title: Multiomics approach showing genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric brain tumors.
abstract: OBJECTIVE
  Based on copy number alterations and transcriptional profiles, the posterior fossa tumors (medulloblastoma (MB), ependymoma and pilocytic astrocytoma) have been classified into various subgroups. The study design was aimed to identify and catalog genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric posterior fossa tumors and matched control tissue through Molecular Inversion Probe (MIP) Based and Human Transcriptome Array.
  
  
  METHODS
  MIP based OncoScan Array and Human Transcriptome Array 2.0 were used to molecularly-categorize histopathologically and immunohistochemically proven tumor samples on the basis of copy number variations and altered gene expression patterns and/or alternative splicing events.
  
  
  RESULTS
  Based on molecular, histopathological/immunohistochemical and age-dependent factors MB was subgrouped into group-3 MB, Wnt and SHH; ependymoma into balanced, numerical and structural/anaplastic; and pilocytic astrocytoma was stratified age-dependently. Compared with the vermis tissue of MB, the vermis tissue of ependymoma showed higher levels of gain and losses compared with their counter tumor parts implicating metastasis within the confined region. Group-3 MB and anaplastic ependymoma represented highest differentially expressed genes both at gene and exon levels in the CN altered regions compared with other subgroups of MB and ependymoma respectively.
  
  
  CONCLUSIONS
  This multiomics approach based molecular characterization of posterior fossa tumors together with clinical and histopathological factors may help us in the area of personalized medicine.
authors.affiliation: Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow 226 003, India. Electronic address: neetuaashi@yahoo.com.
authors.forename: Neetu
authors.initials: N
authors.lastname: Singh
authors.affiliation: Imperial Life Sciences, 463 Phase City 2nd, Sector 37, Gurgaon, Haryana 122001, India.
authors.forename: Dinesh Kumar
authors.initials: DK
authors.lastname: Sahu
authors.affiliation: Department of Biochemistry, King George's Medical University, Lucknow 226 003, India.
authors.forename: Archana
authors.initials: A
authors.lastname: Mishra
authors.affiliation: Department of Pathology, King George's Medical University, Lucknow 226 003, India.
authors.forename: Preeti
authors.initials: P
authors.lastname: Agarwal
authors.affiliation: Department of Pathology, King George's Medical University, Lucknow 226 003, India.
authors.forename: Madhu Mati
authors.initials: MM
authors.lastname: Goel
authors.affiliation: Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India.
authors.forename: Anil
authors.initials: A
authors.lastname: Chandra
authors.affiliation: Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India.
authors.forename: Sunil Kumar
authors.initials: SK
authors.lastname: Singh
authors.affiliation: Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India.
authors.forename: Chhitij
authors.initials: C
authors.lastname: Srivastava
authors.affiliation: Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India.
authors.forename: Bal Krishna
authors.initials: BK
authors.lastname: Ojha
authors.affiliation: Department of Pediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Devendra Kumar
authors.initials: DK
authors.lastname: Gupta
authors.affiliation: Department of Surgical Oncology, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
authors.forename: Ravi
authors.initials: R
authors.lastname: Kant
mesh_terms: D000293:Adolescent; D001932:Brain Neoplasms / Q000235:genetics*; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D056915:DNA Copy Number Variations / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D007194:India; D007223:Infant; D009154:Mutation / Q000235:genetics
keywords: Human Transcriptome Array 2.0; Molecular Inversion Probe Based Array; Pediatric posterior fossa tumors