Impact of Chromatin Structures on DNA Processing for Genomic Analyses

Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP) experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome

Piccolo genotype modulates neural correlates of emotion processing but not executive functioning

Major depressive disorder (MDD) is characterized by affective symptoms and cognitive impairments, which have been associated with changes in limbic and prefrontal activity as well as with monoaminergic neurotransmission. A genome-wide association study implicated the polymorphism rs2522833 in the piccolo (PCLO) gene—involved in monoaminergic neurotransmission—as a risk factor for MDD. However, the role of the PCLO risk allele in emotion processing and executive function or its effect on their neural substrate has never been studied. We used functional magnetic resonance imaging (fMRI) to investigate PCLO risk allele carriers vs noncarriers during an emotional face processing task and a visuospatial planning task in 159 current MDD patients and healthy controls. In PCLO risk allele carriers, we found increased activity in the left amygdala during processing of angry and sad faces compared with noncarriers, independent of psychopathological status. During processing of fearful faces, the PCLO risk allele was associated with increased amygdala activation in MDD patients only. During the visuospatial planning task, we found no genotype effect on performance or on BOLD signal in our predefined areas as a function of increasing task load. The PCLO risk allele was found to be specifically associated with altered emotion processing, but not with executive dysfunction. Moreover, the PCLO risk allele appears to modulate amygdala function during fearful facial processing in MDD and may constitute a possible link between genotype and susceptibility for depression via altered processing of fearful stimuli. The current results may therefore aid in better understanding underlying neurobiological mechanisms in MDD

Deliberate self-harm and attachment: mediating and moderating roles of depression, anxiety, social support and interpersonal problems among Pakistani school going adolescents

Introduction: In Pakistan there is dearth of research on deliberate self-harm (DSH) and its predictors among adolescents. While the lack of research in Pakistan can be partly attributed to the sacrilegious status, criminalization and stigmatization attached to DSH, it is also an attribute of paucity of Urdu versions of the standardized psychological instruments. Previous research in developed countries has indicated that attachment theory can be used as a useful framework to understand the development of austere psychopathologies like DSH, as well as for studying pathways of interaction of interpersonal and intrapersonal factors of psychopathologies. In this study, standardized psychological instruments are translated into Urdu language as a first step. These instruments are then used to study pathways of interaction of interpersonal and intrapersonal factors of DSH, conceptualized within attachment framework. Method: The study was conducted in two steps. In step 1, Youth Health Risk Behavior Survey (YHRB), Inventory of Interpersonal Problems-32 (IIP-32) and Significant Others Scale (SOS), were translated into Urdu language. Along with these scales, Urdu translated versions of Hospital Anxiety and Depression Scale (HADS), Adolescent Relationship Scales Questionnaire (ARSQ), Life Events scale (LES) from CASE questionnaire and Family Affluence Scale-II (FAS-II) were reviewed for accuracy of translation through expert judgement and psychometric evaluation. Secondly, a cross sectional survey was conducted with 1290 adolescents (10 - 19 years age) using the translated Urdu versions of the instruments and demographic pro forma. Structural equation modelling was used to study the pathways of associations between predictors of DSH. Results: The extensive process of translation resulted in establishment of semantic, content, technical and construct equivalence of the translated instruments with the original English versions. Multiple imputation was performed to account for missing values in SPSS 20. Important structural adaptations were made in the scales based on factor analyses conducted in M plus. After modifications, all scales showed satisfactory CFI (≥ 0.90) and RMSEA (≤ 0.06). Results of the survey indicated that the prevalence of DSH (with, without and ambivalent suicidal intentions) was 7%. Two SEM models were constructed involving both mediation and moderation pathways. Results of Model 1 showed association of attachment with DSH was double mediated by social support, depression and anxiety. Model 2 also confirmed association of attachment with DSH with double mediation through relationship style problems, depression and anxiety. In order to understand the contextual picture of the concepts studied in this research both SEM models were also constructed by controlling for demographic factors. This resulted in confirming age, gender and family affluence as significant contributors but with very small effects. Discussion and conclusion: In the present study translation of the instruments helped in building a reservoir for future research. The results of translation and validation of instruments indicated that cultural differences, language needs and age must be accounted for while using standardized psychological instruments. Taking into consideration specific cultural and demographic background of Pakistan, this study also confirms the key role of attachment in influencing interaction of predictors of DSH. It is suggested that intrapersonal and interpersonal factors are influential points of intervention for designing clinical, school and community based awareness and prevention programs for DSH. The thesis also discusses the implications for policy guidelines along with recommendations for future research and other applications of the study

Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA

© 2015 Lanman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Cell-free DNA in the management of colorectal cancer

International audienceColorectal cancer is one of the leading cause of death by cancer worldwide in both men and women. Liquid biopsy belongs nowadays to the landscape of cancer management biological tools. In this chapter, we will describe and discuss the actual, potential and future applications of cfDNA analysis in plasma of patients with colorectal cancer in early or metastatic stage. During the last decade, the development of molecular biology assays like digital PCR or next-generation sequencing made the analysis of cfDNA in plasma possible with an excellent sensitivity and applications like early detection, diagnosis, prognosis, response to treatment, monitoring of an emerging resistance, mapping of the disease molecular landscape or evaluation of the residual disease are now feasible. cfDNA detection has several promising applications in the management of patients with colorectal cancer, but prospective randomised clinical trials are still lacking to make liquid biopsy ready for prime-time