Methodology

"Sequencing-grade" screening for BRCA1 variants by oligo-arrays

Alessandro Monaco^1,4 , Filippo Menolascina^2,4 , Yingdong Zhao³ , Stefania Tommasi⁴ , Marianna Sabatino¹ , Ross Fasano¹ , Angelo Paradiso⁴ , Francesco M Marincola¹ and Ena Wang¹

¹  Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA

²  Department of Bioinformatics, University of Bari, Italy

³  Biometrics Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, Italy

⁴  Clinical Experimental Oncology Laboratory, Istituto Tumori IRCCS "Giovanni Paolo II", Bari, Italy

author email corresponding author email

Journal of Translational Medicine 2008, 6:64doi:10.1186/1479-5876-6-64

Published:	30 October 2008

Abstract

The need for fast, efficient, and less costly means to screen genetic variants associated with disease predisposition led us to develop an oligo-nucleotide array-based process for gene-specific single nucleotide polymorphism (SNP) genotyping. This cost-effective, high-throughput strategy has high sensitivity and the same degree of accuracy as direct sequencing, the current gold standard for genetic screening. We used the BRCA1 breast and ovarian cancer predisposing gene model for the validation of the accuracy and efficiency of our strategy. This process could detect point mutations, insertions or deletions of any length, of known and unknown variants even in heterozygous conditions without affecting sensitivity and specificity. The system could be applied to other disorders and can also be custom-designed to include a number of genes related to specific clinical conditions. This system is particularly useful for the screening of long genomic regions with relatively infrequent but clinically relevant variants, while drastically cutting time and costs in comparison to high-throughput sequencing.