15 results on '"SNPa"'
Search Results
2. DeepSNP: An End-to-End Deep Neural Network with Attention-Based Localization for Breakpoint Detection in Single-Nucleotide Polymorphism Array Genomic Data.
- Author
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Eghbal-Zadeh, Hamid, Fischer, Lukas, Popitsch, Niko, Kromp, Florian, Taschner-Mandl, Sabine, Gerber, Teresa, Bozsaky, Eva, Ambros, Peter F., Ambros, Inge M., Widmer, Gerhard, and Moser, Bernhard A.
- Subjects
- *
DEEP learning , *PHARMACOGENOMICS , *ARTIFICIAL neural networks , *CANCER , *DATA curation , *MACHINE learning - Abstract
Clinical decision-making in cancer and other diseases relies on timely and cost-effective genome-wide testing. Classical bioinformatic algorithms, such as Rawcopy, can support genomic analysis by calling genomic breakpoints and copy-number variations (CNVs), but often require manual data curation, which is error prone, time-consuming, and thus substantially increasing costs of genomic testing and hampering timely delivery of test results to the treating physician. We aimed to investigate whether deep learning algorithms can be used to learn from genome-wide single-nucleotide polymorphism array (SNPa) data and improve state-of-the-art algorithms. We developed, applied, and validated a novel deep neural network (DNN), DeepSNP. A manually curated data set of 50 SNPa analyses was used as truth-set. We show that DeepSNP can learn from SNPa data and classify the presence or absence of genomic breakpoints within large genomic windows with high precision and recall. DeepSNP was compared with well-known neural network models as well as with Rawcopy. Moreover, the use of a localization unit indicates the ability to pinpoint genomic breakpoints despite their exact location not being provided while training. DeepSNP results demonstrate the potential of DNN architectures to learn from genomic SNPa data and encourage further adaptation for CNV detection in SNPa and other genomic data types. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
3. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity
- Author
-
Stefania Tuveri, Koen Debackere, Lukas Marcelis, Nicolas Dierckxsens, Jonas Demeulemeester, Eftychia Dimitriadou, Daan Dierickx, Pierre Lefesvre, Karen Deraedt, Carlos Graux, Lucienne Michaux, Jan Cools, Thomas Tousseyn, Joris Robert Vermeesch, Iwona Wlodarska, Brussels Heritage Lab, Supporting clinical sciences, Experimental Pathology, Pathology, UCL - SSS/IREC/MONT - Pôle Mont Godinne, and UCL - (MGD) Service d'hématologie
- Subjects
CN-LOH ,Cancer Research ,Lymphoma, Large B-Cell, Diffuse/diagnosis ,driver genes ,primary mediastinal B-cell lymphoma ,Loss of Heterozygosity ,Genomics ,mutations ,SNPa ,Mediastinal Neoplasms ,Pathology and Forensic Medicine ,whole exom/genome sequencing ,Mediastinal Neoplasms/genetics ,Mutation ,Genetics ,genomics ,Humans ,loss of heterozygosity ,Lymphoma, Large B-Cell, Diffuse ,mutation - Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumor from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%), and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15), and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as "second hit" in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukemia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma.
- Published
- 2022
4. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity.
- Author
-
UCL - SSS/IREC/MONT - Pôle Mont Godinne, UCL - (MGD) Service d'hématologie, Tuveri, Stefania, Debackere, Koen, Marcelis, Lukas, Dierckxsens, Nicolas, Demeulemeester, Jonas, Dimitriadou, Eftychia, Dierickx, Daan, Lefesvre, Pierre, Deraedt, Karen, Graux, Carlos, Michaux, Lucienne, Cools, Jan, Tousseyn, Thomas, Vermeesch, Joris Robert, Wlodarska, Iwona, UCL - SSS/IREC/MONT - Pôle Mont Godinne, UCL - (MGD) Service d'hématologie, Tuveri, Stefania, Debackere, Koen, Marcelis, Lukas, Dierckxsens, Nicolas, Demeulemeester, Jonas, Dimitriadou, Eftychia, Dierickx, Daan, Lefesvre, Pierre, Deraedt, Karen, Graux, Carlos, Michaux, Lucienne, Cools, Jan, Tousseyn, Thomas, Vermeesch, Joris Robert, and Wlodarska, Iwona
- Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumor from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%), and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15), and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as "second hit" in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukemia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma.
- Published
- 2022
5. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity
- Author
-
Tuveri, Stefania, Debackere, Koenraad, Marcelis, Lukas, Dierckxsens, Nicolas, Demeulemeester, Jonas, Dimitriadou, Eftychia, Dierickx, Daan, Lefesvre, Pierre, Deraedt, Karen, Graux, Carlos, Michaux, Lucienne, Cools, Jan, Tousseyn, Thomas, Vermeesch, Joris Robert, Wlodarska, Iwona, Tuveri, Stefania, Debackere, Koenraad, Marcelis, Lukas, Dierckxsens, Nicolas, Demeulemeester, Jonas, Dimitriadou, Eftychia, Dierickx, Daan, Lefesvre, Pierre, Deraedt, Karen, Graux, Carlos, Michaux, Lucienne, Cools, Jan, Tousseyn, Thomas, Vermeesch, Joris Robert, and Wlodarska, Iwona
- Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumor from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3–248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3–51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%), and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15), and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as “second hit” in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukemia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma., SCOPUS: ar.j, DecretOANoAutActif, info:eu-repo/semantics/published
- Published
- 2022
6. Intra-Tumour Genetic Heterogeneity and Prognosis in High-Risk Neuroblastoma
- Author
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Victoria Castel, Maite Blanquer-Maceiras, Ana P. Berbegall, Rosa Noguera, Susana Martín-Vañó, Samuel Navarro, and Amparo López-Carrasco
- Subjects
Solid tumour ,Cancer Research ,MYCN amplification ,Genetic heterogeneity ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Genomics ,ctDNA ,Biology ,SNPa ,Article ,Oncology ,Mycn amplification ,Genomic Profile ,Cancer research ,genomics ,segmental chromosomal aberration ,High risk neuroblastoma ,Liquid biopsy ,tumour microenvironment ,Survival rate ,RC254-282 - Abstract
Simple Summary Neuroblastoma (NB) is the most common extra-cranial solid paediatric cancer and is responsible for 15% of childhood cancer deaths. Patients with NB are characterized by presenting a very heterogeneous clinic (inter-tumoural heterogeneity) and also both spatial and temporal intra-tumour heterogeneity (ITH) reflected in their genetic aberrations, which may be the consequence of the coexistence of different microenvironments within the tumour. Applying pangenomic techniques to detect genomic aberrations in different biopsies (solid and liquid) of high risk NB (HR-NB) we have detected spatial ITH in a surprisingly high percentage (almost 40%) of the studied cohort. Moreover, a positive association between this heterogeneity and survival has been found. Confirming these results, combining tumour material analysis in a large cohort of HR-NB will have a major impact in the genetic diagnosis routine procedure, and would also entail a revision of the prognosis of patients with ITH. Abstract Spatial ITH is defined by genomic and biological variations within a tumour acquired by tumour cell evolution under diverse microenvironments, and its role in NB patient prognosis is understudied. In this work, we applied pangenomic techniques to detect chromosomal aberrations in at least two different areas of each tumour and/or in simultaneously obtained solid and liquid biopsies, detecting ITH in the genomic profile of almost 40% of HR-NB. ITH was better detected when comparing one or more tumour pieces and liquid biopsy (50%) than between different tumour pieces (21%). Interestingly, we found that patients with ITH analysed by pangenomic techniques had a significantly better survival rate that those with non-heterogeneous tumours, especially in cases without MYCN amplification. Moreover, all patients in the studied cohort with high ITH (defined as 50% or more genomic aberration differences between areas of a tumour or simultaneously obtained samples) survived after 48 months. These results clearly support analysing at least two solid tumour areas (separately or mixed) and liquid samples to provide more accurate genomic diagnosis, prognosis and therapy options in HR-NB.
- Published
- 2021
7. Elementi di governance ambientale tra Stato e Regioni. SNPA un modello a rete federale e federato
- Author
-
Stupazzini, Riccardo
- Subjects
legge 28 giugno 2016 ,LEPTA ,ambiente ,n. 132 ,SNPA ,legge 28 giugno 2016, n. 132 - Published
- 2021
8. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity.
- Author
-
Tuveri S, Debackere K, Marcelis L, Dierckxsens N, Demeulemeester J, Dimitriadou E, Dierickx D, Lefesvre P, Deraedt K, Graux C, Michaux L, Cools J, Tousseyn T, Vermeesch JR, and Wlodarska I
- Subjects
- Genomics, Humans, Loss of Heterozygosity, Mutation, Lymphoma, Large B-Cell, Diffuse diagnosis, Mediastinal Neoplasms genetics
- Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumor from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%), and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15), and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as "second hit" in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukemia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma., (© 2022 Wiley Periodicals LLC.)
- Published
- 2022
- Full Text
- View/download PDF
9. The snpA, a temperature-sensitive suppressor of npgA1, encodes the eukaryotic translation release factor, eRF1, in Aspergillus nidulans
- Author
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Han, Kap-Hoon, Kim, Jee Hyun, Kim, Won-Sin, and Han, Dong-Min
- Subjects
- *
ASPERGILLUS , *GENETICS , *CELL nuclei , *RADIOGENETICS - Abstract
Abstract: The npgA1 mutation causes defects in the outer layer of the cell wall resulting in a colorless colony. In this study, a temperature-sensitive suppressor of npgA1 named snpA was isolated by UV mutagenesis. The suppressing mutant showed pleiotropic phenotypes in cellular structure and developmental processes when incubated at a temperature of 37°C or above. At 37°C, multiple germ tubes emerged from germinating conidia. Moreover, at 42°C conidia germination was delayed more than 12h and hyphal growth was strongly inhibited. The suppressor allele, snpA6, is recessive and maps to the linkage group III. A gene complementing the mutation was identified employing the chromosome III-specific cosmid library. Sequencing analysis revealed that the snpA gene encodes the eukaryotic polypeptide release factor, eRF1. The snpA6 allele contains a G–A mutation resulting in SnpAE117K, which may allow read-through of the nonsense mutation in the npgA1 allele in a similar manner to the yeast omni-potent suppressor SUP45 and SUP35. [Copyright &y& Elsevier]
- Published
- 2005
- Full Text
- View/download PDF
10. Intra-Tumour Genetic Heterogeneity and Prognosis in High-Risk Neuroblastoma.
- Author
-
López-Carrasco, Amparo, Berbegall, Ana P., Martín-Vañó, Susana, Blanquer-Maceiras, Maite, Castel, Victoria, Navarro, Samuel, and Noguera, Rosa
- Subjects
- *
SURVIVAL , *NEUROBLASTOMA , *GENETIC mutation , *GENETICS , *CELL physiology , *CHROMOSOME abnormalities , *DESCRIPTIVE statistics , *GENETIC techniques ,BODY fluid examination - Abstract
Simple Summary: Neuroblastoma (NB) is the most common extra-cranial solid paediatric cancer and is responsible for 15% of childhood cancer deaths. Patients with NB are characterized by presenting a very heterogeneous clinic (inter-tumoural heterogeneity) and also both spatial and temporal intra-tumour heterogeneity (ITH) reflected in their genetic aberrations, which may be the consequence of the coexistence of different microenvironments within the tumour. Applying pangenomic techniques to detect genomic aberrations in different biopsies (solid and liquid) of high risk NB (HR-NB) we have detected spatial ITH in a surprisingly high percentage (almost 40%) of the studied cohort. Moreover, a positive association between this heterogeneity and survival has been found. Confirming these results, combining tumour material analysis in a large cohort of HR-NB will have a major impact in the genetic diagnosis routine procedure, and would also entail a revision of the prognosis of patients with ITH. Spatial ITH is defined by genomic and biological variations within a tumour acquired by tumour cell evolution under diverse microenvironments, and its role in NB patient prognosis is understudied. In this work, we applied pangenomic techniques to detect chromosomal aberrations in at least two different areas of each tumour and/or in simultaneously obtained solid and liquid biopsies, detecting ITH in the genomic profile of almost 40% of HR-NB. ITH was better detected when comparing one or more tumour pieces and liquid biopsy (50%) than between different tumour pieces (21%). Interestingly, we found that patients with ITH analysed by pangenomic techniques had a significantly better survival rate that those with non-heterogeneous tumours, especially in cases without MYCN amplification. Moreover, all patients in the studied cohort with high ITH (defined as 50% or more genomic aberration differences between areas of a tumour or simultaneously obtained samples) survived after 48 months. These results clearly support analysing at least two solid tumour areas (separately or mixed) and liquid samples to provide more accurate genomic diagnosis, prognosis and therapy options in HR-NB. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
11. O Sistema Nacional de Pesquisa Agropecuária: Histórico, Estrutura e Financiamento
- Author
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Pereira, Caroline Nascimento and de Castro, César Nunes
- Subjects
CT-Agro ,ddc:330 ,O3 ,O13 ,SNPA ,sectorial funds ,O38 ,agriculture - Abstract
This article makes an evaluation of the history, structure and financing of the Brazilian agricultural research, evaluating the transfers from the Federal Government to Embrapa and, mainly, the values to CT-Agro, the sectorial fund created to promoting R&D activities related to this sector. The goal is to verify the current constitution of the SNPA and the participation of the sectorial fund for the promotion of innovation in the agricultural sector. In order to do so, the paper analyses the evolution over the years of the SNPA, which includes a diversity of agents that act in networks, with a capacity to interfere in the process of innovation and research. It was observed that the system is well structured and strongly dependent on public resources focused mainly on basic and applied research, carried out via Embrapa or sectoral funds. CT-Agro has small expressive participation in the research structure, but significant importance for market signaling of the government's performance in agricultural R&D.
- Published
- 2017
- Full Text
- View/download PDF
12. I LEPTA come strumento i coordinamento e valutazione della performance
- Author
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Galli, Davide
- Subjects
environment protection ,LEPTA ,Settore SECS-P/07 - ECONOMIA AZIENDALE ,coordinamento ,SNPA ,performance - Published
- 2016
13. Política pública de pesquisa agropecuária no Brasil
- Author
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MOREIRA, G. C., TEIXEIRA, E. C., GUSTAVO CARVALHO MOREIRA, UFV, and ERLY CARDOSO TEIXEIRA, UFV.
- Subjects
Retornos da pesquisa agropecuária ,Embrapa ,SNPA - Abstract
Dada a importância da pesquisa e da inovação para a evolução da agricultura brasileira, principalmente depois da década de 1960, este estudo teve como objetivo verificar historicamente quais foram os incentivos governamentais de investimento em pesquisa agropecuária no País. Destacam- se como principais marcos a criação do Sistema Nacional de Pesquisa Agropecuária (SNPA), o papel da Embrapa, o papel das instituições de pesquisa e assistência técnica estaduais e o papel das universidades e das instituições de fomento. Verifica-se também a necessidade da formação de novas instituições de pesquisa nas regiões Centro-Oeste e Norte para a promoção do desenvolvimento. Por fim, destaca-se como importante agenda de pesquisa a análise do retorno dos investimentos em pesquisa agropecuária no Brasil e seus impactos sobre a sociedade, dada a escassez de tais estudos.
- Published
- 2014
14. Organização da P&D agrícola no Brasil: evolução, experiências e perspectivas de um sistema de inovação para a agricultura
- Author
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MENDES, P. J. V. and SGE.
- Subjects
Brasil ,Agricultura ,Desenvolvimento ,SNPA ,Pesquisa - Abstract
Esta tese tem como objetivo principal identificar fatores relacionados à organização e ao gerenciamento da P, D&I, que possam mostrar o quanto a pesquisa agrícola no Brasil tem sido orientada por tal abordagem. Além disso, explora-se o papel das inovações institucionais e organizacionais como mecanismos importantes para se avançar rumo a um sistema de inovação agrícola (SIA). Made available in DSpace on 2018-08-30T00:34:00Z (GMT). No. of bitstreams: 1 MendesPauleJeanneVieiraD.pdf: 1441350 bytes, checksum: d46ebe0c78a1ae49af3360118861bd2c (MD5) Previous issue date: 2009-07-09 Tese (Doutorado em Política Científica e Tecnológica) - Universidade Estadual de Campinas, Instituto de Geociências, Campinas.
- Published
- 2009
15. A parceria da Embrapa com os sistemas estaduais de pesquisa
- Author
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RODRIGUES, C. M. and CIRO MASCARENHAS RODRIGUES, SSE.
- Subjects
Setor Agrícola ,Difusão de Tecnologia ,Transferência de Tecnologia ,SNPA - Abstract
Para ilustrar a diversidade na atuação dos egressos do Programa de Doutorado em Sociologia da UnB e as possíveis influências do curso no seu desempenho profissional, apresenta-se aqui a experiência de trabalho de quem assumiu a Secretaria Executiva de um dos 16 programas do Sistema Embrapa de Planejamento, aquele que foi criado para estimular a parceria com vistas à modernização institucional dos sistemas estaduais de pesquisa. Made available in DSpace on 2022-08-03T20:19:22Z (GMT). No. of bitstreams: 1 Parceria-da-Embrapa-com-os-sistemas-estaduais.pdf: 292226 bytes, checksum: 18d7b6a7603fc946c363228167694196 (MD5) Previous issue date: 1995
- Published
- 1995
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