Rapid identification of somatic mutations in colorectal and breast cancer tissues using mismatch repair detection (MRD)

Mismatch repair detection (MRD) was used to screen 93 matched tumor‐normal sample pairs and 22 cell lines for somatic mutations in 30 cancer relevant genes. Using a starting amount of only 150 ng of genomic DNA, we screened 102 kb of sequence for somatic mutations in colon and breast cancer. A total of 152 somatic mutations were discovered, encompassing previously reported mutations, such as BRAF V600E and KRAS G12S, G12V, and G13D, as well as novel mutations, including some in genes in which somatic mutations have not previously been reported, such as MAP2K1 and MAP2K2. The distribution of mutations ranged widely within and across tumor types. The functional significance of many of these mutations is not understood, with patterns of selection only evident in KRAS and BRAF in colon cancer. These results present a novel approach to high‐throughput mutation screening using small amounts of starting material and reveal a mutation spectrum across 30 genes in a large cohort of breast and colorectal cancers. Hum Mutat 29(3), 441–450, 2008. © 2008 Wiley‐Liss, Inc.

[1]  Ronald W. Davis,et al.  Multiplexed variation scanning for 1,000 amplicons in hundreds of patients using mismatch repair detection (MRD) on tag arrays. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Alessandra Viel,et al.  Human MRE11 is inactivated in mismatch repair‐deficient cancers , 2002, EMBO reports.

[3]  K. Kinzler,et al.  Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status , 2002, Nature.

[4]  F. Al-Mulla,et al.  Structural differences between valine‐12 and aspartate‐12 Ras proteins may modify carcinoma aggression , 1999, The Journal of pathology.

[5]  D. Barford,et al.  Mechanism of Activation of the RAF-ERK Signaling Pathway by Oncogenic Mutations of B-RAF , 2004, Cell.

[6]  Pablo Rodriguez-Viciana,et al.  Germline Mutations in Genes Within the MAPK Pathway Cause Cardio-facio-cutaneous Syndrome , 2006, Science.

[7]  Nobuyoshi Shimizu,et al.  Presence of epidermal growth factor receptor gene T790M mutation as a minor clone in non-small cell lung cancer. , 2006, Cancer research.

[8]  D. Palli,et al.  MRE11 expression is impaired in gastric cancer with microsatellite instability. , 2004, Carcinogenesis.

[9]  N. Freimer,et al.  Mismatch repair detection (MRD): high-throughput scanning for DNA variations. , 2001, Human molecular genetics.

[10]  P. Gillevet,et al.  Sequencing homopolymer tracts and repetitive elements. , 1996, BioTechniques.

[11]  C. Harris,et al.  Mutations in the p53 tumor suppressor gene: clues to cancer etiology and molecular pathogenesis. , 1994, Cancer research.

[12]  J. Chien,et al.  Heterozygous ATR mutations in mismatch repair-deficient cancer cells have functional significance. , 2005, Cancer research.

[13]  A. Jubb,et al.  Association of k-ras, b-raf, and p53 status with the treatment effect of bevacizumab. , 2005, Journal of the National Cancer Institute.

[14]  W. Park,et al.  Somatic Mutations of ERBB2 Kinase Domain in Gastric, Colorectal, and Breast Carcinomas , 2006, Clinical Cancer Research.

[15]  Lucio Luzzatto,et al.  A quantitative measurement of the human somatic mutation rate. , 2005, Cancer research.

[16]  R. Herrmann,et al.  High frequency of point mutations clustered within the adenosine triphosphate-binding region of BCR/ABL in patients with chronic myeloid leukemia or Ph-positive acute lymphoblastic leukemia who develop imatinib (STI571) resistance. , 2002, Blood.

[17]  Xiao-Fan Wang,et al.  ATR functions as a gene dosage‐dependent tumor suppressor on a mismatch repair‐deficient background , 2004, The EMBO journal.

[18]  Kylie L. Gorringe,et al.  Evidence that both genetic instability and selection contribute to the accumulation of chromosome alterations in cancer. , 2005, Carcinogenesis.

[19]  M. Nei,et al.  Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.

[20]  F. Lozupone,et al.  Mutually exclusive NRASQ61R and BRAFV600E mutations at the single-cell level in the same human melanoma , 2006, Oncogene.

[21]  S. Schwartz,et al.  KRAS and BRAF oncogenic mutations in MSS colorectal carcinoma progression , 2007, Oncogene.

[22]  G. Thomas,et al.  Differential nonsense mediated decay of mutated mRNAs in mismatch repair deficient colorectal cancers. , 2005, Human molecular genetics.

[23]  P. Bork,et al.  Towards a structural basis of human non-synonymous single nucleotide polymorphisms. , 2000, Trends in genetics : TIG.

[24]  S Srivastava,et al.  A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. , 1998, Cancer research.

[25]  Patricia L. Harris,et al.  Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. , 2004, The New England journal of medicine.

[26]  N. Matsubara,et al.  Colorectal cancer with mutation in BRAF, KRAS, and wild-type with respect to both oncogenes showing different patterns of DNA methylation. , 2004, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.