Development and validation of BRCA1 for Next Generation Sequencing (NGS)

This paper presents the profile development of the Cancer susceptibility gene type 1 (BRCA1) that will be used in Next Generation Sequencing (NGS). The developed profile is validated in terms of accuracy for an early detection of breast cancer (BC). Exon 11 is chosen as truncated BRCA1 as it has 3426 nucleotides, which is the longest DNA sequence among exons available in BRCA1. Hayward works also has reported that most of mutation occurs at exon 11 of BRCA1. The detection of BC disease uses DNA sequence alignment method where it identifies similarity region between the truncated sequence of exon 11 and mutated exon 11 sequence of BRCA1. These sequences are aligned based on the well-known Smith-Waterman (SW) algorithm with affine gap penalty score. A custom designed code based on the aforementioned algorithm is implemented in MATLAB. The best matched score and computation time of aligning DNA sequence for early BC detection using SSEARCH35 and MATLAB are compared. With 99.4 percent of accuracy, the truncated exon 11 DNA sequences are sensitive for BC early diagnosis using NGS.