Dovetail Genomics, LLC

Marco Blanchette

Paul Hartley

Christopher John Troll

Richard E Green

Nicholas H Putnam

Daniel S Rokhsar

Martin P Powers

Elizabeth Munding

Disclosed herein are methods, compositions and systems that facilitate accurate phasing of sequence data such as genomic sequence data through the segmentation and rearrangement of nucleic acid molecules in such a way as to preserve individual molecules' phase or physical linkage information. This is variously accomplished by binding molecules independent of their phosphodiester backbones, cleaving the molecules, ligating, and sequencing the molecules through long-read sequencing technology to recover segment sequence information spanning at least more than one segment.

Generation of phased read-sets for genome assembly and haplotype phasing

Provided herein are methods of releasing nucleic acids from a fixed biological sample comprising contacting the fixed tissue sample to an enzyme. The disclosure further provides methods to quantify and deconvolute a population of mRNA spliced variant isoforms from a cellular transcriptome. Additionally provided herein are methods delivering a barcode to a nucleic acid sample using integrases, nucleic acid samples having barcodes, and nucleic acid libraries thereof.

Sample prep for DNA linkage recovery

The disclosure provides methods to isolate genome or chromosome level structural information from preserved samples. In some cases, samples preserved under conditions where long-range nucleic acid information is believed to be irreparably lost, such as FFPE samples, are treated to recover nucleic acid-protein complexes stabilized as part of the sample preservation process. The complexes are processed so as to recover information regarding which nucleic acids are bound to a common complex, and the information is used to recover genomic structural information.

Recovering long-range linkage information from preserved samples

Disclosed herein are methods, compositions and systems that facilitate accurate phasing of sequence data such as genomic sequence data through the segmentation and rearrangement of nucleic acid molecules in such a way as to preserve individual molecules phase or physical linkage information. This is variously accomplished by binding molecules independent of their phosphodiester backbones, cleaving the molecules, ligating, and sequencing the molecules through long-read sequencing technology to recover segment sequence information spanning at least more than one segment.

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Marco Blanchette