientific communication landscape by providing rapid access to research before peer review. medRxiv was launched as a free online repository for preprints in the medical, clinical, and related health sciences in 2019. In this review, we present the uptake of preprint server use in nephrology and discuss specific considerations regarding preprint server use in medicine. Distribution of kidney-related research on preprint servers is rising at an exponential rate. Survey of nephrology journals identified that 15 of 17 (88%) are publishing original research accepted submissions that have been uploaded to preprint servers. After reviewing 52 clinically impactful trials in nephrology discussed in the online Nephrology Journal Club (NephJC), an average lag of 300 days was found between study completion and publication, indicating an opportunity for faster research dissemination. Rapid review of papers discussing benefits and risks of preprint server use from the researcher, publisher, or end user perspective identified 53 papers that met criteria. Potential benefits of biomedical preprint servers included rapid dissemination, improved transparency of the peer review process, greater visibility and recognition, and collaboration. However, these benefits come at the risk of rapid spread of results not yet subjected to the rigors of peer review. Preprint servers shift the burden of critical appraisal to the reader. Media may be especially at risk due to their focus on "late-breaking" information. Preprint servers have played an even larger role when late-breaking research results are of special interest, such as during the global coronavirus disease 2019 pandemic. Coronavirus disease 2019 has brought both the benefits and risks of preprint servers to the forefront. Given the prominent online presence of the nephrology community, it is poised to lead the medicine community in appropriate use of preprint servers.

Using age- and height-adjusted total kidney volume, the Mayo Clinic Imaging Classification provides a validated approach to assess the risk of chronic kidney disease (CKD) progression in autosomal dominant polycystic kidney disease (ADPKD), but requires excluding patients with atypical imaging patterns, whose clinical characteristics have been poorly defined. We report an analysis of the prevalence, clinical and genetic characteristics of patients with atypical polycystic kidney disease by imaging. Patients from the extended Toronto Genetic Epidemiology Study of Polycystic Kidney Disease recruited between 2016 and 2018 completed a standardized clinical questionnaire, kidney function assessment, genetic testing, and kidney imaging by magnetic resonance or computed tomography. We compared the prevalence, clinical features, genetics, and renal prognosis of atypical versus typical polycystic kidney disease by imaging. Forty-six of the 523 (8.8%) patients displayed atypical polycystic kidney disease by imaging; they were older (55 vs. 43 years; P PKD1 or PKD2 mutation (9.2% vs. 80.4%; P

Numerous genes for monogenic kidney diseases with classical patterns of inheritance, as well as genes for complex kidney diseases that manifest in combination with environmental factors, have been discovered. Genetic findings are increasingly used to inform clinical management of nephropathies, and have led to improved diagnostics, disease surveillance, choice of therapy, and family counseling. All of these steps rely on accurate interpretation of genetic data, which can be outpaced by current rates of data collection. In March of 2021, Kidney Diseases: Improving Global Outcomes (KDIGO) held a Controversies Conference on “Genetics in Chronic Kidney Disease (CKD)” to review the current state of understanding of monogenic and complex (polygenic) kidney diseases, processes for applying genetic findings in clinical medicine, and use of genomics for defining and stratifying CKD. Given the important contribution of genetic variants to CKD, practitioners with CKD patients are advised to “think genetic,” which specifically involves obtaining a family history, collecting detailed information on age of CKD onset, performing clinical examination for extrarenal symptoms, and considering genetic testing. To improve the use of genetics in nephrology, meeting participants advised developing an advanced training or subspecialty track for nephrologists, crafting guidelines for testing and treatment, and educating patients, students, and practitioners. Key areas of future research, including clinical interpretation of genome variation, electronic phenotyping, global representation, kidney-specific molecular data, polygenic scores, translational epidemiology, and open data resources, were also identified.

Purpose of review: Patients with autosomal dominant polycystic kidney disease (ADPKD) have kidney cysts and kidney enlargement decades before progressing to advanced chronic kidney disease (CKD), meaning patients live most of their adult life with a chronic medical condition. The coronavirus disease 2019 (COVID-19) pandemic has created common questions among patients with ADPKD. In this review, we discuss COVID-19 concerns centered around a patient with a common clinical vignette. Sources of information: We performed PubMed and Google scholar searches for English, peer-reviewed studies related to “COVID-19,” “ADPKD,” “CKD,” “tolvaptan,” “angiotensin-converting enzyme inhibitors” (ACEi), “angiotensin receptor blockers” (ARB), and “vaccination.” We also evaluated transplant data provided by the Ontario Trillium Gift of Life Network. Methods: Following an assessment of available literature, this narrative review addresses common questions of patients with ADPKD in the context of the COVID-19 pandemic. Key findings: Data regarding the risk of developing COVID-19 and the risk of adverse COVID-19 outcomes in patients with ADPKD remain limited, but patients with ADPKD with impaired estimated glomerular filtration rate (eGFR), kidney transplants, or on dialysis are likely at similar increased risk as those with generally defined CKD. We provide strategies to improve virtual care, which is likely to persist after the pandemic. Current evidence suggests ACEi, ARB, and tolvaptan treatment should be continued unless contraindicated due to severe illness. When available, and in the absence of a severe allergy, vaccination is recommended for all patients with ADPKD. Limitations: This narrative review is limited by a paucity of high-quality data on COVID-19 outcomes in patients specifically with ADPKD. Implications: Patients with ADPKD who have developed advanced CKD, require dialysis, or who have received a kidney transplant are at elevated risk of COVID-19 complications.

BackgroundATP-citrate lyase (ACLY) inhibition is a promising therapeutic target for dyslipidemia, atherosclerotic cardiovascular disease, non-alcoholic steatohepatitis, and metabolic syndrome. Genetic analysis of its role in chronic kidney disease (CKD) has not been performed.MethodsWe constructed a genetic instrument by selecting variants associated with ACLY expression level in the expression quantitative trait loci genetics consortium (eQTLGen) that includes blood samples from 31,684 participants. In a two-sample Mendelian randomization analysis, we then evaluated the effect of genetically predicted ACLY expression on risk of CKD, estimated glomerular filtration rate (eGFR), and microalbuminuria using the CKD Genetics consortium (CKDGen), United Kingdom biobank, and the Finnish Genetics consortium (FinnGen) totaling 66,396 CKD cases and 958,517 controls.ResultsACLY is constitutively expressed in all cell types including in whole blood. The genetic instrument included 13 variants and explained 1.5% of variation in whole blood ACLY gene expression. A 34% reduction in genetically predicted ACLY expression was associated with a 0.04 mmol/L reduced low-density lipoprotein cholesterol (P = 3.4 × 10−4) and a 9% reduced risk of CKD (stage 3,4,5, dialysis or eGFR below 60 ml/min/1.73m2) (OR = 0.91, 95% C.I. 0.85-0.98, P = 0.008), but no association was observed with eGFR nor microalbuminuria.ConclusionMendelian Randomization analysis provides cautious optimism regarding the possibility of ACLY as a therapeutic target for CKD.

Introduction Discordance in kidney disease severity between affected relatives is a recognized feature of autosomal dominant polycystic kidney disease (ADPKD). Here, we report a systematic study of a large cohort of families to define the prevalence and clinical features of intrafamilial discordance in ADPKD. Methods The extended Toronto Genetic Epidemiology Study of Polycystic Kidney Disease (eTGESP) cohort includes 1390 patients from 612 unrelated families with ADPKD ascertained in a regional polycystic kidney disease center. All probands underwent comprehensive PKD1 and PKD2 mutation screening. Total kidney volume by magnetic resonance imaging (MRI) was available in 500 study patients. Results Based on (i) rate of estimated glomerular filtration rate (eGFR) decline, (ii) age at onset of end-stage renal disease (ESRD), and (iii) Mayo Clinic Imaging Classification (MCIC), 20% of patients were classified as having mild disease, and 33% as having severe disease. Intrafamilial ADPKD discordance with at least 1 mild and 1 severe case was observed in 43 of 371 (12%) families, at a similar frequency regardless of the responsible gene (PKD1/PKD2/no mutation detected) or mutation type (protein-truncating versus nontruncating). Intrafamilial discordance was more common in larger families and was present in 30% of families with more than 5 affected members. The heritability of age at onset of ESRD was similar between different mutation types. Conclusion Extreme kidney disease discordance is present in at least 12% of families with ADPKD, regardless of the underlying mutated gene or mutation class. Delineating genetic and environmental modifiers underlying the observed intrafamilial ADPKD variability will provide novel insights into the mechanisms of progression in ADPKD., Graphical abstract

BackgroundClonal hematopoiesis of indeterminate potential (CHIP) is an inflammatory premalignant disorder resulting from acquired genetic mutations in hematopoietic stem cells. CHIP is common in aging populations and associated with cardiovascular morbidity and overall mortality, but its role in chronic kidney disease (CKD) has not been investigated.MethodsWe performed targeted sequencing to detect CHIP mutations in a cohort of 87 adults with eGFR < 60 ml/min/1.73m2. Kidney function, hematologic, and mineral bone disease parameters were assessed cross-sectionally at baseline, and a total of 2,091 creatinine measurements and 3,382 hemoglobin measurements were retrospectively collected over the following 12-year period.ResultsAt baseline, 20 of 87 (23%) cohort participants had CHIP detected. Those with CHIP had lower baseline eGFR (22.3 ± 11.2 vs. 28.2 ± 11.5 ml/min/1.73 m2, P = 0.04) in age- and sex-adjusted regression models. Individuals with CHIP had a 2.5–fold increased risk of incident 50% decline in eGFR or ESKD in a Cox proportional hazard model adjusted for age and sex (95% confidence interval, 1.3–4.7). The annualized rate of eGFR decline adjusted for age and sex was -2.3 ±1.1 ml/min/1.73m2 per year in those with CHIP versus -1.6 ±0.5 ml/min/1.73m2 per year in those without CHIP. Further, those with CHIP had lower hemoglobin at baseline (11.6 ± 0.3 vs. 12.8 ± 0.2 g/dL, P = 0.0003) and throughout the follow-up period despite a greater use of erythropoiesis-stimulating agents.ConclusionIn those with pre-existing CKD, CHIP was associated with lower eGFR at baseline, faster progression of CKD, and anemia.

Sexual dysfunction occurs commonly in people with chronic kidney disease (CKD) and has been recognized as a research priority. We sought to evaluate the current state of the literature addressing sexual dysfunction in people with CKD and identify barriers and strategies to improve our management of this important symptom.OVID Medline and Google Scholar were searched for English, peer-reviewed studies using keywords and terms related to "Chronic Kidney Disease," "sexuality," and "sexual dysfunction OR function."In this narrative review, we describe definitions of sexual dysfunction and contributors exacerbated by CKD, barriers to researching sexual dysfunction in people with CKD, and possible avenues for future research.Sexual dysfunction is common in people with CKD and results from a combination of kidney disease itself, as well as its associated physical (ie, comorbidities) and nonphysical factors. Barriers to the study of sexual dysfunction in CKD include inconsistent disease definitions, stigma, variable efficacy and safety of established therapies, and evolving gender roles in sexual function. Potential avenues for future research to improve the sexual function in people with CKD may include evaluating the safety and efficacy of established therapies in people with CKD using a variety of observational and interventional study designs, engaging people with CKD and multidisciplinary team members in research, and using implementation science methods to translate what is known about sexual function into clinical practice. Concerted efforts are required to break down barriers and improve sexual function in people with CKD. Patients have identified this as an important research priority, and national networks need to direct efforts to reduce symptom burden.This narrative review was limited by a paucity of high-quality studies examining sexual dysfunction specifically in people with kidney disease.Les dysfonctions sexuelles sont fréquentes chez les personnes atteintes d’insuffisance rénale chronique (IRC) et ont été reconnues comme une priorité de recherche. Cette revue avait pour objectif d’évaluer la documentation actuelle traitant du dysfonctionnement sexuel chez les personnes atteintes d’IRC et de répertorier les obstacles à la recherche dans ce domaine et les stratégies qui permettent d’améliorer la gestion de cet important symptôme.Les bases de données OVID Medline et Google Scholar ont été consultées à la recherche des études rédigées en anglais et évaluées par des pairs à l’aide de mots-clés et de termes liés àCette revue narrative présente les définitions de la dysfonction sexuelle et les contributeurs exacerbés par l’IRC. Elle décrit également les obstacles limitant la recherche sur le dysfonctionnement sexuel chez les personnes atteintes d’IRC et cerne de possibles pistes pour les recherches futures.Le dysfonctionnement sexuel est fréquent chez les personnes atteintes d’IRC et résulte d’une combinaison de la néphropathie elle-même et de facteurs physiques (c.-à-d. les maladies concomitantes) et non physiques qui y sont associés. Les obstacles limitant l’étude de la dysfonction sexuelle en contexte d’IRC comprennent: 1) l’incohérence dans les différentes définitions de maladie; 2) la stigmatization; 3) l’efficacité et l’innocuité variables des thérapies existantes; et 4) le caractère évolutif des rôles des genres dans la fonction sexuelle. Les possibles axes de recherche pour les études futures pourraient inclure: 1) l’utilization d’une variété de modèles d’études observationnelles et interventionnelles pour évaluer l’innocuité et l’efficacité des thérapies existantes dans cette population de patients; 2) la participation de patients et de membres de l’équipe multidisciplinaire à la recherche, et 3) l’utilization de méthodes scientifiques de mise en œuvre afin de traduire les connaissances dans la pratique clinique. Des efforts concertés sont nécessaires pour éliminer les obstacles à la recherche et améliorer la fonction sexuelle des personnes atteintes d’IRC. Il s’agit d’une importante priorité de recherche pour les patients, et les réseaux nationaux se doivent d’orienter leurs efforts vers la réduction du fardeau des symptômes.Cette revue narrative était limitée par le manque d’études de haute qualité examinant spécifiquement la dysfonction sexuelle chez les personnes atteintes de néphropathies.

More than 10% of patients with advanced CKD have a rare pathogenic genetic variant that significantly contributes to their disease (1). Ideally, early genetic testing would lead to a specific diagnosis of the underlying cause of CKD which would ultimately prevent or delay progression to kidney failure. Adult-onset conditions for which genetic testing is available in nephrology are wide ranging and include cystic kidney diseases, type IV collagen nephropathy (Alport syndrome), congenital abnormalities of the kidney and urinary tract, nephrotic syndrome including FSGS, tubulopathies including autosomal dominant tubulointerstitial kidney disease, channelopathies including Bartter and Gitelman syndromes, and nephronophthisis among others (2). Using clinical clues to select patients for sequencing can increase the probability of identifying a rare pathogenic variant. In this issue of Kidney360 , Lundquist et al. report their experience using commercial diagnostic genetic panels in an academic adult nephrology clinic to assist the clinical care of patients (3). Using commercial laboratories to provide sequencing, they report identifying pathogenic variants in nine of 19 CKD patients. An additional two patients were cleared for kidney donation because they did not have a familial pathogenic variant. The authors suggest that their experience demonstrates the feasibility of nephrology genetic testing without specific genetics infrastructure, although they admit there were administrative hurdles in obtaining preauthorization for funding and that a genetic counselor was funded by a hospital initiative. Young age at disease onset and clinical clues suggestive of a genetic kidney disease increase the pretest probability of discovering a pathogenic variant (2). Although pediatric nephrologists recognize genetics as a valuable diagnostic tool, it is a paradigm shift to suggest that adult nephrologists can also successfully utilize genetic testing to assist in diagnosis. …

BACKGROUND AND OBJECTIVES: Progression of autosomal dominant polycystic kidney disease (ADPKD) is highly variable. On average, protein-truncating PKD1 mutations are associated with the most severe kidney disease among all mutation classes. Here, we report that patients with protein-truncating PKD1 mutations may also have mild kidney disease, a finding not previously well recognized. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: From the extended Toronto Genetic Epidemiologic Study of Polycystic Kidney Disease, 487 patients had PKD1 and PKD2 sequencing and typical ADPKD imaging patterns by magnetic resonance imaging or computed tomography. Mayo Clinic Imaging Classification on the basis of age- and height-adjusted total kidney volume was used to assess their cystic disease severity; classes 1A or 1B were used as a proxy to define mild disease. Multivariable linear regression was performed to test the effects of age, sex, and mutation classes on log-transformed height-adjusted total kidney volume and eGFR. RESULTS: Among 174 study patients with typical imaging patterns and protein-truncating PKD1 mutations, 32 (18%) were found to have mild disease on the basis of imaging results (i.e., Mayo Clinic Imaging class 1A–1B), with their mutations spanning the entire gene. By multivariable analyses of age, sex, and mutation class, they displayed mild disease similar to patients with PKD2 mutations and Mayo Clinic Imaging class 1A–1B. Most of these mildly affected patients with protein-truncating PKD1 mutations reported a positive family history of ADPKD in preceding generations and displayed significant intrafamilial disease variability. CONCLUSIONS: Despite having the most severe mutation class, 18% of patients with protein-truncating PKD1 mutations had mild disease on the basis of clinical and imaging assessment. PODCAST: This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2021_02_18_CJN11100720_final.mp3

On January 18, 2020, the Nephrology is Back learning day forum was held in Toronto, ON, Canada. The objectives of the meeting were to describe recent advances in nephrology for community and academic nephrologists and patients, and to define challenges and opportunities for integration of new data into clinical practice. The intent was to test a unique forum for continuing medical education integrating physician and patient experiences with the goal of encouraging change in practice.Program content was based on current literature and clinical experience. Additional information was provided by patient partners who attended the meeting to provide their perspective on current issues in nephrology.A steering committee (A.L., A.S., and D.S.) developed goals and an outline for the content to be covered over the course of the meeting and led the recruitment of speakers. Speakers were asked to develop their presentations independently following direction by the committee, based on primary sources, including their own experiences. Presentations were followed by discussion including both physicians and patients, and participants had an opportunity to evaluate the conference and its outcomes.We present a unique approach to providing continuing medical education by including both physicians and patients in the learning process. Patient perspectives accompanying presentations around data and other clinical topics provided a much different environment from other knowledge translation exercises. We believe this represents an innovative approach for knowledge translation that allows physicians to address clinical topics in a novel manner, including the integration of new findings into practice and the need to cascade this education to their peers.Because the conference was a one-time event, it has been difficult to assess the actual clinical impact of the knowledge translation exercise and whether physician behaviors have changed as a result of the activity. The conference could also have included broader representation from across Canada.The success of this test forum among both physicians and patient partners suggests that the inclusion of patient partners in learning could have an important role in future educational initiatives.La journée d’apprentissageLe contenu du programme s’inspirait de la documentation actuelle et de l’expérience clinique. L’invitation de patients partenaires à donner leur point de vue sur les enjeux actuels en néphrologie a fourni des informations supplémentaires.Le comité directeur (AL, AS et DS) a élaboré les objectifs de la réunion et un plan du contenu à couvrir, en plus de diriger le recrutement des intervenants. Ces derniers ont été invités à préparer leur présentation de façon indépendante en suivant les directives du comité, en se basant sur des sources primaires et en intégrant leurs expériences personnelles. Ces présentations ont été suivies de discussions impliquant tant des médecins que des patients, et les participants ont évalué la conférence et ses issues.Nous présentons une approche de formation médicale continue unique qui intègre à la fois l’avis des médecins et de patients partenaires au processus d’apprentissage. Le point de vue des patients sur les données et les autres sujets abordés pendant les présentations a fourni un environnement très différent des exercices d’application des connaissances habituels. Nous sommes d’avis qu’il s’agit d’une approche innovante pour l’application des connaissances et qu’elle offre aux médecins une nouvelle façon d’aborder certains sujets, notamment l’intégration des plus récentes découvertes à la pratique et la nécessité de transmettre ces apprentissages aux pairs.Il s’agissait d’un événement ponctuel. Il est donc difficile d’évaluer l’impact clinique réel de cette conférence sur la transmission des connaissances et de déterminer si les comportements des médecins ont changé à la suite de l’activité. La conférence aurait également bénéficié d’une meilleure représentation au niveau national.Le succès de cette conférence rassemblant à la fois des médecins et des patients partenaires suggère que l’inclusion de ces derniers au processus d’apprentissage pourrait jouer un rôle de premier plan dans les futures activités d’apprentissage.

Purpose: Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressive development of kidney cysts and enlargement and dysfunction of the kidneys. The Consortium of Radiologic Imaging Studies of the Polycystic Kidney Disease (CRISP) cohort revealed that 89.1% had either a PKD1 or PKD2 mutation. Of the CRISP patients with a genetic cause detected, mutations in PKD1 accounted for 85%, while mutations in the PKD2 accounted for the remaining 15%. Here, we report exome sequencing of 16 Saudi patients diagnosed with ADPKD and 16 ethnically matched controls. Methods: Exome sequencing was performed using combinatorial probe-anchor synthesis and improved DNA Nanoballs technology on BGISEQ-500 sequencers (BGI, China) using the BGI Exome V4 (59 Mb) Kit. Identified variants were validated with Sanger sequencing. Results: With the exception of GC-rich exon 1, we obtained excellent coverage of PKD1 (mean read depth = 88) including both duplicated and non-duplicated regions. Of nine patients with typical ADPKD presentations (bilateral symmetrical kidney involvement, positive family history, concordant imaging, and kidney function), four had protein truncating PKD1 mutations, one had a PKD1 missense mutation, and one had a PKD2 mutation. These variants have not been previously observed in the Saudi population. In seven clinically diagnosed ADPKD cases but with atypical features, no PKD1 or PKD2 mutations were identified, but rare predicted pathogenic heterozygous variants were found in cystogenic candidate genes including PKHD1, PKD1L3, EGF, CFTR, and TSC2. Conclusions: Mutations in PKD1 and PKD2 are the most common cause of ADPKD in Saudi patients with typical ADPKD. Abbreviations: ADPKD: Autosomal dominant polycystic kidney disease; CFTR: Cystic fibrosis transmembrane conductance regulator; EGF: Epidermal growth factor; MCIC: Mayo Clinic Imaging Classification; PKD: Polycystic kidney disease; TSC2: Tuberous sclerosis complex 2

Purpose of reviewPreprint servers including arXiv and bioRxiv have disrupted the scientific communication landscape by providing rapid access to pre--peer reviewed research. MedRxiv is a recently launched free online repository for preprints in the health sciences. We sought to summarize potential benefits and risks to preprint server use, from both the researcher and end--user perspective, and evaluate the uptake of preprint servers in the nephrology community.Sources of InformationWe performed a rapid review of articles describing preprint servers and their use. We approached the 20 highest impact nephrology journals regarding their policy towards the use of preprint servers. We evaluated the average time from study completion to publication of impactful articles in nephrology. Finally, we evaluated the number of nephrology articles submitted to preprint servers.FindingsTo date over 600 kidney--related articles have been uploaded to bioRxiv and medRxiv. The average time from study completion to publication was over 10 months. 16 of the top 20 nephrology journals currently accept research submitted to a preprint server. Transparency and collaboration, visibility and recognition, and rapid dissemination of results were identified as benefits of preprint servers. Concerns exist regarding the potential risk of non--peer reviewed medical research being publicly available.LimitationsPreprint servers remain a recent phenomenon in health sciences and their long-- term impact on the medical literature remains to be seen.ImplicationsThe quantity of research submitted to preprint servers is likely to continue to grow. The model for dissemination of research results will need to adapt to incorporate preprint servers.

The prevalence of end-stage renal disease (ESRD) and the number of kidney transplants performed continues to rise every year, straining the procurement of deceased and living kidney allografts and health systems. Genome-wide genotyping and sequencing of diseased populations have uncovered genetic contributors in substantial proportions of ESRD patients. A number of these discoveries are beginning to be utilized in risk stratification and clinical management of patients. Specifically, genetics can provide insight into the primary cause of chronic kidney disease (CKD), the risk of progression to ESRD, and post-transplant outcomes, including various forms of allograft rejection. The International Genetics & Translational Research in Transplantation Network (iGeneTRAiN), is a multi-site consortium that encompasses >45 genetic studies with genome-wide genotyping from over 51,000 transplant samples, including genome-wide data from >30 kidney transplant cohorts (n = 28,015). iGeneTRAiN is statistically powered to capture both rare and common genetic contributions to ESRD and post-transplant outcomes. The primary cause of ESRD is often difficult to ascertain, especially where formal biopsy diagnosis is not performed, and is unavailable in ∼2% to >20% of kidney transplant recipients in iGeneTRAiN studies. We overview our current copy number variant (CNV) screening approaches from genome-wide genotyping datasets in iGeneTRAiN, in attempts to discover and validate genetic contributors to CKD and ESRD. Greater aggregation and analyses of well phenotyped patients with genome-wide datasets will undoubtedly yield insights into the underlying pathophysiological mechanisms of CKD, leading the way to improved diagnostic precision in nephrology.

Background Estimating the prevalence of autosomal dominant polycystic kidney disease (ADPKD) is challenging because of age-dependent penetrance and incomplete clinical ascertainment. Early studies estimated the lifetime risk of ADPKD to be about one per 1000 in the general population, whereas recent epidemiologic studies report a point prevalence of three to five cases per 10,000 in the general population. Methods To measure the frequency of high-confidence mutations presumed to be causative in ADPKD and autosomal dominant polycystic liver disease (ADPLD) and estimate lifetime ADPKD prevalence, we used two large, population sequencing databases, gnomAD (15,496 whole-genome sequences; 123,136 exome sequences) and BRAVO (62,784 whole-genome sequences). We used stringent criteria for defining rare variants in genes involved in ADPKD ( PKD1 , PKD2 ), ADPLD ( PRKCSH , SEC63 , GANAB , ALG8 , SEC61B , LRP5 ), and potential cystic disease modifiers; evaluated variants for quality and annotation; compared variants with data from an ADPKD mutation database; and used bioinformatic tools to predict pathogenicity. Results Identification of high-confidence pathogenic mutations in whole-genome sequencing provided a lower boundary for lifetime ADPKD prevalence of 9.3 cases per 10,000 sequenced. Estimates from whole-genome and exome data were similar. Truncating mutations in ADPLD genes and genes of potential relevance as cyst modifiers were found in 20.2 cases and 103.9 cases per 10,000 sequenced, respectively. Conclusions Population whole-genome sequencing suggests a higher than expected prevalence of ADPKD-associated mutations. Loss-of-function mutations in ADPLD genes are also more common than expected, suggesting the possibility of unrecognized cases and incomplete penetrance. Substantial rare variation exists in genes with potential for phenotype modification in ADPKD.

Background Genome wide association studies of patients with European descent have identified common variants associated with risk of reduced estimated glomerular filtration rate (eGFR). A panel of eight variants were selected to evaluate their association and prevalence in a Saudi Arabian patient cohort with chronic kidney disease (CKD). Methods Eight genetic variants in four genes (SHROOM3, MYH9, SLC7A9, and CST3) were genotyped in 160 CKD patients and 189 ethnicity-matched healthy controls. Genetic variants were tested for association with the development of CKD (eGFR

Genetic testing can improve diagnostic precision in some patients with end-stage renal disease (ESRD) providing the potential for targeted therapy and improved patient outcomes. We sought to describe the genetic architecture of ESRD and Canadian data sources available for further genetic investigation into ESRD.We performed PubMed searches of English, peer-reviewed articles using keywords "chronic kidney disease," "ESRD," "genetics," "sequencing," and "administrative databases," and searched for nephrology-related Mendelian diseases on the Online Mendelian Inheritance in Man database.In this narrative review, we discuss our evolving understanding of the genetic architecture of kidney disease and ESRD, the risks and benefits of using genetic data to help diagnose and manage patients with ESRD, existing public Canadian biobanks and databases, and a vision for future genetic studies of ESRD in Canada.ESRD has a polygenic architecture including rare Mendelian mutations and common small effect genetic polymorphism contributors. Genetic testing will improve diagnostic accuracy and contribute to a precision medicine approach in nephrology. However, the risk and benefits of genetic testing needs to be considered from an individual and societal perspective, and further research is required. Merging existing health data, linking biobanks and administrative databases, and forming Canadian collaborations hold great potential for genetic research into ESRD. Large sample sizes are necessary to perform the suitably powered investigations required to bring this vision to reality.This is a narrative review of the literature discussing future directions and opportunities. It reflects the views and academic biases of the authors.National collaborations will be required to obtain sample sizes required for impactful, robust research. Merging established datasets may be one approach to obtain adequate samples. Patient education and engagement will improve the value of knowledge gained.Le dépistage génétique a le potentiel d’améliorer la précision diagnostique chez certains patients atteints d’insuffisance rénale terminale (IRT), et ouvre la voie à des thérapies ciblées et à de meilleures perspectives de santé pour les patients. Notre objectif est de présenter l’architecture génétique de l’IRT ainsi que les sources de données disponibles au Canada propres à faire avancer la recherche génétique sur l’IRT.Nous avons répertorié des articles rédigés en anglais, révisés par les pairs et publiés sur PubMed à l’aide des mots-clés suivants :Plusieurs aspects sont abordés dans le présent article synthèse : i) l’évolution de notre compréhension de l’architecture génétique de la maladie rénale et de l’IRT; ii) les risques et avantages de recourir aux données génétiques pour faciliter le diagnostic et la prise en charge des patients atteints d’IRT; iii) un répertoire des biobanques et bases de données publiques canadiennes, et iv) une vision pour la recherche en génétique sur l’IRT au Canada.L’IRT présente une architecture polygénique qui comprend de rares mutations mendéliennes et des contributeurs communs de polymorphisme génétique à effets mineurs. Le dépistage génétique contribuera à la précision du diagnostic et à l’adoption d’une médecine de précision en néphrologie. Cependant, les risques et avantages du dépistage génétique doivent être mesurés dans une perspective individuelle et sociétale, et des analyses supplémentaires s’imposent. La colligation des données en santé, des biobanques et des bases de données administratives existantes, couplée à des collaborations nationales, offre un vaste potentiel en recherche génétique sur l’IRT; il reste que des échantillons plus volumineux sont nécessaires pour étayer adéquatement les études qui permettront de concrétiser ce potentiel de recherche.Il s’agit d’un article synthèse de la documentation existante sur les perspectives et orientations d’avenir du point de vue des auteurs; l’article reflète conséquemment leur opinion et parti pris.Il nous faudra établir des collaborations nationales pour composer des échantillons dont la taille permettra de mener des recherches fructueuses et fiables. La colligation des jeux de données existants pourrait s’avérer une première approche à adopter pour y arriver. En outre, l’éducation des patients et leur participation à la recherche bonifieront la valeur des connaissances acquises.

Autosomal dominant polycystic kidney disease (ADPKD) is caused primarily by mutations of two genes, PKD1 and PKD2. In the presence of a positive family history of ADPKD, genetic testing is currently seldom indicated as the diagnosis is mostly based on imaging studies using well-established criteria. Moreover, PKD1 mutation screening is technically challenging due to its large size, complexity (i.e. presence of six pseudogenes with high levels of DNA sequence similarity) and extensive allelic heterogeneity. Despite these limitations, recent studies have delineated a strong genotype–phenotype correlation in ADPKD and begun to unravel the role of genetics underlying cases with atypical phenotypes. Furthermore, adaptation of next-generation sequencing (NGS) to clinical PKD genetic testing will provide a high-throughput, accurate and comprehensive screen of multiple cystic disease and modifier genes at a reduced cost. In this review, we discuss the evolving indications of genetic testing in ADPKD and how NGS-based screening promises to yield clinically important prognostic information for both typical as well as unusual genetic (e.g. allelic or genic interactions, somatic mosaicism, cystic kidney disease modifiers) cases to advance personalized medicine in the era of novel therapeutics for ADPKD.

BACKGROUND: Hereditary hemochromatosis leads to an increased lifetime risk for end-organ damage due to excess iron deposition. Guidelines recommend that genetic testing be performed in patients with clinical suspicion of iron overload accompanied by elevated serum ferritin and transferrin saturation levels.OBJECTIVE: To evaluate guideline adherence and the clinical and economic impact ofHFEgenetic testing.METHODS: The electronic charts of patients submitted forHFEtesting in 2012 were reviewed for genetic testing results, biochemical markers of iron overload and clinical history of phlebotomy.RESULTS: A total of 664 samples were sent for testing, with clinical, biochemical and phlebotomy data available for 160 patients. A positive C282Y homozygote or C282Y/H63D compound heterozygote test result was observed in 18% of patients. Patients with an at-riskHFEgenotype had significantly higher iron saturation, serum iron and hemoglobin (P45% and ferritin level >300 μg/L). Patients were four times more likely to undergo phlebotomy if they were gene test positive (RR 4.29 [95% CI 2.35 to 7.83]; PDISCUSSION: One-half of patients referred for testing did not exhibit biochemical evidence of iron overload. Many patients with biochemical evidence of iron overload, but with negative genetic test results, did not undergo phlebotomy. A requisition to determine clinical indication for testing may reduce the use of theHFEgenetic test. Finally, improvement of current genetic test characteristics would improve rationale for the test.CONCLUSION: A significant proportion of hemochromatosis genetic testing does not adhere to current guidelines and would not alter patient management.

Mutations in PKD1 or PKD2 cause autosomal dominant polycystic kidney disease, which proceeds to kidney failure in 70% of patients between the fourth and seventh decade of life.[1][1] Signs of autosomal dominant polycystic kidney disease (i.e., numerous cysts and enlargement of the kidneys) may be

Genetic loci explain only 25-30 % of the heritability observed in plasma lipid traits. Epistasis, or gene-gene interactions may contribute to a portion of this missing heritability. Using the genetic data from five NHLBI cohorts of 24,837 individuals, we combined the use of the quantitative multifactor dimensionality reduction (QMDR) algorithm with two SNP-filtering methods to exhaustively search for SNP-SNP interactions that are associated with HDL cholesterol (HDL-C), LDL cholesterol (LDL-C), total cholesterol (TC) and triglycerides (TG). SNPs were filtered either on the strength of their independent effects (main effect filter) or the prior knowledge supporting a given interaction (Biofilter). After the main effect filter, QMDR identified 20 SNP-SNP models associated with HDL-C, 6 associated with LDL-C, 3 associated with TC, and 10 associated with TG (permutation P value

Waist circumference (WC) and waist-to-hip ratio (WHR) are surrogate measures of central adiposity that are associated with adverse cardiovascular events, type 2 diabetes and cancer independent of body mass index (BMI). WC and WHR are highly heritable with multiple susceptibility loci identified to date. We assessed the association between SNPs and BMI-adjusted WC and WHR and unadjusted WC in up to 57 412 individuals of European descent from 22 cohorts collaborating with the NHLBI's Candidate Gene Association Resource (CARe) project. The study population consisted of women and men aged 20-80 years. Study participants were genotyped using the ITMAT/Broad/CARE array, which includes ∼50 000 cosmopolitan tagged SNPs across ∼2100 cardiovascular-related genes. Each trait was modeled as a function of age, study site and principal components to control for population stratification, and we conducted a fixed-effects meta-analysis. No new loci for WC were observed. For WHR analyses, three novel loci were significantly associated (P < 2.4 × 10(-6)). Previously unreported rs2811337-G near TMCC1 was associated with increased WHR (β ± SE, 0.048 ± 0.008, P = 7.7 × 10(-9)) as was rs7302703-G in HOXC10 (β = 0.044 ± 0.008, P = 2.9 × 10(-7)) and rs936108-C in PEMT (β = 0.035 ± 0.007, P = 1.9 × 10(-6)). Sex-stratified analyses revealed two additional novel signals among females only, rs12076073-A in SHC1 (β = 0.10 ± 0.02, P = 1.9 × 10(-6)) and rs1037575-A in ATBDB4 (β = 0.046 ± 0.01, P = 2.2 × 10(-6)), supporting an already established sexual dimorphism of central adiposity-related genetic variants. Functional analysis using ENCODE and eQTL databases revealed that several of these loci are in regulatory regions or regions with differential expression in adipose tissue.

Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ∼50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10-7) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification. © 2014 The American Society of Human Genetics.

Introduction Pharmacogenetics attempts to identify inter-individual genetic differences that are predictive of variable drug response and propensity to side effects, with the prospect of assisting physicians to select the most appropriate drug and dosage for treatment. However, many concerns regarding genetic tests exist. We sought to test the opinions of undergraduate science and medical students in southern Ontario universities toward pharmacogenetic testing. Methods and Results Questionnaires were completed by 910 undergraduate medicine and science students from 2005 to 2007. Despite students' concerns that the results of genetic tests may be used for other purposes without consent (71%) or lead to discrimination (78%), an overwhelming number of students were in favor of pharmacogenetic testing (90%). Discussion To our knowledge, this study is the first to survey a large sample for their attitude toward pharmacogenetic testing for psychotropic medications. Our results indicate that, although concerns remain and scientific advancements are required, respondents were in support of pharmacogenetic testing for medications used to treat schizophrenia. © 2014 The Authors. Human Psychopharmacology: Clinical and Experimental published by John Wiley & Sons, Ltd.

Acute kidney injury (AKI) occurs in approximately one quarter of patients undergoing cardiac surgery and is associated with increased short-term and long-term mortality, as well as prolonged time for mechanical ventilation, intensive care, and hospitalization (1,2). AKI is defined by a sudden decrease in glomerular filtration rate typically with reduced urine output over a time period of hours to days; many patients with AKI also require renal replacement therapy (RRT) including hemodialysis or continuous RRT.

Background The genetic etiology of human lipid quantitative traits is not fully elucidated, and interactions between variants may play a role. We performed a gene-centric interaction study for four different lipid traits: low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC), and triglycerides (TG). Results Our analysis consisted of a discovery phase using a merged dataset of five different cohorts (n = 12,853 to n = 16,849 depending on lipid phenotype) and a replication phase with ten independent cohorts totaling up to 36,938 additional samples. Filters are often applied before interaction testing to correct for the burden of testing all pairwise interactions. We used two different filters: 1. A filter that tested only single nucleotide polymorphisms (SNPs) with a main effect of p

Blood pressure (BP) is a heritable determinant of risk for cardiovascular disease (CVD). To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) and pulse pressure (PP), we genotyped ∼50 000 single-nucleotide polymorphisms (SNPs) that capture variation in ∼2100 candidate genes for cardiovascular phenotypes in 61 619 individuals of European ancestry from cohort studies in the USA and Europe. We identified novel associations between rs347591 and SBP (chromosome 3p25.3, in an intron of HRH1) and between rs2169137 and DBP (chromosome1q32.1 in an intron of MDM4) and between rs2014408 and SBP (chromosome 11p15 in an intron of SOX6), previously reported to be associated with MAP. We also confirmed 10 previously known loci associated with SBP, DBP, MAP or PP (ADRB1, ATP2B1, SH2B3/ATXN2, CSK, CYP17A1, FURIN, HFE, LSP1, MTHFR, SOX6) at array-wide significance (P < 2.4 × 10(-6)). We then replicated these associations in an independent set of 65 886 individuals of European ancestry. The findings from expression QTL (eQTL) analysis showed associations of SNPs in the MDM4 region with MDM4 expression. We did not find any evidence of association of the two novel SNPs in MDM4 and HRH1 with sequelae of high BP including coronary artery disease (CAD), left ventricular hypertrophy (LVH) or stroke. In summary, we identified two novel loci associated with BP and confirmed multiple previously reported associations. Our findings extend our understanding of genes involved in BP regulation, some of which may eventually provide new targets for therapeutic intervention.

Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering ∼2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids. © 2012 The American Society of Human Genetics.

Background— Rare variant accumulation studies can implicate genes in disease susceptibility when a significant burden is observed in patients versus control subjects. Such analyses might be particularly useful for candidate genes that are selected based on experiments other than genome-wide association studies (GWAS). We sought to determine whether rare variants in non-GWAS candidate genes identified from mouse models and human mendelian syndromes of hypertriglyceridemia (HTG) accumulate in patients with polygenic adult-onset HTG. Methods and Results— We resequenced protein coding regions of 3 genes with established roles ( APOC2, GPIHBP1 , LMF1 ) and 2 genes recently implicated ( CREB3L3 and ZHX3 ) in TG metabolism. We identified 41 distinct heterozygous rare variants, including 29 singleton variants, in the combined sample; in total, we observed 47 rare variants in 413 HTG patients versus 16 in 324 control subjects (odds ratio=2.3; P =0.0050). Post hoc assessment of genetic burden in individual genes using 3 different tests suggested that the genetic burden was most prominent in the established genes LMF1 and APOC2 , and also in the recently identified CREB3L3 gene. Conclusions— These extensive resequencing studies show a significant accumulation of rare genetic variants in non-GWAS candidate genes among patients with polygenic HTG, and indicate the importance of testing specific hypotheses in large-scale resequencing studies.

Elevated plasma plasminogen activator inhibitor-1 (PAI-1) concentration is associated with cardiovascular disease risk. PAI-1 is the primary inhibitor of fibrinolysis within both the circulation and the arterial wall, playing roles in both atherosclerosis and thrombosis. To define the heritable component, subjects within the population-based SHARE (Study of Health Assessment and Risk in Ethnic groups) and SHARE-AP (Study of Health Assessment and Risk Evaluation in Aboriginal Peoples) studies, composed of Canadians of South Asian (n = 298), Chinese (n = 284), European (n = 227), and Aboriginal (n = 284) descent, were genotyped using the gene-centric Illumina HumanCVD BeadChip. After imputation, more than 150 000 single nucleotide polymorphisms (SNPs) in more than 2000 loci were tested for association with plasma PAI-1 concentration. Marginal association was observed with the PAI-1 locus itself (SERPINE1; P < .05). However, 5 loci (HABP2, HSPA1A, HYAL1, MBTPS1, TARP) were associated with PAI-1 concentration at a P < 1 × 10−5 threshold. The protein products of 2 of these loci, hyaluronan binding protein 2 (HABP2) and hyaluronoglucosaminidase 1 (HYAL1), play key roles in hyaluronan metabolism, providing genetic evidence to link these pathways.

Human genetic variation can modulate pathophysiologic processes that alter susceptibility to complex disease. Recent genomic analyses have sought to identify how common genetic variation alters susceptibility to coronary artery disease (CAD). From genome-wide association studies (GWAS), common genetic variants in several novel chromosomal loci have been associated with CAD. GWAS identified the 9p21 locus as the strongest independent genetic CAD risk factor, along with 11 additional loci that harbor common genetic variants associated with increased CAD risk. A thorough understanding of human genetic variation and genomic analyses will be crucial to understand how GWAS-identified loci increase susceptibility to CAD. This article outlines the relevance of genetic variation in the elucidation of novel CAD risk factors and the clinical utility of genetic variants in the management and treatment of CAD.

With advances in high-throughput genotyping technologies, the rate-limiting step of large-scale genetic investigations has become the collection of sensitive and specific phenotype information in large samples of study participants. Clinicians play a pivotal role for successful genetic studies because sound clinical acumen can substantially increase study power by reducing measurement error and improving diagnostic precision for translational research. Phenomics is the systematic measurement and analysis of qualitative and quantitative traits, including clinical, biochemical, and imaging methods, for the refinement and characterization of a phenotype. Phenomics requires deep phenotyping, the collection of a wide breadth of phenotypes with fine resolution, and phenomic analysis, composed of constructing heat maps, cluster analysis, text mining, and pathway analysis. In this article, we review the components of phenomics and provide examples of their application to genomic studies, specifically for implicating novel disease processes, reducing sample heterogeneity, hypothesis generation, integration of multiple types of data, and as an extension of Mendelian randomization studies.

Received December 23, 2009; accepted February 22, 2010. Because cardiovascular disease (CVD) is the leading cause of morbidity and mortality in the Western world,1 reduction of CVD is the focus of a large body of research. Ever since the initial Framingham study, researchers have sought to identify and validate CVD risk factors, now often referred to as “traditional” risk factors, including age, sex, blood pressure, lipid parameters, diabetes, and smoking.2 More recently, extraordinary efforts have been undertaken to construct large study samples to carry out population-based genome-wide association studies (GWAS) to further deconstruct the heritable component of CVD risk, with the successful identification of molecular determinants, such as the robustly associated chromosome 9p21 locus.3–6 However, a substantial component of heritable CVD risk still exists,7 and new study designs and statistical methods will be necessary for uncovering additional associated variants. Mounting evidence suggests that common complex disorders represent the extremes of quantitative traits.8 The evaluation of individuals with extreme values of a continuously distributed trait in studies seeking to identify quantitative trait loci has a long history in genetics. “Selective genotyping” was first described by Lander and Botstein9 in the context of animal models, and later Carey and Williamson10 and then Risch and Zhang11 described the approach in family-based linkage studies. Schork et al12 demonstrated formally that selective genotyping, or genotyping of the extremes, showed substantial efficiency gains in human genetic association studies. Since the publication by Schork et al, a number of authors have extended the extreme sampling strategy to the use of more general selection strategy designs,13 considerations when loci are multiallelic and exhibit varying strengths of linkage disequilibrium,14 and for use in DNA pooling strategies.15 The various ultrasound techniques used to monitor carotid atherosclerosis, including intima-media …