Version 2 2024-06-04, 06:41Version 2 2024-06-04, 06:41
Version 1 2016-10-20, 13:41Version 1 2016-10-20, 13:41
journal contribution
posted on 2024-06-04, 06:41authored byN Zhang, Y Xu, Martin O'HelyMartin O'Hely, TP Speed, C Scharfe, W Wang
Sequencing by hybridization to oligonucleotides has evolved into an inexpensive, reliable and fast technology for targeted sequencing. Hundreds of human genes can now be sequenced within a day using a single hybridization to a resequencing microarray. However, several issues inherent to these arrays (e.g. cross-hybridization, variable probe/target affinity) cause sequencing errors and have prevented more widespread applications. We developed an R package for resequencing microarray data analysis that integrates a novel statistical algorithm, sequence robust multi-array analysis (SRMA), for rare variant detection with high sensitivity (false negative rate, FNR 5%) and accuracy (false positive rate, FPR 1×10⁻⁵). The SRMA package consists of five modules for quality control, data normalization, single array analysis, multi-array analysis and output analysis. The entire workflow is efficient and identifies rare DNA single nucleotide variations and structural changes such as gene deletions with high accuracy and sensitivity.