The pan-cancer analysis of whole genomes The expansion of whole-genome sequencing studies from individual ICGC and TCGA working groups presented the opportunity to undertake a meta-analysis of genomic features across tumour types. To achieve this, the PCAWG Consortium was established. A Technical Working Group implemented the informatics analyses by aggregating the raw sequencing data from different working groups that studied individual tumour types, aligning the sequences to the human genome and delivering a set of high-quality somatic mutation calls for downstream analysis (Extended Data Fig. 1). Given the recent meta-analysis

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

PCAWG working groups focused on unified analyses of copynumber variation 6 , structural variants 7,8 , germline variants 5 , mutational signatures 9 and identification of driver genes 8 , among others 5. Here, we report the joint analysis of available matched transcriptome and genome profiling for 1,188 samples from 27 tumour types by the PCAWG Transcriptome Working Group 5 , providing the largest, to our knowledge, resource of RNA phenotypes and their underlying genetic changes in cancer so far (Extended Data Fig. 1, Methods, Supplementary Results, Supplementary Table 23). We demonstrate the importance of transcriptomics data in understanding how different dimensions of specific DNA alterations contribute to carcinogenesis and map out the landscape of cancer-related RNA alterations.

Nitrate pollution of the karstic groundwater is an increasingly serious problem with the development of Guiyang, the capital city of Guizhou Province, southwest China. The higher content of NO3- in groundwater compared to surface water during both summer and winter seasons indicates that the karstic groundwater system cannot easily recover once contaminated with nitrate. In order to assess the sources and conversion of nitrate in the groundwater of Guiyang, we analyzed the major ions, delta(15)N-NH4+, delta(15)N-NO3-, and delta(18)O-NO3- in surface and groundwater samples collected during both summer and winter seasons. The results show that nitrate is the major dominant species of nitrogen in most water samples and there is a big variation of nitrate sources in groundwater between winter and summer season, due to fast response of groundwater to rain or surface water in the karst area. Combined with information on NO3- /Cl-, the variations of the isotope values of nitrate in the groundwater show a mixing process of multiple sources of nitrate, especially in the summer season. Chemical fertilizer and nitrification of nitrogen-containing organic materials contribute nitrate to suburban groundwater, while the sewage effluents and denitrification mainly control the nitrate distribution in urban groundwater.