Cancer Genome Nexus – Inocras and Broad Institute:
Novel insights from TCGA Cancer Whole-Genome Analysis
Where We Are Today: The Foundation of Cancer Genomics
The Cancer Genome Atlas (TCGA) project is the NCI’s most comprehensive pan-cancer study, profiling thousands of tumors across 30+ cancer types with multi-omic data spanning genomics, epigenomics, transcriptomics, and proteomics. It has enabled major advances in cancer biology and diagnostics. However, most of TCGA analysis has relied on whole-exome sequencing data, leaving key aspects understudied, including oncogenic driver mutations in non-coding regions, genomic rearrangements (structural variations; SVs), genome-wide copy number alterations (CNA), and mutational signatures. As a result, most routine cancer sequencing and discovery still depends on targeted gene panels that cover only a small fraction of the genome.
Whole Genome Analysis of TCGA Data at Scale
Inocras and Broad Institute researchers have advanced TCGA analysis into the whole genome era , analyzing over 8,000 tumor/normal paired whole cancer genomes released by NCI for the TCGA project. The whole genome analysis was performed using a bioinformatics pipeline by the Broad Institute and CancerVision from Inocras in parallel, and then the variant calls were harmonized and consolidated into a single, frozen, and well-curated dataset to enable a consistent large-scale analysis, and robust benchmarking of computational and AI methods.
Beyond TCGA: Cancer Genome Nexus
At the AACR Annual Meeting 2026, the Broad Institute and Inocras will present novel insights from whole-genome analysis of the TCGA dataset, highlighting their impact on precision oncology and the future of cancer research. Building on this foundation, the conversation will turn to what’s next: Cancer Genome Nexus, a next-generation collaborative initiative now taking shape, designed to scale a robust, standardized whole-genome framework across larger datasets. By integrating harmonized pipelines, curated data, and AI-ready infrastructure, the program aims to accelerate discovery, enable clinical translation, and advance the next generation of cancer intelligence.
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By providing a harmonized, high-quality whole-genome variant dataset across thousands of samples, this collaboration creates a standard reference for cancer whole genome studies that can uncover novel coding and non-coding driver events as well as new potential targets; moreover, it can be used to train next-generation AI and other computational models poised to reveal new insights and transform precision oncology.
Gad Getz, PhD Harvard Medical School, Massachusetts General Hospital Cancer Center, Broad Institute -
The TCGA WGS initiative reflects our belief that the most impactful discoveries will come from open, rigorous, and collaborative science. Through this partnership, we are not just generating findings—we are building the foundation of a new ecosystem to scale whole-genome cancer insights for researchers and clinicians. At the AACR Annual Meeting 2026, we are excited to signal a shift toward a scalable, whole-genome–driven ecosystem for cancer research and clinical translation.
Jehee Suh, MBA CEO Inocras -
While genomic discovery has long centered on protein-coding genes, the vast ‘dark matter’ of the non-coding genome holds important clues to tumorigenesis. By looking at non-coding regulatory sequences, we are identifying candidate driver events that were previously missed by standard sequencing approaches.
Esther Rheinbay, PhD Harvard Medical School, Massachusetts General Hospital Cancer Center, Broad Institute -
The powerful cancer whole genome pipelines of both organizations at production scale have made this project possible, while creating a robust tumor-normal whole genome cancer dataset. The whole genome pipelines and dataset set the gold standard of cancer research, potentially unlocking the next wave of cohort studies, drug discovery, and AI-driven cancer research at a WGS level.
Youngseok Ju, MD, PhD Co-Founder at Inocras, Korea Advanced Institute of Science and Technology
The key insights from this collaboration will be shared in different forums and poster sessions during the AACR Annual Meeting 2026
Broad Institute Educational Session
New Insights from TCGA Whole-Genome Sequencing
Saturday, April 18th, 12:30 PM – 1:30 PM (PST)
Room 33 – Upper Level – Convention Center
Join Professor Getz as he chairs and presents at the Educational Session, The Cancer Genome Atlas (TCGA) has fundamentally reshaped our understanding of cancer genomics. While the initial ~11,000 whole exome sequencing from TCGA yielded many new discoveries, the recent release of high-quality whole-genome sequencing (WGS) data from nearly all tumor/normal pairs enables additional power insights. This educational session will demonstrate the utility of generating and analyzing WGS for tumors. WGS captures comprehensive information beyond the exome, including non-coding elements like promoters, enhancers, and insulators, as well as complex structural variations and full mutational signatures. The TCGA WGS resource is clinically and genomically well-annotated, and its deep, PCR-free coverage extends to challenging genomic regions. This genome-scale data enables machine learning of cancer-specific patterns and increases statistical power for non-coding discoveries. This session will highlight the latest biological insights and technical advantages derived from WGS for advancing precision oncology.
Inocras Exhibitor Spotlight Presentation
TCGA and Beyond: Whole-Genome Data Powering the Next Era of Cancer Intelligence
Monday, April 20th 12:30 PM – 1:30 PM (PST)
Inocras Exhibitor Spotlight Theater A
Learn about a transformational cancer genome initiative by Broad Institute and Inocras, analyzing over 8,000 TCGA tumor–normal samples using whole-genome bioinformatics pipelines from Broad and Inocras. Profs. Getz and Rheinbay (Broad Institute and Massachusetts General Hospital) will present novel findings showing how whole-genome analytics expand the variant landscape, improve driver gene discovery, and enable new actionable insights. Prof. Ju (Inocras) will outline what’s next: Cancer Genome Nexus, a next-generation collaborative initiative that builds on TCGA whole-genome analysis to scale a robust, standardized framework across larger datasets. Join us to learn how cancer whole genome analysis unlocks new insights and explore our next initiative to advance precision oncology.
Cancer Genome Nexus platform designed to empower the collaborative efforts at scale will be presented during the Inocras Exhibitor Spotlight Presentation
This Exhibitor Spotlight Theater is a promotional activity and is not approved for continuing education credit. The content of this Exhibitor Spotlight Theater are the opinions of the presenter and do not represent the position or the opinion of the American Association for Cancer Research® (AACR) or its members.” “Not affiliated with or endorsed by AACR.”
Visit Our Posters
Visit the 16 posters from the TCGA whole genome analysis by the Broad Institute – Inocras collaboration.
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Uncovering therapeutically targetable mutations from The Cancer Genome Atlas (TCGA) whole-genome datasets
Presenter: Ryul Kim/Inocras
April 19th, 2026 2:00 p.m.- 5:00 p.m. | Poster #492
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Origins of Structural Variant Junctional Insertions Across >8,000 TCGA Whole Genomes
Presenter: Youyun Zheng/Beroukhim Lab
April 20th , 2026 2:00 p.m.- 5:00 p.m. | Poster #3247
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Discovery of Coding and Non-coding Driver Mutations Across >8,000 TCGA Whole Genomes
Presenter: Ron Solan/ Gaddy Getz Lab
April 20th, 2026 9:00 a.m.-12:00 p.m. | Poster #2001
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Systematic Discovery of Structural Variant Drivers Across >8,000 TCGA Whole Genomes
Presenter: Antonia Kowalewski/Gaddy Getz Lab
April 20th, 2026 9:00 a.m.-12:00 p.m. | Poster #1989
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Pan-cancer PCR-free whole-genome sequencing refines the somatic driver landscape beyond exome sequencing alone
Presenter: Gengchao Wang/Rheinbay Lab
April 20th, 2026 9:00 a.m.-12:00 p.m. | Poster #1990
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Copy number analysis of regulatory regions reveal recurrent promoter/enhancer somatic copy number alterations across >8000 TCGA samples
Presenter: Haruna Tomono/Meyerson Lab
April 20th, 2026 9:00 a.m.-12:00 p.m. | Poster #1978
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The pan-cancer landscape of chromosome Y alterations
Presenter: Luis Antonio Corchete Sanchez/Rheinbay Lab
April 20th, 2026 9:00 a.m.-12:00 p.m. | Poster #1986
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The landscape of X chromosome copy number alterations in cancer
Presenter: Matthew Joseph Leventhal/Zhang Lab
April 20th, 2026 9:00 a.m.-12:00 p.m. | Poster #2002
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Germline predisposition in The Cancer Genome Atlas (TCGA) whole-genome sequencing datasets
Presenter : Ryul Kim/Inocras
April 20th, 2026 9:00 a.m.-12:00 p.m. | Poster #1991
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Pan-cancer LINE-1 retrotransposition landscapes in TCGA whole-genome sequences
Presenter: Beomki Lee/Kaist
April 20th, 2026 9AM-12 PM | Poster #1980
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Whole-genome sequencing of >8,000 TCGA samples reveals diverse and atypical spectra of homologous recombination deficiency in primary human cancers
Presenter: Joonoh Lim/Inocras
April 20th, 2026 9:00 a.m.-12:00 p.m. | Poster #1977
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Genomic signatures of chromosomal instability from a pan-cancer landscape of haplotype-specific copy-number alterations
Presenter: Chunyang Bao/Inocras
April 21st, 2026 2:00 p.m.-5:00 p.m. | Poster #5934
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Structural Variant Signature Discovery Across >8,000 TCGA Whole Genomes Using QuantHDP
Presenter: Gregory Raskind/Beroukhim Lab
April 22nd 9:00 a.m.-12:00 p.m. | Poster #7274
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Fast and Cost-effective Cloud-based Pipelines to Analyze Cancer Sequencing Data
Presenter: Sam Wiseman/Getz Lab
April 22nd 9:00 a.m.-12:00 p.m. | Poster #6881
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Comprehensive mutation profiling from The Cancer Genome Atlas (TCGA) whole-genome sequencing datasets
Presenter: Chunyang Bao/Inocras
April 22nd, 2026 9:00 a.m.-12:00 p.m. | Poster #7270
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AI-Driven stratification of cancer patients using The Cancer Genome Atlas (TCGA) whole-genome sequencing data
Presenter: Jonghoon Lee/Inocras
April 22nd, 2026 9 AM-12 PM | Poster #7268
Visit Inocras Booth
Visit us at Inocras booth # 3145 to learn more about how Inocras can help advance your research and clinical diagnostics and to learn how to get involved in Cancer Genome Nexus program
Learn about Inocras’ whole genome portfolio – across clinical assays and research solutions
Clinical assays (CAP/CLIA LTD):
- CancerVision™ Whole Genomic Profiling (WGP) test that maximizes cancer insights to guide therapy selection
- MRDVision™ Whole genome based, ultrasensitive, tissue informed MRD test
- RareVision™ Future-proof WGS based genetic test that maximizes diagnostic yield
Research Solutions:
- Comprehensive lab services: WGS, WES, RNA, Methylation, ppmSeq, Single Cell, Spatial
- Bioinformatics excellence: Specialized secondary and tertiary analysis from massive whole genome data
- Custom assay development: Partner with us to design and validate proprietary assays within our regulated environment
Learn more about Inocras solutions
Contact us by email at: inquiry@inocras.com
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