Department of Radiation Oncology and Kimmel Cancer Center, Thomas jefferson University, The intronic G13964C variant in p53 is not a high-risk mutation in familial breast cancer in Australia.

BACKGROUND: Mutations in BRCA1 and BRCA2 account for approximately 50% of breast cancer families with more than four affected cases, whereas exonic mutations in p53, PTEN, CHK2 and ATM may account for a very small proportion. It was recently reported that an intronic variant of p53--G13964C--occurred in three out of 42 (7.1%) \u27hereditary\u27 breast cancer patients, but not in any of 171 \u27sporadic\u27 breast cancer control individuals (P = 0.0003). If this relatively frequent occurrence of G13964C in familial breast cancer and absence in control individuals were confirmed, then this would suggest that the G13964C variant plays a role in breast cancer susceptibility. METHOD: We genotyped 71 familial breast cancer patients and 143 control individuals for the G13964C variant using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis. RESULTS: Three (4.2%; 95% confidence interval [CI] 0-8.9%) G13964C heterozygotes were identified. The variant was also identified in 5 out of 143 (3.5%; 95% CI 0.6-6.4%) control individuals without breast cancer or a family history of breast cancer, however, which is no different to the proportion found in familial cases (P = 0.9). CONCLUSION: The present study would have had 80% power to detect an odds ratio of 4.4, and we therefore conclude that the G13946C polymorphism is not a \u27high-risk\u27 mutation for familial breast cancer

The intronic G13964C variant in p53 is not a high-risk mutation in familial breast cancer in Australia

BACKGROUND: Mutations in BRCA1 and BRCA2 account for approximately 50% of breast cancer families with more than four affected cases, whereas exonic mutations in p53, PTEN, CHK2 and ATM may account for a very small proportion. It was recently reported that an intronic variant of p53 - G13964C - occurred in three out of 42 (7.1%) 'hereditary' breast cancer patients, but not in any of 171 'sporadic' breast cancer control individuals (P = 0.0003). If this relatively frequent occurrence of G13964C in familial breast cancer and absence in control individuals were confirmed, then this would suggest that the G13964C variant plays a role in breast cancer susceptibility. METHOD: We genotyped 71 familial breast cancer patients and 143 control individuals for the G13964C variant using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis. RESULTS: Three (4.2%; 95% confidence interval [CI] 0–8.9%) G13964C heterozygotes were identified. The variant was also identified in 5 out of 143 (3.5%; 95% CI 0.6–6.4%) control individuals without breast cancer or a family history of breast cancer, however, which is no different to the proportion found in familial cases (P = 0.9). CONCLUSION: The present study would have had 80% power to detect an odds ratio of 4.4, and we therefore conclude that the G13946C polymorphism is not a 'high-risk' mutation for familial breast cancer

Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource

INTRODUCTION: The Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab) is a multidisciplinary, collaborative framework for the investigation of familial breast cancer. Based in Australia, the primary aim of kConFab is to facilitate high-quality research by amassing a large and comprehensive resource of epidemiological and clinical data with biospecimens from individuals at high risk of breast and/or ovarian cancer, and from their close relatives. METHODS: Epidemiological, family history and lifestyle data, as well as biospecimens, are collected from multiple-case breast cancer families ascertained through family cancer clinics in Australia and New Zealand. We used the Tyrer-Cuzick algorithms to assess the prospective risk of breast cancer in women in the kConFab cohort who were unaffected with breast cancer at the time of enrolment in the study. RESULTS: Of kConFab's first 822 families, 518 families had multiple cases of female breast cancer alone, 239 had cases of female breast and ovarian cancer, 37 had cases of female and male breast cancer, and 14 had both ovarian cancer as well as male and female breast cancer. Data are currently held for 11,422 people and germline DNAs for 7,389. Among the 812 families with at least one germline sample collected, the mean number of germline DNA samples collected per family is nine. Of the 747 families that have undergone some form of mutation screening, 229 (31%) carry a pathogenic or splice-site mutation in BRCA1 or BRCA2. Germline DNAs and data are stored from 773 proven carriers of BRCA1 or BRCA1 mutations. kConFab's fresh tissue bank includes 253 specimens of breast or ovarian tissue – both normal and malignant – including 126 from carriers of BRCA1 or BRCA2 mutations. CONCLUSION: These kConFab resources are available to researchers anywhere in the world, who may apply to kConFab for biospecimens and data for use in ethically approved, peer-reviewed projects. A high calculated risk from the Tyrer-Cuzick algorithms correlated closely with the subsequent occurrence of breast cancer in BRCA1 and BRCA2 mutation positive families, but this was less evident in families in which no pathogenic BRCA1 or BRCA2 mutation has been detected

Adapting the ASSIST model of informal peer-led intervention delivery to the Talk to FRANK drug prevention programme in UK secondary schools (ASSIST + FRANK): intervention development, refinement and a pilot cluster randomised controlled trial

Background: Illicit drug use increases the risk of poor physical and mental health. There are few effective drug prevention interventions. Objective: To assess the acceptability of implementing and trialling two school-based peer-led drug prevention interventions. Design: Stage 1 – adapt ASSIST, an effective peer-led smoking prevention intervention to deliver information from the UK national drug education website [see www.talktofrank.com (accessed 29 August 2017)]. Stage 2 – deliver the two interventions, ASSIST + FRANK (+FRANK) and FRANK friends, examine implementation and refine content. Stage 3 – four-arm pilot cluster randomised control trial (cRCT) of +FRANK, FRANK friends, ASSIST and usual practice, including a process evaluation and an economic assessment. Setting: Fourteen secondary schools (two in stage 2) in South Wales, UK. Participants: UK Year 8 students aged 12–13 years at baseline. Interventions: +FRANK is a UK informal peer-led smoking prevention intervention provided in Year 8 followed by a drug prevention adjunct provided in Year 9. FRANK friends is a standalone informal peer-led drug prevention intervention provided in Year 9. These interventions are designed to prevent illicit drug use through training influential students to disseminate information on the risks associated with drugs and minimising harms using content from www.talktofrank.com. Training is provided off site and follow-up visits are made in school. Outcomes: Stage 1 – +FRANK and FRANK friends intervention manuals and resources. Stage 2 – information on the acceptability and fidelity of delivery of the interventions for refining manuals and resources. Stage 3 – (a) acceptability of the interventions according to prespecified criteria; (b) qualitative data from students, staff, parents and intervention teams on implementation and receipt of the interventions; (c) comparison of the interventions; and (d) recruitment and retention rates, completeness of primary, secondary and intermediate outcome measures and estimation of costs. Results: +FRANK and FRANK friends were developed with stakeholders [young people, teachers (school management team and other roles), parents, ASSIST trainers, drug agency staff and a public health commissioner] over an 18-month period. In the stage 2 delivery of +FRANK, 12 out of the 14 peer supporters attended the in-person follow-ups but only one completed the electronic follow-ups. In the pilot cRCT, 12 schools were recruited, randomised and retained. The student response rate at the 18-month follow-up was 93% (1460/1567 students). Over 80% of peer supporters invited were trained and reported conversations on drug use and contact with trainers. +FRANK was perceived less positively than FRANK friends. The prevalence of lifetime illicit drug use was 4.1% at baseline and 11.6% at follow-up, with low numbers of missing data for all outcomes. The estimated cost per school was £1942 for +FRANK and £3041 for FRANK friends. All progression criteria were met. Conclusions: Both interventions were acceptable to students, teachers and parents, but FRANK friends was preferred to +FRANK. A limitation of the study was that qualitative data were collected on a self-selecting sample. Future work recommendations include progression to a Phase III effectiveness trial of FRANK friends. Trial registration: Current Controlled Trials ISRCTN14415936. Funding: This project was funded by the National Institute for Health Research (NIHR) Public Health Research programme and will be published in full in Public Health Research; Vol. 5, No. 7. See the NIHR Journals Library website for further project information. The work was undertaken with the support of the Centre for the Development and Evaluation of Complex Interventions for Public Health Improvement (DECIPHer). Joint funding (MR/KO232331/1) from the British Heart Foundation, Cancer Research UK, the Economic and Social Research Council, the Medical Research Council, the Welsh Government and the Wellcome Trust, under the auspices of the UK CRC, is gratefully acknowledged

Tropical rainfall predictions from multiple seasonal forecast systems

We quantify seasonal prediction skill of tropical winter rainfall in 14 climate forecast systems. High levels of seasonal prediction skill exist for year‐to‐year rainfall variability in all tropical ocean basins. The tropical East Pacific is the most skilful region, with very high correlation scores, and the tropical West Pacific is also highly skilful. Predictions of tropical Atlantic and Indian Ocean rainfall show lower but statistically significant scores. We compare prediction skill (measured against observed variability) with model predictability (using single forecasts as surrogate observations). Model predictability matches prediction skill in some regions but it is generally greater, especially over the Indian Ocean. We also find significant inter‐basin connections in both observed and predicted rainfall. Teleconnections between basins due to El Niño–Southern Oscillation (ENSO) appear to be reproduced in multi‐model predictions and are responsible for much of the prediction skill. They also explain the relative magnitude of inter‐annual variability, the relative magnitude of predictable rainfall signals and the ranking of prediction skill across different basins. These seasonal tropical rainfall predictions exhibit a severe wet bias, often in excess of 20% of mean rainfall. However, we find little direct relationship between bias and prediction skill. Our results suggest that future prediction systems would be best improved through better model representation of inter‐basin rainfall connections as these are strongly related to prediction skill, particularly in the Indian and West Pacific regions. Finally, we show that predictions of tropical rainfall alone can generate highly skilful forecasts of the main modes of extratropical circulation via linear relationships that might provide a useful tool to interpret real‐time forecasts

A quantification of uncertainties in historical tropical tropospheric temperature trends from radiosondes

The consistency of tropical tropospheric temperature trends with climate model expectations remains contentious. A key limitation is that the uncertainties in observations from radiosondes are both substantial and poorly constrained. We present a thorough uncertainty analysis of radiosonde‐based temperature records. This uses an automated homogenization procedure and a previously developed set of complex error models where the answer is known a priori. We perform a number of homogenization experiments in which error models are used to provide uncertainty estimates of real‐world trends. These estimates are relatively insensitive to a variety of processing choices. Over 1979–2003, the satellite‐equivalent tropical lower tropospheric temperature trend has likely (5–95% confidence range) been between −0.01 K/decade and 0.19 K/decade (0.05–0.23 K/decade over 1958–2003) with a best estimate of 0.08 K/decade (0.14 K/decade). This range includes both available satellite data sets and estimates from models (based upon scaling their tropical amplification behavior by observed surface trends). On an individual pressure level basis, agreement between models, theory, and observations within the troposphere is uncertain over 1979 to 2003 and nonexistent above 300 hPa. Analysis of 1958–2003, however, shows consistent model‐data agreement in tropical lapse rate trends at all levels up to the tropical tropopause, so the disagreement in the more recent period is not necessarily evidence of a general problem in simulating long‐term global warming. Other possible reasons for the discrepancy since 1979 are: observational errors beyond those accounted for here, end‐point effects, inadequate decadal variability in model lapse rates, or neglected climate forcings

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts