Related Experiment Video
Updated: Dec 8, 2025
11:02
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
19.8K
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples.
J P Torcivia1, R Mazumder1,2
1The Department of Biochemistry and Molecular Medicine, The George Washington University Medical Center, Washington, DC, USA.
Briefings in Bioinformatics
|September 17, 2020
Summary
Genomic sequencing reveals most cancer mutations occur in non-coding DNA. These non-coding regions, particularly on chromosome X, show significant mutations across cancers and races, highlighting their role in oncogenesis.
Area of Science:
- Genomics
- Cancer Biology
- Bioinformatics
Background:
- High-throughput sequencing technology has advanced genomics.
- Non-coding DNA regions play a crucial role in oncogenesis.
- Understanding non-coding mutations is vital for cancer research.
Purpose of the Study:
- To investigate the role of non-coding regions in cancer development.
- To identify significantly mutated regions in the non-coding genome across various cancers and races.
- To explore the potential of non-coding DNA as biomarkers for cancer.
Main Methods:
- Whole-genome tumor-normal paired sequencing of 154 samples across five cancer types.
- Analysis of non-coding regions using sliding window and binning strategies.
- Pan-cancer analysis to identify significantly mutated windows and clusters.
Main Results:
- The majority of cancer-associated mutations (4,432,885) were found in non-coding regions, compared to coding regions (1,412,731).
- Pan-cancer analysis identified numerous significantly mutated windows (292-3881) in the non-coding genome.
- Fifty-nine universally mutated windows were found across all studied races and cancers, with 16 regions identified for further study.
- The X chromosome, particularly Xq11.1, showed a high concentration of universally mutated windows linked to chromosomal instability and oncogenesis.
Conclusions:
- Non-coding regions harbor a significant number of cancer-associated mutations.
- Mutations in large, conserved non-coding regions across cancers and races suggest a role in cancer development.
- Specific regions, such as those on the X chromosome, warrant further investigation for their oncogenic potential.
