Whole-genome characterization of chemoresistant ovarian cancer

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

Whole-genome characterization of chemoresistant ovarian cancer

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

Whole genomes redefine the mutational landscape of pancreatic cancer

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.

Evaluating endogenous repair of focal cartilage defects in C57BL/6 and MRL/MpJ mice using 9.4T magnetic resonance imaging: A pilot study

The use of magnetic resonance imaging (MRI) for evaluating joint injuries is often considered superior to radiography due to the capacity of MRI for visualizing both soft and hard tissues. While longitudinal studies regarding cartilage repair have been undertaken on patients and in larger animal models, a method has yet to be developed for mouse cartilage to be repeatedly and non-invasively evaluated over time. The aim of this pilot study was to investigate if morphological changes following a focal cartilage injury in mice could be measured by 9.4T magnetic resonance imaging. Focal cartilage defects were induced in the left knee of 4-6weeks old C57BL/6 and MRL/MpJ mice. At endpoints 0, 2, and 4weeks post-injury, legs were dissected out and imaged ex vivo. The defect could be detected by MRI immediately after injury, appearing as a hyperintense focal point and with size similar to that of the surgical tool used. Defects were visible in both strains up to 4weeks post-injury, although signal intensity decreased over time. One C57BL/6 in particular, displayed extensive fibrosis in the patellar tendon at 4weeks as assessed by histology, while the MR images of the same animal displayed a clear, structural distinction between the patella and the new tissue growth. Overall, our results suggest that MRI could be used for longitudinal studies in murine cartilage injury models to evaluate certain characteristics of repair not detectable through histology.

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins efforts to improve early detection and treatment outcomes. While large EAC exome sequencing efforts to date have found recurrent loss-of-function mutations, oncogenic driving events have been underrepresented. Here we use a combination of whole-genome sequencing (WGS) and single-nucleotide polymorphism-array profiling to show that genomic catastrophes are frequent in EAC, with almost a third (32%, n=40/123) undergoing chromothriptic events. WGS of 22 EAC cases show that catastrophes may lead to oncogene amplification through chromothripsis-derived double-minute chromosome formation (MYC and MDM2) or breakage-fusion-bridge (KRAS, MDM2 and RFC3). Telomere shortening is more prominent in EACs bearing localized complex rearrangements. Mutational signature analysis also confirms that extreme genomic instability in EAC can be driven by somatic BRCA2 mutations. These findings suggest that genomic catastrophes have a significant role in the malignant transformation of EAC.

Mobile phones in clinical practice: reducing the risk of bacterial contamination

BACKGROUND

Mobile smart phones have become increasingly integrated into the practice of doctors and allied medical professionals. Recent studies suggest them to represent reservoirs for pathogens with potential to cause nosocomial infections. This study aimed to investigate the level of contamination on phones used on surgical wards and identify strategies for their safe use within clinical areas.

METHODS

Fifty mobile phones were taken from members of the multidisciplinary team working in a surgical unit. Phones were swabbed by two trained investigators using a standardised technique and samples streaked out using an automated specimen inoculator onto two types of culture media (Columbia blood agar and MacConkey agar). Colonies were identified and counted by a single trained investigator in a blinded fashion. Simultaneously a questionnaire investigating usage levels of phones was given to 150 healthcare workers.

RESULTS

Sixty per cent of phones sampled had some form of contaminant isolated from their phone. Thirty-one (62%) of phones had only three colonies or less isolated on medium. No pathogenic or drug resistant strains of bacteria were identified. A total of 88% of individuals sampled by questionnaire used their phone within the workplace of which 55% used it for clinical purposes. Sixty-three per cent expected there to be some form of contaminant on their phone with only 37% admitting to cleaning it regularly. Seventy-five per cent of people did not view a ban on phones as a practical solution was they found to be an infection risk.

CONCLUSION

Touch screen smart phones may be used safely in a clinical environment, with a low risk of cross-contamination of nosocomial bacteria to patients, in the setting of effective adherence to hand hygiene policies.

Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling

The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high-density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non-malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5' region of genes (including the proximal promoter, 5'UTR and CpG islands). Approximately 33% DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF-β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT-ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT-PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT-ROBO signaling and up-regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy.

A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing

Somatic rearrangements, which are commonly found in human cancer genomes, contribute to the progression and maintenance of cancers. Conventionally, the verification of somatic rearrangements comprises many manual steps and Sanger sequencing. This is labor intensive when verifying a large number of rearrangements in a large cohort. To increase the verification throughput, we devised a high-throughput workflow that utilizes benchtop next-generation sequencing and in-house bioinformatics tools to link the laboratory processes. In the proposed workflow, primers are automatically designed. PCR and an optional gel electrophoresis step to confirm the somatic nature of the rearrangements are performed. PCR products of somatic events are pooled for Ion Torrent PGM and/or Illumina MiSeq sequencing, the resulting sequence reads are assembled into consensus contigs by a consensus assembler, and an automated BLAT is used to resolve the breakpoints to base level. We compared sequences and breakpoints of verified somatic rearrangements between the conventional and high-throughput workflow. The results showed that next-generation sequencing methods are comparable to conventional Sanger sequencing. The identified breakpoints obtained from next-generation sequencing methods were highly accurate and reproducible. Furthermore, the proposed workflow allows hundreds of events to be processed in a shorter time frame compared with the conventional workflow.

Somatic point mutation calling in low cellularity tumors

Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (http://www.qcmg.org/bioinformatics/qsnp/) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.

Isolation of Aspergillus species from the airway of lung transplant recipients is associated with excess mortality

BACKGROUND

Aspergillus spp. are the leading cause of invasive fungal infection in lung transplant recipients. We investigated the relationship between the isolation of Aspergillus spp. from the respiratory tract of lung transplant recipients and their risk of mortality.

METHODS

A retrospective, observational cohort study of all patients who received lung allografts between January 1999 and May 2011 at a single UK centre was performed. The time from transplantation to death was analysed using Cox regression models. Isolation of Aspergillus spp. from the respiratory tract was included as a covariate in the Cox regression model.

RESULTS

Two hundred-thirteen patients were included. The median follow-up time was 5 years during which 102 patients (47.9%) died. Aspergillus was isolated from 74 (34.7%) patients. Twenty patients (27%) had Aspergillus isolated in the first 60 days post-transplant. Forty-one patients (55.4%) in the Aspergillus group and 61 patients (43.9%) in the non-Aspergillus group died during follow-up. A hazard ratio of 2.2 (95% CI 1.5-3.3; P < 0.001) for death following a positive Aspergillus sample was observed.

CONCLUSION

Isolation of Aspergillus spp. from patients following lung transplantation is associated with a significant increase in mortality. Novel preventative strategies are required to minimise the impact of Aspergillus in lung transplant recipients.

qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles

Tumour cellularity, the relative proportion of tumour and normal cells in a sample, affects the sensitivity of mutation detection, copy number analysis, cancer gene expression and methylation profiling. Tumour cellularity is traditionally estimated by pathological review of sectioned specimens; however this method is both subjective and prone to error due to heterogeneity within lesions and cellularity differences between the sample viewed during pathological review and tissue used for research purposes. In this paper we describe a statistical model to estimate tumour cellularity from SNP array profiles of paired tumour and normal samples using shifts in SNP allele frequency at regions of loss of heterozygosity (LOH) in the tumour. We also provide qpure, a software implementation of the method. Our experiments showed that there is a medium correlation 0.42 (-value = 0.0001) between tumor cellularity estimated by qpure and pathology review. Interestingly there is a high correlation 0.87 (-value 2.2e-16) between cellularity estimates by qpure and deep Ion Torrent sequencing of known somatic KRAS mutations; and a weaker correlation 0.32 (-value = 0.004) between IonTorrent sequencing and pathology review. This suggests that qpure may be a more accurate predictor of tumour cellularity than pathology review. qpure can be downloaded from https://sourceforge.net/projects/qpure/.

Cost-effectiveness of balloon kyphoplasty in patients with symptomatic vertebral compression fractures in a UK setting

SUMMARY

Balloon kyphoplasty (BKP) is a procedure used to treat vertebral compression fractures (VCFs). We developed a cost-effectiveness model to evaluate BKP in United Kingsdom patients with hospitalised VCFs and estimated the cost-effectiveness of BKP compared to non-surgical management. The results indicate that BKP provides a cost-effective alternative for treating these patients.

INTRODUCTION

VCFs of osteoporotic patients are associated with chronic pain, a reduction in health-related quality of life (QoL) and high healthcare costs. BKP is a minimally invasive procedure that has resulted in pain relief, vertebral body height-restoration, decreased kyphosis and improved physical functioning in patients with symptomatic VCFs. BKP was shown to improve health-related QoL in a 12-month interim analysis of a randomised phase-III trial.

METHODS

The objectives of this study were to develop a Markov cost-effectiveness model to evaluate BKP in patients with painful hospitalised VCFs and to estimate the cost-effectiveness of BKP compared with non-surgical management in a UK setting. It was assumed that QoL-benefits found at 12 months linearly approached zero during another 2 years, and that patients receiving BKP warranted six fewer hospital bed days compared with patients given non-surgical management.

RESULTS

The procedure was associated with quality-adjusted life-years (QALY)-gains of 0.17 and cost/QALY-gains at 8,800 pound sterling. The results were sensitive to assumptions about avoided length of hospital-stay and persistence of kyphoplasty-related QoL-benefits.

CONCLUSION

In conclusion, the results indicate that BKP provides a cost-effective alternative for treating patients with hospitalised VCFs in a UK-setting.