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

Abstract Submission for Poster Presentation
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Abstract Title:: The Integrated Oncogenomics Portal (IOCP): A Cloud-Native Pipeline and Database for Processing and Sharing CCDI & other Childhood Cancer Genomics Data 
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. 

Authors::
1. First Name: Vineela
   Last Name: Gangalapudi
   Degree(s): Masters
   Organization: ABCS, FNLCR, NCI Genetics Branch
2. First Name: Hsien Chao
   Last Name: Chou
   Degree(s): Ph.D.
   Organization: NCI Genetics Branch
3. First Name: Xinyu
   Last Name: Wen
   Degree(s): Masters
   Organization: ABCS, FNLCR, NCI Genetics Branch
4. First Name: Jun
   Last Name: Wei
   Degree(s): Ph.D.
   Organization: NCI Genetics Branch
5. First Name: Javed
   Last Name: Khan
   Degree(s): M.D.
   Organization: NCI Genetics Branch
6. First Name: Srujan
   Last Name: Boppana
   Degree(s): Bachelor of Engineering
   Organization: NCI CBIIT
7. First Name: Lauren
   Last Name: Funston
   Degree(s): Bachelors in Computer Science
   Organization: NCI CBIIT
8. First Name: Subhashini
   Last Name: Jagu
   Degree(s): Ph.D.
   Organization: Office of Data Sharing, NCI
9. First Name: Simone
   Last Name: Kats
   Degree(s): Masters
   Organization: Office of Data Sharing, NCI
10. First Name: Bahar
    Last Name: Sayoldin
    Degree(s): Masters
    Organization: FNLCR, Office of Data Sharing, NCI
11. First Name: Catherine
    Last Name: Bullen
    Degree(s): Ph.D.
    Organization: FNLCR, Office of Data Sharing, NCI

Presenting Author:: Vineela Gangalapudi
Institution:: ABCS, FNLCR, NCI Genetics Branch
Email Address:: vineela.gangalapudi@nih.gov