PATTERNS OF SOMATIC MUTATION IN HUMAN CANCER GENOMES
Nature, Vol. 446, No. 7132. (March 2007), pp. 153-8.Cancers arise owing to mutations in a subset of genes that confer growth advantage. The availability of the human genome sequence led us to propose that systematic resequencing of cancer genomes for mutations would lead to the discovery of many additional cancer genes. Here we report more than 1,000 somatic mutations found in 274 megabases (Mb) of DNA corresponding to the coding exons of 518 protein kinase genes in 210 diverse human cancers. There was substantial variation in the number and pattern of mutations in individual cancers reflecting different exposures, DNA repair defects and cellular origins. Most somatic mutations are likely to be 'passengers' that do not contribute to oncogenesis. However, there was evidence for 'driver' mutations contributing to the development of the cancers studied in approximately 120 genes. Systematic sequencing of cancer genomes therefore reveals the evolutionary diversity of cancers and implicates a larger repertoire of cancer genes than previously anticipated.
Christopher Greenman, Philip Stephens, Raffaella Smith, Gillian Dalgliesh, Christopher Hunter, Graham Bignell, Helen Davies, Jon Teague, Adam Butler, Claire Stevens, Sarah Edkins, Sarah O'Meara, Imre Vastrik, Esther Schmidt, Tim Avis, Syd Barthorpe, Gurpreet Bhamra, Gemma Buck, Bhudipa Choudhury, Jody Clements, Jennifer Cole, Ed Dicks, Simon Forbes, Kris Gray, Kelly Halliday, Rachel Harrison, Katy Hills, Jon Hinton, Andy Jenkinson, David Jones, Andy Menzies, Tatiana Mironenko, Janet Perry, Keiran Raine, Dave Richardson, Rebecca Shepherd, Alexandra Small, Calli Tofts, Jennifer Varian, Tony Webb, Sofie West, Sara Widaa, Andy Yates, Daniel Cahill, David Louis, Peter Goldstraw, Andrew Nicholson, Francis Brasseur, Leendert Looijenga, Barbara Weber, Yoke-Eng Chiew, Anna DeFazio, Mel Greaves, Anthony Green, Peter Campbell, Ewan Birney, Douglas Easton, Georgia Chenevix-Trench, Min-Han Tan, Sok Khoo, Bin Teh, Siu Yuen, Suet Leung, Richard Wooster, Andrew Futreal, Michael Stratton
THE GENOME ANALYSIS TOOLKIT: A MAPREDUCE FRAMEWORK FOR ANALYZING NEXT-GENERATION DNA SEQUENCING DATA
Genome Research, Vol. 20, No. 9. (1 September 2010), pp. 1297-1303.10.1101/gr.107524.110 Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly, Mark DePristo
EXPRESSION OF RAD51, BRCA1 AND P53 DOES NOT CORRELATE WITH CELLULAR RADIOSENSITIVITY OF NORMAL HUMAN FIBROBLASTS.
Ir J Med Sci. 2010 Aug 29;
Saleh EM, El-Awady RA
AIMS: To evaluate the potential role of key DNA repair proteins in the sensitivity of normal human fibroblasts to ionising radiations. METHODS: Radiosensitivity of six human fibroblast strains established from skin biopsies of women who had undergone conservative breast surgery and received a curative breast conserving radiotherapy was measured by colony-formation assay. The expression level of RAD51, BRCA1 and p53 proteins were studied using western blot analysis. RESULTS: The six fibroblast strains represent a typical spectrum of normal human radiosensitivity with the surviving fraction measured for a dose of 3.5 Gy (SF3.5) ranging from 0.21 to 0.40. We found that these differences in cell survival did not correlate with the expression of RAD51, BRCA1 nor p53 in the tested normal human fibroblast strains. CONCLUSIONS: We conclude that measurement of protein expression of the three tested genes (RAD51, BRCA1 and p53) did not reflect sensitivity of normal fibroblasts to IR.
SURVIVAL OF COMMERCIAL YEASTS IN THE WINERY ENVIRONMENT AND THEIR PREVALENCE DURING SPONTANEOUS FERMENTATIONS.
J Ind Microbiol Biotechnol. 2010 Aug 31;
Blanco P, Orriols I, Losada A
Inoculation of active dry yeasts during the wine-making process has become a common practice in most wine-producing regions; this practice may affect the diversity of the indigenous population of Saccharomyces cerevisiae in the winery. The aim of this work was to study the incidence of commercial yeasts in the experimental winery of Estación de Viticultura e Enoloxía de Galicia (EVEGA) and their ability to lead spontaneous fermentations. To do this, 64 spontaneous fermentations were carried out in the experimental cellar of EVEGA over a period of 7 years. Samples were taken from must and at the beginning, vigorous and final stages of fermentation. A representative number of yeast colonies was isolated from each sample. S. cerevisiae strains were characterised by analysis of mitochondrial DNA restriction patterns. The results showed that although more than 40 different strains of S. cerevisiae were identified, only 10 were found as the dominant strain or in codominance with other strains in spontaneous fermentations. The genetic profiles (mtDNA-RFLPs) of eight of these strains were similar to those of different commercial yeasts that had been previously used in the EVEGA cellar. The remaining two strains were autochthonous ones that were able to reach implantation frequencies as high of those of commercial yeasts. These results clearly indicated that commercial wine yeasts were perfectly adapted to survive in EVEGA cellar conditions, and they successfully competed with the indigenous strains of S. cerevisiae, even during spontaneous fermentations. On the other hand, autochthonous dominant strains that presented desirable oenological traits could be of interest to preserve wine typicity.
EVIDENCE BASED ON STUDIES OF THE MUS309 MUTANT, DEFICIENT IN DNA DOUBLE-STRAND BREAK REPAIR, THAT MEIOTIC CROSSING OVER IN DROSOPHILA MELANOGASTER IS A TWO-PHASE PROCESS.
Genetica. 2010 Aug 31;
Portin P
The mus309 gene in Drosophila melanogaster encodes a RecQ helicase which is involved in DNA double-strand break (DSB) repair and specifically in the choice between the different pathways of the repair. In a brood pattern analysis of mus309 and wild type females which either had or had not experienced a temperature shock, different parameters of meiotic crossing over including map distances and crossover interference in the X chromosome were measured. The results suggest that, like in other eukaryotes studied, the control of meiotic crossover formation also in D. melanogaster is a two-phase process. The first phase seems to be temperature shock sensitive, independent of the mus309 gene and coincidental with the premeiotic DNA synthesis, thus most likely representing the formation of DSBs. The second phase seems to be temperature shock tolerant, dependent on the mus309 gene, occurring during the meiotic prophase and most likely representing the choice made by the oocyte between the different pathways of the DSB repair. A hypothesis of the localization of chiasmata is also presented, combining the mechanisms of interference and the so-called centromere effect, and based on the balance between the SDSA and DSBR pathways of DSB repair.
DNA BARCODING OF PANAX SPECIES.
Planta Med. 2010 Aug 27;
Zuo Y, Chen Z, Kondo K, Funamoto T, Wen J, Zhou S
Ginsengs ( PANAX, Araliaceae) are among the plants best known for their medicinal properties. Many ginseng species are endangered due to over-exploitation of natural resources - a situation difficult to remedy while there are no reliable, practical methods for species identification. We screened eleven candidate DNA barcoding loci to establish an accurate and effective PANAX species identification system, both for commercial and conservation purposes. We used 95 ginseng samples, representing all the species in the genus. We found considerable differences in the performance of the potential barcoding regions. The sequencing of ATPF-ATPH was unsuccessful due to poly-N structures. The RBCL, RPOB, and RPOC1 regions were found to be mostly invariable, with only four to eight variable sites. Using MATK, PSBK-I, PSBM-TRND, RPS16 and NAD1, we could identify four to six out of eight considerably divergent species but only one to five out of nineteen clusters within the P. BIPINNATIFIDUS species group. PSBA-TRNH and ITS were the most variable loci, working very well both in species and cluster identifications. We demonstrated that the combination of PSBA-TRNH and ITS is sufficient for identifying all the species and clusters in the genus.
CAJANOL INHIBITS THE GROWTHS OF ESCHERICHIA COLI AND STAPHYLOCOCCUS AUREUS BY ACTING ON MEMBRANE AND DNA DAMAGE.
Planta Med. 2010 Aug 27;
Liu XL, Zhang XJ, Fu YJ, Zu YG, Wu N, Liang L, Efferth T
In the present study, the mechanism of antibacterial activity of cajanol extracted from the roots of CAJANUS CAJAN (L.) Millsp. towards ESCHERICHIA COLI ( E. COLI) and STAPHYLOCOCCUS AUREUS ( S. AUREUS) was investigated. The antibacterial activity of cajanol was evaluated towards six bacterial strains ( STAPHYLOCOCCUS EPIDERMIDIS, STAPHYLOCOCCUS AUREUS, BACILLUS SUBTILIS, ESCHERICHIA COLI, PROTEUS VULGARIS, and PSEUDOMONAS AERUGINOSA) by the broth microdilution method. It showed strong antibacterial activity towards all bacteria tested with minimal inhibition concentration (MIC) values ranging from 98.90 microM to 197.8 microM. Cajanol-induced death rates in the most sensitive strains ( E.COLI, 96.55 % and S. AUREUS, 97.25 %) were analyzed by flow cytometry. Furthermore, the activity of cajanol on the membranes of E. COLI and S. AUREUS was investigated by using lecithin, phosphate groups, and fluorescence microscopy. Cajanol-induced DNA damage was observed by agarose gel electrophoresis. In summary, cajanol inhibited E.COLI only by DNA damage, whereas S. AUREUS was inhibited by affecting both, the lecithin and phosphate groups on the cellular membrane and DNA. The present study shows that cajanol possesses antibacterial activity IN VITRO towards both gram-negative and gram-positive bacteria and therefore may be a promising candidate as an antibacterial agent for the therapy of microbial infections.
POLG, BUT NOT PEO1, IS A FREQUENT CAUSE OF CEREBELLAR ATAXIA IN CENTRAL EUROPE.
Mov Disord. 2010 Aug 27;
Schicks Md J, Synofzik Md M, Schulte C, Schöls Md L
Nuclear genes, in particular mitochondrial polymerase gamma (POLG) and PEO1, have been increasingly recognized to cause mitochondrial diseases. Both genes assume a complementary role as part of the mitochondrial DNA (mtDNA) replication fork and, accordingly, seem to present with largely overlapping phenotypical spectra. We assessed the frequency and phenotypic spectrum of PEO1 compared to POLG mutations in a cohort of 80 patients with cerebellar ataxia for which common repeat expansion diseases had been excluded. Patients were selected to present additional features previously described for PEO1 mutations, namely early age of onset, progressive external ophthalmoplegia (PEO), or epilepsy. Whereas PEO1 mutations were not found in our cohort, POLG frequently caused ataxia with PEO (47%), psychiatric comorbidities (20%) and, more rarely, with epilepsy (14%). Thus, PEO1 is rare in Central Europe even in those patients displaying characteristic phenotypic features. In contrast, POLG is rather common in Central European ataxia patients. It should be particularly considered in ataxia patients with PEO, psychiatric comorbidities, and/or sensory neuropathy, even if characteristic mitochondrial extra-CNS features are absent. (c) 2010 Movement Disorder Society.
P53 AND P21(WAF1) ARE RECRUITED TO DISTINCT PML-CONTAINING NUCLEAR FOCI IN IRRADIATED AND NUTLIN-3A-TREATED U2OS CELLS.
J Cell Biochem. 2010 Aug 27;
Shen H, Maki CG
Promyelocytic leukemia nuclear bodies (PML-NBs) are multi-protein complexes that include PML protein and localize in nuclear foci. PML-NBs are implicated in multiple stress responses, including apoptosis, DNA repair, and p53-dependent growth inhibition. ALT-associated PML bodies (APBs) are specialized PML-NBs that include telomere-repeat binding-factor TRF1 and are exclusively in telomerase-negative tumors where telomere length is maintained through alternative (ALT) recombination mechanisms. We compared cell cycle and p53 responses in ALT-positive cancer cells (U2OS) exposed to ionizing radiation (IR) or the p53 stabilizer Nutlin-3a. Both IR and Nutlin-3a caused growth arrest and comparable induction of p53. However, p21, whose gene p53 activates, displayed biphasic induction following IR and monophasic induction following Nutlin-3a. P53 was recruited to PML-NBs 3-4 days after IR, approximately coincident with the secondary p21 increase. These p53/PML-NBs marked sites of apparently unrepaired DNA double-strand breaks (DSBs), identified by colocalization with phosphorylated histone H2AX. Nutlin-3a and IR both caused a large increase in APBs that was dependent on p53 and p21 expression. Moreover, p21, and to a lesser extent p53, was recruited to APBs in a fraction of Nutlin-3a treated cells. These data indicate 1) p53 is recruited to PML-NBs after IR that likely mark unrepaired DSBs, suggesting p53 may either be further activated at these sites and/or function in their repair; 2) p53-p21 pathway activation increases the percentage of APB-positive cells, 3) p21 and p53 are recruited to ALT-associated PML-NBs after Nutlin-3a treatment, suggesting they may play a previously unrecognized role in telomere maintenance. (c) 2010 Wiley-Liss, Inc.
A DOUBLY SIGNAL-AMPLIFIED DNA DETECTION METHOD BASED ON PRE-COMPLEXED [RU(BPY)(3)](2+)-DOPED SILICA NANOPARTICLES.
Chemistry. 2010 Aug 27;
Bae SW, Cho MS, Hur SS, Chae CB, Chung DS, Yeo WS, Hong JI
