A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.We thank the DKFZ Genomics and Proteomics Core Facility and the OICR Genome Technologies Platform for provision of sequencing services. Financial support was provided by the consortium projects READNA under grant agreement FP7 Health-F4-2008-201418, ESGI under grant agreement 262055, GEUVADIS under grant agreement 261123 of the European Commission Framework Programme 7, ICGC-CLL through the Spanish Ministry of Science and Innovation (MICINN), the Instituto de Salud Carlos III (ISCIII) and the Generalitat de Catalunya. Additional financial support was provided by the PedBrain Tumor Project contributing to the International Cancer Genome Consortium, funded by German Cancer Aid (109252) and by the German Federal Ministry of Education and Research (BMBF, grants #01KU1201A, MedSys #0315416C and NGFNplus #01GS0883; the Ontario Institute for Cancer Research to PCB and JDM through funding provided by the Government of Ontario, Ministry of Research and Innovation; Genome Canada; the Canada Foundation for Innovation and Prostate Cancer Canada with funding from the Movember Foundation (PCB). PCB was also supported by a Terry Fox Research Institute New Investigator Award, a CIHR New Investigator Award and a Genome Canada Large-Scale Applied Project Contract. The Synergie Lyon Cancer platform has received support from the French National Institute of Cancer (INCa) and from the ABS4NGS ANR project (ANR-11-BINF-0001-06). The ICGC RIKEN study was supported partially by RIKEN President’s Fund 2011, and the supercomputing resource for the RIKEN study was provided by the Human Genome Center, University of Tokyo. MDE, LB, AGL and CLA were supported by Cancer Research UK, the University of Cambridge and Hutchison-Whampoa Limited. SD is supported by the Torres Quevedo subprogram (MI CINN) under grant agreement PTQ-12-05391. EH is supported by the Research Council of Norway under grant agreements 221580 and 218241 and by the Norwegian Cancer Society under grant agreement 71220-PR-2006-0433. Very special thanks go to Jennifer Jennings for administrating the activity of the ICGC Verification Working Group and Anna Borrell for administrative support.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms1000

Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study.

Background: Acute illness, existing co-morbidities and surgical stress response can all contribute to postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. The aim of this study was prospectively to develop a pragmatic prognostic model to stratify patients according to risk of developing AKI after major gastrointestinal surgery. Methods: This prospective multicentre cohort study included consecutive adults undergoing elective or emergency gastrointestinal resection, liver resection or stoma reversal in 2-week blocks over a continuous 3-month period. The primary outcome was the rate of AKI within 7 days of surgery. Bootstrap stability was used to select clinically plausible risk factors into the model. Internal model validation was carried out by bootstrap validation. Results: A total of 4544 patients were included across 173 centres in the UK and Ireland. The overall rate of AKI was 14·2 per cent (646 of 4544) and the 30-day mortality rate was 1·8 per cent (84 of 4544). Stage 1 AKI was significantly associated with 30-day mortality (unadjusted odds ratio 7·61, 95 per cent c.i. 4·49 to 12·90; P < 0·001), with increasing odds of death with each AKI stage. Six variables were selected for inclusion in the prognostic model: age, sex, ASA grade, preoperative estimated glomerular filtration rate, planned open surgery and preoperative use of either an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker. Internal validation demonstrated good model discrimination (c-statistic 0·65). Discussion: Following major gastrointestinal surgery, AKI occurred in one in seven patients. This preoperative prognostic model identified patients at high risk of postoperative AKI. Validation in an independent data set is required to ensure generalizability

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

Clival-Meckel\u27s Cave Angle: A Predictor of Glycerol Displacement in Percutaneous Glycerol Rhizotomy for Trigeminal Neuralgia.

BACKGROUND AND OBJECTIVES: Percutaneous glycerol rhizotomy successfully treats trigeminal neuralgia although failure rates and durability of the procedure are variable. Some of this variability in clinical outcome might be due to egress of glycerol from Meckel\u27s cave (MC) because of surgical positioning and individual patient anatomy. In this article, we quantitatively analyzed the anatomic variances that affect glycerol fluid dynamics to better predict patients more amenable for percutaneous glycerol injections. METHODS: Computed tomography imaging of 11 cadaveric heads was used to calculate bilateral Clival-Meckel\u27s cave (CMC) and sella-temporal (ST) angles. Twenty-two cadaveric percutaneous injections of dyed glycerol into the Meckel\u27s cave were performed using Härtel\u27s approach, and the fluid movement was documented at prespecified intervals over 1 hour. The relationship between the angles and glycerol migration was studied. RESULTS: Specimens with basal cistern involvement by 60 minutes had significantly greater CMC angles (median [IQR]: basal cistern involvement = 74.5° [59.5°-89.5°] vs no basal cistern involvement = 58.0° [49.0°-67.0°]), U = 6.0, P \u3c .001. This model may predict which patients will experience glycerol migration away from the Gasserian ganglion (area under the curve: 0.950, SE: 0.046, CI: 0.859-1.041, P \u3c .001). Increased ST angle was associated with lateral flow of glycerol (rs = 0.639, P = .001), and CMC angle was associated with total area of dispersion (rs = -0.474, P = .026). CONCLUSION: Anatomic variation in skull base angles affects glycerol migration. Specifically, a more obtuse CMC angle was associated with a higher risk of posterior migration away from the Gasserian ganglion. This may be a reason for differing rates of surgical success. These results suggest that anterior head flexion for 60 minutes may prevent percutaneous glycerol rhizotomy failures and some patients with large CMC angles are more likely to benefit from postinjection head positioning. However, this clinical effect needs validation in vivo

Transpalpebral transorbital neuroendoscopic (TONES) repair of orbital meningoencephalocele: a technical note

Purpose Intraorbital encephalocele (OMEC) is a rare entity in adults, usually secondary to an orbital pathology or prior trauma, in particular orbital roof fractures. Treatment of the OMEC is warranted to alleviate the pulsating exophthalmos and prevent potential visual decline. OMEC and orbital roof fractures have been predominantly treated via a craniotomy with a reconstruction of the orbital roof using various implants. With the advances in the endoscopic techniques, neuroendoscopy found its application in the treatment of orbital pathologies. We report a minimally invasive alternative: endoscopic transorbital repair of OMEC. Material and methods The repair technique is described with illustrations and clinical images. Narrated operative video demonstrating the procedure is provided. Results Illustrative case: 50-year-old female presented with progressive right eye proptosis over 6 months. Computed tomography (CT) demonstrated bony erosion in the lateral orbital roof, and magnetic resonance imaging (MRI) showed a small hyperintense T2-weighted and T1-weighted contrast enhancing lesion in the orbit, in the area of the bony erosion. Intraoperatively, the lesion was found to be an orbital encephalocele. The orbital defect was successfully repaired by employing the 'sandwich' technique, in which a dural substitute reinforced with tissue glue were deployed without repair of the osseous orbital roof. The patient tolerated the procedure well with ultimate resolution of proptosis. The cosmetic outcome was excellent. Conclusion The transorbital neuroendoscopic approach (TONES) presents a feasible, minimally invasive alternative treatment option for circumscribed intraorbital encephaloceles with minimal side effects, well tolerated by patients

Optimizing workflow in combined petrosectomy approaches: surgical technique and case series.

BACKGROUND AND OBJECTIVES: The combined petrosectomy is one of the workhorse skull base approaches to the petroclival region. Traditionally, this approach starts with a temporo-suboccipital craniotomy, followed by the mastoidectomy/anterior petrosectomy, and completed with the dural opening/tumor resection. This sequence of events (neurosurgery-neuro-otology-neurosurgery) involves at least two handoffs and change of surgical teams and instrumentation. This report describes a resequencing of events and a modification on the technique used to craft the temporo-suboccipital craniotomy. With aims to reduce handoffs between surgical teams and improves operating room workflow. METHODS: Adhering to PROCESS guidelines, a case series is provided in addition to the surgical technique and surgical images. RESULTS: This article describes the technique for performing a combined petrosectomy with descriptive illustrations. This shows that the temporal bone drilling may be performed prior to the craniotomy to allow for direct visualization of the dura and sinuses prior to completing the craniotomy. In doing so, only one transition between the otolaryngologist and neurosurgeon is necessary, thereby improving operating room workflow and time management. A series of ten patients is presented illustrating the feasibility of this procedure and providing operative details that were previously absent in the peer-reviewed literature. CONCLUSION: Combined petrosectomy while often performed in a three-step manner with the neurosurgeon starting the craniotomy, can be performed as described here in a two-step manner with similar outcomes and reasonable operating time

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

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.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 (VAFPeer reviewe