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NIH Research Festival

September 16 – 18, 2015

Characterization of genomic alterations in HPV-negative and HPV-positive HNSCC cell lines with high throughput whole exome DNA and transcriptome RNA sequencing

Friday, September 18, 2015 – Poster Session IV
12:00 – 1:30 p.m.

FAES Terrace

NIDCD

GEN-6

Authors

  • H Cheng
  • X Yang
  • H Si
  • A Saleh
  • J Coupar
  • RL Ferris
  • WG Yarbrough
  • ME Prince
  • TE Carey
  • C Van Waes
  • Z Chen

Abstract

Head and neck squamous cell carcinoma (HNSCC) is among the top cancer types with high frequencies of genomic alterations, including mutation and copy number variation (CNV). Recently the Cancer Genome Atlas (TCGA) has profiled over 279 HNSCC tumors and generated a comprehensive genomic characterization of HNSCC. This has led to an urgent need for a panel of HNSCC cell line models with genomic alterations representative of those found by TCGA. We performed whole exome-DNA and transcriptome RNA sequencing on 15 HPV-negative and 11 HPV-positive HNSCC lines. These sequencings were performed on the ABI SOLiD platform with an average depth of 87X and 44X respectively. We identified chromosome losses in 3p, 5q, 8p, 9p and 18q and gains in 3q, 7p and 11q in a significant portion of cell lines, which are consistent with previous karyotype and TCGA CNV studies. Integrative analysis between CNV by exome-seq and gene expression by RNAseq of these cell lines revealed a significant positive correlation in multiple oncogenes including PIK3CA, TP63, CCND1, FADD, BIRC2 and YAP1, which is in concordance with TCGA results. The significantly mutated genes identified by MutSig in TCGA are also frequently mutated in cell lines, including TP53, FAT1 and NOTCH1, etc. Many of the genomic alterations identified converge on the networks previously defined in HNSCC, including the PI3K/AKT/mTOR, NFκB, and RAS/MAPK pathways. Our findings suggest that these cell lines can serve as HNSCC models for mechanistic and therapeutic studies, and thereby provide a valuable resource for the wider biomedical research community.

Scientific Focus Area: Genetics and Genomics

This page was last updated on Friday, March 26, 2021

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2015 program

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Current Research Festival

  • 2025
  • 2024
    • General Schedule of Events
    • 2024 NIH Distinguished Scholars Program
    • Poster Sessions
    • Concurrent Workshops
    • NIH Resource Information Fair
    • National Academy of Science Mini-Symposium
    • Special Wednesday Events
    • Vendor Exhibit Information
    • Green Labs Fair
    • Research Festival Committee
  • 2023
    • General Schedule of Events
    • NIH Early–Career Investigator Lectures
    • Poster Sessions
    • Concurrent Workshops
    • NIH Resource Information Fair
    • Vendor Exhibit Information
    • Research Festival Committee
  • 2021
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    • General Schedule of Events
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    • Poster Session
    • Data Blitz
    • FARE Award Ceremony
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    • Technical Sales Association (TSA) Research Festival Exhibit Tent Show
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  • 2018
    • General Schedule of Events
    • Plenary Sessions
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    • FARE Award Ceremony
    • Special Exhibits on Resources for Intramural Research
    • Technical Sales Association (TSA) Research Festival Exhibit Tent Show
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    • General Schedule of Events
    • Plenary Sessions
    • Concurrent Symposia Sessions
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    • FARE Award Ceremony
    • Future Research Leaders
    • Special Exhibits on Resources for Intramural Research
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    • General Schedule of Events
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    • Browse by Presenter Name
    • Browse by Presenter IC
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    • Tours of the National Library of Medicine and Clinical Center
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  • 2015
    • General Schedule of Events
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