Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterised by the presence of inactivating mutations in the VHL gene in the majority of cases1,2 and by infrequent somatic mutations in known cancer genes. To elucidate further the genetics of ccRCC, we have sequenced 101 cases through 3544 protein coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification, SETD2, a histone H3 lysine 36 methyltransferase and JARID1C (KDM5C), a histone H3 lysine 4 demethylase in addition to mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), we recently reported3. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Additionally, NF2 mutations were found in non-VHL mutated ccRCC and several other likely cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene and that systematic screens will be key to fully elucidating the somatic genetic architecture of cancer.

The cancer genome is moulded by the dual processes of somatic mutation and selection. Homozygous deletions in cancer genomes occur over recessive cancer genes, where they can confer selective growth advantage, and over fragile sites, where they are thought to reflect an increased local rate of DNA breakage. However, most homozygous deletions in cancer genomes are unexplained. Here we identified 2,428 somatic homozygous deletions in 746 cancer cell lines. These overlie 11% of protein-coding genes that, therefore, are not mandatory for survival of human cells. We derived structural signatures that distinguish between homozygous deletions over recessive cancer genes and fragile sites. Application to clusters of unexplained homozygous deletions suggests that many are in regions of inherent fragility, whereas a small subset overlies recessive cancer genes. The results illustrate how structural signatures can be used to distinguish between the influences of mutation and selection in cancer genomes. The extensive copy number, genotyping, sequence and expression data available for this large series of publicly available cancer cell lines renders them informative reagents for future studies of cancer biology and drug discovery.

Somatically acquired epigenetic changes are present in many cancers. Epigenetic regulation is maintained via post-translational modifications of core histones. Here, we describe inactivating somatic mutations in the histone lysine demethylase, UTX, pointing to histone H3 lysine methylation deregulation in multiple tumour types. UTX reintroduction into cancer cells with inactivating UTX mutations resulted in slowing of proliferation and marked transcriptional changes. These data identify UTX as a new human cancer gene.

Large-scale systematic resequencing has been proposed as the key future strategy for the discovery of rare, disease-causing sequence variants across the spectrum of human complex disease. We have sequenced the coding exons of the X chromosome in 208 families with X-linked mental retardation (XLMR), the largest direct screen for constitutional disease-causing mutations thus far reported. The screen has discovered nine genes implicated in XLMR, including SYP, ZNF711 and CASK reported here, confirming the power of this strategy. The study has, however, also highlighted issues confronting whole-genome sequencing screens, including the observation that loss of function of 1% or more of X-chromosome genes is compatible with apparently normal existence.

The in vitro activity of BAY 12-8039, a new fluoroquinolone, was studied in comparison with those of ciprofloxacin, trovafloxacin (CP 99,219), cefpodoxime, and amoxicillin-clavulanate against gram-negative, grampositive, and anaerobic bacteria. Its activity against mycobacteria and chlamydia was also investigated. BAY 12-8039 was active against members of the family Enterobacteriaceae (MIC at which 90% of strains tested were inhibited [MIC 90 s] <1 g/ml, except for Serratia spp. MIC 90 2 g/ml), Neisseria spp. (MIC 90 s, 0.015 g/ml), Haemophilus influenzae (MIC 90 , 0.03 g/ml), and Moraxella catarrhalis (MIC 90 , 0.12 g/ml), and these results were comparable to those obtained for ciprofloxacin and trovafloxacin. Against Pseudomonas aeruginosa, the quinolones were more active than the ␤-lactam agents but BAY-12-8039 was less active than ciprofloxacin. Strains of Stenotrophomonas maltophilia were fourfold more susceptible to BAY 12-8039 and trovafloxacin (MIC 90 s, 2 g/ml) than to ciprofloxacin. BAY 12-8039 was as active as trovafloxacin but more active than ciprofloxacin against Streptococcus pneumoniae (MIC 90 , 0.25 g/ml) and methicillin-susceptible Staphylococcus aureus (MIC 90 s, 0.12 g/ml). The activity of BAY 12-8039 against methicillin-resistant S. aureus (MIC 90 , 2 g/ ml) was lower than that against methicillin-susceptible strains. BAY 12-8039 was active against anaerobes (MIC 90 s < 2 g/ml), being three-to fourfold more active against Bacteroides fragilis, Prevotella spp., and Clostridium difficile than was ciprofloxacin. Against Mycobacterium tuberculosis, BAY 12-8039 exhibited activity comparable to that of rifampin (MICs < 0.5 g/ml). Against Chlamydia trachomatis and Chlamydia pneumoniae BAY 12-8039 was more active (MICs < 0.12 g/ml) than either ciprofloxacin or erythromycin and exhibited a greater lethal effect than either of these two agents. The protein binding of BAY 12-8039 was determined at 1 and 5 g/ml as 30 and 26.4%, respectively. The presence of human serum (at 20 or 70%) had no marked effect on the in vitro activity of BAY 12-8039.