Identifying A Library Member By Means Of A Tag, Label, Or Other Readable Or Detectable Entity Associated With The Library Member (e.g., Decoding Process, Etc.) Patents (Class 506/4)
  • Patent number: 10011871
    Abstract: The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.
    Type: Grant
    Filed: February 15, 2013
    Date of Patent: July 3, 2018
    Assignee: Fred Hutchinson Cancer Research Center
    Inventor: Jason H. Bielas
  • Patent number: 9938578
    Abstract: The present disclosure generally pertains to a multiplex method for analyzing samples comprising using polynucleotide amplification to produce amplified products wherein one or more target sequences are tagged with a non-interfering, non-canceling target-specific polynucleotide identification tag, pyrosequencing the amplified products through the non-canceling target-specific polynucleotide identification tag sequence to detect the presence of one or more specific polynucleotide identification tags. The presence of a specific polynucleotide identification tag being correlated with the presence of a specific target sequence.
    Type: Grant
    Filed: September 24, 2013
    Date of Patent: April 10, 2018
    Assignee: iRepertoire, Inc.
    Inventors: Jian Han, Chunlin Wang
  • Patent number: 9896683
    Abstract: Methods for isolating circulating small RNAs, e.g., microRNA (miRNA), from plasma samples, e.g., that comprise using an alkaline phenol:chloroform extraction, and methods of use thereof, including for the detection, prognosis, and/or monitoring of disease in a subject.
    Type: Grant
    Filed: July 29, 2015
    Date of Patent: February 20, 2018
    Assignees: University of Massachusetts, Firefly BioWorks
    Inventors: Victor Ambros, Rosalind Lee, Anthony Patrick Fusco
  • Patent number: 9897532
    Abstract: A system is disclosed that enables the automated measurement of cellular mechanical parameters at high throughputs. The microfluidic device uses intersecting flows to create an extensional flow region where the cells undergo controlled stretching. Cells are focused into streamlines prior to entering the extensional flow region. In the extensional region, each cell's deformation is measured with an imaging device. Automated image analysis extracts a range of independent biomechanical parameters from the images. These may include cell size, deformability, and circularity. The single cell data that is obtained may then be used to in a variety of ways. Scatter density plots of deformability and circularity may be developed and displayed for the user. Mechanical parameters such as deformability and circularity may be gated or thresholded to identify certain cells of interest or sub-populations of interest. Similarly, the mechanical data obtained using the device may be used as cell signatures.
    Type: Grant
    Filed: November 24, 2014
    Date of Patent: February 20, 2018
    Inventors: Dino Di Carlo, Daniel R. Gossett, Henry T. K. Tse
  • Patent number: 9816088
    Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. In some aspects, such methods may comprise steps of: (a) forming a plurality of first vessels each comprising: (i) a single cell, and (ii) a single solid support; (b) copying onto the single solid support: (i) a first copy of a first cell polynucleotide from the single cell, and (ii) a second copy of a second cell polynucleotide from the single cell; (c) forming a plurality of second vessels each comprising (i) a single solid support from the plurality of first vessels, and (ii) a barcoded polynucleotide; and (d) amplifying (i) the first copy and the second copy with a first primer set, and (ii) the barcode with a second primer set, wherein a primer of the first primer set is complementary to a primer of the second set; and (e) forming first and second single cell barcoded sequences.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: November 14, 2017
    Assignee: AbVitro LLC
    Inventors: Francois Vigneault, Adrian Wrangham Briggs
  • Patent number: 9725765
    Abstract: The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.
    Type: Grant
    Filed: September 10, 2012
    Date of Patent: August 8, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Dmitry Pushkarev, Stephen R. Quake, Ayelet Voskoboynik, Michael Kertesz
  • Patent number: 9670526
    Abstract: Methods and related products are disclosed that improve the probability of interaction between a target molecule and a nanopore by capturing the target molecule on a surface comprising the nanopore. The captured target molecule, the nanopore, or both, are able to move relative to each other along the surface. When the leader of the target molecule is in proximity with the nanopore, interaction of the target portion of the target molecule with the nanopore occurs, thereby permitting sensing of the target portion. Confining the target molecule and nanopore in this manner leads to significantly enhanced interaction with the nanopore.
    Type: Grant
    Filed: November 8, 2013
    Date of Patent: June 6, 2017
    Assignee: Stratos Genomics, Inc.
    Inventors: Mark Stamatios Kokoris, Robert N. McRuer
  • Patent number: 9605311
    Abstract: The present invention relates to compositions, methods and systems for analyzing the methylation state of nucleic acids. Some embodiments relate to a compositions, methods and systems for analyzing the methylation state of DNA with a gene array.
    Type: Grant
    Filed: July 10, 2014
    Date of Patent: March 28, 2017
    Assignee: Illumina, Inc.
    Inventor: Henri A. Kester
  • Patent number: 9523128
    Abstract: The present invention provides nucleic acids and peptides, and methods of using the nucleic acids and peptides to identify subjects at risk for a TDP-43 proteinopathy. The invention also provides for an array comprising the nucleic acids and peptides of the invention.
    Type: Grant
    Filed: October 14, 2014
    Date of Patent: December 20, 2016
    Inventors: Nigel J. Cairns, Robert H. Baloh, Alan Pestronk, Michael A. Gitcho, Alison M. Goate
  • Patent number: 9395359
    Abstract: Arrays of single molecules and methods of producing an array of single molecules are described. Arrays with defined volumes between 10 attoliters and 50 picoliters enable single molecule detection and quantitation.
    Type: Grant
    Filed: March 4, 2015
    Date of Patent: July 19, 2016
    Assignee: Trustees of Tufts College
    Inventors: David R. Walt, David M. Rissin
  • Patent number: 9376691
    Abstract: The present invention provides for a modified host cell comprising a heterologous pinene synthase (PS), or enzymatically active fragment or variant thereof, and optionally a geranyl pyrophosphate synthase (GPPS), or enzymatically active fragment or variant thereof, or a fusion protein comprising: (a) a PS and (b) a GPPS linked by a linker.
    Type: Grant
    Filed: November 27, 2013
    Date of Patent: June 28, 2016
    Assignee: The Regents of the University of California
    Inventors: Pamela P. Peralta-Yahya, Jay D. Keasling
  • Patent number: 9347929
    Abstract: Improved resolution and detection of nanoparticles are achieved when a nanopore connecting liquid compartments in a device running on the Coulter principle is provided with fluid lipid walls. The fluid lipid walls are made of a lipid bilayer, and preferably include lipid anchored mobile ligands as part of the lipid bilayer. By varying the nature and concentration of the mobile ligand in the lipid bilayer, multifunctional coatings of lipids are provided.
    Type: Grant
    Filed: February 20, 2012
    Date of Patent: May 24, 2016
    Assignee: The Regents Of The University Of Michigan
    Inventors: Michael Mayer, Erik Yusko, Jerry Yang
  • Patent number: 9297048
    Abstract: The present invention relates to an antibiotic resistance profile for Neisseria gonorrhoeae by assessing the presence of mutations (e.g., SNP) in antibiotic resistant genes that confer bacterial resistance against antibiotics such as penicillin, tetracycline, fluoroquinolones, cephalosporin, macrolides and spectinomycin. There is provided a method and a kit for generating an antibiotic resistance profile for Neisseria gonorrhoeae by utilizing a multiplex PCR to amplify segments of antibiotic-resistant genes, allele-specific primer extension to detect gene mutation, and detection of such gene mutations with gel electrophoresis, capillary electrophoresis, or DNA microarray. The present method provides useful information to physicians relating the antibiotic susceptibility of Neisseria gonorrhoeae against different classes of antibiotics.
    Type: Grant
    Filed: June 2, 2011
    Date of Patent: March 29, 2016
    Assignee: Medical Diagnostic Laboratories, LLC
    Inventors: Sergey Balashov, Eli Mordechai, Martin E. Adelson, Scott E. Gygax
  • Patent number: 9267174
    Abstract: The invention provides a non-invasive technique for the differential detection of multiple genotypes and/or mutations for a plurality of target genes in a biological sample containing genetic material from different genomic sources. Methods are conducted using multiplex amplification of a plurality of target sequences from the biological sample, and sequencing is used to detect and enumerate genetic mutations and chromosomal abnormalities at the single nucleotide level.
    Type: Grant
    Filed: October 26, 2011
    Date of Patent: February 23, 2016
    Assignee: Stanford University
    Inventors: Stephen R. Quake, Wei Gu, Hei-Mun Christina Fan
  • Patent number: 9193997
    Abstract: Methods are provided for the detection and analysis of clonality in a cell population, where parallel sequencing is applied to a nucleic acid sample obtained from the cell population, optionally a population of lymphocytes. Replicate samples are amplified, and sequenced, where identification of coincident sequences in two or more replicates is indicative of clonal expansion.
    Type: Grant
    Filed: December 15, 2011
    Date of Patent: November 24, 2015
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Andrew Fire, Scott D. Boyd, Jason Merker, Kyunga Seo, Eleanor L. Marshall
  • Patent number: 9139874
    Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template. In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.
    Type: Grant
    Filed: July 6, 2012
    Date of Patent: September 22, 2015
    Assignee: Life Technologies Corporation
    Inventors: Jason Myers, Zhoutao Chen, Devin Dressman, Theo Nikiforov
  • Publication number: 20150148241
    Abstract: The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3? end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers.
    Type: Application
    Filed: February 4, 2015
    Publication date: May 28, 2015
    Applicant: Keygene N.V.
    Inventors: Michael Josephus Theresia VAN EIJK, Taco Peter JESSE
  • Publication number: 20150148240
    Abstract: This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns.
    Type: Application
    Filed: December 19, 2014
    Publication date: May 28, 2015
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Timothy H. Bestor, John R. Edwards, Jingyue Ju, Xiaoxu Li
  • Publication number: 20150141270
    Abstract: Provided is a single-stranded nucleic acid aptamer specifically binding to Klebsiella pneumoniae, and a method for detecting Klebsiella pneumoniae by using the same. The aptamer of the present disclosure, and a method, a composition, a kit or a sensor of using the same may be used to specifically detect Klebsiella pneumoniae present in an aqueous environment, foods, and medical samples and also be applied in fields such as sanitary conditions of foods and medical diagnosis.
    Type: Application
    Filed: July 30, 2014
    Publication date: May 21, 2015
    Inventors: Byoung Chan KIM, Yeon Seok KIM, Jin Yang CHUNG, Jong Soo JURNG, Min Young SONG
  • Publication number: 20150133317
    Abstract: Disclosed herein are compositions and methods for sequencing, analyzing, and utilizing samples such as single samples. Also disclosed herein are compositions and methods for matching together two or more sequences from a sample. Also disclosed herein are compositions and methods for expressing and screening molecules of interest.
    Type: Application
    Filed: April 27, 2012
    Publication date: May 14, 2015
    Applicants: Department of Veterans Affairs, The Board of Trustees of the Leland Stanford Junior University
    Inventors: William H. Robinson, Yann Chong Tan, Jeremy Sokolove
  • Publication number: 20150133320
    Abstract: A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.
    Type: Application
    Filed: January 20, 2015
    Publication date: May 14, 2015
    Applicant: ILLUMINA, INC.
    Inventors: Eric H. Kawashima, Laurent Farinelli, Pascal Mayer
  • Publication number: 20150133318
    Abstract: The instant invention is based, at least in part, on the identification of novel methods for the enzymatic enrichment of capped RNAs. The invention provides, e.g., methods for enrichment of capped RNAs, kits for making such capped RNAs, and compositions of enriched RNAs or cDNA libraries derived therefrom.
    Type: Application
    Filed: April 24, 2014
    Publication date: May 14, 2015
    Inventors: Craig C. MELLO, Weifeng GU
  • Publication number: 20150133319
    Abstract: Methods, kits and systems are disclosed for analyzing one or more molecules in a sample. Analyzing the one or more molecules may comprise quantitation of the one or more molecules. Individual molecules may quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing. Quantitation of individual molecules may further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules. The methods may further comprise amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules. The molecules may be DNA, RNA and/or proteins.
    Type: Application
    Filed: February 27, 2013
    Publication date: May 14, 2015
    Inventors: Glenn K. Fu, Stephen P.A. Fodor, Julie Wilhelmy
  • Publication number: 20150126379
    Abstract: The present invention is directed to a method of detecting a genomic rearrangement in a nucleic acid sample with Long Insert Whole Genome Sequencing (LI-WGS). The method may include obtaining a nucleic acid sample and then fragmenting the nucleic acid sample (e.g., via sonication). In particular, the fragmenting may result in the production of a plurality of inserts. Thereafter, the method comprises purifying the plurality of inserts using magnetic beads and then amplifying the purified plurality of inserts. In addition, the method further comprises sequencing the purified and amplified plurality of inserts. In some aspects, the plurality of inserts have a length of between about 800 and about 1,100 base pairs.
    Type: Application
    Filed: October 28, 2014
    Publication date: May 7, 2015
    Inventors: Winnie Liang, John Carpten, David Craig
  • Publication number: 20150126381
    Abstract: The invention combines the advantages of split and mix synthesis with the advantages of template directed synthesis. The method comprises the steps of: a) adding a linker molecule L to one or more reaction wells; b) adding a molecule fragment to each of said reaction wells; c) adding an oligonucleotide identifier to each of said reaction wells; d) subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; e) combining the contents of said one or more reaction wells; and f) contacting the resulting bifunctional molecule(s) of step e) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c).
    Type: Application
    Filed: January 6, 2015
    Publication date: May 7, 2015
    Inventor: Peter Birk Rasmussen
  • Publication number: 20150126380
    Abstract: The present invention relates to a non-destructive method for analyzing maternal DNA of a seed. In this method the DNA may be dislodged from the seed coat surface and may be used to collect information on the genome of the maternal parent of the seed. Also, the present invention provides a high throughput DNA analysis system for large plant populations.
    Type: Application
    Filed: December 5, 2014
    Publication date: May 7, 2015
    Applicant: Rijk Zwaan Zaadteelt en Zaadhandel B.V.
    Inventor: Cornelis Maria Petrus VAN DUN
  • Publication number: 20150111763
    Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using two or more labels and signal ratios to distinguish bases.
    Type: Application
    Filed: May 2, 2013
    Publication date: April 23, 2015
    Inventor: Mark W. Eshoo
  • Publication number: 20150111762
    Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using one or more labels and signal amplitude to distinguish bases.
    Type: Application
    Filed: May 2, 2013
    Publication date: April 23, 2015
    Inventor: Mark W. Eshoo
  • Patent number: 9012367
    Abstract: Disclosed are a method for rapid screening of suitable translational fusion partners (TFPs) capable of inducing expression or secretory production of non-producible proteins, which are difficult to produce in conventional recombinant production methods, from a variety of genetic sources, and protein secretion-inducing TFPs obtained using the method.
    Type: Grant
    Filed: January 30, 2014
    Date of Patent: April 21, 2015
    Assignee: Korea Research Institute of Bioscience and Biotechnology
    Inventors: Jung-Hoon Sohn, Eui-Sung Choi, Jung-Hoon Bae, Eung-Suck Lee, Mi-Kyung Shin
  • Publication number: 20150099646
    Abstract: The invention relates to PCR-based clonality studies for among others early diagnosis of lymphoproliferative disorders. Provided is a set of nucleic acid amplification primers comprising a forward primer, or a variant thereof, and a reverse primer, or a variant thereof, capable of amplifying a rearrangement selected from the group consisting of a VH-JH IGH rearrangement, a DH-JH IGH rearrangement, a VK-JK IGK rearrangement, a VK/intron-Kde IGK rearrangement, a V?-J? IGL rearrangement, a V?-J? TCRB rearrangement, a D?-J? TCRB rearrangement, a V?-J? TCRG rearrangement, a V?-J? TCRD rearrangement, a D?-D? TCRD rearrangement, a D?-J? TCRD rearrangement, a V?-D? TCRD rearrangement, or a translocation selected from t(11;14) (BCL1-IGH) and t(14;18) (BCL2-IGH). The primers can be used in PCR-based clonality studies for early diagnosis of lymphoproliferative disorders and detection of minimal residual disease (MRD). Also provided is a kit comprising at least one set of primers of the invention.
    Type: Application
    Filed: June 23, 2014
    Publication date: April 9, 2015
    Inventors: Jacobus Johannes Maria Van Dongen, Anthonie Willem Langerak, Eduardus Maria Dominicus Schuuring, Jesus Fernando San Miquel, Ramon Garcia Sanz, Antonio Parreira, John Lewis Smith, Frances Louise Lavender, Gareth John Morgan, Paul Anthony Stuart Evans, Michael Kneba, Michael Hummel, Elizabeth Anne Macintyre, Christian Bastard
  • Publication number: 20150099647
    Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.
    Type: Application
    Filed: August 11, 2014
    Publication date: April 9, 2015
    Inventors: Steven Gordon, Phillip A. Veatch
  • Publication number: 20150099648
    Abstract: The present disclosure relates in part to a method for identifying a soybean germline transformant from a population of soybean transformants by incorporating a selection agent within rooting medium used in tissue culture during the soybean transformation process. The soybean germline transformants are selected from a population of soybean transformants which are comprised of a combination of non-germline and germline soybean transformants. The soybean non-germline transformants are identified and eliminated early in the transformation process. The soybean germline transformants are identified and selected for culturing into mature soybean plants. The method is readily applicable for screening and obtaining a soybean germline transformant at an early stage in the soybean transformation process.
    Type: Application
    Filed: October 2, 2014
    Publication date: April 9, 2015
    Inventors: Sivarama Reddy CHENNAREDDY, Dayakar PAREDDY, Jayakumar Pon SAMUEL, Rodrigo SARRIA-MILAN, Toby CICAK
  • Patent number: 8999897
    Abstract: The use of a tag moiety comprising a biotinylation domain, such as biotin carboxyl carrier protein (BCCP), as a protein folding marker and protein solubility enhancer in the orientated surface capture of products of heterologously expressed genes is described. Methods for increasing the solubility of proteins and determining the folded state of a protein are also disclosed. The uses and methods of the invention can be carried out in a multiplexed manner on more than one protein in the formation of libraries. In addition the nucleic acid molecule encoding the biotinylation domain of the tag moiety can be used to increase the proportion of clones in a library that express the protein of interest.
    Type: Grant
    Filed: January 29, 2003
    Date of Patent: April 7, 2015
    Assignee: Sense Proteomic Limited
    Inventors: Mitali Samaddar, Jonathan Michael Blackburn, Darren James Hart, Michael Richard Dyson
  • Publication number: 20150094213
    Abstract: A method of comparative ligand mapping to identify peptide ligands presented by MHC positive cells that distinguish an infected/transfected cell from an uninfected/non-transfected cell is disclosed.
    Type: Application
    Filed: November 10, 2014
    Publication date: April 2, 2015
  • Publication number: 20150087537
    Abstract: A method for sequencing a polynucleotide sample having a barcode sequence includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined order of nucleotide flows; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-correcting code that is (i) designed based on and adapted for use with the predetermined order of nucleotide flows, and (ii) capable of distinguishing any codeword in the error-correcting code from the other codewords in the error-correcting code in the presence of zero, one, and two errors.
    Type: Application
    Filed: October 3, 2014
    Publication date: March 26, 2015
    Inventor: Earl Hubbell
  • Publication number: 20150087535
    Abstract: Methods and compositions are disclosed for measuring low-abundance DNA variants from a complex mixture of DNA molecules. Embodiments of the methods allow for extremely sensitive detection and can distinguish true variants from sequencer misreads and PCR misincorporations.
    Type: Application
    Filed: March 13, 2013
    Publication date: March 26, 2015
    Inventor: Abhijit Ajit Patel
  • Publication number: 20150087536
    Abstract: The present invention is a method for measuring the amount of at least one molecule in a biological sample, the method comprising a) combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s); b) separating bound from unbound molecules; and c) quantifying the molecule(s) bound to the or each aptamer, wherein quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer. Uses of and products derived from the method are also contemplated.
    Type: Application
    Filed: September 5, 2014
    Publication date: March 26, 2015
    Applicant: Caris Life Sciences Switzerland Holdings GmbH
    Inventors: Clive Gavin BROWN, Koen KAS, Sven Agnes Jan EYCKERMAN
  • Publication number: 20150087534
    Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.
    Type: Application
    Filed: March 6, 2013
    Publication date: March 26, 2015
    Inventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
  • Publication number: 20150080234
    Abstract: The present disclosure provides technologies for achieving cell patterning, as well as patterned cell arrays achieved with such technologies. Provided apparatus and methods are useful in a variety of contexts and provide particular advantages with respect to assessing living cell arrays and/or their responsiveness to stimuli, including identifying and/or characterizing complex cellular responses.
    Type: Application
    Filed: September 16, 2014
    Publication date: March 19, 2015
    Inventors: John Christopher Love, Ayca Yalcin Ozkumur, Brittany Anne Thomas
  • Publication number: 20150080233
    Abstract: A method of generating a high resolution two-dimensional image of a sample comprising cells and extracellular structures is provided. In certain embodiments, the method comprises: labeling a sample with at least one mass tag, thereby producing a labeled sample; scanning the sample with a secondary ion mass spectrometer (SIMS) ion beam to generate a data set that comprises spatially-addressable measurements of the abundance of the mass tag across an area of the sample; and outputting the data set. In many embodiments, the data set contains the identity and abundance of the mass tag. A system for performing the method is also provided.
    Type: Application
    Filed: September 11, 2014
    Publication date: March 19, 2015
    Inventors: Sean C. Bendall, Garry P. Nolan, Robert M. Angelo
  • Publication number: 20150080232
    Abstract: This invention provides nucleoside triphosphate analogues having the structure: wherein B is a base and is adenine, guanine, cytosine, uracil or thymine, wherein R? is an OH or an H, and wherein R? is azidomethyl, a hydrocarbyl, or a substituted hydrocarbyl, and which has a Raman spectroscopy peak with wavenumber from 2000 cm?1 to 2300 cm?1 or a Fourier transform-infrared spectroscopy spectroscopy peak with wavenumber from 2000 cm?1 to 2300 cm?1, and also to methods of DNA sequencing and SNP detection.
    Type: Application
    Filed: May 23, 2012
    Publication date: March 19, 2015
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Jian Wu, Zengmin Li
  • Publication number: 20150080235
    Abstract: Described herein are compositions and methods for diagnosing or monitoring type 1 diabetes.
    Type: Application
    Filed: September 18, 2014
    Publication date: March 19, 2015
    Inventor: Sahar Usmani-Brown
  • Publication number: 20150072874
    Abstract: Provided is a method for detection of HLA-A*31:01 allele. One or more single nucleotide polymorphisms which characterize HLA-A*31:01 are analyzed and the presence or absence of HLA-A*31:01 is determined based on the result of the analysis.
    Type: Application
    Filed: February 28, 2013
    Publication date: March 12, 2015
    Inventors: Masayuki Aoki, Michiaki Kubo, Naoya Hosono
  • Publication number: 20150072875
    Abstract: This disclosure relates to methods for identifying target nucleic acids in a sample by detecting an amplified sequence corresponding to the target using a detectable probe and by monitoring its melting temperature (Tm).
    Type: Application
    Filed: September 2, 2014
    Publication date: March 12, 2015
  • Publication number: 20150072873
    Abstract: A method of retrieving a subset of polynucleotide molecules from a mixture of polynucleotide molecules includes receiving a mixture of nucleotide sequences comprising one or more polynucleotide molecules, synthesizing one or more identifier (ID) regions onto the one or more polynucleotide molecules, and sequencing members of the population of polynucleotide molecules to associate the sequence of one or more of the molecules (the “Polynucleotide Sequence”) with the sequence of the attached ID region (the “ID Sequence”). The method also includes generating a bead-bound library of one or more beads comprising subsets of identical polynucleotide molecules. Each bead is identified by the ID Sequence of the associated Polynucleotide Sequence.
    Type: Application
    Filed: May 2, 2014
    Publication date: March 12, 2015
    Inventors: Austen Heinz, Anselm Levskaya, John T. Mulligan
  • Publication number: 20150065358
    Abstract: The present invention relates to a method for verifying the integrity of biological source samples subjected to multistep bioassays that comprise massively parallel sequencing of the sample genomic nucleic acids. The integrity of the biological source samples is verified using unique marker nucleic acids that are combined with the biological source sample, and are sequenced concomitantly with the genomic nucleic acids of the biological source sample. The method provides verification of individual samples in single- and multiplex massively parallel sequencing assays.
    Type: Application
    Filed: March 30, 2012
    Publication date: March 5, 2015
    Inventors: David A. Comstock, Anupama Srinivasan
  • Publication number: 20150065359
    Abstract: A 3D organotypic culture which phenocopies aggressive, invasive cancer and methods of use thereof are provided.
    Type: Application
    Filed: September 4, 2014
    Publication date: March 5, 2015
    Inventor: Anil K. Rustgi
  • Publication number: 20150057164
    Abstract: Provided is a single construct combining a sequence encoding an RNAi molecule, a sequence encoding a reporter, and a target sequence specific for the RNAi molecule. The construct can be used to determine the potency of the encoded RNAi molecule in a direct and unbiased way. These results can be used to inform the design of potent RNAi molecules of various types and can be extended to several other applications, including: (1) generation of tiled libraries comprising every possible RNAi molecule-encoding sequence for a given gene target; (2) large-scale parallel validation of RNAi molecules targeting many genes to generate validated RNAi molecule-encoding libraries; (3) experimental comparison of design algorithms and strategies; and (4) investigation of RNAi biology in target site mutagenesis assays by screening pools containing single nucleotide changes in target sites and/or in the RNAi molecule to identify the most relevant sequence characteristics of potent RNAi-target site predictions.
    Type: Application
    Filed: November 5, 2014
    Publication date: February 26, 2015
    Inventors: Christof FELLMANN, Scott W. LOWE, Gregory J. HANNON, Johannes Ekkehart ZUBER
  • Publication number: 20150051088
    Abstract: Provided herein is technology relating to next-generation sequencing and particularly, but not exclusively, to methods and compositions for preparing a next-generation sequencing library comprising short overlapping DNA fragments and using the library to sequence one or more target nucleic acids.
    Type: Application
    Filed: August 19, 2014
    Publication date: February 19, 2015
    Inventor: Dae Hyun Kim
  • Publication number: 20150051089
    Abstract: Compositions and methods are described for highly sensitive quantification of the relative representation of DNA from adaptive immune cells (e.g., T and/or B lymphocytes) in DNA extracted from complex mixtures of cells that include cells which are not adaptive immune cells. Included are methods for determining the relative presence in a tumor of tumor infiltrating lymphocytes (TIL), the relative presence of lymphocytes infiltrating a somatic tissue that is the target of an autoimmune disease, and the relative presence of lymphocytes infiltrating a transplanted organ.
    Type: Application
    Filed: August 28, 2014
    Publication date: February 19, 2015
    Inventors: Harlan S. Robins, Robert J. Livingston