The University of New Mexico

Other

Centrillion Technology Holdings Corporation

Armonica Technologies, Inc.

Szauter, Paul

Edwards, Jeremy Scott

Dimmler, Kirsten

Sinclair, Robert B.

Jeremy Scott Edwards

Steven Roy Julien Brueck

Alexander Neumann

Yuliya Kuznetsova

Edgar A Mendoza

C Jeffrey Brinker

Payman Zarkesh-Ha

Wei Zhou

Justin Costa

Xin Jin

Paul Szauter

Robert B Sinclair

Kirsten Dimmler

Anupama Suryanaraya

Olga Amosova

T Scott Pollom

Yaning Li

Steven Rj Brueck

Suzy Chang

Xun Ding

Steven RJ Brueck

This disclosure describes detecting four genetically distinct kinds of inherited myopathy in horses, referred to as Polysaccharide Storage Myopathy type 2 (PSSM2), or in some cases as Myofibrillar Myopathy (MFM).

Methods of detecting inherited myopathies in horses

Methods and apparatus for long read, label-free, optical nanopore long chain molecule sequencing. In general, the present disclosure describes a novel sequencing technology based on the integration of nanochannels to deliver single long-chain molecules with widely spaced (>wavelength), ˜1-nm aperture 'tortuous' nanopores that slow translocation sufficiently to provide massively parallel, single base resolution using optical techniques. A novel, directed self-assembly nanofabrication scheme using simple colloidal nanoparticles is used to form the nanopore arrays atop nanochannels that unfold the long chain molecules. At the surface of the nanoparticle array, strongly localized electromagnetic fields in engineered plasmonic/polaritonic structures allow for single base resolution using optical techniques.

Innovative nanopore sequencing technology

Nucleic acid sequencing methods and systems, the systems including nanochannel chip including: a nanochannel formed in an upper surface of the nanochannel chip and; a roof covering the nanochannel and comprising nanopores and a field enhancement structure; and a barrier disposed in the nanochannel. The method including: introducing a buffer solution including long-chain nucleic acids to the nanochannel chip; applying a voltage potential across the nanochannel chip to drive the nucleic acids through the nanochannel, towards the barrier, and to translocate the nucleic acids through nanopores adjacent to the barrier, such that bases of each of the nucleic acids pass through the field enhancement structure one base at a time and emerge onto an upper surface of the roof; detecting the Raman spectra of the bases of the nucleic acids as each base passes through the electromagnetic-field enhancement structure; and sequencing the nucleic acids based on the detected Raman spectra.

Manipulating the translation of DNA strands across and through nanopore sequencing systems using Raman signatures to identify DNA bases and methods

Methods and apparatus for long read, label-free, optical nanopore long chain molecule sequencing. In general, the present disclosure describes a novel sequencing technology based on the integration of nanochannels to deliver single long-chain molecules with widely spaced (&#x3e;wavelength), &#x2dc;1-nm aperture 'tortuous' nanopores that slow translocation sufficiently to provide massively parallel, single base resolution using optical techniques. A novel, directed self-assembly nanofabrication scheme using simple colloidal nanoparticles is used to form the nanopore arrays atop nanochannels that unfold the long chain molecules. At the surface of the nanoparticle array, strongly localized electromagnetic fields in engineered plasmonic/polaritonic structures allow for single base resolution using optical techniques.

The disclosure describes a method for sequencing long portions of DNA sequence by assembling a plurality of shorter polynucleotide reads. Generally, the method includes annealing a plurality of primers to a denatured DNA molecule, appending a barcode polynucleotide to the 5' end of the primer, subjecting the DNA molecules to a plurality of cycles of (1) pooling, (2) dividing, and (3) appending a barcode polynucleotide to the 5&#x2032; end of the primer, sequencing the barcode polynucleotides and the genomic DNA, and assembling the short read polynucleotide sequences having identical barcode polynucleotides.

Synthetic long read DNA sequencing

Devices that include a substrate; a source region and a drain region formed within the substrate and having a channel region provided therebetween; a first insulating layer formed over the channel region; a first floating gate formed over the first insulating layer, the first floating gate configured to respond to an analyte in a target material; and a second gate formed over the first floating gate, the second gate capacatively coupled but not electrically connected to the first floating gate.

Double gate ion sensitive field effect transistor

Innovative nanopore sequencing technology including a self-assembled porous membrane

Provided herein are methods and compositions for analyzing epigenetic modifications of genomes. The methods and compositions are suited for complete epigenome sequencing of any modification for which an antibody or an affinity binding agent has been developed. In one aspect, provided herein is a method for analyzing epigenetic modification of a genome. In some embodiments of aspects provided herein, the method further comprises sequencing a sequencing library to generate sequence reads, and assembling the sequence reads with aid of a positional barcode sequence information. In some embodiments of aspects provided herein, the method further comprises determining a location of at least two different epigenetic modifications of the nucleic acid. Another aspect of the present disclosure provides a kit for analyzing an epigenetic modification of a nucleic acid.

Methods for phrasing epigenetic modifications of genomes

This disclosure describes, in one aspect, methods for DNA sequencing and performing epigenomic analyses. Generally, the methods include immobilizing a plurality of copies of a DNA molecule on a surface, stretching at least a portion of the immobilized DNA molecules, and sequencing at least a portion of the immobilized, stretched DNA molecules.

DNA sequencing and epigenome analysis

The disclosure describes a method for sequencing long portions of DNA sequence by assembling a plurality of shorter polynucleotide reads. Generally, The method includes annealing a plurality of primers to a denatured DNA molecule, appending a barcode polynucleotide to the 5' end of the primer, subjecting the DNA molecules to a plurality of cycles of (1) pooling, (2) dividing, and (3) appending a barcode polynucleotide to the 5&#x2032; end of the primer, sequencing the barcode polynucleotides and the genomic DNA, and assembling the short read polynucleotide sequences having identical barcode polynucleotides.

We describe ultra-high throughput polony genome sequencing that can permit, for example, generating raw data to re-sequencing the human genome in about one week (including library prep and sequencing) at a reasonable cost. The methods described herein include one or more of the following: (1) increasing polony sequencing read length, (2) improving library construction and emulsions protocols, (3) increasing bead density and/or moving to alternative clonal amplication strategies (other than emulsion PCR or ePCR), (4) extending software capabilities to allow SNP calls from our new sequencing raw data, (5) Dual Primer Emulsion PCR, and (6) diagnostic method exploiting one or more of the foregoing.

Polony sequencing methods

This disclosure describes, in one aspect, a method for preparing DNA molecule for sequencing. Generally, the method includes fragmenting the DNA molecule into double-stranded fragments; amplifying at least a portion of the double-stranded fragments; circularizing the fragments so that the first end of the fragment comprises a first loop connecting the strands and the second end of the fragment comprises a second loop connecting the strands; annealing a first sequencing primer to the first loop oriented to sequence at least a portion of one strand of the fragment; and annealing a second sequencing primer to the second loop oriented to sequence at least a portion of the other strand of the fragment. In another aspect, this disclosure describes a method for sequencing a DNA molecule. Generally, the method includes fragmenting the DNA molecule into double-stranded fragments; amplifying at least a portion of the double-stranded fragments; circularizing the fragments so that the first end of the fragment comprises a first loop connecting the strands and the second end of the fragment comprises a second loop connecting the strands; and sequencing at least one of the DNA strands.

Growing community of inventors

Albuquerque, NM, United States of America

Jeremy Scott Edwards