Diagnostic Utility of Exome Sequencing for Kidney Disease.

BACKGROUND: Exome sequencing is emerging as a first-line diagnostic method in some clinical disciplines, but its usefulness has yet to be examined for most constitutional disorders in adults, including chronic kidney disease, which affects more than 1 in 10 persons globally. METHODS: We conducted exome sequencing and diagnostic analysis in two cohorts totaling 3315 patients with chronic kidney disease. We assessed the diagnostic yield and, among the patients for whom detailed clinical data were available, the clinical implications of diagnostic and other medically relevant findings. RESULTS: In all, 3037 patients (91.6%) were over 21 years of age, and 1179 (35.6%) were of self-identified non-European ancestry. We detected diagnostic variants in 307 of the 3315 patients (9.3%), encompassing 66 different monogenic disorders. Of the disorders detected, 39 (59%) were found in only a single patient. Diagnostic variants were detected across all clinically defined categories, including congenital or cystic renal disease (127 of 531 patients [23.9%]) and nephropathy of unknown origin (48 of 281 patients [17.1%]). Of the 2187 patients assessed, 34 (1.6%) had genetic findings for medically actionable disorders that, although unrelated to their nephropathy, would also lead to subspecialty referral and inform renal management. CONCLUSIONS: Exome sequencing in a combined cohort of more than 3000 patients with chronic kidney disease yielded a genetic diagnosis in just under 10% of cases. (Funded by the National Institutes of Health and others.).

Implementation of App-Based Diabetes Medication Management: Outpatient and Perioperative Clinical Decision Support.

PURPOSE OF REVIEW: Outpatient and perioperative therapeutic decision making for patients with diabetes involves increasingly complex medical-decision making due to rapid advances in knowledge and treatment modalities. We sought to review mobile decision support tools available to clinicians for this essential and increasingly difficult task, and to highlight the development and implementation of novel mobile applications for these purposes. RECENT FINDINGS: We found 211 mobile applications related to diabetes from the search, but only five were found to provide clinical decision support for outpatient diabetes management and none for perioperative decision support. We found a dearth of tools for clinicians to navigate these tasks. We highlight key aspects for effective development of future diabetes decision support. These include just-in-time availability, respect for the five rights of clinical decision support, and integration with clinical workflows including the electronic medical record.

Understanding genetic learning needs of people affected by rare disease.

Nearly 350 million people worldwide are affected by a rare disease (RD) and ~80% of RDs have a genetic type, underscoring the need for access to reliable genomics education. Patient assistance in resource development can help ensure content is appropriate. The aim of this study was to define the needs and practical usage of the RD community to inform the scope and content of an online genetic course targeted toward the entire RD ecosystem. A high-level online survey (OS) was disseminated to 586 RD patients and family members/caregivers. A total of 251 individuals responded to the OS. Eight respondents were invited to participate in a follow-up focus group (FG). Nearly 87% of OS respondents have made efforts previously to learn more about genetics and 95.6% indicated a current interest in genetic education. Navigating healthcare systems, information sharing, and advocacy support were driving factors for this desire. Respondents indicated difficulty finding information on gene function, genetic testing, disease pathogenesis, and scientific advances. FG outcomes dove deeper into psychological needs including reducing emotional burden, alleviating fear of the unknown and seeking hope. Research identified high levels of interest in genetic education across all stages of the RD journey. Key themes identified in this study may help guide genetic counselors as they create their own patient and family-facing content.

Follow-up of multiple aneuploidies and single monosomies detected by noninvasive prenatal testing: implications for management and counseling.

OBJECTIVES: To determine the underlying biological basis for noninvasive prenatal testing (NIPT) results of multiple aneuploidies or autosomal monosomies. METHODS: Retrospective analysis of 113,415 tests to determine the study cohort, consisting of 138 (0.12%) cases reported as a single autosomal monosomy (n = 65), single trisomy with a sex chromosome aneuploidy (n = 36), or with multiple aneuploidies (n = 37). Clinical outcome information was reviewed and stratified into eight categories according to whether the karyotype or sonographic information agreed or disagreed with sequencing results. RESULTS: Of 67 cases with fetal or neonatal karyotypes available, 16 (24%) were partially or fully concordant with the NIPT result, 4 (6%) had aneuploidy on a reference chromosome, and 47 (70%) had normal fetal chromosomes, in which 5/47 had maternal malignancies reported. One case of maternal mosaic trisomy 8 was also detected. Of cases with no fetal karyotype information, ten had an abnormal clinical outcome, one was a normal live birth, and one reported maternal malignancy. CONCLUSIONS: Noninvasive prenatal test results of autosomal monosomy or multiple aneuploidies are rare but have a diversity of underlying biologic causes. Some reflect the fetal karyotype; some reflect the presence of other maternal or fetal chromosome abnormalities, and a small number are linked to maternal disease.

Noninvasive prenatal testing in the general obstetric population: clinical performance and counseling considerations in over 85 000 cases.

OBJECTIVE: The primary goal of this study was to provide clinically relevant information for appropriate patient counseling. METHOD: Demographics and test metrics were reviewed for 86 658 clinical cases. Outcome information was requested for samples reported as aneuploidy detected or suspected for chromosomes 21, 18, or 13; voluntary outcome reporting was encouraged for all discordant outcomes. RESULTS: Of 86 658 cases, 85 298 (98.4%) met inclusion criteria for result reporting. Of the 1360 (1.6%) cancellations, only 101 (0.1%) were for technical reasons. Average time to result was 3.3 business days. Aneuploidy was detected or suspected in 2142 (2.5%) samples. For aneuploidy detected cases with known clinical outcomes, the overall positive predictive value (PPV) was 83.5% (608/728); observed PPVs for trisomies 21, 18, and 13 ranged from 50.0 to 92.8%. As individual PPVs are determined by a patient's prior risk, we developed a chart for counseling patients on positive predictive value based on maternal age. CONCLUSION: This large-scale report reinforces that noninvasive prenatal testing is a highly accurate screen for fetal aneuploidy in the general obstetric population. Test improvements have facilitated a reduction in failure rates, time to result, and borderline results/unclassifiable results. We have developed a positive predictive value counseling tool to ensure appropriate patient education, counseling, and clinical utilization.

Geographic differences in genetic susceptibility to IgA nephropathy: GWAS replication study and geospatial risk analysis.

IgA nephropathy (IgAN), major cause of kidney failure worldwide, is common in Asians, moderately prevalent in Europeans, and rare in Africans. It is not known if these differences represent variation in genes, environment, or ascertainment. In a recent GWAS, we localized five IgAN susceptibility loci on Chr.6p21 (HLA-DQB1/DRB1, PSMB9/TAP1, and DPA1/DPB2 loci), Chr.1q32 (CFHR3/R1 locus), and Chr.22q12 (HORMAD2 locus). These IgAN loci are associated with risk of other immune-mediated disorders such as type I diabetes, multiple sclerosis, or inflammatory bowel disease. We tested association of these loci in eight new independent cohorts of Asian, European, and African-American ancestry (N = 4,789), followed by meta-analysis with risk-score modeling in 12 cohorts (N = 10,755) and geospatial analysis in 85 world populations. Four susceptibility loci robustly replicated and all five loci were genome-wide significant in the combined cohort (P = 5×10⁻³²-3×10⁻¹°), with heterogeneity detected only at the PSMB9/TAP1 locus (I²â€Š= 0.60). Conditional analyses identified two new independent risk alleles within the HLA-DQB1/DRB1 locus, defining multiple risk and protective haplotypes within this interval. We also detected a significant genetic interaction, whereby the odds ratio for the HORMAD2 protective allele was reversed in homozygotes for a CFHR3/R1 deletion (P = 2.5×10⁻4). A seven-SNP genetic risk score, which explained 4.7% of overall IgAN risk, increased sharply with Eastward and Northward distance from Africa (r = 0.30, P = 3×10⁻¹²8). This model paralleled the known East-West gradient in disease risk. Moreover, the prediction of a South-North axis was confirmed by registry data showing that the prevalence of IgAN-attributable kidney failure is increased in Northern Europe, similar to multiple sclerosis and type I diabetes. Variation at IgAN susceptibility loci correlates with differences in disease prevalence among world populations. These findings inform genetic, biological, and epidemiological investigations of IgAN and permit cross-comparison with other complex traits that share genetic risk loci and geographic patterns with IgAN.

Nutritional control of antibiotic resistance via an interface between the phosphotransferase system and a two-component signaling system.

Enterococci are ubiquitous inhabitants of the gastrointestinal (GI) tract. However, antibiotic-resistant enterococci are also major causes of hospital-acquired infections. Enterococci are intrinsically resistant to cephalosporins, enabling growth to abnormally high densities in the GI tract in patients during cephalosporin therapy, thereby promoting dissemination to other sites where they cause infection. Despite its importance, many questions about the underlying basis for cephalosporin resistance remain. A specific two-component signaling system, composed of the CroS sensor kinase and its cognate response regulator (CroR), is required for cephalosporin resistance in Enterococcus faecalis, but little is known about the factors that control this signaling system to modulate resistance. To explore the signaling network in which CroR participates to influence cephalosporin resistance, we employed a protein fragment complementation assay to detect protein-protein interactions in E. faecalis cells, revealing a previously unknown association of CroR with the HPr protein of the phosphotransferase system (PTS) responsible for carbohydrate uptake and catabolite control of gene expression. Genetic and physiological analyses indicate that association with HPr restricts the ability of CroR to promote cephalosporin resistance and gene expression in a nutrient-dependent manner. Mutational analysis suggests that the interface used by HPr to associate with CroR is distinct from the interface used to associate with other cellular partners. Our results define a physical and functional connection between a critical nutrient-responsive signaling system (the PTS) and a two-component signaling system that drives antibiotic resistance in E. faecalis, and they suggest a general strategy by which bacteria can integrate their nutritional status with diverse environmental stimuli.

Impact of noninvasive prenatal testing in regionally dispersed medical centers in the United States.

OBJECTIVE: Noninvasive prenatal testing using cell-free DNA is a new alternative to screen for common fetal aneuploidies. It is not known what impact regional location may play on noninvasive prenatal testing implementation and downstream invasive prenatal procedure use in the United States. STUDY DESIGN: Six different regionally based centers collected data on noninvasive prenatal testing indication and results between February and November 2012, as well as their invasive prenatal procedure rates before and after offering noninvasive prenatal testing. Statistical analyses were performed using the 2-proportion Z-test. RESULTS: Of 1477 patients who underwent noninvasive prenatal testing; 693 (47%) were from centers in the West; 522 (35.3%) from centers in the East; and 262 (17.7%) from 1 center in the Midwest. Statistically significant differences were observed between West Coast and nonWest Coast sites for gestational age (14.1 weeks; P ≤ .0001). Advanced maternal age (AMA-only) was the most frequent indication in 5 of 6 sites (range, 21.8-62.9%) A total of 98 invasive prenatal procedures performed on 94 (6.4%) patients of which 64 (65.3%) were performed at centers in the West. More invasive procedures were performed following negative noninvasive prenatal testing results (n = 61) than abnormal noninvasive prenatal testing results (n = 30). The overall rate of patients undergoing invasive procedure after an abnormal noninvasive prenatal testing result was 32.6% (30 of 92). All 6 centers reported a decrease in invasive procedure volume after noninvasive prenatal testing introduction. CONCLUSION: This study demonstrates differences in clinical implementation of noninvasive prenatal testing across regionally dispersed centers in the United States, suggesting patient demographics and views toward prenatal testing influence use as well as downstream management.

Next Generation sequencing is the impetus for the next generation of laboratory-based genetic counselors.

Next generation sequencing (NGS) is dramatically increasing the number of clinically available genetic tests and thus the number of patients in which such testing may be indicated. The complex nature and volume of the reported results requires professional interpretation of the testing in order to translate and synthesize the meaning and potential benefit to patients, and genetic counselors are uniquely suited to provide this service. The increased need for genetic counselors in this role, coupled with the time required and a limited number of trained and available counselors presents a challenge to current models for making genetic testing available to patients and their healthcare providers effectively and efficiently. The employment of genetic counselors at genetic/genomic laboratories is one model to expand the resources for providing this service. In this article, we briefly review the advent of NGS and its clinical applications, examine the core skills of genetic counselors and delineate the expanding roles and responsibilities of laboratory-based genetic counselors. We also propose changes to the genetic counseling training program curriculum to account for the increasing opportunities for genetic counselors to contribute and thrive within genetic testing laboratories.

Iridescent colour production in hairs of blind golden moles (Chrysochloridae).

Relative to other metazoans, the mammalian integument is thought to be limited in colour. In particular, while iridescence is widespread among birds and arthropods, it has only rarely been reported in mammals. Here, we examine the colour, morphology and optical mechanisms in hairs from four species of golden mole (Mammalia: Chrysochloridae) that are characterized by sheens ranging from purple to green. Microspectrophotometry reveals that this colour is weak and variable. Iridescent hairs are flattened and have highly reduced cuticular scales, providing a broad and smooth surface for light reflection. These scales form multiple layers of light and dark materials of consistent thickness, strikingly similar to those in the elytra of iridescent beetles. Optical modelling suggests that the multi-layers produce colour through thin-film interference, and that the sensitivity of this mechanism to slight changes in layer thickness and number explains colour variability. While coloured integumentary structures are typically thought to evolve as sexual ornaments, the blindness of golden moles suggests that the colour may be an epiphenomenon resulting from evolution via other selective factors, including the ability to move and keep clean in dirt and sand.