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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
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Characterizing Mutational Load and Clonal Composition of Human Blood
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Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.

Kevin Hadi1, Xiaotong Yao2, Julie M Behr2

  • 1Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA.

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|October 2, 2020
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Summary

Researchers discovered three new types of complex DNA rearrangements in cancer genomes: pyrgo, rigma, and tyfonas. These findings, based on genome graph analysis, reveal new insights into cancer development and potential therapeutic targets.

Keywords:
aneuploidycancer evolutioncancer genomicschromothripsisfragile sitesgenome graphsmutational processesphasingstructural variationsuperenhancers

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Area of Science:

  • Genomics
  • Cancer Biology
  • Bioinformatics

Background:

  • Somatic DNA rearrangements are common in cancer genomes.
  • Many rearrangements are difficult to classify into simple or complex structural variant categories.

Purpose of the Study:

  • To apply a novel genome graph computational paradigm to analyze junction copy number (JCN) in tumor whole-genome sequences.
  • To uncover and characterize novel complex DNA rearrangement phenomena.

Main Methods:

  • Analysis of junction copy number (JCN) topology using a genome graph computational paradigm.
  • Whole-genome sequencing of 2,778 tumor samples.
  • Clustering of tumors based on genome graph-derived features.

Main Results:

  • Identification of three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas.
  • Pyrgo (duplications) linked to early replication, superenhancers, and breast/ovarian cancers.
  • Rigma (deletions) linked to late replication, fragile sites, and gastrointestinal cancers.
  • Tyfonas (inversions) linked to protein-coding fusions, hypermutation, and acral melanomas.
  • Tumor subgroups associated with DNA repair defects and poor prognosis were identified.

Conclusions:

  • The genome graph approach reveals novel complex genomic rearrangements in cancer.
  • These phenomena (pyrgo, rigma, tyfonas) have distinct genomic contexts and cancer associations.
  • Genomic features identified subgroups linked to DNA repair and prognosis, suggesting therapeutic implications.