Top PDF Frequent mutations in EGFR, KRAS and TP53 genes in human lung cancer tumors detected by ion torrent DNA sequencing.

Frequent mutations in EGFR, KRAS and TP53 genes in human lung cancer tumors detected by ion torrent DNA sequencing.

Frequent mutations in EGFR, KRAS and TP53 genes in human lung cancer tumors detected by ion torrent DNA sequencing.

As there is increasing awareness about the changes in lung cancer cells in recent times, newer drugs that specifically target these changes have been developed. These targeted drugs either work synergistically with the chemotherapy drugs or by themselves with much lesser toxicity due to a selective effect as an alternative to a more systemic modulation of proteins associated with oncogenesis. EGFR inhibitors (Afatinib, Erlotinib, and Gefitinib) and VEGF inhibitors (Bevacizumab) are currently used for target therapies for NSCLC patients with mutations in the VEGF and EGFR [26]. Erlotinib is a drug that blocks EGFR from signaling the cell to grow. It prevents the progression of lung cancer, specifically in non-smoking women, and is mostly used in advanced NSCLC treatment that was not responsive to chemo- therapy. It is also used as the first treatment in patients whose cancers have a mutation in the EGFR gene [27]. Cetuximab is a monoclonal antibody that targets EGFR which is also used in advanced NSCLC in combination with standard chemotherapy as part of first-line treatment [28]. Like erlotinib, afatinib is a drug that blocks the growth signal from EGFR and used for advanced NSCLCs that have mutations in the EGFR gene [29]. Some younger, non-smokers with adenocarcinomas are found to have an ALK/EML4 fusion oncogene which is currently a target for the drug Crizotinib [30]. Other drugs currently used to treat lung cancers are not gene-specific, and instead target general molecular pathways like folate anitmetabolites (methotrexate and peme- trexed), mitotic inhibitors (docetaxel, piclitaxel, and vinorelbine), topoisomerase inhibitors (etopophos and topotecan), and nucleo- side analogs which interfere with DNA synthesis (carboplatin, cisplatin, and gemciabine) [31,32]. Inhibitors of EGFR-directed tyrosine kinase are established to be an effective treatment option for advanced NSCLC not responding to chemotherapy. However, EGFR-directed monoclonal antibodies in combination with platinum-based first-line chemotherapy, cetuximab combined with cisplatin/vinorelbine and bevacizumab in combination with platinum-based chemotherapy resulted in better survival com- pared to chemotherapy alone in patients with advanced EGFR- positive NSCLC [33]. Other targeted therapies including dual and
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PIK3CA and TP53 gene mutations in human breast cancer tumors frequently detected by ion torrent DNA sequencing.

PIK3CA and TP53 gene mutations in human breast cancer tumors frequently detected by ion torrent DNA sequencing.

Breast cancer is the most common malignancy and the leading cause of cancer deaths in women worldwide. While specific genetic mutations have been linked to 5–10% of breast cancer cases, other environmental and epigenetic factors influence the development and progression of the cancer. Since unique mutations patterns have been observed in individual cancer samples, identification and characterization of the distinctive breast cancer molecular profile is needed to develop more effective target therapies. Until recently, identifying genetic cancer mutations via personalized DNA sequencing was impractical and expensive. The recent technological advancements in next-generation DNA sequencing, such as the semiconductor-based Ion Torrent sequencing platform, has made DNA sequencing cost and time effective with more reliable results. Using the Ion Torrent Ampliseq Cancer Panel, we sequenced 737 loci from 45 cancer-related genes to identify genetic mutations in 105 human breast cancer samples. The sequencing analysis revealed missense mutations in PIK3CA, and TP53 genes in the breast cancer samples of various histologic types. Thus, this study demonstrates the necessity of sequencing individual human cancers in order to develop personalized drugs or combination therapies to effectively target individual, breast cancer-specific mutations.
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Molecular typing of lung adenocarcinoma on cytological samples using a multigene next generation sequencing panel.

Molecular typing of lung adenocarcinoma on cytological samples using a multigene next generation sequencing panel.

Identification of driver mutations in lung adenocarcinoma has led to development of targeted agents that are already approved for clinical use or are in clinical trials. Therefore, the number of biomarkers that will be needed to assess is expected to rapidly increase. This calls for the implementation of methods probing the mutational status of multiple genes for inoperable cases, for which limited cytological or bioptic material is available. Cytology specimens from 38 lung adenocarcinomas were subjected to the simultaneous assessment of 504 mutational hotspots of 22 lung cancer-associated genes using 10 nanograms of DNA and Ion Torrent PGM next-generation sequencing. Thirty-six cases were successfully sequenced (95%). In 24/36 cases (67%) at least one mutated gene was observed, including EGFR, KRAS, PIK3CA, BRAF, TP53, PTEN, MET, SMAD4, FGFR3, STK11, MAP2K1. EGFR and KRAS mutations, respectively found in 6/36 (16%) and 10/36 (28%) cases, were mutually exclusive. Nine samples (25%) showed concurrent alterations in different genes. The next-generation sequencing test used is superior to current standard methodologies, as it interrogates multiple genes and requires limited amounts of DNA. Its applicability to routine cytology samples might allow a significant increase in the fraction of lung cancer patients eligible for personalized therapy.
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Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq.

Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq.

We selected five different fibroblast cell strains (MRC-5, BJ, IMR-90, WI-38 and HFF) and monitored their replicative behavior during passaging into senescence. The similarities in gene expression profiles of primary human fibroblast strains derived from embryonic lung and fore- skin were revealed by us previously [76]. We extended our previous study [76] with data obtained from further three fibroblast strains (BJ, IMR-90 and WI-38) in this study in order to essentially extend the statistical basis for deducing common age-driven changes in the tran- scriptome. In our analysis, the cell strains were derived from a single vial and were maintained in culture as triplicates from an early population doubling (PD) time point until they achieved senescence at late PDs (Fig 1A). The growth curve (Fig 1B) reveals that the starting PD of each of the fibroblasts differs according to the prehistory of the cells before arriving in our labora- tory. For MRC-5 fibroblasts, the start PD was 30 for fresh vials ordered from ATCC. For BJ, IMR-90 and WI-38 the start PD was between 20 and 30. HFF cells were freshly isolated from foreskin of young boys below the age of 10 at University of Erlangen. When the HFF strain samples were received for culture, the start PD was 14. The cell strain specific transition into senescence of each of the fibroblast cell strains was detected by the induction of SA-βGal with age. The assay was performed at intervals of every four PDs (Fig 1C). The induction of senes- cence was earliest in HFF and IMR-90 strains (Fig 1C) during their span in culture compared to the other three fibroblast cell strains while SA-β Gal increase was late for BJ fibroblasts. Indeed, BJ fibroblasts showed the most extended replicative lifespan (Fig 1B). IMR-90 and WI- 38 fibroblasts, both derived from female lung, had the least cumulative PDs approaching repli- cative senescence much earlier than the other fibroblast cell strains (Fig 1B and 1C). Cell strain specific differences in growth and transition into senescence were reported and discussed by us before in a quantitative study [48]. Reassuringly, the growth curves of the fibroblast strains in our study are very similar to previously undertaken studies on fibroblast strains [48, 77, 78, 79]. In particular the growth curve we obtained for HFF is almost identical to the one obtained for HDFs in a previous study of gene expression profiles of replicative senescence [70].
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Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de Barretos, Barretos, SP, Brazil

Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de Barretos, Barretos, SP, Brazil

DHPLC was carried out using a WAVE MD 4000 DNA Fragment Analysis System equipped with a DNASep Car- tridge (Transgenomic Inc., Omaha NE, USA) as described elsewhere (Fackenthal et al., 2005). The HRM curve analy- sis was performed in a LightScanner instrument (Idaho Tecnology Inc.) using the Light Scanner Mastermix with LCGreen dye (Idaho Tecnology Inc.). Heterozygous pro- files were identified by visual inspection of the chromato- grams/melting curves and putative sequence variants were re-analyzed by bi-directional sequencing on a MegaBACE 1000 (Amersham Biosciences, Buckinghamshire, UK) or an ABI-PRISM 3100 Genetic Analyzer (Applied Biosys- tems, Foster City, USA) using an independent PCR prod- uct. Sequence alterations were classified based on data available in the Breast Cancer Information Core (BIC, 2014), ClinVar (Landrum et al., 2014), Universal Mutation database - UMD (Caputo et al., 2012) and AlignGVGD (Tavtigian et al., 2006). New or pathogenic mutations were also searched in The Human Gene Mutation Database (HGMD, 2014,) and LOVD (Vallée et al., 2012). All the 18 HBOC families were screened for BRCA1 genomic rear- rangements and 10 of these families were screened for BRCA2 genomic rearrangements using Multiplex Liga- tion-dependent Probe Amplification (MLPA) methodology using the SALSA P002B BRCA1 and SALSA P045 BRCA2 MLPA probe mix assays (MRC-Holland, Amsterdam, The Netherlands) as recommended by the manufacturer (MRC-Holland) and information on copy number was ex- tracted with Coffalyser V9.4 Software (MRC-Holland). All analyses were performed in duplicate and in at least two in- dependent experiments.
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Use of multiplex allele-specific polymerase chain reaction (MAS-PCR) to detect multidrug-resistant tuberculosis in Panama.

Use of multiplex allele-specific polymerase chain reaction (MAS-PCR) to detect multidrug-resistant tuberculosis in Panama.

The frequency of individual genetic mutations conferring drug resistance (DR) to Mycobacterium tuberculosis has not been studied previously in Central America, the place of origin of many immigrants to the United States. The current gold standard for detecting multidrug-resistant tuberculosis (MDR-TB) is phenotypic drug susceptibility testing (DST), which is resource-intensive and slow, leading to increased MDR-TB transmission in the community. We evaluated multiplex allele- specific polymerase chain reaction (MAS-PCR) as a rapid molecular tool to detect MDR-TB in Panama. Based on DST, 67 MDR-TB and 31 drug-sensitive clinical isolates were identified and cultured from an archived collection. Primers were designed to target five mutation hotspots that confer resistance to the first-line drugs isoniazid and rifampin, and MAS-PCR was performed. Whole-genome sequencing confirmed DR mutations identified by MAS-PCR, and provided frequencies of genetic mutations. DNA sequencing revealed 70.1% of MDR strains to have point mutations at codon 315 of the katG gene, 19.4% within mabA-inhA promoter, and 98.5% at three hotspots within rpoB. MAS-PCR detected each of these mutations, yielding 82.8% sensitivity and 100% specificity for isoniazid resistance, and 98.4% sensitivity and 100% specificity for rifampin resistance relative to DST. The frequency of individual DR mutations among MDR strains in Panama parallels that of other TB-endemic countries. The performance of MAS-PCR suggests that it may be a relatively inexpensive and technically feasible method for rapid detection of MDR-TB in developing countries.
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Bracken fern-induced malignant tumors in rats: absence of mutations in p53, H-ras and K-ras and no microsatellite instability

Bracken fern-induced malignant tumors in rats: absence of mutations in p53, H-ras and K-ras and no microsatellite instability

Since we did not find mutation in the p53 and ras genes in the malignant tumors that we obtained after bracken fern treatment of the rats, we decided to study the so-called “mutator pathway”. To test this hypothesis, we have searched seven of the malignant tumors (from which we had matching normal tissue) for MSI. The MSI is caused by a failure of the DNA mismatch repair system to repair errors that occur during the replication of DNA and is characterized by the accelerated accumulation of single nucleotide mutations and alterations in the length of simple, repetitive microsatellite sequences that occur ubiqui- tously throughout the genome. We analyzed five rat microsatellite loci: IGHE, ADRB2, PRLR and PBPC2 (di- or tetra-nucleotide loci) that had been previously analyzed in colon tumors induced by heterocyclic amines in rats and shown to be suitable for screening for instability [17]. The IVD locus was chosen because it is a poly A repeat with 20 nucleotides [18], similar to the BAT26 locus that has been proposed as the most sensitive marker for MSI in human tumors [29]. Our results show convincingly that, bracken fern induced malignant tumors in rats do not present genuine mi- crosatellite instability. For humans, a workshop of the National Cancer Institute established international criteria for determination of microsatellite instability in colorectal cancers and validated a panel of five microsatellites [30]. The same observations are true for gastric tumors, where it has been proposed that tumors with high frequency MSI (MSI-H) can be detected analyzing only the BAT26 locus [31]. Thus, we believe that the markers we used were enough to reveal if any tumor presented MSI-H.
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Human Capital and the Recent Fall of Earnings Inequality in Brazil

Human Capital and the Recent Fall of Earnings Inequality in Brazil

where is a set of linear restrictions that transforms the unrestricted model (1) on restricted model (2). 8 In our case, the restriction implies that the age, trend and (orthogonal) time dummies are sufficient to explain the behavior of each estimated statistic order across cells and over time. Imposing the restrictions means estimating weighted least squares regressions on the grouped data, for each quantile and education group separately. This procedure will give us consistent estimates of . Under the null that the restrictions are valid, the minimized value follows a chi-square distribution with degrees of freedom equal to the number of restrictions. In order to construct the test statistics, we only have to sum up the weighted squared residuals, that is, the estimated percentiles minus the predicted values minus the orthogonal time dummies.
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Clinical analysis of 152 cases of multiple primary malignant tumors in 15,398 patients with malignant tumors.

Clinical analysis of 152 cases of multiple primary malignant tumors in 15,398 patients with malignant tumors.

MPMTs are a rare phenomenon in tumorigenesis. In recent years, several papers examining MPMTs have been published, but the reported prevalence differs significantly. The prevalence of MPMTs in foreign studies ranged from 11.0% to 21.0% [4–5]; however, the prevalence of MPMTs was reported to be 0.4%-2.4% [9] in China. In our dataset obtained from the First Hospital of Jilin University, China between January 2010 and November 2013, the prevalence of MPMTs was 0.99%, which is similar to the prevalence in China but less than that reported in other countries, such as Sweden [5]. The reasons for the lower prevalence in China may in- clude the following: 1. Misdiagnosis: Doctors are not on the lookout for MPMTs, and some pa- tients who suffer from MPMTs may be misdiagnosed with metastatic carcinoma. 2. Difficulty of detection: The primary cancer may be very small and difficult to detect at the time of presen- tation. Furthermore, autopsies are rarely performed, which can also result in misdiagnosis. 3. Misregistration: Some patients may develop MPMTs during the progression of their primary cancer but fail to present to the hospital in a timely manner, leading to the lack of documenta- tion of their MPMTs. 4. Time span: Time span of the study, starting recently in 2010, covers
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Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART.

Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART.

The L63P, V77I, and I93L mutations in the protease region were found in patient No. 1 and L63P and I64V in patient No 2. The HIVdb genotypic resistance interpretation algorithm clas- sifies these mutations as “other mutationsand refers them as accessory mutations. Such muta- tions are not associated with antiretroviral resistance. The L63P mutation is a common polymorphism in patients receiving PI; V77I is a common polymorphism associated with treatment with Nelfinavir (NFV) and the I93L mutation is also a common polymorphism asso- ciated with PI therapy in subtype B viruses. The HIVdb does not show comment for the I64V mutation. However, resistance mutations in the protease gene are classified as “major” or “minor” in the 2014 Update of the Drug Resistance Mutation in HIV-1 from the International Antiviral Society-USA (IAS-USA) [23]. According to the IAS-USA list, all the mutations in protease region of our patients are defined as minor resistance mutations. L63P is associated with Lopinavir (LPV) minor resistance; V77I with NFV, Indinavir (IDV), and Saquinavir (SQV) minor resistance; I93L and I64L are related to minor resistance against Atazanavir (ATV). The minor mutations do not have a substantial effect on the phenotype and often are generally considered to be accessory mutations but they may improve replication of viruses containing major mutations [23]. Comparing viral rebounds in each patient, it was observed that substitutions in the protease-coding region were the same in each rebound, it may thus be suggested that selection of new mutations was not induced during the three periods of inter- ruption/resumption. Instead, mutations detected in the protease may have been present before the STI scheme was initiated although it is hard to make correct interpretations of the data without a baseline sequence prior to the STI program. These mutations were also found in the previous study using standard genotyping to assess the effect of the STI [6]. Additionally, another study also reported the presence of these changes in naïve patients [24]. In the present work, the mutations in the protease were always detected as a high-abundance and variation in their frequency never was shown (Table 5). These observations may suggest that the STI pro- gram, as planned in this study, could be safe by not selecting mutations associated with resis- tance to PI.
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Editor’s Pick: PSMA-Specific Ligands in Prostate Cancer Diagnosis and Therapy

Editor’s Pick: PSMA-Specific Ligands in Prostate Cancer Diagnosis and Therapy

16. Smith-Jones PM et al. Radiolabeled monoclonal antibodies speciic to the extracellular domain of prostate-speciic membrane antigen: preclinical studies in nude mice bearing LNCaP human prostate tumor. J Nucl Med. 2003;44(4):610-7. 17. Elsässer-Beile U et al. A new generation of monoclonal and recombinant antibodies against cell-adherent prostate speciic membrane antigen for diagnostic and therapeutic targeting of prostate cancer. Prostate. 2006;66(13):1359-70. 18. Grauer LS et al. Identiication, puriication, and subcellular localization of prostate-speciic membrane antigen PSM’ protein in the LNCaP prostatic carcinoma cell line. Cancer Res. 1998;58(21):4787-9. 19. Pandit-Taskar N et al. A Phase I/II Study for Analytic Validation of 89Zr- J591 ImmunoPET as a Molecular Imaging Agent for Metastatic Prostate Cancer. Clin Cancer Res. 2015. [Epub ahead of print]. 20. Tagawa ST et al. Phase II study of Lutetium-177-labeled anti-prostate-
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Distinct Clinicopathological Patterns of Mismatch Repair Status in Colorectal Cancer Stratified by KRAS Mutations.

Distinct Clinicopathological Patterns of Mismatch Repair Status in Colorectal Cancer Stratified by KRAS Mutations.

A significant association was found between the presence of lymph node metastases and pMMR tumors stratified by KRAS mutation status. Our findings revealed that pMMR tumors with KRAS mutation demonstrated more positive lymph nodes and pTNM III-IV stage of dis- ease than tumors with KRAS(-)/pMMR status. This is consistent with findings from a smaller report, which demonstrated that the frequency of KRAS mutations was higher in pMMR lymph node positive tumors as compared to pMMR lymph node negative tumors [36,37]. Our results indicate that the majority of pMMR tumors needed KRAS mutation to be able to metastasize and this activation was crucial for neoplastic cells to acquire invasive potential. Mutations in KRAS oncogene lead to alterations in encoded amino acids adjacent to the GTP binding pocket and reduced the GTPase activity of KRAS protein after guanine nucleotide acti- vating protein (GAP) binding [38]. Both in vitro and in vivo experimental models, transfection of mutated, constitutively active forms of KRAS oncogene into previously noncancerous cells can lead to invasive and metastatic phenotypes. Ectopic expression of active KRAS in the mu- rine NIH 3T3 fibroblast cell line resulted in increased invasion and acquisition of metastatic properties [39]. Using tail vein injection of transformed cells, in vivo models were observed by liver and lung metastasis [40]. In addition to the evidence obtained from cell and animal experiments, clinical studies have also displayed significant lymph node metastasis in KRAS (+)/pMMR tumors [36,41]. Gene expression profiling reveals that genes involoving epithelial mesenchymal transition and matrix remodeling that can facilitate tumor invasion and metasta- sis are up-regulated in mutant KRAS-pMMR tumors [42]. Consequently, KRAS oncogenic activation was shown to be an important mediator of tumor cell invasion and metastasis in pMMR tumors.
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Incidence and imaging characteristics of skeletal metastases detected by bone scintigraphy in lung cancer patients

Incidence and imaging characteristics of skeletal metastases detected by bone scintigraphy in lung cancer patients

16. Bury T, Barreto A, Daenen F, Barthelemy N, Ghaye B, Rigo P. Fluorine-18 deoxyglucose positron emission tomography for the detection of bone metastases in patients with non-small cell lung cancer. Eur J Nucl Med 1998; 25(9): 1244−7. 17. Kao CH, Hsieh JF, Tsai SC, Ho YJ, Yen RF. Comparison and

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A bumpy ride on the diagnostic bench of massive parallel sequencing, the case of the mitochondrial genome.

A bumpy ride on the diagnostic bench of massive parallel sequencing, the case of the mitochondrial genome.

FastQ files from all datasets, generated by either the Ion Torrent PGM or MiSeq platforms, were mapped to the mitochondrial revised Cambridge Reference Sequence (rCRS, NC 012920.1) using BWA-MEM (version 0.7.5) [6]. As a metric for coverage bias, the relative coverage was used. Applying the SAMtools software (version 0.1.18) [7] the number of reads mapping to each reference base was counted. The mean coverage was calculated by averaging this value across each base in the sequence. By computing the ratio of the coverage of a given reference base and the mean coverage of all reference bases, the relative coverage was obtained. This was calculated for the plus and minus strand separately, for the total coverage of both strands together, and was presented in graphical illustrations. To visualize the relative coverage resulting from all different protocols and methods tested, circular plots were generated with the freeware Circos-0.64 software [8]. The Circos plots demonstrated in this article are restricted to sample 1, as the coverage profiles were consistent across all samples. To compare different methodologies, datasets were down sampled to an average coverage of 3000 using Picard (http://picard.sourceforge.net). The average relative cov- erage was collected for all samples processed with the same protocol resulting in seven datasets (Ion Torrent standard, Ion Torrent without amplification step, Ion Torrent Covaris, Ion Torrent NEBNext dsDNA Fragmentase, TruSeq Covaris, TruSeq NEBNext dsDNA Fragmentase and Nextera XT). For each dataset the fraction with a relative coverage ,0.50; ,0.25; ,0.10; ,0.05 and ,0.01 was determined. To identify the nucleotide composition of undercovered regions GC, AT along with CT, AG, AC and GT dinucleotide motif plots were created and correlated to the total relative coverage, as well as the relative coverage from each strand separately. Both the incidence (in percentages) of the dinucleotide motifs in the mtDNA molecule, and the relative coverage were calculated in bins of 150 nucleotides and illustrated as bias plots.
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Clinics  vol.67 número10

Clinics vol.67 número10

Nuclear genomic instability was assessed by PCR analysis of 13 STR markers. The TPOX, D3S1358, FGA, D7S820, TH01, D13S317 and D16S539 loci were amplified with the fluor- escent AmpFlSTR Identifiler Genotyping system according to the manufacturer’s recommendations (Applied Biosystems, USA) and then analyzed using the automated ABI3100 Genetic Analyzer platform and GeneMapper Software (Applied Biosystem, USA). The D13S790 locus was amplified with an independent FAM-fluorescent system and analyzed using the ABI3100 Genetic Analyzer platform (Applied Biosystems, USA). The D2S123, D3S1611, D17S796, intron 12 BRCA1 and intron 1 TP53 loci were analyzed using silver nitrate staining following a 6% denaturing polyacrylamide gel electrophoresis. Nuclear genome instability was assessed by observing the allelic imbalances, which are usually identified as LOH. Supplementary Table 1 shows the STR loci localizations and the primer sequences. When the allelic patterns differed between the matched normal and tumor DNAs, the PCRs and electrophoresis were performed twice. Eventually, the lymphocyte DNAs of patients were also genotyped and compared to normal and tumor DNAs to confirm results. In a previous study, TP53 mutation detection was performed for exons 4-9 (13). The association analyses were performed with Fisher’s exact test with a significance level of 95% using GraphPadH software.
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TOX3 mutations in breast cancer.

TOX3 mutations in breast cancer.

mutations have a potential deleterious effect on protein secondary structure or function. Of these, one is expressed by the tumour and therefore potentially pathogenic (p.Leu129Phe, exon 3). The other two are not expressed by the corresponding tumours, and therefore are unlikely to be disease-causing. The variability of preferential expression of the mutant vs wild-type allele in the samples without LOH can be an indication of differential allelic methylation within the tumours, which can lead to loss of expression from one allele. However, all mutations detected in our samples were outside of the HMG-box region (Figure 1B), suggesting that the DNA binding ability of the mutant proteins should not be affected.
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PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011.

PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011.

Many interesting lectures were given at the ISMB 2011 conference in Vienna. In my opinion, one of the outstanding sessions in the conference was the work dedicated to understanding the mysterious role and function of proteins encoded by chimeric transcripts, which was presented by Milana Frenkel-Morgenstern, a post- doctorate fellow in the CNIO in Madrid, Spain. Alternative splicing is thought to influence more than 70% of human genes and has a major contribution to both transcriptomic and protemic diversity. It has been shown to have a role in several genetic diseases as well as in cancer development. Chimeric transcripts may be generated by trans-splicing of pre- mRNAs or, alternatively, through gene fusion following translocations and rear- rangements. Chimeric transcripts are of special interest since many of them have been shown to be associated with cancer. Nevertheless, very few chimeric tran- scripts, and especially their associated protein products, have been characterized. Their functional importance has remained mysterious and prompted the questions in the work presented by Dr. Frenkel-Mor- genstern. The major aim of her work was to detect and functionally characterize the chimeric proteins products associated with genome-wide detection of chimeras by computational methods. Dr. Frenkel-Mor- genstern explained that a significant pro- portion of the chimera transcripts were
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Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors

Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors

The literature on the role of mitochondrial DNA mutations in cancer is in many cases contradictory. Some authors have claimed that mtDNA somatic muta- tions are accumulated in cancer cells due to a relaxation of the negative selection acting at the population level, thus consistent with neutrality [18]. Some mathematical models taking into account several parameters (as mtDNA point mutation fractions in a variety of human tissues) [19] showed that the homoplasy of the cancer somatic mtDNA mutations can be explained by random processes of drift, without the need to invoke positive selection for these mutations. However, other authors [20] have argued that the available data support strong selection against detrimental mtDNA mutations in tumor cells, so that intact mitochondria are required for successful tumorigenesis. Zhidkov et al. [21] analyzed two datasets of somatic cancer mutations typed by the high throughput mitochondrial sequencing array (Mito- Chip) concluding that the patterns of mutation in tumors are similar to the ones that occur in human evo- lution, so that both are shaped by similar selective con- strains. These authors saw that somatic cancer mutations match the ones occurring in deep branches of the tree. Palanichamy and Zhang [22] showed that caution should be applied to the interpretation of data from MitoChip studies, as the application of phyloge- netic quality control criteria led to the identification of many sample mix-ups; including in the dataset [23] which constituted 83 of the 98 samples analyzed in [21], where at least five samples had leucocytes belonging to one haplogroup and tumor to a clearly different hap- logroup (sometimes as far apart as African from Eura- sian haplogroups), clearly the result of sample mix-ups. Research on the role of mtDNA mutations in cancer has a long history filled with controversy; however, none of these works dealing with selection of the somatic can- cer mtDNA mutations addressed the particular pheno- type of oncocytic tumors, which is so clearly associated with mitochondrial dysfunction. To focus the point we consider the question of whether the predicted patho- genicity of somatic mtDNA mutations is higher in onco- cytic tumors than in non-oncocytic tumors.
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A genomewide screen for suppressors of Alu-mediated rearrangements reveals a role for PIF1.

A genomewide screen for suppressors of Alu-mediated rearrangements reveals a role for PIF1.

present here suggesting that loss of PIF1 function may contribute to breast carcinogenesis. However, for many genes it is well known that findings in mouse mutants cannot necessarily be extrapolated to humans. For example, early attempts to develop mouse models of BRCA1-linked breast cancer were unsuccessful (reviewed in [60]). Early embryonic lethality precluded tumor development in Brca1 (2/2) mice. Surprisingly, conventional null or hypomor- phic Brca1 alleles revealed lack of tumor formation in heterozy- gous mice. However, homozygous mice with certain hypomorphic Brca1 alleles can survive to adulthood and display an increased susceptibility to a range of tumors, including mammary carcino- mas [61]. Tumors can also be induced by conditional inactivation of Brca1 in breast epithelial cells through cre/loxP-mediated recombination [62]. Inactivation of Brca1 alone in murine ovarian surface epithelium resulted in an increased accumulation of premalignant changes, but no tumor formation [63]. Importantly, somatic loss of both Brca1 and p53 resulted in the rapid and efficient formation of highly proliferative, poorly differentiated estrogen receptor-negative mammary tumors that closely mimic human BRCA-mutated breast cancers with basal-like phenotypes [64] suggesting that other genetic events contribute to tumorigen- esis. Approximately 50% of familial breast cancer remains unresolved- that is disease cannot be explained by loss of function mutations in known breast cancer genes. Thus other genes are worthy of in-depth genomic analysis in unresolved families regardless of their associated mouse phenotype.
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MiR-132 suppresses the migration and invasion of lung cancer cells via targeting the EMT regulator ZEB2.

MiR-132 suppresses the migration and invasion of lung cancer cells via targeting the EMT regulator ZEB2.

A total of 90 cases of NSCLC specimens were obtained from General Hospital of Tianjin Medical University. All 90 patients hadn’t received radiation therapy or chemotherapy prior to the surgery. Tissue samples for use were stored in liquid nitrogen. The TNM staging system of the UICC (1997) was used to classify the specimens and the survival times which were calculated from the operation day to death via the evaluation of recurrence and metastasis until the last follow-up date. The following-up of the surviving patients averaged 32.55 months and ranged from 1 to 96 months. The study has been approved by hospital ethical committee. Clinicopathological information of the patients about age, tumor size, histological type, differentiation, stage and lymph node metastasis was obtained from patient records, which were summarized in Table 1.
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