TY - GEN
T1 - Detection of novel tandem duplication with next-generation sequencing
AU - Liu, Xuan
AU - Choi, Shing Wan
AU - Wong, Thomas K.F.
AU - Lam, Tak Wah
AU - Yiu, Siu Ming
PY - 2011
Y1 - 2011
N2 - Detection of structural variations is an important problem. With the next generation sequencing technology, it is relatively easier to obtain a set of paired-end short reads from an individual (the donor). By aligning these reads onto a reference genome (the reference), we are able to detect some of the structural variations that exist between the donor and the reference. A number of tools were developed in this direction. However, these tools are not able to detect all types of variations. In particular, they do not perform well for the detection of tandem duplications which are found to be associated with some diseases. In this paper, we try to solve this problem and developed algorithm to identify novel tandem duplications that exist in donor and vice versa. Experimental results on both simulated and real datasets showed that our solutions are effective.
AB - Detection of structural variations is an important problem. With the next generation sequencing technology, it is relatively easier to obtain a set of paired-end short reads from an individual (the donor). By aligning these reads onto a reference genome (the reference), we are able to detect some of the structural variations that exist between the donor and the reference. A number of tools were developed in this direction. However, these tools are not able to detect all types of variations. In particular, they do not perform well for the detection of tandem duplications which are found to be associated with some diseases. In this paper, we try to solve this problem and developed algorithm to identify novel tandem duplications that exist in donor and vice versa. Experimental results on both simulated and real datasets showed that our solutions are effective.
KW - Novel tandem duplication detection
KW - Structural variations
UR - http://www.scopus.com/inward/record.url?scp=84858955423&partnerID=8YFLogxK
U2 - 10.1145/2147805.2147861
DO - 10.1145/2147805.2147861
M3 - Conference contribution
SN - 9781450307963
T3 - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
SP - 415
EP - 419
BT - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
T2 - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011
Y2 - 1 August 2011 through 3 August 2011
ER -