TY - GEN
T1 - SeqBBS
T2 - 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013
AU - Li, Hua
AU - Vallandingham, Jim
AU - Chen, Jie
PY - 2013
Y1 - 2013
N2 - Following the breakthrough of the microarray technology, the next generation sequencing (NGS) technology further advanced approaches in modern biomedical research. The high-throughput NGS technology is now frequently used in profiling tumor and control samples for the study of DNA copy number variants (CNVs). In particular, the ratio of read count of the tumor sample to that of the control sample is popularly used for identifying CNV regions. We illustrate that a change-point (or a breakpoint) detection method, along with a Bayesian approach, is particularly suitable for identifying CNVs in the reads ratio data. We have written our algorithm into a user friendly R-package, SeqBBS (stands for Bayesian breakpoints search for sequencing data) and applied our method to the sequencing data of reads ratio between the breast tumor cell lines HCC1954 and its matched normal cell line BL1954. Breakpoints that separate different CNV regions are successfully identified.
AB - Following the breakthrough of the microarray technology, the next generation sequencing (NGS) technology further advanced approaches in modern biomedical research. The high-throughput NGS technology is now frequently used in profiling tumor and control samples for the study of DNA copy number variants (CNVs). In particular, the ratio of read count of the tumor sample to that of the control sample is popularly used for identifying CNV regions. We illustrate that a change-point (or a breakpoint) detection method, along with a Bayesian approach, is particularly suitable for identifying CNVs in the reads ratio data. We have written our algorithm into a user friendly R-package, SeqBBS (stands for Bayesian breakpoints search for sequencing data) and applied our method to the sequencing data of reads ratio between the breast tumor cell lines HCC1954 and its matched normal cell line BL1954. Breakpoints that separate different CNV regions are successfully identified.
UR - http://www.scopus.com/inward/record.url?scp=84897710552&partnerID=8YFLogxK
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U2 - 10.1109/GENSIPS.2013.6735925
DO - 10.1109/GENSIPS.2013.6735925
M3 - Conference contribution
AN - SCOPUS:84897710552
SN - 9781479934621
T3 - Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics
SP - 40
EP - 43
BT - 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Proceedings
Y2 - 17 November 2013 through 19 November 2013
ER -