Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis

Advances in next-generation sequencing (NGS) have facilitated parallel analysis of multiple genes enabling the implementation of cost-effective, rapid, and high-throughput methods for the molecular diagnosis of multiple genetic conditions, including the identification of BRCA1 and BRCA2 mutations in high-risk patients for hereditary breast and ovarian cancer. We clinically validated a NGS pipeline designed to replace Sanger sequencing and multiplex ligation-dependent probe amplification analysis and to facilitate detection of sequence and copy number alterations in a single test focusing on a BRCA1/BRCA2 gene analysis panel. Our custom capture library covers 46 exons, including BRCA1 exons 2, 3, and 5 to 24 and BRCA2 exons 2 to 27, with 20 nucleotides of intronic regions both 5′ and 3′ of each exon. We analyzed 402 retrospective patients, with previous Sanger sequencing and multiplex ligation-dependent probe amplification results, and 240 clinical prospective patients. One-hundred eighty-three unique variants, including sequence and copy number variants, were detected in the retrospective (n = 95) and prospective (n = 88) cohorts. This standardized NGS pipeline demonstrated 100% sensitivity and 100% specificity, uniformity, and high-depth nucleotide coverage per sample (approximately 7000 reads per nucleotide). Subsequently, the NGS pipeline was applied to the analysis of larger gene panels, which have shown similar uniformity, sample-to-sample reproducibility in coverage distribution, and sensitivity and specificity for detection of sequence and copy number variants

Exploration of Shared Genetic Architecture Between Subcortical Brain Volumes and Anorexia Nervosa

In MRI scans of patients with anorexia nervosa (AN), reductions in brain volume are often apparent. However, it is unknown whether such brain abnormalities are influenced by genetic determinants that partially overlap with those underlying AN. Here, we used a battery of methods (LD score regression, genetic risk scores, sign test, SNP effect concordance analysis, and Mendelian randomization) to investigate the genetic covariation between subcortical brain volumes and risk for AN based on summary measures retrieved from genome-wide association studies of regional brain volumes (ENIGMA consortium, n = 13,170) and genetic risk for AN (PGC-ED consortium, n = 14,477). Genetic correlations ranged from − 0.10 to 0.23 (all p > 0.05). There were some signs of an inverse concordance between greater thalamus volume and risk for AN (permuted p = 0.009, 95% CI: [0.005, 0.017]). A genetic variant in the vicinity of ZW10, a gene involved in cell division, and neurotransmitter and immune system relevant genes, in particular DRD2, was significantly associated with AN only after conditioning on its association with caudate volume (pFDR = 0.025). Another genetic variant linked to LRRC4C, important in axonal and synaptic development, reached significance after conditioning on hippocampal volume (pFDR = 0.021). In this comprehensive set of analyses and based on the largest available sample sizes to date, there was weak evidence for associations between risk for AN and risk for abnormal subcortical brain volumes at a global level (that is, common variant genetic architecture), but suggestive evidence for effects of single genetic markers. Highly powered multimodal brain- and disorder-related genome-wide studies are needed to further dissect the shared genetic influences on brain structure and risk for AN

Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci. However, the nature and mechanisms of these pleiotropic effects remain unclear. We performed analyses of 232,964 cases and 494,162 controls from genome-wide studies of anorexia nervosa, attention-deficit/hyper-activity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, and Tourette syndrome. Genetic correlation analyses revealed a meaningful structure within the eight disorders, identifying three groups of inter-related disorders. Meta-analysis across these eight disorders detected 109 loci associated with at least two psychiatric disorders, including 23 loci with pleiotropic effects on four or more disorders and 11 loci with antagonistic effects on multiple disorders. The pleiotropic loci are located within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes. These findings have important implications for psychiatric nosology, drug development, and risk prediction.Peer reviewe

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Background Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors. Results Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged. Conclusions Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.Peer reviewe

Alcoholism: Pathophysiology of a Disease

Editor’s introduction The first component of the patient-centered method distinguishes disease and illness. Effective care requires clinicians’ understanding and facility with both concepts. Dr Woodside explores the ‘body-as-machinef portion of the first component as he leads readers toward an appreciation of the illness experience. Exploring evidence and implications of the disease concept of alcoholism, this chapter begins with a review of the historical evolution of the concept of alcoholism as a disease: speeches by Abraham Lincoln and editorials from the JAMA in the 1890s, writings from the founders of Alcoholics Anonymous (AA), and the American Medical Association s (AMA) declaration of alcoholism as a disease in the 1950s. This is followed by a review of the scientific evidence supporting the disease concept. Investigations demonstrating genetic transmission including twin and adoption studies are presented along with research leading toward biochemical markers, and ‘valid’ biological bases for disease. Dr Woodside also reviews emergent literature describing the neurobiologic role of the mesolimbic dopamine system in craving and in the maintenance of drinking behavior. Case studies demonstrating patterns of inheritance facilitate his discussion, particularly as this relates to the perspective of an alcoholdependent person attempting to recover. The disease concept is described as playing a valuable role in mitigating shame and promoting acceptance of a recovery process. Taking this broader perspective, the disease concept has important implications for society’s approach to alcoholism, the responsibility of the healthcare industry, and third-party payers

Female Smokers Have Increased Postoperative Narcotic Requirements

This study investigated the influence of tobacco use on postoperative narcotic requirements of female patients following pelvic surgery. The history of tobacco use was taken by telephone survey, and the amount of postoperative narcotic used was obtained from a retrospective review of the patients’ hospital charts. Postoperative narcotic use for patients who never smoked was 10.9 mg/12 hr (n = 83, S.E. = 0.5), for former smokers was 13.0 mg/12 hr (n = 33, S.E. = 0.8) and for current smokers was 13.1 mg/12 hr (n = 53, S.E. = 0.7). Patients who never smoked used significantly less narcotic than former smokers (p =.02) or current smokers (p =.007). There was no difference between current and former smokers. Patients who have smoked required more narcotic for postoperative pain control. This effect was equally strong for former as for current smokers

Mapping network champion behavior in B2B electronic venturing

Abstract This study examines the concept of a new venture, B2B e-market in the light of participants who are involved in its innovation and diffusion processes. Our assessment results in the development of two key working propositions. The first proposition attempts to explain the relationship of the participants in the network and their contribution to innovation and diffusion processes over time. The second proposition attempts to explain how network champions (NC) contribute by bringing suppliers and buyers together in an electronic marketplace over time. In particular, this research adds to the industrial marketing literature by applying a case research method that is particularly useful for operationalizing theory development in business-to-business environments.