Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Teo, Audrey; Verzotto, Davide; Yao, Fei; Nagarajan, Niranjan; Hillmer, Axel
• Is Part Of: GigaScience. Volume 4:Issue 1(2015)
• Page Start: 1
• Page End: 6
• Publication Date: 2015-12
• Subjects: Optical mapping -- Genomic mapping -- Cancer genome -- Genome structure -- Single-molecule restriction mapping; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1186/s13742-015-0106-1
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract Background Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35–300 bases remains a challenge. Single-molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and as such are suitable for the identification of large-scale genome structural variations, and forde novo genome assemblies when combined with short-read NGS data. Here we present optical mapping data for two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116. Findings High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs, followed by DNA extraction under mild conditions. Genomic DNA was digested withKpn I and 310, 000 and 296, 000 DNA molecules (≥150 kb and 10 restriction fragments), respectively, were analyzed per cell line using the Argus optical mapping system. Maps were aligned to the human reference by OPTIMA, a new glocal alignment method. Genome coverage of 6.8× and 5.7× was obtained, respectively; 2.9× and 1.7× more than the coverage obtained with previously available software. Conclusions Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-basedde novo assemblies. OPTIMA is an efficient new alignment method; our optical mapping data provide a resource for genome structure analyses of the human HapMap reference cell line GM12878, and the colorectal cancer cell line HCT116.