10X, BioNano Publishes De Novo Assembly

By Bio-IT World Staff

May 10, 2016 Yesterday, 10x Genomics announced the publication of a study in Nature Methods highlighting the benefits of their GemCode Technology to generate high-quality assemblies of complex genomes with their proprietary Linked-Read approach. (doi:10.1038/nmeth.3865) The article demonstrates a new strategy for performing rapid, accurate and cost-effective de novo genome assembly using 10x Genomics’ Linked-Reads in combination with technologies from BioNano. 

The GemCode Platform was officially launched last year. A new instrument was announced in February that  uses the same basic technology, but supports a roughly tenfold improvement in the number of separate barcodes that can be used on one sample, up to around one million.

“After working in this field for many years, we are very excited to find a clear path to de novo sequence assembly of complex genomes,” said study author Pui-Yan Kwok, University of California, San Francisco, in the press release.  "The 10X Genomics’ Linked-Read data is the critical component that allows us to build long-range phased assemblies and map breakpoints of structural variations to single basepair resolution.  Our approach makes high quality de novo genome sequence assemblies readily accessible to any researcher interested in genome analysis.”

The study evaluated the combination of 10x Genomics’ Linked-Reads with Illumina short reads and BioNano’s genome map data to achieve de novo genome assembly. For proof-of-concept, de novo assembly of human genome NA12878 was conducted. As a result, the 10x-BioNano assembly showed higher contiguity than and comparable accuracy with previous high-quality NA12878 assemblies performed with PacBio and Illumina-based systems with mate-pair libraries. The assembly also spanned repetitive and other complex regions. As a result of the assembly, approximately 14.3 Mb of novel genome sequences were obtained.

“The results of this study clearly show the unique value of using Linked-Reads to provide long-range information for a better understanding of genome structure, phasing and de novo assembly,” said Serge Saxonov, co-founder and chief executive officer of 10x Genomics in a statement.  

In addition to scientists from 10x Genomics and BioNano Genomics, the study included researchers from The Cardiovascular Research Institute; the Institute for Human Genetics; the Department of Dermatology, University of California San Francisco and the Department of Molecular and Cell Biology, University of Cape Town.