TY - JOUR
T1 - SRMA
T2 - An r package for resequencing array data analysis
AU - Zhang, Nianxiang
AU - Xu, Yan
AU - O'hely, Martin
AU - Speed, Terence P.
AU - Scharfe, Curt
AU - Wang, Wenyi
N1 - Funding Information:
Funding: Michael & Susan Dell Foundation (to N.Z.); U.S. National Institutes of Health through the following grants: P30 CA016672 (to N.Z. and W.W.), R01 EY016240 (to Y.X. and C.S.), 5R01 GM083084-03 (to T.P.S.). M.O’H and T.P.S acknowledge the NHMRC for support through an Australia Fellowship. P30 CA016672 (to N.Z. and W.W.), and R01 EY016240 (to T.P.S. and C.S.).
PY - 2012/7
Y1 - 2012/7
N2 - 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.
AB - 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.
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U2 - 10.1093/bioinformatics/bts286
DO - 10.1093/bioinformatics/bts286
M3 - Article
C2 - 22581181
AN - SCOPUS:84864122072
SN - 1367-4803
VL - 28
SP - 1928
EP - 1930
JO - Bioinformatics
JF - Bioinformatics
IS - 14
M1 - bts286
ER -