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 scale1-3. 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 promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.

Inhibition of the human flexion reflex by low intensity, high frequency transcutaneous electrical nerve stimulation (TENS) has a gradual onset and offset

The present study examines the inhibitory effect of segmentally applied TENS on the nociceptive component of the flexion reflex elicited in various lower limb muscles, in an attempt to gain some insight into the underlying mechanism. The flexion reflex from 11 normal subjects was recorded electromyographically from the biceps femoris (BF), the tibialis anterior (TA), and in 2 subjects, the hip flexor (HF), in the manner described in a previous paper [9]. Amplitude and area values of the flexion reflex of each muscle were computerized prior to, during, and 50 min after the application of placebo or low intensity TENS at 100 Hz, for 30 min to the low back, at levels of segmental innervation (L4-S1) similar to those of the muscles under study. In the majority of subjects, we found that: Low intensity TENS caused a significant inhibition of the flexion reflex in proximal limb flexors. Thus, the BF measured 64% and 52%, and the HF 45% and 51%, of their respective mean control amplitude and area values at the time of maximum inhibition during TENS. Moreover, less reduction of the mean values of the flexion reflex was observed in the TA, a distal limb (ankle) flexor. It is noteworthy that in both the BF and HF, the time to peak maximum inhibitory effect took 30 and 20 min respectively after the onset of TENS, and the flexion reflex often did not return to control values even at 40-50 min after TENS. In contrast, placebo TENS application resulted in no significant change of the flexion reflex in all the muscles examined. These findings showed that prolonged stimulation of large diameter fibers by conventional TENS application to the lumbosacral level, exerts a progressive and long latency inhibitory influence on a number of lower limb flexor motoneurons. In keeping with functional demand, this effect was found to be more prominent on the proximal than distal limb muscles. Furthermore, a gradual onset and offset of this inhibitory action is consistent with the results of some investigators demonstrating the possible involvement of endogenous opioids.