Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Tumour assessment in advanced melanoma: value of FDG-PET/CT in patients with elevated serum S-100B

PURPOSE: To evaluate the usefulness of PET/CT in melanoma patients with an elevated serum S-100B tumour marker level. METHODS: Out of 165 consecutive high-risk melanoma patients referred for PET/CT imaging, 47 had elevated (>0.2 microg/l) S-100B serum levels and a contemporaneous 18F-FDG PET/CT scan. PET/CT scans were evaluated for the presence of metastases. To produce a composite reference standard, we used cytological, histological, MRI and PET/CT follow-up findings as well as clinical and S-100B follow-up. RESULTS: Among the 47 patients with increased S-100B levels, PET/CT correctly identified metastases in 38 (30 distant metastases and eight lymph node metastases). In one patient with cervical lymph node metastases, PET/CT was negative. Eight patients had no metastases and PET/CT correctly excluded metastases in all of them. Overall sensitivity for metastases was 97% (38/39), specificity 100% (8/8) and accuracy 98% (46/47). S-100B was significantly higher in patients with distant metastases (mean 1.93 microg/l, range 0.3-14.3 microg/l) than in patients with lymph node metastases (mean 0.49 microg/l, range 0.3-1.6 microg/l, p=0.003) or patients without metastases (mean 0.625 microg/l, range 0.3-2.6 microg/l, p=0.007). However, 6 of 14 patients with a tumour marker level of 0.3 microg/l had no metastases. CONCLUSION: In melanoma patients with elevated S-100B tumour marker levels, FDG-PET/CT accurately identifies lymph node or distant metastases and reliably excludes metastases. Because of the significant number of false positive S-100B tumour marker determinations (17%), we recommend repetition of tumour marker measurements if elevated S-100B levels occur before extensive imaging is used

On Quantitative Comparative Research in Communication and Language Evolution

Quantitative comparison of human language and natural animal communication requires improved conceptualizations. We argue that an infrastructural approach to development and evolution incorporating an extended interpretation of the distinctions among illocution, perlocution, and meaning (Austin 1962; Oller and Griebel 2008) can help place the issues relevant to quantitative comparison in perspective. The approach can illuminate the controversy revolving around the notion of functional referentiality as applied to alarm calls, for example in the vervet monkey. We argue that referentiality offers a poor point of quantitative comparison across language and animal communication in the wild. Evidence shows that even newborn human cry could be deemed to show functional referentiality according to the criteria typically invoked by advocates of referentiality in animal communication. Exploring the essence of the idea of illocution, we illustrate an important realm of commonality among animal communication systems and human language, a commonality that opens the door to more productive, quantifiable comparisons. Finally, we delineate two examples of infrastructural communicative capabilities that should be particularly amenable to direct quantitative comparison across humans and our closest relatives