Childhood Cancer Data Initiative Annual Symposium (Abstract Registration): Submission #64

Abstract Submission for Poster Presentation
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Abstract Title:: AI-driven multimodal analysis integrating WSI, Methyl-Seq, and OncoKids Cancer Panel to improve diagnostic precision of pediatric tumors.
Abstract::
Previously, we added clinical and genomic data from more than 1,000 pediatric cancer patients from our racially and ethnically diverse patient population at Children’s Hospital Los Angeles (CHLA) to the CCDI (dbGaP Study Accession: phs002518). We are now augmenting this dataset with new types of data, and to develop tools for integrating the diverse datasets in CCDI to improve diagnosis and treatment of all children with cancer. To date, almost 700 CNS and non-CNS solid tumors in our cohort have been identified, screened, and key whole slide images (WSI) selected. We developed a computational pipeline to access and organize metadata for each WSI, and to quantitatively assess tumor morphology of WSI slides. In parallel, we have also generated whole-genome enzymatic methyl-seq data from 170 CNS tumors, and developed a methyl-seq bioinformatics pipeline with a CNS tumor classifier compatible with methyl-seq data. Tools to leverage these multimodal data to improve diagnosis and characterization of the tumors is an active area of investigation. We have trained a CNS tumor classifier applicable with Methylseq samples. Our pipeline is fully automated from raw bioinformatics processing to a classification report detailing predicted classification, classification score, UMAP clustering analysis, copy number profiling, and quality control metrics. Additionally, we have developed AI/ML tools to converge results from WSI analysis, methylation values, and OncoKids Cancer Panel results to enhance diagnostic decision-making.  Our long-term goals are to incorporate additional data formats into our suite of multimodal analytic tools and to make these tools available to the CCDI community.

Abstract:: https://events.cancer.gov/system/files/webform/ccdi_symposium_abstract/150572/CHLA%20P30%20CCDI%20Abstract_final%20for%20CCDI.docx
Authors::
1. First Name: Alexander 
   Middle Initial: L.
   Last Name: Markowitz
   Degree(s): PhD 
   Organization: Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA
2. First Name: Jennifer
   Last Name: Cotter
   Degree(s): MD
   Organization: Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles; Department of Pathology, Keck School of Medicine, University of Southern California; Los Angeles, CA
3. First Name: David
   Middle Initial: N.
   Last Name: Buckley
   Degree(s): MS, PhD
   Organization: Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA
4. First Name: Shengmei 
   Last Name: Zhou
   Degree(s): MD
   Organization: Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles; Department of Pathology, Keck School of Medicine, University of Southern California; Los Angeles, CA
5. First Name: William
   Last Name: Mango
   Organization: Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA
6. First Name: Bruce
   Last Name: Pawel
   Degree(s): MD
   Organization: Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles; Department of Pathology, Keck School of Medicine, University of Southern California; Los Angeles, CA
7. First Name: Fariba
   Last Name: Navid
   Organization: Cancer and Blood Disease Institute, Children’s Hospital Los Angeles; Department of Pediatrics, Keck School of Medicine, University of Southern California; Los Angeles, CA
8. First Name: Jaclyn
   Last Name: Biegel
   Degree(s): PhD, FACMG
   Organization: Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles; Department of Pathology, Keck School of Medicine, University of Southern California; Los Angeles, CA
9. First Name: James
   Middle Initial: F.
   Last Name: Amatruda
   Degree(s): MD, PhD
   Organization: Cancer and Blood Disease Institute, Children’s Hospital Los Angeles; Departments of Pediatrics and Medicine, Keck School of Medicine, University of Southern California; Los Angeles, CA

Presenting Author:: Alexander L Markowitz, PhD
Institution:: Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA
Email Address:: amarkowitz@chla.usc.edu