Cancer gene mutation discovery and detection using array-based resequencing

Torstein Tengs ,Jc Lee,J Guillermo Páez ,Georgia Giannoukos ,Xiaojun Zhao ,Thomas Laframboise ,R K Thomas

doi:10.1186/bcr1181

Abstract

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.

Highlights

Endocrine therapy for breast cancer is a major modality for the treatment of breast cancer, producing response rates between 30% and 40% of unselected patients with the minimum of toxicity
We have shown that overexpression of TGF-β1 in mammary epithelial cells suppresses the development of carcinomas and that expression of a dominant negative type II TGF-β receptor (DNIIR) in mammary epithelial cells under control of the MMTV promoter/enhancer increases the incidence of erbB2 in carcinomas accompanied by Tgfbr2fspKO fibroblasts
We found that the frequency of the IVS10-6T>G is characterized by multiple physiologic abnormalities, including mutation was not increased in breast cancer cases as compared with neurodegeneration, immunologic abnormalities, cancer predisposition, controls

Summary

Introduction

Endocrine therapy for breast cancer is a major modality for the treatment of breast cancer, producing response rates between 30% and 40% of unselected patients with the minimum of toxicity. Several human genetic diseases are known to be or suspected to be due to defects in DNA repair or cell cycle control Some of these patients are radiation sensitive and/or predisposed for cancer as a cause of mutations in genes involved in these cellular pathways. Microarray-based comparative genomic hybridization (arrayCGH) allows the construction of high-resolution genome-wide maps of copy number alterations, and statistical software packages are available for exploring and analysing array-CGH data (see, for example, [2,3]), facilitating the delineation of the boundaries of CNAs in individual tumors and thereby localizing and identifying potential oncogenes and tumor suppressor genes. The aim of this study was to evaluate the prognostic value of gene expression-based classification as well as established prognostic markers, including mutation status of the TP53 gene, in a group of breast cancer patients with long-term (>10 years) fol The aim of this study was to compare MR spectroscopic findings from breast cancer tissue with histological grading of tumor and patient lymph node status

Methods

Results

Conclusion