Aug 30, 2016

Accessible de novo assembly of phased genomes

Shauna Clark

DNA sequencing has been an important tool for improving our understating of human genetic variation; however, limitations for gaining a complete genomic picture still exist.  One such hurdle is the current haploid representation of a diploid human genome.  When represented in this manner, the human genome reference takes the average over haplotypes, which doesn’t work very well when maternal and paternal alleles differ from each other and/or the reference.  The ability to assemble phased de novo human genomes will help provide a more complete picture of human genetic variation, especially for complex structural variations and important cis v. trans variant relationships.

The article, "A hybrid approach for de novo human genome sequence assembly and phasing" (Kwok, et al.)

in the May 2016 issue of Nature Methods demonstrates a new strategy for performing rapid, accurate and cost-effective de novo genome assembly using 10x Genomics’ Linked-Reads in combination with other technologies.   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 to 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.

"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 Pui-Yan Kwok, M.D., Ph.D., Henry Bachrach Distinguished Professor at the University of California, San Francisco.  "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 paper is available online from Nature Methods here:

Read the 10x Genomics press release here:

To learn more about 10x Genomics’ de novo Assembly Solutions, visit /products.