Abstract 1739: The prevalence of KRAS, PIK3CA, and BRAF mutant subpopulations in tumors may be impacting the success of personalized cancer treatment
Authors: Myers Meagan B. , Wang Yiying , McKim Karen L. , McKinzie Page B. , Parsons Barbara L. 
Published: August 2012

Tumor mutations are being used as predictive biomarkers of response, in order to select the most effective treatment for individual cancer patients. Currently, this is being done without sufficient characterization of relevant oncogene mutations as quantitative biomarkers. The goal of the current study was to define normal and pathological levels of the most prevalent hotspot mutations in the KRAS, PIK3CA, and BRAF genes, to establish the frequency with which the mutations occur as subpopulations, and what diagnostic sensitivity is needed to detect defined percentages of tumors carrying mutant subpopulations. Therefore, the sensitive Allele-specific Competitive Blocker-PCR (ACB-PCR) was used to quantify the levels of specific hotspot point mutations in a panel of normal human tissues and tumors. The mutations examined have established significance in terms of personalized cancer treatment, specifically KRAS G12D, KRAS G12V, BRAF V600E, and PIK3CA H1047R. The tissues examined included lung, colon, pancreas, and thyroid. In colon tumors, the 5th, 25th, 50th, 75th, and 95th percentiles of KRAS G12D mutant fraction (MF) are 1.7 x 10−5, 7.4 x 10−5, 3.0 x 10−4, 2.8 x 10−2, and 8.4 x 10−1, respectively. In lung tumors, the 5th, 25th, 50th, 75th, and 95th percentiles of KRAS G12V MF are 7.0 x 10−6, 1.1 x 10−5, 3.3 x 10−5, 2.3 x 10−2, and 1.2 x 10−1, respectively. Based on the data across these tissue types, 67.5% of tumors carry KRAS G12D or G12V mutation at a subpopulation frequency higher than that observed in normal tissue. Only 18.1% of tumors had a KRAS MF α10−1 (i.e., that detectable by DNA sequencing). From these data it was determined a diagnostic with a sensitivity of 10−2 or 10−3 would detect 27.7% or 43.4% of these tumors, respectively. Surprisingly, analysis of KRAS mutation in papillary thyroid tumors showed KRAS G12V mutations were present above normal thyroid levels, but as subpopulations in 42.1% of papillary thyroid tumors, even though the COSMIC database indicates this mutation occurs in only 0.15% of papillary thyroid tumors. The occurrence of these KRAS G12V mutations was positively correlated with percent tumor necrosis. For PIK3CA H1047R mutation in colon tumors, the 5th, 25th, 50th, 75th, and 95th percentiles are 1.2 x 10−6, 5.3 x 10−4, 7.6 x 10−4, 1.1 x 10−3, and 4.2 x 10−2, respectively. Data on BRAF V600E shows it occurs primarily as large subpopulations in papillary thyroid tumors. For effective development of personalized cancer treatment, quantitative and sensitive analyses of tumor mutations are needed to establish the effect of mutant subpopulations on patient response and/or relapse. Because so many tumors carry KRAS mutation, therapies targeting KRAS mutant cells are needed for use in conjunction with therapies directed against other targets. The views presented do not necessarily reflect those of the US FDA.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1739. doi:1538-7445.AM2012-1739