Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

<p>Abstract</p> <p>Background</p> <p>Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions. Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered. Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated. This inefficient approach to primer design is further intensified in a high-throughput laboratory, where hundreds of genes may be targeted in one experiment.</p> <p>Results</p> <p>We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline. Investigators may specify target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. In the process of improving our sequencing success rate, which currently exceeds 95% for exons, we have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. We reveal the laboratory protocols and their associated, empirically determined computational parameters, as well as describe the novel computational methods which may benefit others in future primer design research.</p> <p>Conclusion</p> <p>The high-throughput PCR primer design pipeline has been very successful in providing the basis for high-quality directed sequencing results and for minimizing costs associated with labor and reprocessing. The modular architecture of the primer design software has made it possible to readily integrate additional primer critique tests based on iterative feedback from the laboratory. As a result, the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing.</p

Cognitive behaviour therapy response and dropout rate across purging and nonpurging bulimia nervosa and binge eating disorder : DSM-5 implications

Background: With the imminent publication of the new edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), there has been a growing interest in the study of the boundaries across the three bulimic spectrum syndromes [bulimia nervosa-purging type (BN-P), bulimia nervosa-non purging type (BN-NP) and binge eating disorder (BED)]. Therefore, the aims of this study were to determine differences in treatment response and dropout rates following Cognitive Behavioural Therapy (CBT) across the three bulimic-spectrum syndromes. Method: The sample comprised of 454 females (87 BED, 327 BN-P and 40 BN-NP) diagnosed according to DSM-IV-TR criteria who were treated with 22 weekly outpatient sessions of group CBT therapy. Patients were assessed before and after treatment using a food and binging/purging diary and some clinical questionnaires in the field of ED. "Full remission" was defined as total absence of binging and purging (laxatives and/or vomiting) behaviors and psychological improvement for at least 4 (consecutive). Results: Full remission rate was found to be significantly higher in BED (69.5%) than in both BN-P (p < 0.005) and BN-NP (p < 0.001), which presented no significant differences between them (30.9% and 35.5%). The rate of dropout from group CBT was also higher in BED (33.7%) than in BN-P (p < 0.001) and BN-NP (p < 0.05), which were similar (15.4% and 12.8%, respectively). Conclusions: Results suggest that purging and non-purging BN have similar treatment response and dropping out rates, whereas BED appears as a separate diagnosis with better outcome for those who complete treatment. The results support the proposed new DSM-5 classification

Effectiveness of a web-based treatment program using intensive therapeutic support for female patients with bulimia nervosa, binge eating disorder and eating disorders not otherwise specified: study protocol of a randomized controlled trial

Background: Disordered eating behavior and body dissatisfaction affect a large proportion of the Dutch population and account for severe psychological, physical and social morbidity. Yet, the threshold for seeking professional care is still high. In the Netherlands, only 7.5% of patients with bulimia nervosa and 33% of patients with anorexia nervosa are treated within the mental health care system. Easily accessible and low-threshold interventions, therefore, are needed urgently. The internet has great potential to offer such interventions. The aim of this study is to determine whether a web-based treatment program for patients with eating disorders can improve eating disorder psychopathology among female patients with bulimia nervosa, binge eating disorder and eating disorders not otherwise specified. Methods/design: This randomized controlled trial will compare the outcomes of an experimental treatment group to a waiting list control group. In the web-based treatment program, participants will communicate personally and asynchronously with their therapists exclusively via the internet. The first part of the program will focus on analyzing eating attitudes and behaviors. In the second part of the program participants will learn how to change their attitudes and behaviors. Participants assigned to the waiting list control group will receive no-reply email messages once every two weeks during the waiting period of 15 weeks, after which they can start the program. The primary outcome measure is an improvement in eating disorder psychopathology as determined by the Eating Disorder Examination Questionnaire. Secondary outcomes include improvements in body image, physical and mental health, body weight, self-esteem, quality of life, and social contacts. In addition, the participants’ motivation for treatment and their acceptability of the program and the therapeutic alliance will be measured. The study will follow the recommendations in the CONSORT statement relating to designing and reporting on RCTs. Discussion: This study protocol presents the design of a RCT for evaluating the effectiveness of a web-based treatment program using intensive therapeutic support for female patients with bulimia nervosa, binge eating disorder and eating disorders not otherwise specified

Irritable bowel syndrome and functional dyspepsia in patients with eating disorders ‐ a systematic review

Objectives: The prevalence of eating disorders is rising worldwide. The low body weight in anorexia nervosa as well as the increase in body mass index due to binge eating disorder are contributing to a strikingly high morbidity and mortality. In a similar pattern, the prevalence and burden of the disease of functional gastrointestinal disorders such as functional dyspepsia and irritable bowel syndrome is increasing. As gastrointestinal complaints are commonly reported by patients with eating disorders, the question arose whether there is a relationship between eating disorders and functional gastrointestinal disorders. Methods: To address the need to better understand the interplay between eating disorders and functional gastrointestinal disorders as well as factors that might influence this connection, the data bases Medline, Web of Science and Embase were systematically searched. Results: After removal of duplicates the search yielded 388 studies which were screened manually. As a result, 36 publications were selected for inclusion in this systematic review. Conclusion: The occurrence of functional gastrointestinal disorders like irritable bowel syndrome and functional dyspepsia in patients with eating disorders is considerably high and often associated with psychological, hormonal and functional alterations. In the future, further research addressing the underlying mechanisms accounting for this relationship is required