Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line
Tóm tắt
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 for de 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. 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 with KpnI 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. Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-based de 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.
Tài liệu tham khảo
Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, et al. Origins and functional impact of copy number variation in the human genome. Nature. 2010;464(7289):704–12. doi:10.1038/nature08516.
Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363–76. doi:10.1038/nrg2958.
Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, et al. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell. 2010;143(5):837–47. doi:10.1016/j.cell.2010.10.027.
Yao F, Kausalya JP, Sia YY, Teo ASM, Lee WH, Ong AGM, et al. Recurrent fusion genes in gastric cancer: CLDN18-ARHGAP26 induces loss of epithelial integrity. Cell Rep. 2015. doi:10.1016/j.celrep.2015.06.020.
Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol. 2013;31(2):135–41. doi:10.1038/nbt.2478.
Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. GigaScience. 2014;3:11. doi:10.1186/2047-217X-3-11.
Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol. 2012;30(8):771–6. doi:10.1038/nbt.2303.
Ray M, Goldstein S, Zhou S, Potamousis K, Sarkar D, Newton MA, et al. Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis. BMC Genomics. 2013;14:505. doi:10.1186/1471-2164-14-505.
Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, et al. High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A. 2010;107(24):10848–53. doi:10.1073/pnas.0914638107.
Antonacci F, Kidd JM, Marques-Bonet T, Teague B, Ventura M, Girirajan S, et al. A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nat Genet. 2010;42(9):745–50. doi:10.1038/ng.643.
Verzotto D, Teo ASM, Hillmer AM, Nagarajan N, Index-based map-to-sequence alignment in large eukaryotic genomes. Fifth RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-Seq 2015). Warsaw, Poland: Cold Spring Harbor Labs Journals; 2015. doi:10.1101/017194.
Verzotto D, Teo ASM, Hillmer AM, Nagarajan N. OPTIMA: Sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis. GigaScience (accepted).
Verzotto D, Teo ASM, Hillmer AM, Nagarajan N. Supporting software for OPTIMA, a tool for sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis. GigaScience Database. 2015. http://dx.doi.org/10.5524/100165.
Anantharaman TS, Mishra B, Schwartz DC. Genomics via optical mapping. II: Ordered restriction maps. J Comput Biol. 1997;4(2):91–118.
Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56–65. doi:10.1038/nature11632.
Teo ASM, Verzotto D, Yao F, Nagarajan N, Hillmer AM. Supporting single-molecule optical genome mapping data from a human HapMap and a colorectal cancer cell line. GigaScience Database. http://dx.doi.org/10.5524/100182.