Detecting copy number changes and structural rearrangements using DNA sequencing Book Section
| Author: | Seshan, V. E. |
| Editors: | Datta, S.; Nettleton, D. |
| Article/Chapter Title: | Detecting copy number changes and structural rearrangements using DNA sequencing |
| Title Series: | Frontiers in Probability and the Statistical Sciences |
| Abstract: | Chromosomal abnormalities in the form of deletions, duplications, inversions and translocations are common in cancer. These changes feed the oncogenic process by affecting genes that are involved in tumor growth. Next generation sequencing has aided our ability to study these changes at very high resolution. In this chapter we will describe the nature of these data and the information contained in them for the detection of the structural changes. We will present the circular binary segmentation algorithm for the segmentation of array based copy number data and adapt it to NGS data. We will also present a method for the detection of somatic structural rearrangement. We will illustrate these methods using data from breast cancer cell line (tumor) along with its blood (normal) counterpart generated by the cancer cell-line encyclopedia project. |
| Keywords: | chromosome; gene; biology; algorithm; tumors; hybridization; circular binary segmentation; resolution; array cgh data; comparative genomic; cancer |
| Book Title: | Statistical Analysis of Next Generation Sequencing Data |
| ISBN: | 978-3-319-07212-8 |
| Publisher: | Springer |
| Publication Place: | Cham, Switzerland |
| Date Published: | 2014-01-01 |
| Start Page: | 355 |
| End Page: | 378 |
| Language: | English |
| ACCESSION: | WOS:000358056800019 |
| PROVIDER: | wos |
| DOI: | 10.1007/978-3-319-07212-8_18 |
| Notes: | Book Chapter: 18 -- Source: Wos |
