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SRMA: an R package for resequencing array data analysis

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journal contribution
posted on 2024-06-04, 06:41 authored by N 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.

History

Journal

Bioinformatics

Volume

28

Pagination

1928-1930

Location

Oxford, Eng.

Open access

  • Yes

ISSN

1367-4803

eISSN

1460-2059

Language

eng

Publication classification

C Journal article, C1.1 Refereed article in a scholarly journal

Copyright notice

2012, The Authors

Issue

14

Publisher

Oxford University Press