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1.
Cell ; 148(1-2): 59-71, 2012 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-22265402

RESUMO

Genomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in a one-step catastrophic event termed chromothripsis. We report the whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome), uncovering massive, complex chromosome rearrangements. Integrating TP53 status with microarray and deep sequencing-based DNA rearrangement data in additional patients reveals a striking association between TP53 mutation and chromothripsis in SHH-MBs. Analysis of additional tumor entities substantiates a link between TP53 mutation and chromothripsis, and indicates a context-specific role for p53 in catastrophic DNA rearrangements. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings connect p53 status and chromothripsis in specific tumor types, providing a genetic basis for understanding particularly aggressive subtypes of cancer.


Assuntos
Neoplasias Encefálicas/genética , Rearranjo Gênico , Meduloblastoma/genética , Proteína Supressora de Tumor p53/genética , Animais , Criança , Aberrações Cromossômicas , Variações do Número de Cópias de DNA , Análise Mutacional de DNA , Modelos Animais de Doenças , Humanos , Leucemia Mieloide Aguda/genética , Síndrome de Li-Fraumeni/fisiopatologia , Camundongos , Pessoa de Meia-Idade
2.
Nature ; 547(7663): 311-317, 2017 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-28726821

RESUMO

Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and 'enhancer hijacking' events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma.


Assuntos
Análise Mutacional de DNA , Genoma Humano/genética , Meduloblastoma/classificação , Meduloblastoma/genética , Sequenciamento Completo do Genoma , Carcinogênese/genética , Proteínas de Transporte/genética , Estudos de Coortes , Metilação de DNA , Conjuntos de Dados como Assunto , Epistasia Genética , Genômica , Humanos , Terapia de Alvo Molecular , Proteínas Musculares/genética , Mutação , Oncogenes/genética , Fatores de Transcrição/genética , Proteínas Wnt/genética
3.
Bioinformatics ; 37(23): 4559-4561, 2021 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-34623383

RESUMO

SUMMARY: A main task in computational cancer analysis is the identification of patient subgroups (i.e. cohorts) based on metadata attributes (patient stratification) or genomic markers of response (biomarkers). Coral is a web-based cohort analysis tool that is designed to support this task: Users can interactively create and refine cohorts, which can then be compared, characterized and inspected down to the level of single items. Coral visualizes the evolution of cohorts and also provides intuitive access to prevalence information. Furthermore, findings can be stored, shared and reproduced via the integrated session management. Coral is pre-loaded with data from over 128 000 samples from the AACR Project GENIE, the Cancer Genome Atlas and the Cell Line Encyclopedia. AVAILABILITY AND IMPLEMENTATION: Coral is publicly available at https://coral.caleydoapp.org. The source code is released at https://github.com/Caleydo/coral. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Antozoários , Neoplasias , Animais , Genoma , Software , Internet
4.
Bioinformatics ; 35(17): 3140-3142, 2019 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-30657871

RESUMO

SUMMARY: Ordino is a web-based analysis tool for cancer genomics that allows users to flexibly rank, filter and explore genes, cell lines and tissue samples based on pre-loaded data, including The Cancer Genome Atlas, the Cancer Cell Line Encyclopedia and manually uploaded information. Interactive tabular data visualization that facilitates the user-driven prioritization process forms a core component of Ordino. Detail views of selected items complement the exploration. Findings can be stored, shared and reproduced via the integrated session management. AVAILABILITY AND IMPLEMENTATION: Ordino is publicly available at https://ordino.caleydoapp.org. The source code is released at https://github.com/Caleydo/ordino under the Mozilla Public License 2.0. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Genômica , Neoplasias , Linhagem Celular Tumoral , Genoma , Humanos , Software
5.
Nature ; 511(7510): 428-34, 2014 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-25043047

RESUMO

Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and group 4 subgroup medulloblastomas account for most paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family proto-oncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1 or GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate 'enhancer hijacking' as an efficient mechanism driving oncogene activation in a childhood cancer.


Assuntos
Proteínas de Ligação a DNA/genética , Elementos Facilitadores Genéticos/genética , Variação Estrutural do Genoma/genética , Meduloblastoma/genética , Oncogenes/genética , Proteínas Proto-Oncogênicas/genética , Proteínas Repressoras/genética , Fatores de Transcrição/genética , Animais , Criança , Cromossomos Humanos Par 9/genética , Proteínas de Ligação a DNA/metabolismo , Humanos , Meduloblastoma/classificação , Meduloblastoma/patologia , Camundongos , Proteínas Proto-Oncogênicas/metabolismo , Proteínas Repressoras/metabolismo , Fatores de Transcrição/metabolismo
6.
Lancet Oncol ; 19(6): 785-798, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29753700

RESUMO

BACKGROUND: Medulloblastoma is associated with rare hereditary cancer predisposition syndromes; however, consensus medulloblastoma predisposition genes have not been defined and screening guidelines for genetic counselling and testing for paediatric patients are not available. We aimed to assess and define these genes to provide evidence for future screening guidelines. METHODS: In this international, multicentre study, we analysed patients with medulloblastoma from retrospective cohorts (International Cancer Genome Consortium [ICGC] PedBrain, Medulloblastoma Advanced Genomics International Consortium [MAGIC], and the CEFALO series) and from prospective cohorts from four clinical studies (SJMB03, SJMB12, SJYC07, and I-HIT-MED). Whole-genome sequences and exome sequences from blood and tumour samples were analysed for rare damaging germline mutations in cancer predisposition genes. DNA methylation profiling was done to determine consensus molecular subgroups: WNT (MBWNT), SHH (MBSHH), group 3 (MBGroup3), and group 4 (MBGroup4). Medulloblastoma predisposition genes were predicted on the basis of rare variant burden tests against controls without a cancer diagnosis from the Exome Aggregation Consortium (ExAC). Previously defined somatic mutational signatures were used to further classify medulloblastoma genomes into two groups, a clock-like group (signatures 1 and 5) and a homologous recombination repair deficiency-like group (signatures 3 and 8), and chromothripsis was investigated using previously established criteria. Progression-free survival and overall survival were modelled for patients with a genetic predisposition to medulloblastoma. FINDINGS: We included a total of 1022 patients with medulloblastoma from the retrospective cohorts (n=673) and the four prospective studies (n=349), from whom blood samples (n=1022) and tumour samples (n=800) were analysed for germline mutations in 110 cancer predisposition genes. In our rare variant burden analysis, we compared these against 53 105 sequenced controls from ExAC and identified APC, BRCA2, PALB2, PTCH1, SUFU, and TP53 as consensus medulloblastoma predisposition genes according to our rare variant burden analysis and estimated that germline mutations accounted for 6% of medulloblastoma diagnoses in the retrospective cohort. The prevalence of genetic predispositions differed between molecular subgroups in the retrospective cohort and was highest for patients in the MBSHH subgroup (20% in the retrospective cohort). These estimates were replicated in the prospective clinical cohort (germline mutations accounted for 5% of medulloblastoma diagnoses, with the highest prevalence [14%] in the MBSHH subgroup). Patients with germline APC mutations developed MBWNT and accounted for most (five [71%] of seven) cases of MBWNT that had no somatic CTNNB1 exon 3 mutations. Patients with germline mutations in SUFU and PTCH1 mostly developed infant MBSHH. Germline TP53 mutations presented only in childhood patients in the MBSHH subgroup and explained more than half (eight [57%] of 14) of all chromothripsis events in this subgroup. Germline mutations in PALB2 and BRCA2 were observed across the MBSHH, MBGroup3, and MBGroup4 molecular subgroups and were associated with mutational signatures typical of homologous recombination repair deficiency. In patients with a genetic predisposition to medulloblastoma, 5-year progression-free survival was 52% (95% CI 40-69) and 5-year overall survival was 65% (95% CI 52-81); these survival estimates differed significantly across patients with germline mutations in different medulloblastoma predisposition genes. INTERPRETATION: Genetic counselling and testing should be used as a standard-of-care procedure in patients with MBWNT and MBSHH because these patients have the highest prevalence of damaging germline mutations in known cancer predisposition genes. We propose criteria for routine genetic screening for patients with medulloblastoma based on clinical and molecular tumour characteristics. FUNDING: German Cancer Aid; German Federal Ministry of Education and Research; German Childhood Cancer Foundation (Deutsche Kinderkrebsstiftung); European Research Council; National Institutes of Health; Canadian Institutes for Health Research; German Cancer Research Center; St Jude Comprehensive Cancer Center; American Lebanese Syrian Associated Charities; Swiss National Science Foundation; European Molecular Biology Organization; Cancer Research UK; Hertie Foundation; Alexander and Margaret Stewart Trust; V Foundation for Cancer Research; Sontag Foundation; Musicians Against Childhood Cancer; BC Cancer Foundation; Swedish Council for Health, Working Life and Welfare; Swedish Research Council; Swedish Cancer Society; the Swedish Radiation Protection Authority; Danish Strategic Research Council; Swiss Federal Office of Public Health; Swiss Research Foundation on Mobile Communication; Masaryk University; Ministry of Health of the Czech Republic; Research Council of Norway; Genome Canada; Genome BC; Terry Fox Research Institute; Ontario Institute for Cancer Research; Pediatric Oncology Group of Ontario; The Family of Kathleen Lorette and the Clark H Smith Brain Tumour Centre; Montreal Children's Hospital Foundation; The Hospital for Sick Children: Sonia and Arthur Labatt Brain Tumour Research Centre, Chief of Research Fund, Cancer Genetics Program, Garron Family Cancer Centre, MDT's Garron Family Endowment; BC Childhood Cancer Parents Association; Cure Search Foundation; Pediatric Brain Tumor Foundation; Brainchild; and the Government of Ontario.


Assuntos
Biomarcadores Tumorais/genética , Neoplasias Cerebelares/genética , Metilação de DNA , Testes Genéticos/métodos , Mutação em Linhagem Germinativa , Meduloblastoma/genética , Modelos Genéticos , Adolescente , Adulto , Neoplasias Cerebelares/mortalidade , Neoplasias Cerebelares/patologia , Neoplasias Cerebelares/terapia , Criança , Pré-Escolar , Análise Mutacional de DNA , Feminino , Perfilação da Expressão Gênica , Predisposição Genética para Doença , Hereditariedade , Humanos , Lactente , Masculino , Meduloblastoma/mortalidade , Meduloblastoma/patologia , Meduloblastoma/terapia , Linhagem , Fenótipo , Valor Preditivo dos Testes , Intervalo Livre de Progressão , Estudos Prospectivos , Reprodutibilidade dos Testes , Estudos Retrospectivos , Fatores de Risco , Transcriptoma , Sequenciamento do Exoma , Adulto Jovem
7.
Nature ; 488(7409): 100-5, 2012 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-22832583

RESUMO

Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.


Assuntos
Neoplasias Cerebelares/genética , Genoma Humano/genética , Meduloblastoma/genética , Envelhecimento/genética , Sequência de Aminoácidos , Transformação Celular Neoplásica , Neoplasias Cerebelares/classificação , Neoplasias Cerebelares/diagnóstico , Neoplasias Cerebelares/patologia , Criança , Cromatina/metabolismo , Cromossomos Humanos/genética , RNA Helicases DEAD-box/genética , DNA Helicases/genética , Proteínas de Ligação a DNA/genética , Genômica , Proteínas Hedgehog/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Histona Desmetilases/genética , Humanos , Meduloblastoma/classificação , Meduloblastoma/diagnóstico , Meduloblastoma/patologia , Metilação , Mutação/genética , Taxa de Mutação , Proteínas de Neoplasias/genética , Proteínas Nucleares/genética , Proteínas de Fusão Oncogênica/genética , Receptores Patched , Receptor Patched-1 , Fosfoproteínas Fosfatases/genética , Poliploidia , Receptores de Superfície Celular/genética , Análise de Sequência de RNA , Transdução de Sinais , Proteínas com Domínio T/genética , Fatores de Transcrição/genética , Proteínas Wnt/metabolismo , beta Catenina/genética
8.
Nature ; 488(7409): 49-56, 2012 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-22832581

RESUMO

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-ß signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.


Assuntos
Neoplasias Cerebelares/classificação , Neoplasias Cerebelares/genética , Genoma Humano/genética , Variação Estrutural do Genoma/genética , Meduloblastoma/classificação , Meduloblastoma/genética , Proteínas de Transporte/genética , Neoplasias Cerebelares/metabolismo , Criança , Variações do Número de Cópias de DNA/genética , Duplicação Gênica/genética , Genes myc/genética , Genômica , Proteínas Hedgehog/metabolismo , Humanos , Meduloblastoma/metabolismo , NF-kappa B/metabolismo , Proteínas do Tecido Nervoso/genética , Proteínas de Fusão Oncogênica/genética , Proteínas/genética , RNA Longo não Codificante , Transdução de Sinais , Fator de Crescimento Transformador beta/metabolismo , Translocação Genética/genética
9.
Genome Res ; 24(7): 1193-208, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24714809

RESUMO

The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.


Assuntos
Drosophila melanogaster/genética , Variação Genética , Genoma de Inseto , Fenótipo , Animais , Cromatina/genética , Cromatina/metabolismo , Drosophila melanogaster/microbiologia , Feminino , Ligação Genética , Tamanho do Genoma , Estudo de Associação Genômica Ampla , Genótipo , Técnicas de Genotipagem , Sequenciamento de Nucleotídeos em Larga Escala , Mutação INDEL , Desequilíbrio de Ligação , Masculino , Anotação de Sequência Molecular , Polimorfismo de Nucleotídeo Único , Característica Quantitativa Herdável , Reprodutibilidade dos Testes
10.
Genome Res ; 23(3): 568-79, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23222910

RESUMO

Genomic structural variation (SV) is a major determinant for phenotypic variation. Although it has been extensively studied in humans, the nucleotide resolution structure of SVs within the widely used model organism Drosophila remains unknown. We report a highly accurate, densely validated map of unbalanced SVs comprising 8962 deletions and 916 tandem duplications in 39 lines derived from short-read DNA sequencing in a natural population (the "Drosophila melanogaster Genetic Reference Panel," DGRP). Most SVs (>90%) were inferred at nucleotide resolution, and a large fraction was genotyped across all samples. Comprehensive analyses of SV formation mechanisms using the short-read data revealed an abundance of SVs formed by mobile element and nonhomologous end-joining-mediated rearrangements, and clustering of variants into SV hotspots. We further observed a strong depletion of SVs overlapping genes, which, along with population genetics analyses, suggests that these SVs are often deleterious. We inferred several gene fusion events also highlighting the potential role of SVs in the generation of novel protein products. Expression quantitative trait locus (eQTL) mapping revealed the functional impact of our high-resolution SV map, with quantifiable effects at >100 genic loci. Our map represents a resource for population-level studies of SVs in an important model organism.


Assuntos
Drosophila melanogaster/genética , Genoma de Inseto , Variação Estrutural do Genoma , Análise de Sequência de DNA/métodos , Animais , Mapeamento Cromossômico , Feminino , Regulação da Expressão Gênica , Genótipo , Desequilíbrio de Ligação , Masculino , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
11.
Bioinformatics ; 28(18): i333-i339, 2012 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-22962449

RESUMO

MOTIVATION: The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs. RESULTS: We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity. AVAILABILITY: DELLY is available at www.korbel.embl.de/software.html CONTACT: tobias.rausch@embl.de.


Assuntos
Variação Estrutural do Genoma , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Software , Mapeamento Cromossômico/métodos , Genoma Humano , Genômica/métodos , Humanos , Deleção de Sequência
12.
Anal Chem ; 84(7): 3417-26, 2012 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-22390817

RESUMO

Mass spectrometry allows sensitive, automated, and high-throughput analysis of small molecules. In principle, tandem mass spectrometry allows us to identify "unknown" small molecules not in any database, but the automated interpretation of such data is in its infancy. Fragmentation trees have recently been introduced for the automated analysis of the fragmentation patterns of small molecules. We present a method for the automated comparison of such fragmentation patterns, based on aligning the compounds' fragmentation trees. We cluster compounds based solely on their fragmentation patterns and show a good agreement with known compound classes. Fragmentation pattern similarities are strongly correlated with the chemical similarity of molecules. We present a tool for searching a database for compounds with fragmentation pattern similar to an unknown sample compound. We apply this tool to metabolites from Icelandic poppy. Our method allows fully automated computational identification of small molecules that cannot be found in any database.


Assuntos
Espectrometria de Massas/métodos , Estatística como Assunto/métodos , Análise por Conglomerados , Bases de Dados Factuais , Papaver/química
13.
PLoS Comput Biol ; 6(11): e1000988, 2010 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-21085617

RESUMO

Copy-number variations (CNVs) are widespread in the human genome, but comprehensive assignments of integer locus copy-numbers (i.e., copy-number genotypes) that, for example, enable discrimination of homozygous from heterozygous CNVs, have remained challenging. Here we present CopySeq, a novel computational approach with an underlying statistical framework that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can incorporate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. We benchmarked CopySeq by genotyping 500 chromosome 1 CNV regions in 150 personal genomes sequenced at low-coverage. The assessed copy-number genotypes were highly concordant with our performed qPCR experiments (Pearson correlation coefficient 0.94), and with the published results of two microarray platforms (95-99% concordance). We further demonstrated the utility of CopySeq for analyzing gene regions enriched for segmental duplications by comprehensively inferring copy-number genotypes in the CNV-enriched >800 olfactory receptor (OR) human gene and pseudogene loci. CopySeq revealed that OR loci display an extensive range of locus copy-numbers across individuals, with zero to two copies in some OR loci, and two to nine copies in others. Among genetic variants affecting OR loci we identified deleterious variants including CNVs and SNPs affecting ~15% and ~20% of the human OR gene repertoire, respectively, implying that genetic variants with a possible impact on smell perception are widespread. Finally, we found that for several OR loci the reference genome appears to represent a minor-frequency variant, implying a necessary revision of the OR repertoire for future functional studies. CopySeq can ascertain genomic structural variation in specific gene families as well as at a genome-wide scale, where it may enable the quantitative evaluation of CNVs in genome-wide association studies involving high-throughput sequencing.


Assuntos
Variações do Número de Cópias de DNA , Genômica/métodos , Receptores Odorantes/genética , Mapeamento Cromossômico , Bases de Dados Genéticas , Variação Genética , Genética Populacional , Genoma , Genótipo , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Reação em Cadeia da Polimerase , Polimorfismo de Nucleotídeo Único , Análise de Componente Principal , Reprodutibilidade dos Testes , Análise de Sequência de DNA , Software , População Branca
14.
Cancer Immunol Res ; 7(11): 1891-1899, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31484656

RESUMO

Drugs targeting the programmed cell death protein 1 (PD-1) pathway are approved as therapies for an increasing number of cancer entities, including renal cell carcinoma. Despite a significant increase in overall survival, most treated patients do not show durable clinical responses. A combination of checkpoint inhibitors could provide a promising improvement. The aim of the study was to determine the most promising checkpoint blockade combination for renal cell carcinoma patients. Tumor-infiltrating lymphocytes (TIL) and autologous peripheral blood mononuclear cells (PBMC) were isolated from patients undergoing surgery for primary tumors. Cells were stained for multicolor flow cytometry to determine the (co)expression of five inhibitory receptors (iR), PD-1, LAG-3, Tim-3, BTLA, and CTLA-4, on T-cell populations. The function of these TILs was assessed by intracellular cytokine staining after in vitro stimulation in the presence or absence of PD-1 ± LAG-3 or Tim-3-specific antibodies. Although the percentage of iR+ T cells was low in PBMCs, both CD4+ and CD8+ T cells showed increased frequencies of PD-1+, LAG-3+, and Tim-3+ cells on TILs. The most frequent iR combination was PD-1 and LAG-3 on both CD4+ and CD8+ TILs. Blockade of PD-1 resulted in significant LAG-3, but not Tim-3, upregulation. The dual blockade of PD-1 and LAG-3, but not PD-1 and Tim-3, led to increased IFNγ release upon in vitro stimulation. Together, these data suggest that dual blockade of PD-1 and LAG-3 is a promising checkpoint blockade combination for renal cell carcinoma.


Assuntos
Antígenos CD/imunologia , Carcinoma de Células Renais/imunologia , Neoplasias Renais/imunologia , Linfócitos do Interstício Tumoral/imunologia , Receptor de Morte Celular Programada 1/imunologia , Subpopulações de Linfócitos T/imunologia , Idoso , Anticorpos Bloqueadores/imunologia , Antígenos CD/metabolismo , Carcinoma de Células Renais/patologia , Receptores Coestimuladores e Inibidores de Linfócitos T/imunologia , Receptores Coestimuladores e Inibidores de Linfócitos T/metabolismo , Feminino , Humanos , Interferon gama/metabolismo , Neoplasias Renais/patologia , Leucócitos Mononucleares/imunologia , Leucócitos Mononucleares/metabolismo , Linfócitos do Interstício Tumoral/metabolismo , Masculino , Pessoa de Meia-Idade , Receptor de Morte Celular Programada 1/metabolismo , Subpopulações de Linfócitos T/metabolismo , Proteína do Gene 3 de Ativação de Linfócitos
15.
Sci Rep ; 9(1): 11661, 2019 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-31406271

RESUMO

SMARCA4/BRG1 and SMARCA2/BRM, the two mutually exclusive catalytic subunits of the BAF complex, display a well-established synthetic lethal relationship in SMARCA4-deficient cancers. Using CRISPR-Cas9 screening, we identify SMARCA4 as a novel dependency in SMARCA2-deficient esophageal squamous cell carcinoma (ESCC) models, reciprocal to the known synthetic lethal interaction. Restoration of SMARCA2 expression alleviates the dependency on SMARCA4, while engineered loss of SMARCA2 renders ESCC models vulnerable to concomitant depletion of SMARCA4. Dependency on SMARCA4 is linked to its ATPase activity, but not to bromodomain function. We highlight the relevance of SMARCA4 as a drug target in esophageal cancer using an engineered ESCC cell model harboring a SMARCA4 allele amenable to targeted proteolysis and identify SMARCA4-dependent cell models with low or absent SMARCA2 expression from additional tumor types. These findings expand the concept of SMARCA2/SMARCA4 paralog dependency and suggest that pharmacological inhibition of SMARCA4 represents a novel therapeutic opportunity for SMARCA2-deficient cancers.


Assuntos
DNA Helicases/antagonistas & inibidores , Neoplasias Esofágicas/tratamento farmacológico , Carcinoma de Células Escamosas do Esôfago/tratamento farmacológico , Proteínas Nucleares/antagonistas & inibidores , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/genética , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Sistemas CRISPR-Cas/genética , Linhagem Celular Tumoral , Sobrevivência Celular/genética , DNA Helicases/genética , Epigênese Genética , Neoplasias Esofágicas/genética , Neoplasias Esofágicas/patologia , Carcinoma de Células Escamosas do Esôfago/genética , Carcinoma de Células Escamosas do Esôfago/patologia , Edição de Genes , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Técnicas de Silenciamento de Genes , Técnicas de Inativação de Genes , Humanos , Mutação com Perda de Função , Terapia de Alvo Molecular/métodos , Proteínas Nucleares/genética , RNA Guia de Cinetoplastídeos/genética , RNA Interferente Pequeno/metabolismo , Mutações Sintéticas Letais , Fatores de Transcrição/deficiência
16.
Bioinformatics ; 23(13): 1708-9, 2007 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-17463016

RESUMO

UNLABELLED: Faspad is a user-friendly tool that detects candidates for linear signaling pathways in protein interaction networks based on an approach by Scott et al. (Journal of Computational Biology, 2006). Using recent algorithmic insights, it can solve the underlying NP-hard problem quite fast: for protein networks of typical size (several thousand nodes), pathway candidates of length up to 13 proteins can be found within seconds and with a 99.9% probability of optimality. Faspad graphically displays all candidates that are found; for evaluation and comparison purposes, an overlay of several candidates and the surrounding network context can also be shown. AVAILABILITY: Faspad is available as free software under the GPL license at http://theinf1.informatik.uni-jena.de/faspad/ and runs under Linux and Windows.


Assuntos
Algoritmos , Expressão Gênica/fisiologia , Modelos Biológicos , Mapeamento de Interação de Proteínas/métodos , Proteoma/metabolismo , Transdução de Sinais/fisiologia , Software , Simulação por Computador
17.
Artigo em Inglês | MEDLINE | ID: mdl-30136970

RESUMO

Storing analytical provenance generates a knowledge base with a large potential for recalling previous results and guiding users in future analyses. However, without extensive manual creation of meta information and annotations by the users, search and retrieval of analysis states can become tedious. We present KnowledgePearls, a solution for efficient retrieval of analysis states that are structured as provenance graphs containing automatically recorded user interactions and visualizations. As a core component, we describe a visual interface for querying and exploring analysis states based on their similarity to a partial definition of a requested analysis state. Depending on the use case, this definition may be provided explicitly by the user by formulating a search query or inferred from given reference states. We explain our approach using the example of efficient retrieval of demographic analyses by Hans Rosling and discuss our implementation for a fast look-up of previous states. Our approach is independent of the underlying visualization framework. We discuss the applicability for visualizations which are based on the declarative grammar Vega and we use a Vega-based implementation of Gapminder as guiding example. We additionally present a biomedical case study to illustrate how KnowledgePearls facilitates the exploration process by recalling states from earlier analyses.

18.
Nat Genet ; 49(1): 65-74, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27869826

RESUMO

Extensive prior research focused on somatic copy-number alterations (SCNAs) affecting cancer genes, yet the extent to which recurrent SCNAs exert their influence through rearrangement of cis-regulatory elements (CREs) remains unclear. Here we present a framework for inferring cancer-related gene overexpression resulting from CRE reorganization (e.g., enhancer hijacking) by integrating SCNAs, gene expression data and information on topologically associating domains (TADs). Analysis of 7,416 cancer genomes uncovered several pan-cancer candidate genes, including IRS4, SMARCA1 and TERT. We demonstrate that IRS4 overexpression in lung cancer is associated with recurrent deletions in cis, and we present evidence supporting a tumor-promoting role. We additionally pursued cancer-type-specific analyses and uncovered IGF2 as a target for enhancer hijacking in colorectal cancer. Recurrent tandem duplications intersecting with a TAD boundary mediate de novo formation of a 3D contact domain comprising IGF2 and a lineage-specific super-enhancer, resulting in high-level gene activation. Our framework enables systematic inference of CRE rearrangements mediating dysregulation in cancer.


Assuntos
Variações do Número de Cópias de DNA/genética , Elementos Facilitadores Genéticos/genética , Regulação Neoplásica da Expressão Gênica , Proteínas Substratos do Receptor de Insulina/genética , Fator de Crescimento Insulin-Like II/genética , Neoplasias/genética , Estudos de Associação Genética , Predisposição Genética para Doença , Humanos , Regiões Promotoras Genéticas
19.
Curr Biol ; 26(1): 38-51, 2016 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-26687625

RESUMO

Embryogenesis is remarkably robust to segregating mutations and environmental variation; under a range of conditions, embryos of a given species develop into stereotypically patterned organisms. Such robustness is thought to be conferred, in part, through elements within regulatory networks that perform similar, redundant tasks. Redundant enhancers (or "shadow" enhancers), for example, can confer precision and robustness to gene expression, at least at individual, well-studied loci. However, the extent to which enhancer redundancy exists and can thereby have a major impact on developmental robustness remains unknown. Here, we systematically assessed this, identifying over 1,000 predicted shadow enhancers during Drosophila mesoderm development. The activity of 23 elements, associated with five genes, was examined in transgenic embryos, while natural structural variation among individuals was used to assess their ability to buffer against genetic variation. Our results reveal three clear properties of enhancer redundancy within developmental systems. First, it is much more pervasive than previously anticipated, with 64% of loci examined having shadow enhancers. Their spatial redundancy is often partial in nature, while the non-overlapping function may explain why these enhancers are maintained within a population. Second, over 70% of loci do not follow the simple situation of having only two shadow enhancers-often there are three (rols), four (CadN and ade5), or five (Traf1), at least one of which can be deleted with no obvious phenotypic effects. Third, although shadow enhancers can buffer variation, patterns of segregating variation suggest that they play a more complex role in development than generally considered.


Assuntos
Elementos Facilitadores Genéticos , Regulação da Expressão Gênica no Desenvolvimento , Animais , Drosophila , Desenvolvimento Embrionário/genética , Transcrição Gênica
20.
G3 (Bethesda) ; 3(8): 1213-24, 2013 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-23550136

RESUMO

HeLa is the most widely used model cell line for studying human cellular and molecular biology. To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. Effective design and interpretation of molecular genetic studies performed using HeLa cells require accurate genomic information. Here we present a detailed genomic and transcriptomic characterization of a HeLa cell line. We performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile. Segmentation of the genome according to copy number revealed a remarkably high level of aneuploidy and numerous large structural variants at unprecedented resolution. Some of the extensive genomic rearrangements are indicative of catastrophic chromosome shattering, known as chromothripsis. Our analysis of the HeLa gene expression profile revealed that several pathways, including cell cycle and DNA repair, exhibit significantly different expression patterns from those in normal human tissues. Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins. This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology.


Assuntos
Genoma Humano , Alelos , Variações do Número de Cópias de DNA , Bases de Dados Genéticas , Frequência do Gene , Genômica , Células HeLa , Humanos , Modelos Biológicos , Mutação , Interferência de RNA , Análise de Sequência de DNA , Análise de Sequência de RNA , Transcriptoma
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