Innovation and Partnerships Office

Long-range Barcode Labeled Sequencing for Efficient Genome and Metagenome Assembly IB-3019

APPLICATIONS OF TECHNOLOGY:

  • Reduces complexity of genome
  • Differentiates similar regions from mixed genomes, i.e., mixed cancer and normal cells from cancer tissue
  • Enables haplotype genome sequencing
  • Enables complex genome and metagenome assembly

ADVANTAGES:

  • Sequences and assembles a large number of long single DNA molecules without indexing during library construction
  • Cost effective and easy to process
  • Operates with extremely low DNA quantities
  • No cloning required

ABSTRACT:

Scientists at Berkeley Lab have developed a Long-range Barcode Labeling Sequencing (LBL-Seq) technology that can be used to sequence thousands of large, single DNA molecules (>10kb) in parallel using short read sequencers. The scientists demonstrated that >10kb DNA can be inserted into emulsion droplets and amplified to generate enough barcode labeled DNA material for mulitplex sequencing. Until now, it had not been possible to use a single 10kb DNA molecule as a sequencing template.

The Berkeley Lab technology applies many emulsion droplets for clonal amplification of thousands of large, single DNA molecules using hundreds of barcoded primers. By sequencing barcode labeled DNA and sorting reads based on their barcode sequences, short reads derived from the original DNA can be used for assembly of large contigs corresponding to original DNA templates.

LBL-Seq reduces the complexity of the original genomic DNA samples and enables assembly of long contigs from complex genomes containing a high percentage of repetitive sequences. Long contig sequences can be used to detect genetic variations in the DNA sample. Since barcoded reads are derived from large, single DNA molecules, the assembled sequences contain haploid genotype information, which can be used to differentiate closely related chromosomes in the polyploid genome.

LBL-Seq can be used to efficiently sequence and assemble a metagenome with reduced complexity. This is achieved by random selection of a limited number of large, single DNA molecules for amplification and deep sequencing coverage to these DNA molecules. Barcode labeling of DNA using LBL-Seq further reduces complexity because sequence reads can be binned into small data sets and assembled into large contigs, which are useful for annotation of genes and pathways in microbial community.

DEVELOPMENT STAGE:  Proven principle.

STATUS: Patent pending. Available for licensing or collaborative research.

SEE THESE OTHER BERKELEY LAB TECHNOLOGIES IN THIS FIELD:

Lab-on-a-Chip Device for Massively Parallel DNA Assembly and Functional Screening, EJIB-2934

j5: Automated DNA Assembly Design Software, ECRB-2836

REFERENCE NUMBER: IB-3019