Temperature-tolerant COLD-PCR reduces temperature stringency and enables robust mutation enrichment

E. Castellanos-Rizaldos, Pingfang Liu, Coren A. Milbury, Minakshi Guha, Angela Brisci, Laura Cremonesi, Maurizio Ferrari, Harvey Mamon, G. Mike Makrigiorgos

Research output: Contribution to journalArticle

Abstract

BACKGROUND: Low-level mutations in clinical tumor samples often reside below mutation detection limits, thus leading to false negatives that may impact clinical diagnosis and patient management. COLD-PCR (co-amplification at lower denaturation temperature PCR) is a technology that magnifies unknown mutations during PCR, thus enabling downstream mutation detection. However, a practical difficulty in applying COLD-PCR has been the requirement for strict control of the denaturation temperature for a given sequence, to within ±0.3°C. This requirement precludes simultaneous mutation enrichment in sequences of substantially different melting temperature (Tm) and limits the technique to a single sequence at a time. We present a temperature-tolerant (TT) approach (TT-COLD-PCR) that reduces this obstacle. METHODS: We describe thermocycling programs featuring a gradual increase of the denaturation temperature during COLD-PCR. This approach enabled enrichment of mutations when the cycling achieves the appropriate critical denaturation temperature of each DNA amplicon that is being amplified. Validation was provided for KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) and TP53 (tumor protein p53) exons 6-9 by use of dilutions of mutated DNA, clinical cancer samples, and plasma-circulating DNA. RESULTS: A single thermocycling program with a denaturation-temperature window of 2.5-3.0°C enriches mutations in all DNA amplicons simultaneously, despite their different Tms. Mutation enrichments of 6-9-fold were obtained with TT-full-COLD-PCR. Higher mutation enrichments were obtained for the other 2 forms of COLD-PCR, fast-COLD-PCR, and ice-COLD-PCR. CONCLUSIONS: Low-level mutations in diverse amplicons with different Tms can be mutation enriched via TT-COLD-PCR provided that their Tms fall within the denaturation-temperature window applied during amplification. This approach enables simultaneous enrichment of mutations in several amplicons and increases significantly the versatility of COLD-PCR.

Original languageEnglish
Pages (from-to)1130-1138
Number of pages9
JournalClinical Chemistry
Volume58
Issue number7
DOIs
Publication statusPublished - Jul 2012

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ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

Castellanos-Rizaldos, E., Liu, P., Milbury, C. A., Guha, M., Brisci, A., Cremonesi, L., Ferrari, M., Mamon, H., & Makrigiorgos, G. M. (2012). Temperature-tolerant COLD-PCR reduces temperature stringency and enables robust mutation enrichment. Clinical Chemistry, 58(7), 1130-1138. https://doi.org/10.1373/clinchem.2012.183095