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1.  Assessing the agreement of biomarker data in the presence of left-censoring 
BMC Nephrology  2014;15:144.
In many clinical biomarker studies, Lin’s concordance correlation coefficient (CCC) is commonly used to assess the level of agreement of a biomarker measured under two different conditions. However, measurement of a specific biomarker typically cannot provide accurate numerical values below the lower limit of detection (LLD) of the assay, which results in left-censored data. Most researchers discard the data below the LLD or apply simple data imputation methods in the presence of left-censored data, such as replacing values below the LLD with a fixed number less than or equal to the LLD. This is not statistically optimal, because it often leads to biased estimates and overestimates the precision.
We describe a simple method using a bivariate normal distribution in this situation and apply SAS statistical software to arrive at the maximum likelihood (ML) estimate of the parameters and construct the estimate of the CCC. We conduct a computer simulation study to investigate the statistical properties of the ML method versus the data deletion and simple data imputation method. We also contrast the methods with real data using two urine biomarkers, Interleukin 18 and Cystatin C.
The computer simulation studies confirm that the ML procedure is superior to the data deletion and simple data imputation procedures. In all of the simulated scenarios, the ML method yields the smallest relative bias and the highest percentage of the 95% confidence intervals that include the true value of the CCC. In the first simulation scenario (sample size of 100 paired data points, 25% left-censoring for both members of the pair, true CCC of 0.238), the relative bias is −1.43% for the ML method, −40.97% for the data deletion method, and it ranges between −12.94% and −21.72% for the simple data imputation methods. Similarly, when the left-censoring for one of the members of the data pairs increases from 25% to 40%, the relative bias displays the same pattern for all methods.
When estimating the CCC from paired biomarker data in the presence of left-censored values, the ML method works better than data deletion and simple data imputation methods.
PMCID: PMC4236661  PMID: 25186769
2.  A Prospective Controlled Study of Kidney Donors: Baseline and 6-Month Follow-up 
Most previous studies of living kidney donors have been retrospective and have lacked suitable healthy controls. Needed are prospective controlled studies to better understand the effects of a mild reduction in kidney function from kidney donation in otherwise normal individuals.
Study Design
Prospective, controlled, observational cohort study.
Setting & Participants
Consecutive patients approved for donation at 8 transplant centers in the US were asked to participate. For every donor enrolled, an equally healthy control with 2 kidneys who theoretically would have been suitable to donate a kidney was also enrolled.
Kidney donation.
At baseline pre-donation and at 6 months after donation, a medical history, vital signs, measured (iohexol) glomerular filtration rate and other measurements were collected. There were 201 donors and 198 controls that completed both baseline and 6 month visits and form the basis of this report.
Compared to controls, donors had 28% lower glomerular filtration rate at 6 months (94.6±15.1 [SD] v. 67.6±10.1 mL/min/1.73m2; P<0.001), associated with a 23% greater parathyroid hormone (42.8±15.6 v. 52.7±20.9 pg/mL; P<0.001), 5.4% lower serum phosphate (3.5±0.5 v. 3.3±0.5 mg/dL; P<0.001), 3.7% lower hemoglobin (13.6±1.4 v. 13.1±1.2 g/dL; P<0.001), 8.2% greater uric acid (4.9±1.2 v. 5.3±1.1 mg/dL; P<0.001), 24% greater homocysteine (1.20±0.34 v. 1.49±0.43 mg/L; P<0.001), and 1.5% lower high density lipoprotein cholesterol (54.9±16.4 v. 54.1±13.9 mg/dL; P=0.03) level. There were no differences in albumin-creatinine ratios (5.0 [IQR, 4.0-6.6] v. 5.0 [IQR, 3.3-5.4] mg/g; P=0.5), office blood pressure, or glucose homeostasis.
Short duration of follow-up and possible bias resulting from an inability to screen controls with kidney and vascular imaging performed in donors.
Kidney donors have some, but not all, abnormalities typically associated with mild chronic kidney disease 6 months after donation. Additional follow up is warranted.
PMCID: PMC3724758  PMID: 23523239
3.  NPHS2 Variation in Sporadic Focal Segmental Glomerulosclerosis 
Mutations in NPHS2, the gene that encodes podocin, are well-established causes of both familial and sporadic steroid-resistant focal segmental glomerulosclerosis (FSGS) in the pediatric population, but have not been well-characterized in late-onset disease. To investigate the role of NPHS2 polymorphisms in sporadic cases of late-onset FSGS, we studied 377 biopsy-confirmed FSGS cases and 919 controls. We identified 18 single nucleotide polymorphisms (SNPs) by resequencing a subgroup of cases and controls, and subsequently genotyped African-American and European-American cases and controls for five missense SNPs, three SNPs within introns, and four SNPs in the 3′ untranslated region. No homozygotes or compound heterozygotes were observed for any missense mutation. R138Q carriers were more frequent among FSGS cases relative to controls (OR = 4.9, P = 0.06), but heterozygosity for the other four missense mutations was equally distributed among FSGS cases and controls. Finally, a common haplotype of noncoding SNPs carried by 20% of African-Americans, but not observed in European-Americans, was strongly associated with a 50% reduction in risk for sporadic FSGS (OR = 0.5, P = 0.001). These results indicate that genetic variation or mutation of NPHS2 may play a role in late-onset sporadic FSGS.
PMCID: PMC4096868  PMID: 17942957
4.  Understanding the rise in cardiovascular diseases in Africa: harmonising H3Africa genomic epidemiological teams and tools 
Cardiovascular Journal of Africa  2014;25(3):134-136.
Cardiovascular diseases, principally ischaemic heart disease and stroke, are the leading causes of global mortality and morbidity. Together with other non-communicable diseases, they account for more than 60% of global deaths and pose major social, economic and developmental challenges worldwide. In Africa, there is now compelling evidence that the major cardiovascular disease (CVD) risk factors are on the rise, and so are the related fatal and non-fatal sequelae, which occur at significantly younger ages than seen in high-income countries. In order to tackle this rising burden of CVD, the H3Africa Cardiovascular Working Group will hold an inaugural workshop on 30 May 2014 in Cape Town, South Africa. The primary workshop objectives are to enhance our understanding of the genetic underpinnings of the common major CVDs in Africa and strengthen collaborations among the H3Africa teams and other researchers using novel genomic and epidemiological tools to contribute to reducing the burden of CVD on the continent.
PMCID: PMC4120122  PMID: 24878536
cardiovascular diseases; H3Africa; Africa; genomics; epidemiology
5.  Pain, sleep disturbance and survival in hemodialysis patients 
Patients’ perception of pain during hemodialysis (HD) and at times between HD treatment and its association with survival have not been well studied in end-stage renal disease (ESRD). We evaluated the experience of pain during HD and at times when the patient was not receiving HD, and assessed possible associations of the perception of pain and sleep disturbance with patient survival.
A total of 128 ESRD patients treated with HD completed questionnaires on psychosocial status, quality of life and sleep disorders. A modified McGill Pain questionnaire was used to assess the nature, location, frequency, intensity and duration of pain both during and at times between HD sessions. The Pittsburgh Sleep Quality Index was used to screen for sleep disturbances over a 30-day period.
Controlling for age, diabetes mellitus, serum albumin concentration and human immunodeficiency virus infection, there was a significant association between mortality and both frequency and intensity of pain while patients were not on HD. There was no association between survival and duration of pain while off HD or any of the pain parameters while patients were on HD. There was no association between survival and the presence of a sleep disorder.
Pain perception while off HD may be of more importance to patients than pain during HD. The mechanisms underlying the association are unknown but may involve linkage of pain with severity of medical illness or the generation of a maladaptive cytokine response. Multicenter prospective studies of pain interventions using well-validated pain perception tools are needed to establish causal relationships. Interventions directed toward treating pain on non-HD days may improve ESRD patient survival.
PMCID: PMC3283168  PMID: 21771748
chronic kidney disease; depression; satisfaction with life; satisfaction with care; psychosocial
6.  A Genome-Wide Search for Linkage of Estimated Glomerular Filtration Rate (eGFR) in the Family Investigation of Nephropathy and Diabetes (FIND) 
PLoS ONE  2013;8(12):e81888.
Estimated glomerular filtration rate (eGFR), a measure of kidney function, is heritable, suggesting that genes influence renal function. Genes that influence eGFR have been identified through genome-wide association studies. However, family-based linkage approaches may identify loci that explain a larger proportion of the heritability. This study used genome-wide linkage and association scans to identify quantitative trait loci (QTL) that influence eGFR.
Genome-wide linkage and sparse association scans of eGFR were performed in families ascertained by probands with advanced diabetic nephropathy (DN) from the multi-ethnic Family Investigation of Nephropathy and Diabetes (FIND) study. This study included 954 African Americans (AA), 781 American Indians (AI), 614 European Americans (EA) and 1,611 Mexican Americans (MA). A total of 3,960 FIND participants were genotyped for 6,000 single nucleotide polymorphisms (SNPs) using the Illumina Linkage IVb panel. GFR was estimated by the Modification of Diet in Renal Disease (MDRD) formula.
The non-parametric linkage analysis, accounting for the effects of diabetes duration and BMI, identified the strongest evidence for linkage of eGFR on chromosome 20q11 (log of the odds [LOD] = 3.34; P = 4.4×10−5) in MA and chromosome 15q12 (LOD = 2.84; P = 1.5×10−4) in EA. In all subjects, the strongest linkage signal for eGFR was detected on chromosome 10p12 (P = 5.5×10−4) at 44 cM near marker rs1339048. A subsequent association scan in both ancestry-specific groups and the entire population identified several SNPs significantly associated with eGFR across the genome.
The present study describes the localization of QTL influencing eGFR on 20q11 in MA, 15q21 in EA and 10p12 in the combined ethnic groups participating in the FIND study. Identification of causal genes/variants influencing eGFR, within these linkage and association loci, will open new avenues for functional analyses and development of novel diagnostic markers for DN.
PMCID: PMC3866106  PMID: 24358131
7.  Development and Standardization of a Furosemide Stress Test to Predict the Severity of Acute Kidney Injury 
Critical Care  2013;17(5):R207.
In the setting of early acute kidney injury (AKI), no test has been shown to definitively predict the progression to more severe stages.
We investigated the ability of a furosemide stress test (FST) (one-time dose of 1.0 or 1.5 mg/kg depending on prior furosemide-exposure) to predict the development of AKIN Stage-III in 2 cohorts of critically ill subjects with early AKI. Cohort 1 was a retrospective cohort who received a FST in the setting of AKI in critically ill patients as part of Southern AKI Network. Cohort 2 was a prospective multicenter group of critically ill patients who received their FST in the setting of early AKI.
We studied 77 subjects; 23 from cohort 1 and 54 from cohort 2; 25 (32.4%) met the primary endpoint of progression to AKIN-III. Subjects with progressive AKI had significantly lower urine output following FST in each of the first 6 hours (p<0.001). The area under the receiver operator characteristic curves for the total urine output over the first 2 hours following FST to predict progression to AKIN-III was 0.87 (p = 0.001). The ideal-cutoff for predicting AKI progression during the first 2 hours following FST was a urine volume of less than 200mls(100ml/hr) with a sensitivity of 87.1% and specificity 84.1%.
The FST in subjects with early AKI serves as a novel assessment of tubular function with robust predictive capacity to identify those patients with severe and progressive AKI. Future studies to validate these findings are warranted.
PMCID: PMC4057505  PMID: 24053972
8.  Emergency department visits, use of imaging and drugs for urolithiasis have increased in the United States 
Kidney international  2013;83(3):479-486.
The occurrence of urolithiasis in the United States has increased, however, information on long-term trends, including recurrence rates, is lacking. Here we describe national trends in rates of emergency department visits, use of imaging, and drug treatment primarily using the National Hospital Ambulatory Medical Care Surveys to describe trends and the National Health and Nutrition Examination Survey to determine the frequency of lifetime passage of kidney stones. Emergency department visit rates for urolithiasis increased from 178 to 340 visits per 100,000 individuals from 1992 to 2009. Increases in visit rates were greater in women, Caucasians and in those 25–44 years of age. The use of computed tomography in urolithiasis patients more than tripled, from 21% to 71%. Medical expulsive therapy was used in 14% of patients with a urolithiasis diagnosis in 2007–2009. Among National Health and Nutrition Examination Survey participants who reported a history of kidney stones, 22.4% had passed three or more stones. Hence, emergency department urolithiasis visit rates have increased significantly, as has the use of computed tomography in the United States. Further research is necessary to determine whether recurrent stone formers receive unnecessary radiation exposure during diagnostic evaluation in the emergency department, and allow development of corresponding evidence-based guidelines.
PMCID: PMC3587650  PMID: 23283137
Computed Tomography; Radiation; NHAMCS
9.  Genomewide Linkage Scan for Diabetic Renal Failure and Albuminuria: The FIND Study 
American Journal of Nephrology  2011;33(5):381-389.
Diabetic nephropathy (DN) is a leading cause of mortality and morbidity in patients with type 1 and type 2 diabetes. The multicenter FIND consortium aims to identify genes for DN and its associated quantitative traits, e.g. the urine albumin:creatinine ratio (ACR). Herein, the results of whole-genome linkage analysis and a sparse association scan for ACR and a dichotomous DN phenotype are reported in diabetic individuals.
A genomewide scan comprising more than 5,500 autosomal single nucleotide polymorphism markers (average spacing of 0.6 cM) was performed on 1,235 nuclear and extended pedigrees (3,972 diabetic participants) ascertained for DN from African-American (AA), American-Indian (AI), European-American (EA) and Mexican-American (MA) populations.
Strong evidence for linkage to DN was detected on chromosome 6p (p = 8.0 × 10−5, LOD = 3.09) in EA families as well as suggestive evidence for linkage to chromosome 7p in AI families. Regions on chromosomes 3p in AA, 7q in EA, 16q in AA and 22q in MA displayed suggestive evidence of linkage for urine ACR. The linkage peak on chromosome 22q overlaps the MYH9/APOL1 gene region, previously implicated in AA diabetic and nondiabetic nephropathies.
These results strengthen the evidence for previously identified genomic regions and implicate several novel loci potentially involved in the pathogenesis of DN.
PMCID: PMC3078269  PMID: 21454968
Albuminuria; Diabetes mellitus; Renal failure; End-stage renal disease; Linkage; Allelic association
10.  Genetic Association and Gene-Gene Interaction Analyses in African American Dialysis Patients With Nondiabetic Nephropathy 
African Americans (AAs) have increased susceptibility to non-diabetic nephropathy relative to European Americans.
Study Design
Follow-up of a pooled genome-wide association study (GWAS) in AA dialysis patients with nondiabetic nephropathy; novel gene-gene interaction analyses.
Setting & Participants
Wake Forest sample: 962 AA nondiabetic nephropathy cases; 931 non-nephropathy controls. Replication sample: 668 Family Investigation of Nephropathy and Diabetes (FIND) AA nondiabetic nephropathy cases; 804 non-nephropathy controls.
Individual genotyping of top 1420 pooled GWAS-associated single nucleotide polymorphisms (SNPs) and 54 SNPs in six nephropathy susceptibility genes.
APOL1 genetic association and additional candidate susceptibility loci interacting with, or independently from, APOL1.
The strongest GWAS associations included two non-coding APOL1 SNPs, rs2239785 (odds ratio [OR], 0.33; dominant; p = 5.9 × 10−24) and rs136148 (OR, 0.54; additive; p = 1.1 × 10−7) with replication in FIND (p = 5.0 × 10−21 and 1.9 × 10−05, respectively). Rs2239785 remained significantly associated after controlling for the APOL1 G1 and G2 coding variants. Additional top hits included a CFH SNP(OR from meta-analysis in above 3367 AA cases and controls, 0.81; additive; p = 6.8 × 10−4). The 1420 SNPs were tested for interaction with APOL1 G1 and G2 variants. Several interactive SNPs were detected, the most significant was rs16854341 in the podocin gene (NPHS2) (p = 0.0001).
Non-pooled GWAS have not been performed in AA nondiabetic nephropathy.
This follow-up of a pooled GWAS provides additional and independent evidence that APOL1 variants contribute to nondiabetic nephropathy in AAs and identified additional associated and interactive non-diabetic nephropathy susceptibility genes.
PMCID: PMC3259209  PMID: 22119407
African American; APOL1; CFH; end-stage renal disease; FIND; FSGS; hypertension
11.  Depression in African-American patients with kidney disease. 
Journal of the National Medical Association  2002;94(8 Suppl):92S-103S.
There are few data on the epidemiology, consequences and treatment of depression in African-American patients with kidney disease in the US, even though such patients disproportionately bear the burden of this illness. This paper reviews data on the diagnosis and pathogenesis of depression and its consequences in patients with and without kidney disease, in addition to work on the epidemiology of depression in the African-American population and in the US End-stage Renal Disease (ESRD) program. African Americans are thought to have similar susceptibility to the development of depression as other populations in the US, but diminished access to care for this group of patients may be associated with differential outcomes. Data are presented from longitudinal studies of psychosocial outcomes in a population comprising primarily African-American patients with ESRD, and is reviewed the treatment of depression in patients with and without kidney disease. There are few studies of the management of depression that focus on minority populations. The authors agree with recommendations that treatment trials should include minority patients, patients with medical comorbidities, and the elderly, and assess function and quality of life as outcomes. The relationships between age, marital status and satisfaction, ethnicity, and perception of quality of life and depressive affect level and diagnosis of depression, and medical outcomes have not been determined in ESRD patients, or in African-American patients with ESRD. There are few studies of drugs for the treatment of depression in ESRD patients, and only one small randomized controlled trial. These have shown that therapy with selective serotonin reuptake inhibitors appears to be a safe treatment option for patients with ESRD. The long-term effectiveness of therapy, and its association with clinically important outcomes such as perception of quality of life, compliance, and survival have not been evaluated in ESRD patients. Also, therapeutic effectiveness and outcomes have not been assessed in minority populations with ESRD. These issues need to be addressed to optimize the management of depression in African Americans with kidney disease.
PMCID: PMC2594165  PMID: 12152919
12.  Design and Rationale of Health-Related Quality of Life and Patient-Reported Outcomes Assessment in the Frequent Hemodialysis Network Trials 
Blood Purification  2011;31(1-3):151-158.
End-stage renal disease patients experience significant impairments in health-related quality of life (HRQOL). Testing various strategies to improve patient HRQOL in multicenter clinical trials, such as the Frequent Hemodialysis Network (FHN) trials is vitally important. Aims: Theaim of this paper is to describe the design and conduct of HRQOL and patient-reported outcomes (PRO) assessment in the FHN trials.
In the FHN trials, HRQOL was examined as a multidimensional concept, and the SF-36 RAND Physical Health Composite score was one of the co-primary outcomes. The instruments completed to assess HRQOL included the Medical Outcomes Study Short Form SF-36, Health Utilities Index 3, Sleep Problems Index, Beck Depression Inventory and feeling thermometer. These instruments have been shown to have high reliability, validity and responsiveness to change in the end-stage renal disease population. Additional items evaluating PRO including sexual function, time to recovery after dialysis and patients’ self-perceived burden to caregiver were also assessed. All questionnaires were administered by trained interviewers using computer-assisted telephone interviewing to ensure blinding and minimizing selection bias. Interim analysis reveals that these instruments can be used to collect a comprehensive set of HRQOL measures with minimal patient burden.
Accurate measurement of HRQOL and PRO can help us test whether hemodialysis interventions improve the health and well-being of this compromised patient population. We have shown that a comprehensive set of HRQOL measures can be centrally collected through telephone interviews in a blinded fashion, in a way that is well tolerated with minimum respondent burden.
PMCID: PMC3202955  PMID: 21228584
Health-related quality of life; Frequent Hemodialysis Network; End-stage renal disease
13.  Elevated depressive affect is associated with adverse cardiovascular outcomes among African Americans with chronic kidney disease 
Kidney international  2011;80(6):670-678.
This study was designed to examine the impact of elevated depressive affect on health outcomes among participants with hypertensive chronic kidney disease in the African-American Study of Kidney Disease and Hypertension (AASK) Cohort Study. Elevated depressive affect was defined by Beck Depression Inventory II (BDI-II) thresholds of 11 or more, above 14, and by 5-Unit increments in the score. Cox regression analyses were used to relate cardiovascular death/hospitalization, doubling of serum creatinine/end-stage renal disease, overall hospitalization, and all-cause death to depressive affect evaluated at baseline, the most recent annual visit (time-varying), or average from baseline to the most recent visit (cumulative). Among 628 participants at baseline, 42% had BDI-II scores of 11 or more and 26% had a score above 14. During a 5-year follow-up, the cumulative incidence of cardiovascular death/hospitalization was significantly greater for participants with baseline BDI-II scores of 11 or more compared with those with scores <11. The baseline, time-varying, and cumulative elevated depressive affect were each associated with a significant higher risk of cardiovascular death/hospitalization, especially with a time-varying BDI-II score over 14 (adjusted HR 1.63) but not with the other outcomes. Thus, elevated depressive affect is associated with unfavorable cardiovascular outcomes in African Americans with hypertensive chronic kidney disease.
PMCID: PMC3237701  PMID: 21633409
AASK (African American Study of Kidney Disease and Hypertension); cardiovascular events; chronic kidney disease; depression
14.  Sociodemographic factors contribute to the depressive affect among African Americans with chronic kidney disease 
Kidney international  2010;77(11):1010-1019.
Depression is common in end-stage renal disease and is associated with poor quality of life and higher mortality; however, little is known about depressive affect in earlier stages of chronic kidney disease. To measure this in a risk group burdened with hypertension and kidney disease, we conducted a cross-sectional analysis of individuals at enrollment in the African American Study of Kidney Disease and Hypertension Cohort Study. Depressive affect was assessed by the Beck Depression Inventory II and quality of life by the Medical Outcomes Study-Short Form and the Satisfaction with Life Scale. Beck Depression scores over 14 were deemed consistent with an increased depressive affect and linear regression analysis was used to identify factors associated with these scores. Among 628 subjects, 166 had scores over 14 but only 34 were prescribed antidepressants. The mean Beck Depression score of 11.0 varied with the estimated glomerular filtration rate (eGFR) from 10.7 (eGFR 50–60) to 16.0 (eGFR stage 5); however, there was no significant independent association between these. Unemployment, low income, and lower quality and satisfaction with life scale scores were independently and significantly associated with a higher Beck Depression score. Thus, our study shows that an increased depressive affect is highly prevalent in African Americans with chronic kidney disease, is infrequently treated with antidepressants, and is associated with poorer quality of life. Sociodemographic factors have especially strong associations with this increased depressive affect. Because this study was conducted in an African-American cohort, its findings may not be generalized to other ethnic groups.
PMCID: PMC3114445  PMID: 20200503
AASK (African American Study of Kidney Disease and Hypertension); chronic kidney disease; clinical epidemiology; depression; quality of life
15.  Genome-wide linkage scans for type 2 diabetes mellitus in four ethnically diverse populations; significant evidence for linkage on chromosome 4q in African Americans: the Family Investigation of Nephropathy and Diabetes (FIND) Research Group 
Previous studies have shown that, in addition to environmental influences, type 2 diabetes mellitus (T2DM) has a strong genetic component. The goal of the current study is to identify regions of linkage for T2DM in ethnically diverse populations.
Phenotypic and genotypic data were obtained from African American (AA; total number of individuals (N)=1004), American Indian (AI; N=883), European American (EA; N=537), and Mexican American (MA; N=1634) individuals from the Family Investigation of Nephropathy and Diabetes. Nonparametric linkage analysis, using an average of 4,404 SNPs, was performed in relative pairs affected with T2DM in each ethnic group. In addition, family-based tests were performed to detect association with T2DM.
Statistically significant evidence for linkage was observed on chromosomes 4q21.1 (LOD=3.13; genome-wide p=0.04) in AA. In addition, a total of eleven regions showed suggestive evidence for linkage (estimated at LOD>1.71), with the highest LOD scores on chromosomes 12q21.31 (LOD=2.02) and 22q12.3 (LOD=2.38) in AA, 2p11.1 (LOD=2.23) in AI, 6p12.3 (LOD=2.77) in EA, and 13q21.1 (LOD=2.24) in MA. While no region overlapped across all ethnic groups, at least five loci showing LOD>1.71 have been identified in previously published studies.
The results from this study provide evidence for the presence of genes affecting T2DM on chromosomes 4q, 12q, and 22q in AA, 6p in EA, 2p in AI, and 13q in MA. The strong evidence for linkage on chromosome 4q in AA provides important information given the paucity of diabetes genetic studies in this population.
PMCID: PMC2783577  PMID: 19795399
FIND; Type 2 Diabetes; linkage analysis; ethnicity
16.  The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of Health–Centers for Disease Control and Prevention Multidisciplinary Workshop 
The increasing availability of personal genomic tests has led to discussions about the validity and utility of such tests and the balance of benefits and harms. A multidisciplinary workshop was convened by the National Institutes of Health and the Centers for Disease Control and Prevention to review the scientific foundation for using personal genomics in risk assessment and disease prevention and to develop recommendations for targeted research. The clinical validity and utility of personal genomics is a moving target with rapidly developing discoveries but little translation research to close the gap between discoveries and health impact. Workshop participants made recommendations in five domains: (1) developing and applying scientific standards for assessing personal genomic tests; (2) developing and applying a multidisciplinary research agenda, including observational studies and clinical trials to fill knowledge gaps in clinical validity and utility; (3) enhancing credible knowledge synthesis and information dissemination to clinicians and consumers; (4) linking scientific findings to evidence-based recommendations for use of personal genomics; and (5) assessing how the concept of personal utility can affect health benefits, costs, and risks by developing appropriate metrics for evaluation. To fulfill the promise of personal genomics, a rigorous multidisciplinary research agenda is needed.
PMCID: PMC2936269  PMID: 19617843
behavioral sciences; epidemiologic methods; evidence-based medicine; genetics; genetic testing; genomics; medicine; public health
17.  The assessment, serial evaluation, and subsequent sequelae of acute kidney injury (ASSESS-AKI) study: design and methods 
BMC Nephrology  2010;11:22.
The incidence of acute kidney injury (AKI) has been increasing over time and is associated with a high risk of short-term death. Previous studies on hospital-acquired AKI have important methodological limitations, especially their retrospective study designs and limited ability to control for potential confounding factors.
The Assessment, Serial Evaluation, and Subsequent Sequelae of Acute Kidney Injury (ASSESS-AKI) Study was established to examine how a hospitalized episode of AKI independently affects the risk of chronic kidney disease development and progression, cardiovascular events, death, and other important patient-centered outcomes. This prospective study will enroll a cohort of 1100 adult participants with a broad range of AKI and matched hospitalized participants without AKI at three Clinical Research Centers, as well as 100 children undergoing cardiac surgery at three Clinical Research Centers. Participants will be followed for up to four years, and will undergo serial evaluation during the index hospitalization, at three months post-hospitalization, and at annual clinic visits, with telephone interviews occurring during the intervening six-month intervals. Biospecimens will be collected at each visit, along with information on lifestyle behaviors, quality of life and functional status, cognitive function, receipt of therapies, interim renal and cardiovascular events, electrocardiography and urinalysis.
ASSESS-AKI will characterize the short-term and long-term natural history of AKI, evaluate the incremental utility of novel blood and urine biomarkers to refine the diagnosis and prognosis of AKI, and identify a subset of high-risk patients who could be targeted for future clinical trials to improve outcomes after AKI.
PMCID: PMC2944247  PMID: 20799966
18.  MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis 
Nature genetics  2008;40(10):1175-1184.
The increased burden of chronic kidney and end-stage kidney diseases (ESKD) in populations of African ancestry has been largely unexplained. To identify genetic variants predisposing to idiopathic and HIV-1–associated focal segmental glomerulosclerosis (FSGS), we carried out an admixture-mapping linkage-disequilibrium genome scan on 190 African American individuals with FSGS and 222 controls. We identified a chromosome 22 region with a genome-wide logarithm of the odds (lod) score of 9.2 and a peak lod of 12.4 centered on MYH9, a functional candidate gene expressed in kidney podocytes. Multiple MYH9 SNPs and haplotypes were recessively associated with FSGS, most strongly a haplotype spanning exons 14 through 23 (OR = 5.0, 95% CI = 3.5–7.1; P = 4 × 10−23, n = 852). This association extended to hypertensive ESKD (OR = 2.2, 95% CI = 1.5–3.4; n = 433), but not type 2 diabetic ESKD (n = 476). Genetic variation at the MYH9 locus substantially explains the increased burden of FSGS and hypertensive ESKD among African Americans.
PMCID: PMC2827354  PMID: 18794856
19.  Heritability of the Severity of Diabetic Retinopathy: The FIND-Eye Study 
Diabetic retinopathy (DR) and diabetic nephropathy (DN) are serious microvascular complications of diabetes mellitus. Correlations between severity of DR and DN and computed heritability estimates for DR were determined in a large, multiethnic sample of diabetic families. The hypothesis was that (1) the severity of DR correlates with the presence and severity of nephropathy in individuals with diabetes mellitus, and (2) the severity of DR is under significant familial influence in members of multiplex diabetic families.
The Family Investigation of Nephropathy and Diabetes (FIND) was designed to evaluate the genetic basis of DN in American Indians, European Americans, African Americans, and Mexican Americans. FIND enrolled probands with advanced DN, along with their diabetic siblings who were concordant and discordant for nephropathy. These diabetic family members were invited to participate in the FIND-Eye study to determine whether inherited factors underlie susceptibility to DR and its severity. FIND-Eye participants underwent eye examinations and had fundus photographs taken. The severity of DR was graded by using the Early Treatment Diabetic Retinopathy Study Classification (ETDRS). Sib–sib correlations were calculated with the SAGE 5.0 program FCOR, to estimate heritability of retinopathy severity.
This report summarizes the results for the first 2368 diabetic subjects from 767 families enrolled in FIND-Eye; nearly 50% were Mexican American, the largest single ethnicity within FIND. The overall prevalence of DR was high; 33.4% had proliferative DR; 7.5%, 22.8%, and 9.5% had severe, moderate, and mild nonproliferative DR, respectively; 26.6% had no DR. The severity of DR was significantly associated with severity of DN, both by phenotypic category and by increasing serum creatinine concentration (χ2 = 658.14, df = 20; P < 0.0001). The sib–sib correlation for DR severity was 0.1358 in the total sample and 0.1224 when limited to the Mexican-American sample. Broad sense heritabilities for DR were 27% overall and 24% in Mexican-American families. The polygenic heritability of liability for proliferative DR approximated 25% in this FIND-Eye sample.
These data confirm that the severity of DR parallels the presence and severity of nephropathy in individuals with diabetes mellitus. The severity of DR in members of multiplex diabetic families appears to have a significant familial connection.
PMCID: PMC2583147  PMID: 18765632
20.  Psychosocial Status of Hemodialysis Patients One Year After Hurricane Katrina 
Hemodialysis patients experience a high degree of psychosocial impairment.
The psychosocial status of hemodialysis patients after Hurricane Katrina was evaluated using the Hurricane Coping Self-Efficacy (HCSE) measure, the Short Form-12 Health Survey (physical component summary [PCS] and mental component summary [MCS]), and the Center for Epidemiologic Studies Short Depression Scale (CES-D). These scales were administered to 391 hemodialysis patients (86% participation rate), 7 to 14 months after Hurricane Katrina.
The mean score (standard deviation) was 36.2 (9.6) for the HCSE scale, 37.1 (10.9) and 46.7 (12.7) for the PCS and MCS, respectively, and 10.0 (6.5) on the CES-D. Symptoms of depression (CES-D scores ≥10) were present in 45.5% of patients. After age, race and gender adjustment, evacuating less than 2 days prior to Hurricane Katrina making landfall and more fear of dying were associated with less favorable scores on the HCSE, MCS and CES-D scales. Patients placed in a shelter and with a longer displacement had significantly lower MCS scores and more depressive symptoms. More depressive symptoms were observed among patients hospitalized in the month following the storm. Those who evacuated to a hotel, with more fear of dying and who were hospitalized in the month following Hurricane Katrina had lower scores on the PCS.
Impaired psychosocial status was common among dialysis patients surviving Hurricane Katrina and associated with reduced coping. These data demonstrate the need for screening and management of psychosocial issues in hemodialysis patients after disasters.
PMCID: PMC2644213  PMID: 18703900
hemodialysis; natural disasters; psychosocial status
21.  A genome-wide admixture scan identifies MYH9 as a candidate locus associated with non-diabetic end stage renal disease in African Americans 
Nature genetics  2008;40(10):1185-1192.
End stage renal disease (ESRD) has a four times higher incidence in African Americans compared to European Americans. This led to the hypothesis that susceptibility alleles for ESRD have a higher frequency in West African than European gene pool. We performed a genome-wide admixture scan in 1,372 ESRD cases and 806 controls and demonstrated a highly significant association between excess African ancestry and non-diabetic ESRD (LOD 5.70) but not diabetic ESRD (LOD 0.47) on chromosome 22q12. Each copy of the European ancestral allele conferred a relative risk of 0.50 (95% credible interval 0.39 – 0.63) compared to African ancestry. Multiple common SNPs (allele frequency ranging from 0.2 to 0.6) in the gene that encodes non-muscle myosin heavy chain type II isoform A (MYH9) were associated with 2-4 times greater risk of non-diabetic ESRD and accounted for a large proportion of the excess risk of ESRD observed in African compared to European Americans.
PMCID: PMC2614692  PMID: 18794854
22.  Associations of race and ethnicity with anemia management among patients initiating renal replacement therapy. 
BACKGROUND: Many patients initiate renal replacement therapy with suboptimal anemia management. The factors contributing to this remain largely unknown. The aim of this study was to assess the associations of race and ethnicity with anemia care prior to the initiation of renal replacement therapy. METHODS: Using data from the medical evidence form filed for patients who initiated renal replacement therapy between 1995-2003, we assessed racial and ethnic differences in pre-end-stage renal disease hematocrit levels, the use of erythropoiesis stimulation agents (ESAs), the proportion of patients with hematocrit levels > or = 33% and the proportion of patients with hematocrit levels < 33% that did not receive ESA. We also examined secular trends in racial and ethnic differences in these parameters. RESULTS: In multivariable analyses, non-Hispanic blacks had lower hematocrit levels (delta hematocrit = -0.97%, 95% CI: -1.00-0.94%), and were less likely to receive ESA (OR = 0.82, 95% CI: 0.81-0.84), to initiate renal replacement therapy with hematocrit > or = 33% (OR = 0.78, 95% CI: 0.77-0.79) or to receive ESA if the hematocrit was < 33% (OR = 0.79, 95% CI: 0.77-0.80) than non-Hispanic whites. White Hispanics also had lower hematocrit levels (delta hematocrit = -0.42%, 95% CI:-0.47% to -0.37%), and were less likely to receive ESA (OR = 0.86, 95% CI: 0.85-0.88), to have hematocrit levels > or = 33% (OR = 0.91, 95% CI: 0.89-0.93) or to receive ESA if the hematocrit was < 33% (OR = 0.85, 95% CI: 0.83-0.87) than non-Hispanic whites. These disparities persisted over the eight-year study period. CONCLUSIONS: African-American race and Hispanic ethnicity are associated with suboptimal pre-end-stage renal disease anemia management. Efforts to improve anemia care should incorporate targeted interventions to decrease these disparities.
PMCID: PMC2574315  PMID: 18020096
23.  The severity of acute kidney injury predicts progression to chronic kidney disease 
Kidney International  2011;79(12):1361-1369.
Acute kidney injury (AKI) is associated with progression to advanced chronic kidney disease (CKD). We tested whether patients who survive AKI and are at higher risk for CKD progression can be identified during their hospital admission, thus providing opportunities to intervene. This was assessed in patients in the Department of Veterans Affairs Healthcare System hospitalized with a primary diagnosis indicating AKI (ICD9 codes 584.xx). In the exploratory phase, three multivariate prediction models for progression to stage 4 CKD were developed. In the confirmatory phase, the models were validated in 11,589 patients admitted for myocardial infarction or pneumonia during the same time frame that had RIFLE codes R, I, or F and complete data for all predictor variables. Of the 5351 patients in the AKI group, 728 entered stage 4 CKD after hospitalization. Models 1, 2, and 3 were all significant with ‘c' statistics of 0.82, 0.81, and 0.77, respectively. In model validation, all three were highly significant when tested in the confirmatory patients, with moderate to large effect sizes and good predictive accuracy (‘c' 0.81–0.82). Patients with AKI who required dialysis and then recovered were at especially high risk for progression to CKD. Hence, the severity of AKI is a robust predictor of progression to CKD.
PMCID: PMC3257034  PMID: 21430640
acute kidney injury; acute renal failure; albumin; chronic kidney disease; predicts; severity

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