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Open Access

Cancer gene mutation discovery and detection using array-based resequencing

  • T Tengs1, 2,
  • JC Lee1, 2,
  • JG Paez1, 3,
  • X Zhao1,
  • T LaFramboise1,
  • G Giannoukos2 and
  • RK Thomas1, 2
Breast Cancer Research20057(Suppl 2):P4.51

Published: 17 June 2005


Cancer ResearchGene MutationSplice SiteSomatic MutationNSCLC Patient

We set out to determine the feasibility of using microarray-based resequencing for cancer gene mutation screening by designing GeneChip CustomSeq Resequencing arrays (Affymetrix, Santa Clara, CA, USA) for interrogation of ARAF, BRAF, CDK4, CDK6, CDKN2A, KLF6, HRAS, KRAS, MET, NRAS, PTEN, RAF1, RB1, RET and TP53 (164 exons in total). Arrays also included four intronic bases on either side of the exons to cover splice sites, thus the arrays covered a total of 23,966 bases. Overall performance was very good, with accuracy >99.99% and coverage ~97.5%. Twenty NSCLC samples were analyzed using the arrays, and several well-characterized somatic mutations and germline variants were found. The most significant novel finding was the detection of a transforming MET mutation (T1010I) in a NSCLC patient.

Authors’ Affiliations

Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
The Broad Institute of MIT and Harvard, Cambridge, USA
Merck, Boston, USA


© BioMed Central 2005