The genomic landscape of tuberous sclerosis complex
暂无分享,去创建一个
Orrin Devinsky | Hope Northrup | Juliann Shih | Julie Koeman | Hui Shen | Wanding Zhou | Andrew D Cherniack | D. Weisenberger | Hui Shen | O. Devinsky | A. Cherniack | Wanding Zhou | J. Shih | S. Cottingham | Julie M. Koeman | J. MacKeigan | D. Krueger | H. Northrup | Kristin E Dittenhafer-Reed | M. Bowman | Jeffrey P MacKeigan | Daniel J Weisenberger | Katie R. Martin | Darcy A Krueger | Mary E Winn | S. Deroos | Katie R Martin | K. Au | Megan J Bowman | Kit Sing Au | Kellie A Sisson | Sandra L Cottingham | Steven T DeRoos | M. Winn | Kristin E. Dittenhafer-Reed | Kellie A. Sisson
[1] Mauricio O. Carneiro,et al. From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.
[2] Fred A. Wright,et al. Integrated study of copy number states and genotype calls using high-density SNP arrays , 2009, Nucleic acids research.
[3] S. Verhoef,et al. High rate of mosaicism in tuberous sclerosis complex. , 1999, American journal of human genetics.
[4] J. Wheless,et al. Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States , 2007, Genetics in Medicine.
[5] H. Northrup,et al. Tuberous Sclerosis Complex Consensus Conference: Revised Clinical Diagnostic Criteria , 1998, Journal of child neurology.
[6] H. Onda,et al. Heterozygosity for the tuberous sclerosis complex (TSC) gene products results in increased astrocyte numbers and decreased p27-Kip1 expression in TSC2+/− cells , 2002, Oncogene.
[7] A. Wilm,et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets , 2012, Nucleic acids research.
[8] D. Kwiatkowski,et al. Sun exposure causes somatic second-hit mutations and angiofibroma development in tuberous sclerosis complex. , 2014, Human molecular genetics.
[9] A. Stemmer-Rachamimov,et al. Survey of somatic mutations in tuberous sclerosis complex (TSC) hamartomas suggests different genetic mechanisms for pathogenesis of TSC lesions. , 2001, American journal of human genetics.
[10] Gary D Bader,et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types , 2013, Scientific Reports.
[11] A. McMahon,et al. Atlas of gene expression in the developing kidney at microanatomic resolution. , 2008, Developmental cell.
[12] A. Byars,et al. Everolimus for subependymal giant-cell astrocytomas in tuberous sclerosis. , 2010, The New England journal of medicine.
[13] H. Kazazian. Processed pseudogene insertions in somatic cells , 2014, Mobile DNA.
[14] G. Zamboni,et al. The Perivascular Epithelioid Cell and Related Lesions , 1997 .
[15] D. Kwiatkowski,et al. Mosaicism in tuberous sclerosis as a potential cause of the failure of molecular diagnosis. , 1999, The New England journal of medicine.
[16] C. Perou,et al. Allele-specific copy number analysis of tumors , 2010, Proceedings of the National Academy of Sciences.
[17] A. Wilfong,et al. Long-term treatment of epilepsy with everolimus in tuberous sclerosis , 2016, Neurology.
[18] R. Pieters,et al. Low frequency of DNMT3A mutations in pediatric AML, and the identification of the OCI-AML3 cell line as an in vitro model , 2012, Leukemia.
[19] T. Sepp,et al. Loss of heterozygosity in tuberous sclerosis hamartomas. , 1996, Journal of medical genetics.
[20] N. Rensing,et al. Inflammatory mechanisms contribute to the neurological manifestations of tuberous sclerosis complex , 2015, Neurobiology of Disease.
[21] W. Shi,et al. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote , 2013, Nucleic acids research.
[22] A. Green,et al. The tuberous sclerosis gene on chromosome 9q34 acts as a growth suppressor. , 1994, Human molecular genetics.
[23] Hongbing Zhang,et al. Pathogenesis of Tuberous Sclerosis Subependymal Giant Cell Astrocytomas: Biallelic Inactivation of TSC1 or TSC2 Leads to mTOR Activation , 2004, Journal of neuropathology and experimental neurology.
[24] Ravi Bhargava,et al. Cortical tubers, cognition, and epilepsy in tuberous sclerosis. , 2011, Pediatric neurology.
[25] R. Lazarus,et al. Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations , 2007, Human Genetics.
[26] Steven J. M. Jones,et al. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. , 2016, The New England journal of medicine.
[27] T. Robbins,et al. Renal Involvement in Tuberous Sclerosis , 1991, Annals of the New York Academy of Sciences.
[28] Andrew Menzies,et al. Processed pseudogenes acquired somatically during cancer development , 2014, Nature Communications.
[29] Y. Ben-Ari,et al. Selective suppression of excessive GluN2C expression rescues early epilepsy in a tuberous sclerosis murine model , 2014, Nature Communications.
[30] P. Laird,et al. Low-level processing of Illumina Infinium DNA Methylation BeadArrays , 2013, Nucleic acids research.
[31] Vincent J Schmithorst,et al. Sirolimus for angiomyolipoma in tuberous sclerosis complex or lymphangioleiomyomatosis. , 2008, The New England journal of medicine.
[32] J. Brugarolas,et al. Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications , 2013, Nature Protocols.
[33] D. Kwiatkowski,et al. Mutational analysis in a cohort of 224 tuberous sclerosis patients indicates increased severity of TSC2, compared with TSC1, disease in multiple organs. , 2001, American journal of human genetics.
[34] G. Getz,et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers , 2011, Genome Biology.
[35] P. V. van Rijen,et al. Gene Expression Analysis of Tuberous Sclerosis Complex Cortical Tubers Reveals Increased Expression of Adhesion and Inflammatory Factors , 2009, Brain pathology.
[36] A. Engel,et al. Cortical Tuber Count: A Biomarker Indicating Neurologic Severity of Tuberous Sclerosis Complex , 1997, Journal of child neurology.
[37] Kai Ye,et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..
[38] M. Baybis,et al. Expression of ICAM-1, TNF-α, NFκB, and MAP kinase in tubers of the tuberous sclerosis complex , 2003, Neurobiology of Disease.
[39] O. Hofmann,et al. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research , 2016, Nucleic acids research.
[40] B. Scheithauer,et al. Allelic loss is frequent in tuberous sclerosis kidney lesions but rare in brain lesions. , 1996, American journal of human genetics.
[41] A. Fernandez-Flores. Evidence on the neural crest origin of PEComas. , 2011, Romanian journal of morphology and embryology = Revue roumaine de morphologie et embryologie.
[42] S. Thomas,et al. Identification and characterization of the tuberous sclerosis gene on chromosome 16 , 1993, Cell.
[43] Charity W. Law,et al. voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.
[44] Matthew E. Ritchie,et al. limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.
[45] Doron Lancet,et al. GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data , 2016, Omics : a journal of integrative biology.
[46] E. Aronica,et al. Inflammatory processes in cortical tubers and subependymal giant cell tumors of tuberous sclerosis complex , 2008, Epilepsy Research.
[47] J. Osborne,et al. Epidemiology of Tuberous Sclerosis , 1991, Annals of the New York Academy of Sciences.
[48] O. Devinsky,et al. Severity of manifestations in tuberous sclerosis complex in relation to genotype , 2014, Epilepsia.
[49] Aaron R. Quinlan,et al. GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations , 2013, PLoS Comput. Biol..
[50] E. Thiele,et al. Efficacy and safety of everolimus for subependymal giant cell astrocytomas associated with tuberous sclerosis complex (EXIST-1): a multicentre, randomised, placebo-controlled phase 3 trial , 2013, The Lancet.
[51] A. Ouweland,et al. Mutational analysis of the TSC1 and TSC2 genes in a diagnostic setting: genotype – phenotype correlations and comparison of diagnostic DNA techniques in Tuberous Sclerosis Complex , 2005, European Journal of Human Genetics.
[52] D. Krueger,et al. Tuberous Sclerosis Complex Surveillance and Management: Recommendations of the 2012 International Tuberous Sclerosis Complex Consensus Conference , 2013, Pediatric neurology.
[53] C. Crowson,et al. Causes of death in patients with tuberous sclerosis. , 1991, Mayo Clinic proceedings.
[54] A. Sivachenko,et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.
[55] P. Crino,et al. The tuberous sclerosis complex. , 2006, The New England journal of medicine.
[56] P. Argani,et al. Cathepsin K expression in the spectrum of perivascular epithelioid cell (PEC) lesions of the kidney , 2012, Modern Pathology.
[57] S Povey,et al. Identification of the tuberous sclerosis gene TSC1 on chromosome 9q34. , 1997, Science.
[58] E. Aronica,et al. Fetal Brain Lesions in Tuberous Sclerosis Complex: TORC1 Activation and Inflammation , 2013, Brain pathology.
[59] Alcino J. Silva,et al. Reversal of learning deficits in a Tsc2+/− mouse model of tuberous sclerosis , 2008, Nature Medicine.
[60] Wei Shi,et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..
[61] J. Krischer,et al. Efficacy and safety of sirolimus in lymphangioleiomyomatosis. , 2011, The New England journal of medicine.
[62] Ling Lin,et al. Mosaic and Intronic Mutations in TSC1/TSC2 Explain the Majority of TSC Patients with No Mutation Identified by Conventional Testing , 2015, PLoS genetics.
[63] David Chen,et al. Everolimus for angiomyolipoma associated with tuberous sclerosis complex or sporadic lymphangioleiomyomatosis (EXIST-2): a multicentre, randomised, double-blind, placebo-controlled trial , 2013, The Lancet.
[64] W. Stanford,et al. The neural crest lineage as a driver of disease heterogeneity in Tuberous Sclerosis Complex and Lymphangioleiomyomatosis , 2014, Front. Cell Dev. Biol..
[65] G. Dressler,et al. The genetics and epigenetics of kidney development. , 2013, Seminars in nephrology.
[66] B. Scheithauer,et al. Markers of cellular proliferation are expressed in cortical tubers , 2003, Annals of neurology.
[67] F. Cunningham,et al. The Ensembl Variant Effect Predictor , 2016, Genome Biology.
[68] J. Xu,et al. Tsc1 mutant neural stem/progenitor cells exhibit migration deficits and give rise to subependymal lesions in the lateral ventricle. , 2011, Genes & development.
[69] G. Watkins,et al. Tuberin and hamartin are aberrantly expressed and linked to clinical outcome in human breast cancer: the role of promoter methylation of TSC genes. , 2005, European journal of cancer.
[70] J. Cheadle,et al. Cognitive deficits in Tsc1+/−mice in the absence of cerebral lesions and seizures , 2007, Annals of neurology.
[71] J. Blenis,et al. Molecular mechanisms of mTOR-mediated translational control , 2009, Nature Reviews Molecular Cell Biology.
[72] Ash A. Alizadeh,et al. Robust enumeration of cell subsets from tissue expression profiles , 2015, Nature Methods.
[73] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[74] Zechen Chong,et al. TransVar: a multilevel variant annotator for precision genomics , 2015, Nature Methods.
[75] J. García-Verdugo,et al. Sustained activation of mTOR pathway in embryonic neural stem cells leads to development of tuberous sclerosis complex-associated lesions. , 2011, Cell stem cell.
[76] A. Knudson. Mutation and cancer: statistical study of retinoblastoma. , 1971, Proceedings of the National Academy of Sciences of the United States of America.
[77] P. Finan,et al. TBC1D7 is a third subunit of the TSC1-TSC2 complex upstream of mTORC1. , 2012, Molecular cell.
[78] Li Ding,et al. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes , 2013, Genome Biology.
[79] Hesheng Liu,et al. Decreased language laterality in tuberous sclerosis complex: A relationship between language dominance and tuber location as well as history of epilepsy , 2012, Epilepsy & Behavior.
[80] M. Wigler,et al. Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.
[81] S. Bosari,et al. Growth Factors , Cytokines , Cell Cycle Molecules The Methylation of the TSC 2 Promoter Underlies the Abnormal Growth of TSC 2 Angiomyolipoma-Derived Smooth Muscle Cells , 2009 .
[82] M. DePristo,et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.
[83] Ben-Ari FuchsShani,et al. GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data , 2016 .
[84] Trevor J Pugh,et al. Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development , 2016, PLoS genetics.