Article thumbnail

Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing

By Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew JG Simpson and Robert L Strausberg
Topics: Research
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:3156953
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles

Citations

  1. (2007). A: Widespread monoallelic expression on human autosomes. Science
  2. AG: High incidence of MGMT and RARbeta promoter methylation in primary glioblastomas: association with histopathological characteristics, inflammatory mediators and clinical outcome.
  3. (2008). al: An integrated genomic analysis of human glioblastoma multiforme. Science
  4. (2009). al: Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature
  5. (2007). al: Genome-wide association study identifies novel breast cancer susceptibility loci. Nature
  6. (2007). al: The genomic landscapes of human breast and colorectal cancers. Science
  7. al: The landscape of somatic copy-number alteration across human cancers.
  8. (2004). Allele-specific gene expression uncovered. Trends Genet
  9. (2007). Allele-specific histone modifications regulate expression of the Dlk1-Gtl2 imprinted domain. Genomics
  10. (2008). Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer. PLoS Biol
  11. (2008). Cancer genomics and genetics of FGFR2.
  12. Catalogue of Somatic Mutations in Cancer - COSMIC.
  13. (2007). Chanock SJ: A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet
  14. (2007). de la Chapelle A, Plass C: Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia. Cell
  15. (2008). de la Chapelle A: Germline allele-specific expression of TGFBR1 confers an increased risk of colorectal cancer. Science
  16. (2007). Dimri GP: Mel-18 acts as a tumor suppressor by repressing Bmi-1 expression and downregulating Akt activity in breast cancer cells. Cancer Res
  17. (2000). DM: Association between loss of heterozygosity of BRCA1 and BRCA2 and morphological attributes of sporadic breast cancer.
  18. (2009). ES: High-resolution mapping of copynumber alterations with massively parallel sequencing. Nat Methods
  19. et al: A comprehensive catalogue of somatic mutations from a human cancer genome.
  20. et al: Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. PLoS One 5:e9317.
  21. (2004). Foulkes WD: BRCA1 and BRCA2: 1994 and beyond. Nat Rev Cancer
  22. (2005). Futscher BW: Epigenetic silencing of DSC3 is a common event in human breast cancer. Breast Cancer Res
  23. (2004). Gazdar AF: Aberrant methylation of trail decoy receptor genes is frequent in multiple tumor types.
  24. (2008). Genetic instability caused by loss of MutS homologue 3 in human colorectal cancer. Cancer Res
  25. (2009). GM: Digital RNA allelotyping reveals tissuespecific and allele-specific gene expression in human. Nat Methods
  26. (2008). Hudson TJ: Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet
  27. (1997). Ito H: PRLTS gene alterations in human prostate cancer.
  28. (2007). JH: Aberrant hypermethylation of the FGFR2 gene in human gastric cancer cell lines. Biochem Biophys Res Commun
  29. (2010). JK: Understanding mechanisms underlying human gene expression variation with RNA sequencing.
  30. (2005). Kemp CJ: Tumor suppressor genetics. Carcinogenesis
  31. (2002). Kinzler KW: Allelic variation in human gene expression. Science
  32. (2003). MP: Allelic variation in gene expression is common in the human genome. Genome Res
  33. (2007). MR: Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res
  34. MR: Signatures of mutation and selection in the cancer genome.
  35. (2002). MYEOV, a gene at 11q13, is coamplified with CCND1, but epigenetically inactivated in a subset of esophageal squamous cell carcinomas.
  36. (2009). of 14Identification of regions correlating MGMT promoter methylation and gene expression in glioblastomas. Neuro Oncol
  37. (2008). P: BCR expression is decreased in meningiomas showing loss of heterozygosity of 22q within a new minimal deletion region. Cancer Genet Cytogenet
  38. (2008). Protein phosphatase and TRAIL receptor genes as new candidate tumor genes on chromosome 8p in prostate cancer. Cancer Genomics Proteomics
  39. (2004). Radvanyi F: Inhibition of human bladder tumour cell growth by fibroblast growth factor receptor 2b is independent of its kinase activity. Involvement of the carboxy-terminal region of the receptor. Oncogene
  40. (1999). Radvanyi F: Tumour suppressive properties of fibroblast growth factor receptor 2-IIIb in human bladder cancer. Oncogene
  41. (2009). RL: Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci USA
  42. (1993). Role for DNA methylation in genomic imprinting. Nature
  43. (2009). Sanada Y: Methylation of the MGMT gene is frequently detected in advanced gastric carcinoma. Anticancer Res
  44. (2009). Sanada Y: MGMT gene is aberrantly methylated from the early stages of colorectal cancers. Hepatogastroenterology
  45. (2006). Scherneck S: Genetic background of different cancer cell lines influences the gene set involved in chromosome 8 mediated breast tumor suppression. Genes Chromosomes Cancer
  46. (2007). Syvanen AC: Allelic imbalance in gene expression as a guide to cisacting regulatory single nucleotide polymorphisms in cancer cells. Nucleic Acids Res
  47. The Single Nucleotide Polymorphism database (dbSNP).
  48. (2008). Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc Natl Acad Sci USA
  49. Tsung EF, et al: A small-cell lung cancer genome with complex signatures of tobacco exposure.
  50. (2005). Vasicek TJ: An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res
  51. (2008). Velculescu VE: Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci USA
  52. (2006). Velculescu VE: The consensus coding sequences of human breast and colorectal cancers. Science
  53. (2002). Vogelstein B: Small changes in expression affect predisposition to tumorigenesis. Nat Genet