Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2019 Dec 11;9:18795. doi: 10.1038/s41598-019-55455-6

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Identification of amplicon structure (AS) using copy number variation (CNV) and structural variation (SV). Following low coverage whole genome sequencing of tumor DNA we detected and analyzed structural variation (SV) using BreakDancer and enumerated copy number (CN) using Control-FREEC. The data was integrated and further analyzed using FindAmpliconSTructure: FAST, to identify regions with genomic amplification and infer amplicon structure (AS). (A) Identification of inverted duplication (ID) based amplification: A break-point of type Inversion (INV) was found by BreakDancer between Pos1 and Pos2 (chr2: 209,745,116 and chr2: 209,749,286). A segment (chr2:208,605,000-209,745,000 in 7 copies) was found by FreeC, the right edge of which coincides with Pos1 and Pos2. This combination delineates an amplicon structure of Inverted duplication (ID), in which the segment is repeated head-to-head. (B) Identification of tandem repeat (TR) based amplification: A break-point of type Internal-Translocation (ITX) was found by BreakDancer between Pos1 and Pos2 (chr4: 49,121,104 and chr4: 49,151,838). A segment (chr4: 49,080,000-49,170,000 in 54 copies) was found by FreeC, coinciding with Pos1 and Pos2, as shown. This combination delineates an amplicon structure of Tandem Repeat (TR), in which the segment is repeated head-to-tail. (C) Identification of double minute (DM) based amplification: A break-point of type inter-chromosomal translocation (CTX) was found by BreakDancer between Pos1 and Pos2 (chr5: 3,209,205 and chr8: 119,804,561). Two segments were found by FreeC (chr5: 2,145,000-3,210,000 in 12 copies, and chr8: 117,405,000-119,805,000 in 12 copies), one edge of each segment coincides with one of the break-points’ positions. This combination delineates an amplicon structure of Double Minute (DM), in which segments from different chromosomes are linked. The following link to a session in UCSC Browser⁵³ shows the CN and SV tracks of samples.