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The current study aimed to identify new breast and/or ovarian cancer predisposition genes. For that, whole‐exome sequencing (WES) was performed in the germline DNA of 52 non‐BRCA1/BRCA2/TP53 mutation carrier women at high‐risk for hereditary breast and ovarian cancer (HBOC). All variants were classified using information from population and disease specific databases, in silico prediction tools and the American College of Medical Genetics and Genomics (ACMG) criteria. Loss of heterozygosity (LOH) of tumor samples and segregation analyses were performed whenever possible. The variants identified were investigated in a second, independent cohort of 17 BC cases. Pathogenic/Likely Pathogenic variants were identified in known cancer genes such as CHEK2, MUTYH, PMS2, and RAD51C. Rare and potentially pathogenic variants were identified in DNA repair genes (FAN1, POLQ, and RAD54L) and other cancer‐related genes such as DROSHA and SLC34A2. Interestingly, the variant c.149T>G in the FAN1 gene was identified in two unrelated families, and exhibited LOH in the tumor tissue of one of them. In conclusion, this is the largest Brazilian WES study involving families at high‐risk for HBOC which has brought novel insights into the role of potentially new genetic risk factors for hereditary breast and ovarian cancer., The current study aimed to identify new breast and/or ovarian cancer predisposition genes. Rare and potentially pathogenic variants were identified in DNA repair genes (FAN1, POLQ, and RAD54L) and other cancer‐related genes such as DROSHA and SLC34A2. This is the largest Brazilian WES study involving families at high‐risk for hereditary breast and ovarian cancer which has brought novel insights into the role of potentially new genetic risk factors for hereditary breast and ovarian cancer.

Individuals spread information about their lives, their career, and their recently purchased items. In addition, considering that the customer’s opinions may influence their friendship circle, neighbors, and work colleagues, they constitute a very important factor to consider in future actions of companies. In this paper, we present an approach based on probabilistic cellular automata and ordinary differential equations for modeling the consumer market, inspired by a biological system of an infectious disease-spreading model. However, instead of spreading a disease, consumers spread their opinion to other individuals, thereby having consequences on sales levels. Using marketing, the economic situation, and individual opinion as input variables of the consumer market model, simulation output (generated demand) is then used in the business game, helping the mediator (teacher) to create different scenarios and giving feedback to the student at simulation runtime, even if many players are involved in the game. Analytical and numerical simulations show that the proposed approach allows the teacher to create virtual markets for the players just by setting the parameters that describe a scenario, increasing the dynamism of the game, saving time, and allowing the mediator to focus on other important subjects, such as the teaching concepts of business strategies and decision support. Moreover, simulations are conducted to demonstrate the applicability of the proposed model in real life problems, such as the electro-domestic market.

Manipulation of qudits in optical tables is a difficult and nonscalable task. The use of integrated optical circuits opens new possibilities for the generation, manipulation, and characterization of high dimensional states besides the ease of transmission of these states through an optical fiber. In this work we propose photonic circuits to perform minimum quantum state tomography of path qudits and show how to determine all the constituents parameters of these circuits (beam splitters and phase shifters). Our strategies were based on the symmetries of the involved POVMs (positive operator-valued measures) suggested for minimum tomography and allowed us to obtain interferometers smaller than those obtained by other already known methods. The calculations of the transmittances and reflectivities of the beam splitters were made using the definition of probability operators in extended Hilbert spaces and the application of Naimark's theorem. The employment of equidistant states for the definition of the POVM elements allowed us to develop a recipe applicable to the tomography of qudits of any dimension, generalizing our scheme., 7+\epsilon pages, 4 figures, comments are welcome

Wetlands cover approximately 6% of the Earth's surface. They are frequently found at the interface between terrestrial and aquatic ecosystems and are strongly dependent on the water cycle. For this reason, wetlands are extremely vulnerable to the effects of climate change. Mangroves and floodplain ecosystems are some of the most important environments for the Amazonian population, as a source of proteins and income, and are thus the types of wetlands chosen for this review. Some of the main consequences that can be predicted from climate change for wetlands are modifications in hydrological regimes, which can cause intense droughts or inundations. A possible reduction in rainfall can cause a decrease of the areas of mangroves and floodplains, with a consequent decline in their species numbers. Conversely, an increase in rainfall would probably cause the substitution of plant species, which would not be able to survive under new conditions for a long period. An elevation in water temperature on the floodplains would cause an increase in frequency and duration of hypoxic or anoxic episodes, which might further lead to a reduction in growth rates or the reproductive success of many species. In mangroves, an increase in water temperature would influence the sea level, causing losses of these environments through coastal erosion processes. Therefore, climate change will likely cause the loss of, or reduction in, Amazonian wetlands and will challenge the adaptability of species, composition and distribution, which will probably have consequences for the human population that depend on them.

BRCA1 germline mutation is closely associated with triple-negative breast cancer. BRCA deficiency leads to impaired DNA repair and tumor development, and understanding this deficiency, in both hereditary and sporadic scenarios, is of great clinical and biological interest. Here, we investigated germline or somatic events that might lead to BRCA1 impairment in triple-negative breast cancer. We also analyzed the clinical implications associated with BRCA deficiency. Next-generation sequencing for the BRCA1/2 genes and multiplex ligation-dependent probe amplification (MLPA) for the BRCA1 gene were performed for mutation screening. A customized bisulfite next-generation sequencing approach was used for assessing BRCA1 promoter methylation status in tumor tissue. A total of 131 triple-negative cases were assessed, and germline pathogenic variants were detected in 13.0% of all cases and in 26% of cases diagnosed in young women. Most germline pathogenic variants (88.2%) occurred in the BRCA1 gene. BRCA1 promoter hypermethylation was detected in 20.6% of tumors; none of these tumors were in BRCA1/2 pathogenic variant carriers. BRCA1 impairment by either germline or somatic events was significantly more frequent in young women (55% in those ≤ 40 years; 33% in those 41–50 years; 22% in those > 50 years of age) and associated with better overall and disease-free survival rates in this group of patients. BRCA1 deficiency was recurrent in early-onset triple-negative breast cancer in Brazilian patients and associated with improved survival. With the new treatment modalities being investigated, including poly (ADP-ribose)-polymerase (PARP) inhibitor therapy, our results suggest that a significant proportion of young women with this subtype of tumor might benefit from PARP inhibitor treatment, which warrants further investigation.

List of genes selected for copy number validation of 9 focal rearrangements using real-time quantitative PCR (qPCR) with TaqMan Gene Copy Number assays. (DOC 34Â kb)

List of genes selected for copy number validation of 9 focal rearrangements using real-time quantitative PCR (qPCR) with TaqMan Gene Copy Number assays. (DOC 34Â kb)

Prostate cancer is a heterogeneous and multifocal disease. In general, it presents an indolent behavior, being asymptomatic in many cases. However, in some cases, the tumor rapidly progresses to metastatic disease leading to patient death. The Gleason score (GS) is the main prognostic factor for localized disease and its classification is based on the sum of the primary and the secondary histologic pattern, ranging from 2 to 10. Despite being the main classification method, GS alone does not provide accurate information about patient outcome, since patients with the same score can have different behaviors, particularly in intermediate GS (7-8). Therefore, in this study we investigated genomic alterations in patients with intermediate GS that presented biochemical recurrence (BCR) compared to patients without recurrence, aiming to improve prognosis and also to reveal biologic pathways involved with tumor aggressiveness. Forty-three prostate adenocarcinoma patients with intermediate GS (7-8) that underwent radical prostatectomy at the A.C. Camargo Cancer Center were selected and divided into 2 groups, 21 patients with and 22 patients without BCR, respectively. From these 43 patients we obtained genomic DNA from 35 paired tumor/normal samples and 8 tumors and performed targeted-sequencing of 58 carefully selected genes, including 24 genes frequently mutated in prostate cancer and 34 genes mutated in other solid tumors, using the TruSeq Custom Amplicon kit and the NextSeq platform (Illumina). Sequencing reads were aligned to reference human genome (hg19) using the BWA software, generating >1000X average coverage per sample. To identify somatic mutations, we used the MuTect variant caller followed by Varseq software for selecting SNVs (single nucleotide variants) and indels with a minimum coverage of 100X and minimum allele frequency of 2% in the tumor that leads to missense, nonsense, splice site, or frameshift alterations. A total of 292 variants were identified in prostate tumor samples, 250 SNVs and 42 indels, with an average of 8 alterations per tumor (ranging from 0 to 91). We detected 95 (77 SNVs and 18 Indels) somatic variants in the group of tumors with BCR and 197 (173 SNVs and 24 Indels) somatic variants in the group of tumors without BCR; however, no statistically significant difference in terms of number of variants was detected between the two groups (p-value = 0.30). Of the 58 genes investigated, 45 were affected in at least one patient (77.6%), suggesting that the custom panel is enriched in genes mutated in prostate cancer. Among the top mutated genes (affected by more than 10 variants) we detected genes involved with chromatin modification enzymes, such as KMT2D, KDM5C, KDM6A, CHD5, and BRCA2, as well as genes related to developmental gr In the next step we propose to investigate associations between somatic mutations and clinicopathologic characteristics, especially with the occurrence of biochemical relapse, in an attempt to improve prognosis and better estimate the risk of recurrence. Citation Format: Isabella Meira, Bruna Barros, Rodrigo Ramalho, José Kroll, Renan Almeida, Sandro de Souza, Isabela da Cunha, Gustavo Guimarães, Dirce Carraro, Elisa Ferreira. Identification of somatic alterations in prostate adenocarcinoma with intermediate Gleason score with and without biochemical recurrence [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A19.

Intra-tumor genetic heterogeneity is a possible cause of therapy resistance and has consequences in the disease progression and patient survival. Triple-negative breast cancer (TNBC) is associated with rapid growth, early metastasis, and worse prognosis than other breast cancer subtypes. Close association has been identified between TNBC and germline loss-of-function mutations in BRCA1 gene which trigger the tumorigenic process in hereditary TNBC. Although at genomic level, TNBC was previously characterized as more heterogeneous than other breast cancer subtypes, the difference in genomic, epigenomic, and transcriptional variability between two groups of TNBC—sporadic (BRCA1-proficent) and hereditary (BRCA1-associated)—remains unclear. Here, we investigated both sporadic and hereditary TNBC, by using data from copy-number alterations (CNAs) array, methylation array, and RNA-Seq. A total of 80 samples, 40 TNBC BRCA1-proficient (classified as sporadic), 18 TNBC with BRCA1 germline mutation (classifed as hereditary) and 22 normal breast tissues used as controls, were used. Data from methylation and CNA arrays were analyzed with the RnBeads and snapCGH softwares, respectively. RNA-seq data was analyzed mainly with the STAR aligner, Bioconductor-GenomicFeatures and DESeq2 softwares. To assess the intragroup genomic, transcriptional, and epigenomic variability we used the inter-quantile difference between patients of the same group. Our results clearly demonstrated that the TNBC BRCA1-proficient group has a higher intragroup heterogeneity than the BRCA1-mutated group regarding (i) global pattern of gene expression, (ii) number and intensity of CNAs (copy number alterations), and (iii) level of promoter methylation. Moreover, normal breast samples showed the lowest intra-group heterogeneity for the last two features. Then, our results show higher genomic, transcriptional, and epigenomic variability in sporadic than hereditary TNBC and motivates further molecular subtyping of the sporadic TNBCs, which may reveal new targets to improve TNBC treatment. Citation Format: Kivvi Duarte de Mello Nakamura, Rodrigo Fernandes Ramalho, Rafael Canfield Brianese, Ana Krepischi, Bruna D. F. Barros, Dirce Maria Carraro. Intragroup genomic, transcriptional, and epigenomic variability is higher in sporadic than in BRCA1-associated hereditary triple-negative breast tumors [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A25.

Background: Melanoma is a highly aggressive skin cancer; approximately 10% of melanomas are caused by germline mutations, mainly affecting the p16 isoform of the CDKN2A gene (responsible for up to 40% of the familial melanoma). Other genes exhibiting moderate- to high-penetrant mutations have been recently associated with melanoma susceptibility but in low frequency. Therefore, the majority of the melanoma-prone patients remain without the identification of genetic etiology. Objective: In order to find new genes potentially related to melanoma predisposition, we performed whole-exome sequencing of 10 affected individuals from 5 unrelated families. All patients were negative for CDKN2A/CDK4/TERT promoter/MITF (E318K) mutations. Materials and Methods: Melanoma-prone patients were ascertained based on either the classical criteria for familial melanoma syndrome or based on evidence of a strong genetic predisposition (occurrence of ≥2 primary melanomas). Whole-exome sequencing was performed using the Ion Proton Sequencer (Life Technologies). Our experimental design was performed using at least 20x each base pair sequencing as confidence pattern and the most interesting variants were prioritized, when identified on the two probands from the same family, using the VarSeq software 1.4.2. Once we obtained the most interesting germline rare variants we designed a panel for the validation of these variants through the target sequencing (Ion Proton Thermo Fisher Scientific Inc). Results: We identified 214 rare nonsynonymous variants. We selected a set with 63 rare germline variants potentially damaging the protein function and associated to important cellular pathways to perform validation (4 LoF variants classified as frameshift). All variants were validated by resequencing using probes specifically designed for the rare selected variants; some of them already associated to melanoma, skin pigmentation, melanoma, and/or cancer susceptibility. Conclusion: This study provides new knowledge about melanoma predisposition in the Brazilian population, in which the risk is smaller to develop this disease than in other populations, and also highlighted possible new risk factor or predisposition genes for hereditary melanoma syndrome. Citation Format: Felipe Fidalgo, Luciana Facure, Bruna Barros, Renan Valieris, Giovana Torrezan, Bianca de Sá, Amanda Nóbrega, Maria Isabel Achatz, João Duprat, Carla Rosenberg, Sandro Souza, Ana Krepischi, Dirce Maria Carraro. Identification of new promising germline variants in melanoma-prone patients [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A20.

Background: Triple-negative breast cancer (TNBC) is a breast cancer subtype that accounts for 15-20% of all breast cancer cases. TNBC treatment is challenging because it does not respond to conventional hormonal and available target therapies, which are effective in other subtypes, making systemic chemotherapy the mainstay treatment. Moreover, TNBC displays higher aggressiveness and distinct metastatic pattern compared to other breast tumors, resulting in worse prognosis and survival. We and others have identified high prevalence of BRCA1 germline mutation in TNBC. However, BRCA1 deficiency may also be caused by somatic gene promoter methylation among other mechanisms. BRCA1/2 deficiency may lead to impairment of DNA repair and tumor development. Hence, understanding the mechanisms of BRCA deficiency in driving this tumor subtype, in both hereditary and sporadic scenery, is of great clinical and biologic interest. Methods: We included in this study TNBC samples unselected for age or family history and attending A. C. Camargo Cancer Center. Tumor tissues were screened for point mutation in BRCA1/2 using next-generation sequencing (NGS). Sanger sequencing was performed in both tumor and normal tissue/leucocyte for categorizing the pathogenic mutations in germline or somatic. Multiplex Ligation-dependent Probe Amplification (MLPA) was used to investigate BRCA1 copy number alterations (CNA) resulting from large rearrangements in tumor and leucocyte. Additionally, for BRCA1 gene silencing investigation a customized bisulfite NGS approach was performed to assess the BRCA1 promoter methylation in tumor tissue. Results: Point mutations were screened in 131 TNBC tumor samples, detecting a total of 18 pathogenic mutations (13.7%)---16 (88.8%) in BRCA1 and 2 (11.2%) in BRCA2. No large rearrangement was detected by MLPA in tumor tissue or leucocyte. Mutations classified as germline accounted for the majority of the pathogenic mutations detected in tumor tissue (93.75% - 15/16)---81.25% (13/16) in BRCA1 and 12.5% (2/16) in BRCA2. Only one somatic mutation was detected (6.25% - 1/16) in BRCA1 gene. Considering early onset TNBC (≤40 year of age) the germline mutation rate increased to 25% (8/32), mainly in BRCA1 gene (22% - 7/32). BRCA1 promoter hypermethylation in tumor was detected in 20.6%, all in sporadic TNBC, with a slight increase to 28% in early onset cases. Ultimately, BRCA impairment by either constitutive or somatic events was identified in 34% (45/131) of the cases and was significantly more frequent in young women (56% in ≤40; 33% in 41-50; 23% in >50 year of age; p=0.007) and associated with better overall and disease-free survival rates in this group of patients. Conclusions: We observed that a high number of the TNBC cases are hereditary and BRCA1-related, especially in young women. For the sporadic cases, BRCA1 gene silencing was also a recurrent event. Taken together, our data showed that BRCA1 impairment (either by germline mutation or somatic promoter hypermethylation) was present at high frequency in the early-onset cases and was associated with better survival for these patients. With the new treatment modalities including Poly (ADP-ribose) polymerase (PARP) inhibitors being investigated, our results shed light that a significant proportion of young women with TNBC might benefit from PARP-inhibitor and future investigation in this subject is warranted. Citation Format: Rafael Canfield Brianese, Kivvi D. M. Nakamura, Fernanda G. S. R. Almeida, Rodrigo F. Ramalho, Elisa N. Ferreira, Bruna D. F. Barros, Maria N. C. Formiga, Victor P. Andrade, Vladmir C. C. Lima, Dirce M. Carraro. BRCA1 deficiency is a recurrent event in early onset triple-negative breast cancer (TNBC): A comprehensive analysis of germline mutations and somatic promoter methylation [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A49.

Wilms tumour (WT) is an embryonal kidney neoplasia for which very few driver genes have been identified. Here we identify DROSHA mutations in 12% of WT samples (26/222) using whole-exome sequencing and targeted sequencing of 10 microRNA (miRNA)-processing genes. A recurrent mutation (E1147K) affecting a metal-binding residue of the RNase IIIb domain is detected in 81% of the DROSHA-mutated tumours. In addition, we identify non-recurrent mutations in other genes of this pathway (DGCR8, DICER1, XPO5 and TARBP2). By assessing the miRNA expression pattern of the DROSHA-E1147K-mutated tumours and cell lines expressing this mutation, we determine that this variant leads to a predominant downregulation of a subset of miRNAs. We confirm that the downregulation occurs exclusively in mature miRNAs and not in primary miRNA transcripts, suggesting that the DROSHA E1147K mutation affects processing of primary miRNAs. Our data underscore the pivotal role of the miRNA biogenesis pathway in WT tumorigenesis, particularly the major miRNA-processing gene DROSHA., Wilms tumour (WT) is the most common paediatric kidney cancer and few driver genes related to its development have been identified. Here, the authors identify DROSHA mutations that may contribute to WT tumorigenesis through their effect on primary microRNA processing.

Background The identification of molecular alterations that trigger Wilms tumor (WT) development is crucial to understanding the tumorigenesis of this malignancy. Currently, it is estimated that WTX and WT1 genomic losses together with CTNNB1 point mutations occur in about 30% of WTs. However, the majority of cases remain without any identified driver mutation. Results from a previous study by our group pointed to APC and PLCG2 as candidate genes altered in WT [1]. Given the advent of modern DNA sequencing technologies, it is now feasible to evaluate large genomic regions spanning complete genes (exons and introns), allowing the description of the mutation patterns occurring in tumor cells. Thus, the aim of this study was to identify point mutations and indels in the complete sequence of APC, CTNNB1, WT1, WTX and PLCG2 genes in order to characterize both the exonic mutational spectrum and the intronic nucleotide substitution pattern. Material and methods The complete genomic regions of the selected genes, spanning a total of 430 kb, were amplified by long-range PCR in 15 WTs and 3 non-neoplasic control samples, giving a total of 60 amplicons per sample (10 kb on average). The resulting amplicons were mixed at equimolar concentrations and, for each sample, the Ion PGM library preparation protocol was performed. The libraries of the 18 barcoded samples were combined in four sequencing pools that were individually submitted to an Ion PGM™ Sequencer run on an Ion 316™ Chip. Point mutation and indels not present in the non-neoplasic controls were selected for capillary sequencing validation. The validated

TP53 protein is one of the most important and studied human tumor suppressors. Whereas TP53 drives the malignant transformation and is the most frequently mutated gene in human cancers, the location and the type of its mutations for specific tumor types in ethnically admixed populations have not been evaluated. In this study we employed an amplicon panel to capture and to deep-sequence all the exons of TP53 in a series of 29 tumor biopsy samples derived from Brazilian individuals diagnosed with gastric adenocarcinomas (GACs), which were compared to Asian and Europeans. TP53 sequences were obtained from Brazilian samples with the Ion Torrent AmpliSeq TP53-panel and determined in the Ion PGM Torrent and Ion Proton platforms. We generated a mean of 7.25 million reads per patient, resulting in a median coverage >13,000X. All samples were covered above 6,400X. The mutations observed here were compared to those described in patients from different ethnic groups obtained from TCGA composed for 103 Asians patients (Japan, Hong-Kong, South Korea, Vietnam) and 78 cases of Europeans. The Asian and European populations showed higher prevalence of intestinal type GAC (53.7% and 61.6%, respectively) in contrast to our cohort, in which 69% of the patients had diffuse-type GACs (pA p.Arg282Trp in the DNA binding domain in exon 8, was found in all three sample groups studied, suggesting a possible role for this mutation in GAC pathogenesis. Although TP53 is the most frequently mutated gene in GACs we found no specific patterns that could explain the differences in the clinical behavior of this tumor between Asian and non-Asian patients. Further analyses are being performed trying to correlate mutations in TP53 and other genes with the different clinical outcomes observed in GACs from Asians and non-Asians, and in a setting of high genetic admixture, as observed in Brazil. Citation Format: Melissa Pool Pizzi, Helano Carioca Freitas, Maria Galli Amorim, Bruna Durães de Figueiredo Barros, Frederico Omar Gleber-Netto, Ana Flávia Mattos Costa, Maria Dirlei Begnami, Adriane Graicer Pelosof, Diana Noronha Nunes, Emmanuel Dias-Neto. Gastric adenocarcinoma TP53 mutations in an ethnically admixed population. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3697.

Detection of tumor DNA in urine has been shown as viable method of diagnosis not only for urinary tract (e.g., kidney and bladder) cancers but also for other types, e.g. prostate. Applications of such method, resemble those which use plasma DNA and include cancer detection, monitoring of tumor growth or recurrence and response to chemotherapy or radiation therapy. As far as we know, there is a lack of studies applying urine DNA detection in Wilms tumor (WT), an embryonary kidney cancer type. Here we show evidences of detection for two somatic variants in the urine DNA of one WT patient. By using NGS exome sequencing of tumor tissue and leukocytes samples of the same patient we were able to find new somatic variants: a frame-shift indel in TNRC18 and a misssense SNV in INTS1 gene. Target sequencing applied to the DNA from the patient's urine revealed the presence of these two somatic variants. More interestingly, both variants could not be found in the urine DNA of this patient after treatment (chemotherapy and nephrectomy). Additionally, these genes are poorly characterized in WT contributing for the comprehension of the cellular processes that are operating in tumorigenesis of WT. Altogether, our findings contribute with the mutational repertoire of WT and reveals the potential of using urine DNA sequencing as a noninvasive cancer screening approach. Citation Format: Ana C. K. Miguez, Rodrigo F. Ramalho, Elisa N. Ferreira, Bruna D. F. Barros, Claudia A. A. de Paula, Renan Valieris, Louise D. C. Mota, Jorge E. Souza, Isabela W. Cunha, Cecília L. Costa, Sandro J. de Souza, Dirce M. Carraro. Urine as a potential liquid biopsy for detecting tumor DNA in Wilms tumor patient: Detection of somatic mutations in urine opens perspectives of monitoring chemotherapy response in WT patients. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A32.

Background: Wilms Tumor (WT) is the most common pediatric kidney cancer and in approximately 2% of cases presents a familial predisposition. In both sporadic and inherited WT cases, several genes have been identified as being somatically mutated. The most frequent WT mutated genes are WT1, CTNNB1 and WTX, that together account for approximately 30% of cases. In addition, mutation in other genes such as TP53, IGF2, DIS3L2, FBXW7, MYCN, and DICER have also been described in few cases. However, up to 60-70% of Wilms tumors remain without any associated driver mutation. In this sense, the aim of this project was to identify novel somatic and de novo alterations possibly associated with WT tumorigenesis through exome sequencing. Methods: The study design consisted of performing exome sequencing of 4 samples related to a sporadic WT patient: patient blood and tumor samples, in addition to mother's and father's blood samples. Coding regions of genomic DNA were enriched using SureSelect Human All Exon 50Mb Kit (Agilent). Libraries construction and sequencing at SOLiD 4 and 5500xl were performed following the manufacturer's instructions. Resulting sequences were mapped to a reference genome with Bioscope and NovoalignCS software. Sequence variants were identified with SAMtools and filtered if present on dbSNP database. Initially a small set of de novo and somatic mutations were selected to be validated by sanger sequencing. Results: From 84 unknown de novo alterations, we selected 11 for validation according to the following criteria: all loss of function variants (1 splice site and 2 nonsenses; 8 missense variants that were classified as pathogenic in the prediction programs SIFT and/or Polyphen2 and were not at highly repetitive or homologous regions of the genome. From these 11 candidates, only one was confirmed to be a de novo mutation, while the remaining ten were either false positive or inherited variants. Regarding somatic alterations, 8 candidate mutations were identified and selected for validation. After sanger sequencing, only one was validated as a somatic mutation, one variant was also present in patient's blood and 6 alterations were not confirmed in the tumor, suggesting it to be sequencing artifacts. The gene affected by the validated somatic mutation encodes an important protein involved in RNA regulation and cell differentiation, and was not described to be mutated in any tumor type until now. Remarkably, this somatic mutation affects a highly conserved amino acid of this gene and this residue is a known binding site for a magnesium cofactor that is essential for the protein activity. The presence of this mutation was further evaluated in a cohort of 97 Wilms tumor samples and found to be present in 10% of cases. Preliminary functional studies of HEK293 cells transfected with an expression vector of this mutation demonstrated an impaired activity of the mutated protein. Conclusion: In this study we were able to identify one de novo and one somatic novel mutations in Wilms tumor. Initial results from our group suggest that this somatic mutation represents a driver and frequent event in this type of tumor. Citation Format: Giovana T. Torrezan, Elisa N. Ferreira, Mayra T M Castro, Adriana M. Nakahata, Pedro A. Galante, Daniel T. Ohara, Bruna D. Barros, Mariana Maschietto, Isabela W. Cunha, Cecilia M L Costa, Beatriz D. Camargo, Dirce M. Carraro. Identification of somatic and de novo mutations by exome sequencing in sporadic Wilms tumor. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A29.

In this paper we study the propagation of acoustic waves in a one-dimensional medium with a short range correlated elasticity distribution. In order to generate local correlations we consider a disordered binary distribution in which the effective elastic constants can take on only two values, η(A) and η(B). We add an additional constraint that the η(A) values appear only in finite segments of length n. This is a generalization of the well-known random-dimer model. By using an analytical procedure we demonstrate that the system displays n - 1 resonances with frequencies ω(r). Furthermore, we apply a numerical transfer matrix formalism and a second-order finite-difference method to study in detail the waves that propagate in the chain. Our results indicate that all the modes with ω ≠ ω(r) decay and the medium transmits only the frequencies ω(r).

Superradiance in an ensemble of atoms leads to the collective enhancement of radiation in a particular mode shared by the atoms in their spontaneous decay from an excited state. The quantum aspects of this phenomenon are highlighted when such collective enhancement is observed in the emission of a single quantum of light. Here we report a further step in exploring experimentally the nonclassical features of superradiance by implementing the process not only with single excitations, but also in a two-excitations state. Particularly we measure and theoretically model the wave-packets corresponding to superradiance in both the single-photon and two-photons regimes. Such progress opens the way to the study and future control of the interaction of nonclassical light modes with collective quantum memories at higher photon numbers., 5 pages, 4 figures. V2: substantial changes on the introductory part of the paper

Background Genome-wide profiling of rare tumors is crucial for improvement of diagnosis, treatment, and, consequently, achieving better outcomes. Desmoplastic small round cell tumor (DSRCT) is a rare type of sarcoma arising from mesenchymal cells of abdominal peritoneum that usually develops in male adolescents and young adults. A specific translocation, t(11;22)(p13;q12), resulting in EWS and WT1 gene fusion is the only recurrent molecular hallmark and no other genetic factor has been associated to this aggressive tumor. Here, we present a comprehensive genomic profiling of one DSRCT affecting a 26-year-old male, who achieved an excellent outcome. Methods We investigated somatic and germline variants through whole-exome sequencing using a family based approach and, by array CGH, we explored the occurrence of genomic imbalances. Additionally, we performed mate-paired whole-genome sequencing for defining the specific breakpoint of the EWS-WT1 translocation, allowing us to develop a personalized tumor marker for monitoring the patient by liquid biopsy. Results We identified genetic variants leading to protein alterations including 12 somatic and 14 germline events (11 germline compound heterozygous mutations and 3 rare homozygous polymorphisms) affecting genes predominantly involved in mesenchymal cell differentiation pathways. Regarding copy number alterations (CNA) few events were detected, mainly restricted to gains in chromosomes 5 and 18 and losses at 11p, 13q, and 22q. The deletions at 11p and 22q indicated the presence of the classic translocation, t(11;22)(p13;q12). In addition, the mapping of the specific genomic breakpoint of the EWS-WT1 gene fusion allowed the design of a personalized biomarker for assessing circulating tumor DNA (ctDNA) in plasma during patient follow-up. This biomarker has been used in four post-treatment blood samples, 3 years after surgery, and no trace of EWS-WT1 gene fusion was detected, in accordance with imaging tests showing no evidence of disease and with the good general health status of the patient. Conclusions Overall, our findings revealed genes with potential to be associated with risk assessment and tumorigenesis of this rare type of sarcoma. Additionally, we established a liquid biopsy approach for monitoring patient follow-up based on genomic information that can be similarly adopted for patients diagnosed with a rare tumor. Electronic supplementary material The online version of this article (doi:10.1186/s40246-016-0092-0) contains supplementary material, which is available to authorized users.

Background Wilms tumor (WT) has a not completely elucidated pathogenesis. DNA copy number alterations (CNAs) are common in cancer, and often define key pathogenic events. The aim of this work was to investigate CNAs in order to disclose new candidate genes for Wilms tumorigenesis. Results Array-CGH of 50 primary WTs without pre-chemotherapy revealed a few recurrent CNAs not previously reported, such as 7q and 20q gains, and 7p loss. Genomic amplifications were exclusively detected in 3 cases of WTs that later relapsed, which also exhibited an increased frequency of gains affecting a 16.2 Mb 1q21.1-q23.2 region, losses at 11p, 11q distal, and 16q, and WT1 deletions. Conversely, aneuploidies of chromosomes 13 and 19 were found only in WTs without further relapse. The 1q21.1-q23.2 gain associated with WT relapse harbours genes such as CHD1L, CRABP2, GJA8, MEX3A and MLLT11 that were found to be over-expressed in WTs. In addition, down-regulation of genes encompassed by focal deletions highlighted new potential tumor suppressors such as CNKSR1, MAN1C1, PAQR7 (1p36), TWIST1, SOSTDC1 (7p14.1-p12.2), BBOX and FIBIN (11p13), and PLCG2 (16q). Conclusion This study confirmed the presence of CNAs previously related to WT and characterized new CNAs found only in few cases. The later were found in higher frequency in relapsed cases, suggesting that they could be associated with WT progression. Electronic supplementary material The online version of this article (doi:10.1186/s13039-016-0227-y) contains supplementary material, which is available to authorized users.