Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers

Jesus Gonzalez-Bosquet, Jacob Calcei, Jun S. Wei, Montserrat Garcia-Closas, Mark E. Sherman, Stephen Hewitt, Joseph Vockley, Jolanta Lissowska, Hannah P. Yang, Javed Khan, Stephen Chanock

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderatethroughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

Original languageEnglish (US)
Article numbere14522
JournalPLoS One
Volume6
Issue number1
DOIs
StatePublished - 2011

Fingerprint

Nucleic Acid Denaturation
somatic mutation
melting
Melting
Paraffin
Mutation
neoplasms
DNA
alkanes
Tumors
Neoplasms
mutation
Sensitivity and Specificity
Screening
sampling
Genes
Endometrial Neoplasms
screening
Ovarian Neoplasms
Freezing

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Gonzalez-Bosquet, J., Calcei, J., Wei, J. S., Garcia-Closas, M., Sherman, M. E., Hewitt, S., ... Chanock, S. (2011). Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers. PLoS One, 6(1), [e14522]. https://doi.org/10.1371/journal.pone.0014522

Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers. / Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S.; Garcia-Closas, Montserrat; Sherman, Mark E.; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P.; Khan, Javed; Chanock, Stephen.

In: PLoS One, Vol. 6, No. 1, e14522, 2011.

Research output: Contribution to journalArticle

Gonzalez-Bosquet, J, Calcei, J, Wei, JS, Garcia-Closas, M, Sherman, ME, Hewitt, S, Vockley, J, Lissowska, J, Yang, HP, Khan, J & Chanock, S 2011, 'Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers', PLoS One, vol. 6, no. 1, e14522. https://doi.org/10.1371/journal.pone.0014522
Gonzalez-Bosquet, Jesus ; Calcei, Jacob ; Wei, Jun S. ; Garcia-Closas, Montserrat ; Sherman, Mark E. ; Hewitt, Stephen ; Vockley, Joseph ; Lissowska, Jolanta ; Yang, Hannah P. ; Khan, Javed ; Chanock, Stephen. / Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers. In: PLoS One. 2011 ; Vol. 6, No. 1.
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