Prediction of acute myeloid leukaemia risk in healthy individuals.

The incidence of acute myeloid leukaemia (AML) increases with age and mortality exceeds 90% when diagnosed after age 65. Most cases arise without any detectable early symptoms and patients usually present with the acute complications of bone marrow failure1. The onset of such de novo AML cases is typically preceded by the accumulation of somatic mutations in preleukaemic haematopoietic stem and progenitor cells (HSPCs) that undergo clonal expansion2,3. However, recurrent AML mutations also accumulate in HSPCs during ageing of healthy individuals who do not develop AML, a phenomenon referred to as age-related clonal haematopoiesis (ARCH)4-8. Here we use deep sequencing to analyse genes that are recurrently mutated in AML to distinguish between individuals who have a high risk of developing AML and those with benign ARCH. We analysed peripheral blood cells from 95 individuals that were obtained on average 6.3 years before AML diagnosis (pre-AML group), together with 414 unselected age- and gender-matched individuals (control group). Pre-AML cases were distinct from controls and had more mutations per sample, higher variant allele frequencies, indicating greater clonal expansion, and showed enrichment of mutations in specific genes. Genetic parameters were used to derive a model that accurately predicted AML-free survival; this model was validated in an independent cohort of 29 pre-AML cases and 262 controls. Because AML is rare, we also developed an AML predictive model using a large electronic health record database that identified individuals at greater risk. Collectively our findings provide proof-of-concept that it is possible to discriminate ARCH from pre-AML many years before malignant transformation. This could in future enable earlier detection and monitoring, and may help to inform intervention.

Posttraumatic stress disorder and complex posttraumatic stress disorder in UK police officers.

BACKGROUND: We investigated work-related exposure to stressful and traumatic events in police officers, including repeated exposure to traumatic materials, and predicted that ICD-11 complex PTSD (CPTSD) would be more prevalent than posttraumatic stress disorder (PTSD). The effects of demographic variables on exposure and PTSD were examined, along with whether specific types of exposure were uniquely associated with PTSD or CPTSD. METHODS: An online survey covering issues about trauma management, wellbeing and working conditions was disseminated via social media and official policing channels throughout the UK. In total, 10 401 serving police officers self-identified as having been exposed to traumatic events. Measurement of PTSD and CPTSD utilised the International Trauma Questionnaire. RESULTS: The prevalence of PTSD was 8.0% and of CPTSD was 12.6%. All exposures were associated with PTSD and CPTSD in bivariate analyses. Logistic regression indicated that both disorders were more common in male officers, and were associated independently with frequent exposure to traumatic incidents and traumatic visual material, and with exposure to humiliating behaviours and sexual harassment, but not to verbal abuse, threats or physical violence. Compared to PTSD, CPTSD was associated with exposure to humiliating behaviours and sexual harassment, and also with lower rank and more years of service. CONCLUSIONS: CPTSD was more common than PTSD in police officers, and the data supported a cumulative burden model of CPTSD. The inclusion in DSM-5 Criterion A of work-related exposure to traumatic materials was validated for the first time. Levels of PTSD and CPTSD mandate enhanced occupational mental health services.

Impairment in active navigation from trauma and Post-Traumatic Stress Disorder.

The study investigated the impact of trauma exposure and of Post-Traumatic Stress Disorder (PTSD) on spatial processing and active navigation in a sample (n=138) comprising civilians (n=91), police officers (n=22) and veterans (n=27). Individuals with previous trauma exposure exhibited significantly poorer hippocampal-dependent (allocentric) navigation performance on active navigation in a virtual environment (the Alternative Route task) regardless of whether or not they had PTSD (scoring above 20 on the PTSD Diagnostic Scale). No effect of trauma exposure was found in static perspective taking (the Four Mountains task). Moreover, an associative information processing bias in those with PTSD interfered with ability to use hippocampal-dependent processing in active navigation. This study provides new evidence of impaired active navigation in individuals with trauma exposure and highlights the importance of considering the relationship between trauma and spatial processing in clinical and occupational settings.

Estimating the total prevalence of PTSD among the UK police force: Formal comment on Stevelink et al. (2020).

Two recent surveys have reported widely differing prevalence rates for posttraumatic stress disorder (PTSD) within the U.K. police force. Stevelink et al. (2020) reported a rate of 3.9% whereas a survey conducted for the charity Police Care UK reported a rate of 20.6%. In this comment we discuss how definitions and methodological factors can impact prevalence rates. We consider a number of possible reasons for the discrepancy between the surveys, and conclude that it is most likely a method artefact. Stevelink et al.'s survey reported the prevalence of recent-onset DSM-IV PTSD only, whereas the Police Care UK survey reported the total ICD-11 PTSD and Complex PTSD prevalence, regardless of when in the person's career the traumatic events occurred. Analysing the Police Care UK data using Stevelink et al.'s procedures produced practically identical prevalence rates, suggesting that the discrepancy was apparent rather than real.

Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival.

Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR = 0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR = 1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features.

Digitizing a Face-to-Face Group Fatigue Management Program: Exploring the Views of People With Multiple Sclerosis and Health Care Professionals Via Consultation Groups and Interviews.

BACKGROUND: Fatigue is one of the most common and debilitating symptoms of multiple sclerosis (MS) and is the main reason why people with MS stop working early. The MS Society in the United Kingdom funded a randomized controlled trial of FACETS-a face-to-face group-based fatigue management program for people with multiple sclerosis (pwMS)-developed by members of the research team. Given the favorable trial results and to help with implementation, the MS Society supported the design and printing of the FACETS manual and materials and the national delivery of FACETS training courses (designed by the research team) for health care professionals (HCPs). By 2015 more than 1500 pwMS had received the FACETS program, but it is not available in all areas and a face-to-face format may not be suitable for, or appeal to, everyone. For these reasons, the MS Society funded a consultation to explore an alternative Web-based model of service delivery. OBJECTIVE: The aim of this study was to gather views about a Web-based model of service delivery from HCPs who had delivered FACETS and from pwMS who had attended FACETS. METHODS: Telephone consultations were undertaken with FACETS-trained HCPs who had experience of delivering FACETS (n=8). Three face-to-face consultation groups were held with pwMS who had attended the FACETS program: London (n=4), Liverpool (n=4), and Bristol (n=7). The interviews and consultation groups were digitally recorded and transcribed. A thematic analysis was undertaken to identify key themes. Toward the end of the study, a roundtable meeting was held to discuss outcomes from the consultation with representatives from the MS Society, HCPs, and pwMS. RESULTS: Key challenges and opportunities of designing and delivering an integrated Web-based version of FACETS and maintaining user engagement were identified across 7 themes (delivery, online delivery, design, group, engagement, interactivity, and HCP relationships). Particularly of interest were themes related to replicating the group dynamics and the lack of high-quality solutions that would support the FACETS' weekly homework tasks and symptom monitoring and management. CONCLUSIONS: A minimum viable Web-based version of FACETS was suggested as the best starting point for a phased implementation, enabling a solution that could then be added to over time. It was also proposed that a separate study should look to create a free stand-alone digital toolkit focusing on the homework elements of FACETS. This study has commenced with a first version of the toolkit in development involving pwMS throughout the design and build stages to ensure a user-centered solution.

Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases.

We integrated clinical, genomic, and transcriptomic data from 224 primaries and 95 metastases from 289 patients to characterize progression of pancreatic ductal adenocarcinoma (PDAC). Driver gene alterations and mutational and expression-based signatures were preserved, with truncations, inversions, and translocations most conserved. Cell cycle progression (CCP) increased with sequential inactivation of tumor suppressors, yet remained higher in metastases, perhaps driven by cell cycle regulatory gene variants. Half of the cases were hypoxic by expression markers, overlapping with molecular subtypes. Paired tumor heterogeneity showed cancer cell migration by Halstedian progression. Multiple PDACs arising synchronously and metachronously in the same pancreas were actually intra-parenchymal metastases, not independent primary tumors. Established clinical co-variates dominated survival analyses, although CCP and hypoxia may inform clinical practice.

Impact of Chemical-Induced Mutational Load Increase on Immune Checkpoint Therapy in Poorly Responsive Murine Tumors.

A recurring historic finding in cancer drug development is encouraging antitumor effects observed in tumor-bearing mice that fail to translate into the clinic. An intriguing exception to this pattern is immune checkpoint therapy, as the sustained tumor regressions observed in subsets of cancer patients are rare in mice. Reasoning that this may be due in part to relatively low mutational loads of mouse tumors, we mutagenized transplantable mouse tumor cell lines EMT-6/P, B16F1, RENCA, CT26, and MC38 in vitro with methylnitro-nitrosoguanidine (MNNG) or ethylmethane sulfonate (EMS) and tested their responsiveness to PD-L1 blockade. Exome sequencing confirmed an increase in somatic mutations by mutagen treatment, an effect mimicked in EMT-6 variants chronically exposed in vivo to cisplatin or cyclophosphamide. Certain mutagenized variants of B16F1, EMT-6/P, CT26, and MC38 (but not RENCA) were more immunogenic than their parents, yet anti-PD-L1 sensitization developed only in some EMT-6/P and B16F1 variants. Treatment response patterns corresponded with changes in immune cell infiltration and especially increases in CD8+ T cells. Chronically cisplatin-exposed EMT-6 variants were also more responsive to anti-PD-L1 therapy. Although tumor PD-L1 expression was upregulated in in vivo chemotherapy-exposed variants, PD-L1 expression levels were not consistently associated with anti-PD-L1 treatment activity across mutagenized or chemotherapy-exposed variants. In summary, mutagenized and more immunogenic mouse tumors were not universally sensitized to PD-L1 blockade. Chemically mutagenized variants may be useful to evaluate the impact of immunologically "hot" or "cold" tumors with a high mutational load, to which certain chemotherapy agents may contribute, on immunotherapy outcomes. Mol Cancer Ther; 17(4); 869-82. ©2018 AACR.

Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial.

Purpose: To perform real-time whole genome sequencing (WGS) and RNA sequencing (RNASeq) of advanced pancreatic ductal adenocarcinoma (PDAC) to identify predictive mutational and transcriptional features for better treatment selection.Experimental Design: Patients with advanced PDAC were prospectively recruited prior to first-line combination chemotherapy. Fresh tumor tissue was acquired by image-guided percutaneous core biopsy for WGS and RNASeq. Laser capture microdissection was performed for all cases. Primary endpoint was feasibility to report WGS results prior to first disease assessment CT scan at 8 weeks. The main secondary endpoint was discovery of patient subsets with predictive mutational and transcriptional signatures.Results: Sixty-three patients underwent a tumor biopsy between December 2015 and June 2017. WGS and RNASeq were successful in 62 (98%) and 60 (95%), respectively. Genomic results were reported at a median of 35 days (range, 19-52 days) from biopsy, meeting the primary feasibility endpoint. Objective responses to first-line chemotherapy were significantly better in patients with the classical PDAC RNA subtype compared with those with the basal-like subtype (P = 0.004). The best progression-free survival was observed in those with classical subtype treated with m-FOLFIRINOX. GATA6 expression in tumor measured by RNA in situ hybridization was found to be a robust surrogate biomarker for differentiating classical and basal-like PDAC subtypes. Potentially actionable genetic alterations were found in 30% of patients.Conclusions: Prospective genomic profiling of advanced PDAC is feasible, and our early data indicate that chemotherapy response differs among patients with different genomic/transcriptomic subtypes. Clin Cancer Res; 24(6); 1344-54. ©2017 AACR.

The Impact of the Brain-Derived Neurotrophic Factor Gene on Trauma and Spatial Processing.

The influence of genes and the environment on the development of Post-Traumatic Stress Disorder (PTSD) continues to motivate neuropsychological research, with one consistent focus being the Brain-Derived Neurotrophic Factor (BDNF) gene, given its impact on the integrity of the hippocampal memory system. Research into human navigation also considers the BDNF gene in relation to hippocampal dependent spatial processing. This speculative paper brings together trauma and spatial processing for the first time and presents exploratory research into their interactions with BDNF. We propose that quantifying the impact of BDNF on trauma and spatial processing is critical and may well explain individual differences in clinical trauma treatment outcomes and in navigation performance. Research has already shown that the BDNF gene influences PTSD severity and prevalence as well as navigation behaviour. However, more data are required to demonstrate the precise hippocampal dependent processing mechanisms behind these influences in different populations and environmental conditions. This paper provides insight from recent studies and calls for further research into the relationship between allocentric processing, trauma processing and BDNF. We argue that research into these neural mechanisms could transform PTSD clinical practice and professional support for individuals in trauma-exposing occupations such as emergency response, law enforcement and the military.

Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.

RLS and blood donation.

BACKGROUND AND PURPOSE: The link between brain iron deficiency and RLS is now well established. In a related observation, several conditions that can deplete iron stores have been linked to increased probability of RLS. Blood donation has been linked to iron deficiency. It has thus been hypothesized that donating blood may be a risk factor for developing RLS. PATIENTS AND METHODS: Two thousand and five UK blood donors, ranging from first-time donors to some who had donated more than 70 times, completed the validated Cambridge-Hopkins RLS questionnaire (CH-RLSq) following their donation session. The questionnaire included a set of questions designed to diagnose RLS. The donors' histories of blood donations were determined both from self-report and from the National Blood Service database. RESULTS: A number of statistical models were constructed to determine whether the probability of RLS diagnosis was related to the history of blood donations. Controlling for age and sex, no evidence was found to suggest that a greater number or frequency of blood donations increased the risk of RLS. Even amongst sub-groups especially vulnerable to iron depletion through blood donation, such as vegetarians or low weight individuals, no evidence for an increased risk of RLS could be found. CONCLUSIONS: We found no evidence that the frequency or number of blood donations up to the UK maximum of three times a year would increase the risk of RLS.