Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability

Anna De Grassi, Cinzia Segala, Fabio Iannelli, Sara Volorio, Lucio Bertario, Paolo Radice, Loris Bernard, Francesca D. Ciccarelli

Research output: Contribution to journalArticle

Abstract

Early detection of cancer-associated genomic instability is crucial, particularly in tumour types in which this instability represents the essential underlying mechanism of tumourigenesis. Currently used methods require the presence of already established neoplastic cells because they only detect clonal mutations. In principle, parallel sequencing of single DNA filaments could reveal the early phases of tumour initiation by detecting low-frequency mutations, provided an adequate depth of coverage and an effective control of the experimental error. We applied ultradeep sequencing to estimate the genomic instability of individuals with hereditary non-polyposis colorectal cancer (HNPCC). To overcome the experimental error, we used an ultraconserved region (UCR) of the human genome as an internal control. By comparing the mutability outside and inside the UCR, we observed a tendency of the ultraconserved element to accumulate significantly fewer mutations than the flanking segments in both neoplastic and nonneoplastic HNPCC samples. No difference between the two regions was detectable in cells from healthy donors, indicating that all three HNPCC samples have mutation rates higher than the healthy genome. This is the first, to our knowledge, direct evidence of an intrinsic genomic instability of individuals with heterozygous mutations in mismatch repair genes, and constitutes the proof of principle for the development of a more sensitive molecular assay of genomic instability.

Original languageEnglish
Article numbere1000275
JournalPLoS Biology
Volume8
Issue number1
DOIs
Publication statusPublished - Jan 2010

Fingerprint

Genomic Instability
mutation
genomics
Colorectal Neoplasms
colorectal neoplasms
Mutation Rate
Mutation
Genes
neoplasms
Tumors
DNA Mismatch Repair
Human Genome
DNA Sequence Analysis
Early Detection of Cancer
genome
Neoplasms
Genome
Assays
Repair
sampling

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)

Cite this

De Grassi, A., Segala, C., Iannelli, F., Volorio, S., Bertario, L., Radice, P., ... Ciccarelli, F. D. (2010). Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability. PLoS Biology, 8(1), [e1000275]. https://doi.org/10.1371/journal.pbio.1000275

Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability. / De Grassi, Anna; Segala, Cinzia; Iannelli, Fabio; Volorio, Sara; Bertario, Lucio; Radice, Paolo; Bernard, Loris; Ciccarelli, Francesca D.

In: PLoS Biology, Vol. 8, No. 1, e1000275, 01.2010.

Research output: Contribution to journalArticle

De Grassi, Anna ; Segala, Cinzia ; Iannelli, Fabio ; Volorio, Sara ; Bertario, Lucio ; Radice, Paolo ; Bernard, Loris ; Ciccarelli, Francesca D. / Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability. In: PLoS Biology. 2010 ; Vol. 8, No. 1.
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