Childhood Cancer Data Initiative Annual Symposium (Abstract Registration): Submission #86

serial: '86'
sid: '193899'
uuid: aecd4801-d974-4aca-82d9-6a7553e21359
uri: /nci/ccdisymposium/abstract
created: '1788551142'
completed: '1788554480'
changed: '1788554480'
in_draft: '0'
current_page: ''
remote_addr: 10.208.24.244
uid: '0'
langcode: en
webform_id: ccdi_symposium_abstract
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entity_id: '2139'
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notes: ''
metatag: meta
data:
  authors_:
    - add_author_degree: Masters
      add_author_first_name: Vineela
      add_author_last_name: Gangalapudi
      add_author_middle: ''
      add_author_organization: 'ABCS, FNLCR, NCI Genetics Branch'
    - add_author_degree: Ph.D.
      add_author_first_name: 'Hsien Chao'
      add_author_last_name: Chou
      add_author_middle: ''
      add_author_organization: 'NCI Genetics Branch'
    - add_author_degree: Masters
      add_author_first_name: Xinyu
      add_author_last_name: Wen
      add_author_middle: ''
      add_author_organization: 'ABCS, FNLCR, NCI Genetics Branch'
    - add_author_degree: Ph.D.
      add_author_first_name: Jun
      add_author_last_name: Wei
      add_author_middle: ''
      add_author_organization: 'NCI Genetics Branch'
    - add_author_degree: M.D.
      add_author_first_name: Javed
      add_author_last_name: Khan
      add_author_middle: ''
      add_author_organization: 'NCI Genetics Branch'
    - add_author_degree: 'Bachelor of Engineering'
      add_author_first_name: Srujan
      add_author_last_name: Boppana
      add_author_middle: ''
      add_author_organization: 'NCI CBIIT'
    - add_author_degree: 'Bachelors in Computer Science'
      add_author_first_name: Lauren
      add_author_last_name: Funston
      add_author_middle: ''
      add_author_organization: 'NCI CBIIT'
    - add_author_degree: Ph.D.
      add_author_first_name: Subhashini
      add_author_last_name: Jagu
      add_author_middle: ''
      add_author_organization: 'Office of Data Sharing, NCI'
    - add_author_degree: Masters
      add_author_first_name: Simone
      add_author_last_name: Kats
      add_author_middle: ''
      add_author_organization: 'Office of Data Sharing, NCI'
    - add_author_degree: Masters
      add_author_first_name: Bahar
      add_author_last_name: Sayoldin
      add_author_middle: ''
      add_author_organization: 'FNLCR, Office of Data Sharing, NCI'
    - add_author_degree: Ph.D.
      add_author_first_name: Catherine
      add_author_last_name: Bullen
      add_author_middle: ''
      add_author_organization: 'FNLCR, Office of Data Sharing, NCI'
  abstract: |-
    NCI’s Childhood Cancer Data Initiative(CCDI) is assembling high-value pediatric cancer datasets, creating a critical need for scalable, reproducible infrastructure to transform them into harmonized, interpretable, and reusable results. The Integrated Oncogenomics Portal(IOCP) addresses this need through a cloud-native analysis pipeline and data portal that identify clinically and biologically relevant genomic alterations and enable interactive exploration at the patient, cohort, and cancer-type levels. 

    The first component is a nextflow pipeline, with parallel hg19/hg38 builds, covering RNA and DNA analysis: somatic-germline variant calling, copy-number, fusions, TMB, MSI, mutational signatures, HLA/neoantigen prediction. It is version-controlled and portable across cloud platforms; genomic datasets can be read directly from their source location without the need to transfer. We are currently processing the PediatricMATCH cohort(phs002883), followed by BeatAML(phs002599), MCI(phs002790), and Oncokids(phs002518). 

    The second component disseminates results through cloud oncogenomics database enabling case and cohort-level exploration, interactive-IGV, survival-analyses, and AVIA annotation integrating genomic, population, functional, cancer-specific, and clinical evidence for variant interpretation and prioritization. Pipeline results are also published to CCDI cBioPortal Cancer Data Explore for standardized OncoPrint visualization and cross-cohort queries. By integrating CCDI cohorts with published pediatric cancer genomic datasets, IOCP combines analytical depth with broad interoperability. 

    IOCP provides a reproducible framework for advancing CCDI’s goal of interoperable pediatric cancer research through harmonized and discoverable genomic results. Beyond CCDI cohorts, the database integrates published pediatric cancer genomics data and offers an LLM-enabled conversational interface letting users query in natural language and receive responses grounded in IOCP data. 
  abstract_title_: 'The Integrated Oncogenomics Portal (IOCP): A Cloud-Native Pipeline and Database for Processing and Sharing CCDI & other Childhood Cancer Genomics Data '
  email_address_: vineela.gangalapudi@nih.gov
  institution_: 'ABCS, FNLCR, NCI Genetics Branch'
  presenting_author_: 'Vineela Gangalapudi'