Provided are integrated analysis devices having features of macroscale and nanoscale dimensions, and devices that have reduced background signals and that reduce quenching of fluorophores disposed within the devices. Related methods of manufacturing these devices and of using these devices are also provided.
Disclosed herein includes systems, devices, and methods for determining a B-allele frequency (BAF) value (e.g., a normalized BAF value) of a SNP for a test sample obtained from a test subject (e.g., a human subject) from genome mapping (GM) data, such as optical genome mapping (OGM) data or electronic genome mapping (EGM) data.
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
An imaging apparatus and software for genomic analysis in
scientific or medical research; an imaging system, namely,
an imaging apparatus and software sold as a unit, for
genomic analysis in scientific or medical research; software
for genomic analysis used for medical diagnostic purposes;
solid state substrates, namely, plates, chips, and wafers
for use in scientific or medical research, having a pattern
of channels for confining and linearizing biopolymer samples
(term considered too vague by the International Bureau
pursuant to Rule 13 (2) (b) of the Regulations); disposable
substrates, namely, plates, chips, and wafers for use in
scientific or medical research, having a pattern of channels
to facilitate genomic imaging and analysis (term considered
too vague by the International Bureau pursuant to Rule 13
(2) (b) of the Regulations); medical diagnostic imaging
software. A medical diagnostic imaging system, namely, an imaging
apparatus for genomic analysis (term considered too vague by
the International Bureau pursuant to Rule 13 (2) (b) of the
Regulations); a medical imaging apparatus for genomic
analysis (term considered too vague by the International
Bureau pursuant to Rule 13 (2) (b) of the Regulations);
solid state substrates, namely, plates, chips, and wafers
for use in clinical medicine, having a pattern of channels
for confining and linearizing biopolymer samples (term
considered too vague by the International Bureau pursuant to
Rule 13 (2) (b) of the Regulations); disposable substrates,
namely, plates, chips, and wafers for use in clinical
medicine, having a pattern of channels to facilitate genomic
imaging and analysis (term considered too vague by the
International Bureau pursuant to Rule 13 (2) (b) of the
Regulations).
4.
METHODS AND DEVICES FOR SINGLE-MOLECULE WHOLE GENOME ANALYSIS
Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g. determining structural variations and copy number variations between individuals.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Downloadable or recorded software in the field of genomic
bioinformatics for processing, storing, analyzing,
presenting, interpreting, and sharing genomic data; software
for genomic analysis used for medical diagnostic purposes,
or in scientific, clinical, or medical research; genomic
data analysis software. Software as a service (SAAS) or platform as a service (PAAS)
featuring software in the field of genomics for processing,
storing, analyzing, presenting, interpreting, and sharing
genomic data; product research and development and
consulting services for others in the fields of genomic
bioinformatics and data analysis; genomic data analysis
services for scientific, clinical, and medical research
purposes. Genomic data analysis services for medical diagnostic
purposes.
09 - Scientific and electric apparatus and instruments
Goods & Services
Nucleic acid extraction and purification system, comprised
of laboratory equipment, namely, a laboratory apparatus that
utilizes isotachophoresis to extract, purify, isolate and
concentrate nucleic acid from biological samples
incorporating downloadable software, and nucleic acid
fluidics chips.
09 - Scientific and electric apparatus and instruments
Goods & Services
(1) Nucleic acid extraction and purification system, comprised of laboratory equipment, namely, a laboratory apparatus that utilizes isotachophoresis to extract, purify, isolate and concentrate nucleic acid from biological samples incorporating downloadable software, and nucleic acid fluidics chips.
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
(1) An imaging apparatus and software for genomic analysis in scientific or medical research; an imaging system, namely, an imaging apparatus and software sold as a unit, for genomic analysis in scientific or medical research; software for genomic analysis used for medical diagnostic purposes; solid state substrates, namely, plates, chips, and wafers for use in scientific or medical research, having a pattern of channels for confining and linearizing biopolymer samples (term considered too vague by the International Bureau pursuant to Rule 13 (2) (b) of the Regulations); disposable substrates, namely, plates, chips, and wafers for use in scientific or medical research, having a pattern of channels to facilitate genomic imaging and analysis (term considered too vague by the International Bureau pursuant to Rule 13 (2) (b) of the Regulations); medical diagnostic imaging software.
(2) A medical diagnostic imaging system, namely, an imaging apparatus for genomic analysis (term considered too vague by the International Bureau pursuant to Rule 13 (2) (b) of the Regulations); a medical imaging apparatus for genomic analysis (term considered too vague by the International Bureau pursuant to Rule 13 (2) (b) of the Regulations); solid state substrates, namely, plates, chips, and wafers for use in clinical medicine, having a pattern of channels for confining and linearizing biopolymer samples (term considered too vague by the International Bureau pursuant to Rule 13 (2) (b) of the Regulations); disposable substrates, namely, plates, chips, and wafers for use in clinical medicine, having a pattern of channels to facilitate genomic imaging and analysis (term considered too vague by the International Bureau pursuant to Rule 13 (2) (b) of the Regulations).
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
(1) Downloadable or recorded software in the field of genomic bioinformatics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data; software for genomic analysis used for medical diagnostic purposes, or in scientific, clinical, or medical research; genomic data analysis software. (1) Software as a service (SAAS) or platform as a service (PAAS) featuring software in the field of genomics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data; product research and development and consulting services for others in the fields of genomic bioinformatics and data analysis; genomic data analysis services for scientific, clinical, and medical research purposes.
(2) Genomic data analysis services for medical diagnostic purposes.
G01N 35/02 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
G01N 35/02 - Automatic analysis not limited to methods or materials provided for in any single one of groups Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
Top Hat illumination biological sample imaging devices are provided. Aspects of the imaging devices include: a laser illumination source configured to produce a collimated gaussian beam having a specific diameter; a beam converter configured to convert the collimated gaussian beam into a collimated, uniform irradiance over a region in space; a sample interrogation location in light receiving relationship with the beam converter; and a detector in light receiving relationship with a biological sample interrogation location. Also provided are methods of using the devices, e.g., in genome mapping and other applications.
G01N 21/84 - Systems specially adapted for particular applications
G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
Top Hat illumination biological sample imaging devices are provided. Aspects of the imaging devices include: a laser illumination source configured to produce a collimated gaussian beam having a specific diameter; a beam converter configured to convert the collimated gaussian beam into a collimated, uniform irradiance over a region in space; a sample interrogation location in light receiving relationship with the beam converter; and a detector in light receiving relationship with a biological sample interrogation location. Also provided are methods of using the devices, e.g., in genome mapping and other applications.
Disclosed herein include embodiments of a method of positioning (or leveling or moving) a sample (e.g., adjusting the tip-axis and the tilt axis of the sample or T nT motion stage). A sample can be provided. The sample can be in a sample chip or cartridge. In some embodiments, a method of positioning a sample can comprise: providing a sample. The method can comprise: placing the sample, or the sample chip or cartridge, on (or onto or into) a sample carrier of a TnT motion stage of a motion platform of the present disclosure. The TnT motion stage can be on an x-y motion stage of the motion platform.
Disclosed herein include a motion platform comprising a base; an x-y motion stage on the base; a tip-axis adjustment engagement component (e.g., a pawl) and/or a tilt-axis adjustment pawl engagement component (e.g., a pawl) on the base; a tip and tilt (TnT) motion stage on the x-y motion stage. The TnT motion stage can comprise: a sample carrier, two tip-axis goniometers with different slopes relative to one axis of the x-axis and the y-axis, and/or a tilt-axis slanted linear bearing. The TnT motion stage can comprise: a tip-axis complementary adjustment engagement component (e.g., a notch), and a tilt-axis complementary adjustment engagement component (e.g., a notch).
Methods are provided for detecting and quantitating molecules using fluidics. In some embodiments, the methods comprise minimizing or eliminating biases caused by label density, or minimizing or eliminated biases caused by factors other than label density. In some embodiments, the methods comprise automated identification of genetic structural variation. In some embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.
Disclosed herein includes systems, devices, and methods for determining a B-allele frequency (BAF) value (e.g., a normalized BAF value) of a SNP for a test sample obtained from a test subject (e.g., a human subject) from optical genome mapping (OGM) data.
G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G16B 20/40 - Population geneticsLinkage disequilibrium
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
An imaging apparatus and software for genomic analysis in
scientific or medical research; an imaging system, namely,
an imaging apparatus and software sold as a unit, for
genomic analysis in scientific or medical research; software
for genomic analysis used for medical diagnostic purposes;
solid state substrates, namely, plates, chips, and wafers
for use in scientific or medical research, having a pattern
of channels for confining and linearizing biopolymer
samples; disposable substrates, namely, plates, chips, and
wafers for use in scientific or medical research, having a
pattern of channels to facilitate genomic imaging and
analysis; software for genomic analysis. A medical diagnostic imaging system, namely, an imaging
apparatus for genomic analysis; a medical imaging apparatus
for genomic analysis; solid state substrates, namely,
plates, chips, and wafers for use in clinical medicine,
having a pattern of channels for confining and linearizing
biopolymer samples; disposable substrates, namely, plates,
chips, and wafers for use in clinical medicine, having a
pattern of channels to facilitate genomic imaging and
analysis.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Reagents for use in preparing molecules for genomic research
and analysis; a kit for extracting and labeling biopolymers
for research purposes, containing enzymes, color reagents,
buffers, and other reagents; polynucleotide isolation and
purification kit consisting of enzymes, color reagents,
buffers, and other reagents used for scientific or medical
research purposes; kits for extracting and labeling
polynucleotide molecules for research purposes, containing
enzymes, color reagents, buffers, and other reagents;
reagents for use in preparing polynucleotide molecules for
genomic research; diagnostic kits containing enzymes, color
reagents, buffers, and other reagents for extracting and
labeling polynucleotide molecules. Reagents for use in clinical medicine for preparing
molecules for genomic analysis; a medical diagnostic kit
containing enzymes, color reagents, buffers, and other
reagents for extracting and labeling biopolymers. An imaging system, namely, an imaging apparatus and
software, for the analysis of biopolymer samples in
scientific or medical research; software used in the
analysis of biopolymer samples for medical diagnostic
purposes; software used in the analysis of biopolymer
samples for scientific or medical research; an imaging
apparatus for use in the analysis of biopolymer samples in
scientific or medical research; nanofluidic devices, namely,
solid state substrates in the nature of plates, chips and
wafers, and software, both of the foregoing for genomic
imaging and analysis; an imaging apparatus and software for
genomic analysis in scientific or medical research; an
imaging system, namely, an imaging apparatus and software
sold as a unit, for genomic analysis in scientific or
medical research; software for genomic analysis used for
medical diagnostic purposes, or in scientific, clinical or
medical research; genomic data analysis software; software
for interpreting and analyzing data generated by an imaging
apparatus for the purpose of studying biopolymer samples;
solid state substrates, namely, plates, chips, and wafers
for use in scientific or medical research, having a pattern
of channels for confining and linearizing biopolymer
samples; disposable substrates, namely, plates, chips, and
wafers for use in scientific or medical research, having a
pattern of channels to facilitate genomic imaging and
analysis; solid state substrates, namely, plates, chips and
wafers having a plurality of fluid passageways for confining
and linearizing macromolecules including biopolymer
molecules for scientific or medical research; nanochannel
wafers, for scientific or medical research, used in
instruments for genomic analysis; downloadable or recorded
software in the field of genomic bioinformatics for
processing, storing, analyzing, presenting, interpreting,
and sharing genomic data. A medical diagnostic imaging system, namely, an imaging
apparatus and software sold as a unit and used in the
analysis of biopolymer samples; a medical diagnostic imaging
apparatus used in the analysis of biopolymer samples; a
medical diagnostic imaging system, namely, an imaging
apparatus and software sold as a unit for genomic analysis;
a medical imaging apparatus for genomic analysis; solid
state substrates, namely, plates, chips, and wafers for use
in clinical medicine, having a pattern of channels for
confining and linearizing biopolymer samples; disposable
substrates, namely, plates, chips, and wafers for use in
clinical medicine, having a pattern of channels to
facilitate genomic imaging and analysis; medical diagnostic
solid state substrates, namely, plates, chips and wafers for
confining and linearizing macromolecules including
biopolymer molecules; nanochannel wafers, for use in
clinical medicine, used in instruments for genomic analysis;
medical specimen collection and transportation kit comprised
of blood collection tubes, foam container for tubes,
absorbent pad, biohazard bag, medical indicator marker and
labels, for molecular and genetic testing for disorders of
childhood development. Product research and development and consulting services for
others in the fields of biopolymer imaging and analysis;
genomic mapping, genomic imaging, and genomic analysis
services for scientific research purposes; medical,
pharmaceutical, biotechnology, and scientific research and
consulting services in the field of genetics, namely,
analysis of relationships between genetic variants and
neurodevelopmental disorders, genetic research, bio-marker
discovery research, and pheno-typing for identifying,
testing and developing diagnostics and treatments for human
diseases and human disorders; software as a service (SAAS)
or platform as a service (PAAS) featuring software in the
field of genomics for processing, storing, analyzing,
presenting, interpreting, and sharing genomic data; product
research and development and consulting services for others
in the fields of genomic bioinformatics and data analysis;
genomic data analysis services for scientific, clinical, and
medical research purposes. Genomic mapping, genomic imaging, genomic analysis, and
genomic data analysis services for medical diagnostic
purposes; providing medical analysis services in the nature
of relationships between genetic variants and
neurodevelopmental disorders for identifying, testing, and
developing diagnostic tools and treatments for such
disorders; medical testing services, namely, molecular and
genetic testing for disorders of childhood development;
providing information related to medical testing services
via an internet website for medical professionals and
medical patients; providing molecular and genetic medical
testing results via the internet.
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
Solid state substrates, namely, plates, chips, and wafers
for use in scientific or medical research, having a pattern
of channels for confining and linearizing biopolymer
samples; disposable substrates, namely, plates, chips, and
wafers for use in scientific or medical research, having a
pattern of channels to facilitate genomic imaging and
analysis. Solid state substrates, namely, plates, chips, and wafers
for use in clinical medicine, having a pattern of channels
for confining and linearizing biopolymer samples; disposable
substrates, namely, plates, chips, and wafers for use in
clinical medicine, having a pattern of channels to
facilitate genomic imaging and analysis.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
(1) Reagents for use in preparing molecules for genomic research and analysis; a kit for extracting and labeling biopolymers for research purposes, containing enzymes, color reagents, buffers, and other reagents; polynucleotide isolation and purification kit consisting of enzymes, color reagents, buffers, and other reagents used for scientific or medical research purposes; kits for extracting and labeling polynucleotide molecules for research purposes, containing enzymes, color reagents, buffers, and other reagents; reagents for use in preparing polynucleotide molecules for genomic research; diagnostic kits containing enzymes, color reagents, buffers, and other reagents for extracting and labeling polynucleotide molecules.
(2) Reagents for use in clinical medicine for preparing molecules for genomic analysis; a medical diagnostic kit containing enzymes, color reagents, buffers, and other reagents for extracting and labeling biopolymers.
(3) An imaging system, namely, an imaging apparatus and software, for the analysis of biopolymer samples in scientific or medical research; software used in the analysis of biopolymer samples for medical diagnostic purposes; software used in the analysis of biopolymer samples for scientific or medical research; an imaging apparatus for use in the analysis of biopolymer samples in scientific or medical research; nanofluidic devices, namely, solid state substrates in the nature of plates, chips and wafers, and software, both of the foregoing for genomic imaging and analysis; an imaging apparatus and software for genomic analysis in scientific or medical research; an imaging system, namely, an imaging apparatus and software sold as a unit, for genomic analysis in scientific or medical research; software for genomic analysis used for medical diagnostic purposes, or in scientific, clinical or medical research; genomic data analysis software; software for interpreting and analyzing data generated by an imaging apparatus for the purpose of studying biopolymer samples; solid state substrates, namely, plates, chips, and wafers for use in scientific or medical research, having a pattern of channels for confining and linearizing biopolymer samples; disposable substrates, namely, plates, chips, and wafers for use in scientific or medical research, having a pattern of channels to facilitate genomic imaging and analysis; solid state substrates, namely, plates, chips and wafers having a plurality of fluid passageways for confining and linearizing macromolecules including biopolymer molecules for scientific or medical research; nanochannel wafers, for scientific or medical research, used in instruments for genomic analysis; downloadable or recorded software in the field of genomic bioinformatics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data.
(4) A medical diagnostic imaging system, namely, an imaging apparatus and software sold as a unit and used in the analysis of biopolymer samples; a medical diagnostic imaging apparatus used in the analysis of biopolymer samples; a medical diagnostic imaging system, namely, an imaging apparatus and software sold as a unit for genomic analysis; a medical imaging apparatus for genomic analysis; solid state substrates, namely, plates, chips, and wafers for use in clinical medicine, having a pattern of channels for confining and linearizing biopolymer samples; disposable substrates, namely, plates, chips, and wafers for use in clinical medicine, having a pattern of channels to facilitate genomic imaging and analysis; medical diagnostic solid state substrates, namely, plates, chips and wafers for confining and linearizing macromolecules including biopolymer molecules; nanochannel wafers, for use in clinical medicine, used in instruments for genomic analysis; medical specimen collection and transportation kit comprised of blood collection tubes, foam container for tubes, absorbent pad, biohazard bag, medical indicator marker and labels, for molecular and genetic testing for disorders of childhood development. (1) Product research and development and consulting services for others in the fields of biopolymer imaging and analysis; genomic mapping, genomic imaging, and genomic analysis services for scientific research purposes; medical, pharmaceutical, biotechnology, and scientific research and consulting services in the field of genetics, namely, analysis of relationships between genetic variants and neurodevelopmental disorders, genetic research, bio-marker discovery research, and pheno-typing for identifying, testing and developing diagnostics and treatments for human diseases and human disorders; software as a service (SAAS) or platform as a service (PAAS) featuring software in the field of genomics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data; product research and development and consulting services for others in the fields of genomic bioinformatics and data analysis; genomic data analysis services for scientific, clinical, and medical research purposes.
(2) Genomic mapping, genomic imaging, genomic analysis, and genomic data analysis services for medical diagnostic purposes; providing medical analysis services in the nature of relationships between genetic variants and neurodevelopmental disorders for identifying, testing, and developing diagnostic tools and treatments for such disorders; medical testing services, namely, molecular and genetic testing for disorders of childhood development; providing information related to medical testing services via an internet website for medical professionals and medical patients; providing molecular and genetic medical testing results via the internet.
23.
NANONOZZLE DEVICE ARRAYS: THEIR PREPARATION AND USE FOR MACROMOLECULAR ANALYSIS
Constricted nanochannel devices suitable for use in analysis of macromolecular structure, including DNA sequencing, are disclosed. Also disclosed are methods for fabricating such devices and for analyzing macromolecules using such devices.
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
10 - Medical apparatus and instruments
Goods & Services
Medical testing services, namely, genomic mapping, genomic imaging, and genomic analysis services for medical diagnostic purposes; providing an internet website for medical professionals and medical patients featuring information in the field of medical testing services for diagnostic or treatment purposes; providing medical information, namely, reporting of molecular and genetic medical testing results to medical patients and medical professionals via the internet Medical specimen collection and transportation kit comprised of collection tubes, foam container for tubes, absorbent pad, biohazard bag, marker, labels, mail packaging, forms and instructions, all for testing of patient samples for medical and/or diagnostic purposes
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Downloadable or recorded software in the field of genomic
bioinformatics for processing, storing, analyzing,
presenting, interpreting, and sharing genomic data; software
for genomic analysis used for medical diagnostic purposes,
or in scientific, clinical, or medical research; genomic
data analysis software. Software as a service (SAAS) or platform as a service (PAAS)
featuring software in the field of genomics for processing,
storing, analyzing, presenting, interpreting, and sharing
genomic data; product research and development and
consulting services for others in the fields of genomic
bioinformatics and data analysis; genomic data analysis
services for scientific, clinical, and medical research
purposes. Genomic data analysis services for medical diagnostic
purposes.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Downloadable or recorded software in the field of genomic
bioinformatics for processing, storing, analyzing,
presenting, interpreting, and sharing genomic data; software
for genomic analysis used for medical diagnostic purposes,
or in scientific, clinical, or medical research; genomic
data analysis software. Software as a service (SAAS) or platform as a service (PAAS)
featuring software in the field of genomics for processing,
storing, analyzing, presenting, interpreting, and sharing
genomic data; product research and development and
consulting services for others in the fields of genomic
bioinformatics and data analysis; genomic data analysis
services for scientific, clinical, and medical research
purposes. Genomic data analysis services for medical diagnostic
purposes.
27.
Integrated analysis devices and related fabrication methods and analysis techniques
Provided are integrated analysis devices having features of macroscale and nanoscale dimensions, and devices that have reduced background signals and that reduce quenching of fluorophores disposed within the devices. Related methods of manufacturing these devices and of using these devices are also provided.
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
An imaging apparatus and recorded software for genomic analysis in scientific or medical research; An imaging system, namely, an imaging apparatus and recorded software sold as a unit, for genomic analysis in scientific or medical research; downloadable and recorded software for genomic analysis used for medical diagnostic purposes; Solid state substrates, namely, plates, chips, and wafers for use in scientific or medical research, having a pattern of channels for confining and linearizing biopolymer samples; Disposable substrates, namely, plates, chips, and wafers for use in scientific or medical research, having a pattern of channels to facilitate genomic imaging and analysis A medical diagnostic imaging system, namely, an imaging apparatus with integrated recorded software sold as a unit for genomic analysis; A medical imaging apparatus for genomic analysis; Solid state substrates, namely, plates, chips, and wafers for use in clinical medicine, having a pattern of channels for confining and linearizing biopolymer samples; Disposable substrates, namely, plates, chips, and wafers for use in clinical medicine, having a pattern of channels to facilitate genomic imaging and analysis
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Reagents for use in preparing molecules for genomic research and analysis; a kit for extracting and labeling biopolymers for research purposes, containing enzymes, color reagents, buffers, and other reagents; Polynucleotide isolation and purification kit consisting of enzymes, color reagents, buffers, and other reagents used for scientific or medical research purposes; kits for extracting and labeling polynucleotide molecules for research purposes, containing enzymes, color reagents, buffers, and other reagents; reagents for use in preparing polynucleotide molecules for genomic research; diagnostic kits containing enzymes, color reagents, buffers, and other reagents for extracting and labeling polynucleotide molecules Reagents for use in clinical medicine for preparing molecules for genomic analysis; a medical diagnostic kit containing enzymes, color reagents, buffers, and other reagents for extracting and labeling biopolymers An imaging system, namely, an imaging apparatus and downloadable and recorded software, for the analysis of biopolymer samples in scientific or medical research; downloadable and recorded software used in the analysis of biopolymer samples for medical diagnostic purposes; downloadable and recorded software used in the analysis of biopolymer samples for scientific or medical research; an imaging apparatus for use in the analysis of biopolymer samples in scientific or medical research; Nanofluidic devices, namely, solid state substrates in the nature of plates, chips and wafers, and downloadable and recorded software, both of the foregoing for genomic imaging and analysis; An imaging apparatus and downloadable and recorded software for genomic analysis in scientific or medical research; an imaging system, namely, an imaging apparatus and downloadable and recorded software sold as a unit, for genomic analysis in scientific or medical research; downloadable and recorded software for genomic analysis used for medical diagnostic purposes, and in scientific, clinical, and medical research; downloadable and recorded genomic data analysis software; downloadable and recorded software for interpreting and analyzing data generated by an imaging apparatus for the purpose of studying biopolymer samples; Solid state substrates, namely, plates, chips, and wafers for use in scientific or medical research, having a pattern of channels for confining and linearizing biopolymer samples; disposable substrates, namely, plates, chips, and wafers for use in scientific or medical research, having a pattern of channels to facilitate genomic imaging and analysis; Solid state substrates, namely, plates, chips and wafers having a plurality of fluid passageways for confining and linearizing macromolecules including biopolymer molecules for scientific or medical research; nanochannel wafers, for scientific or medical research, used in instruments for genomic analysis; downloadable and recorded software in the field of genomic bioinformatics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data A medical diagnostic imaging system, namely, an imaging apparatus with integrated recorded software sold as a unit and used in the analysis of biopolymer samples; a medical diagnostic imaging apparatus used in the analysis of biopolymer samples; A medical diagnostic imaging system, namely, an imaging apparatus with integrated recorded software sold as a unit for genomic analysis; a medical imaging apparatus for genomic analysis; Solid state substrates, namely, plates, chips, and wafers for use in clinical medicine, having a pattern of channels for confining and linearizing biopolymer samples; disposable substrates, namely, plates, chips, and wafers for use in clinical medicine, having a pattern of channels to facilitate genomic imaging and analysis; Medical diagnostic solid state substrates, namely, plates, chips and wafers for confining and linearizing macromolecules including biopolymer molecules; nanochannel wafers, for use in clinical medicine, used in instruments for genomic analysis; medical specimen collection and transportation kit comprised of blood collection tubes, foam container for tubes, absorbent pad, biohazard bag, marker, labels, mail packaging, forms and instructions, for molecular and genetic testing for disorders of childhood development product research and development and consulting services for others in the fields of biopolymer imaging and analysis; genomic mapping, genomic imaging, and genomic analysis services for scientific research purposes; medical, pharmaceutical, biotechnology, and scientific research and consulting services in the field of genetics, namely, analysis of relationships between genetic variants and neurodevelopmental disorders, genetic research, bio-marker discovery research, and pheno-typing for identifying, testing and developing diagnostics and treatments for human diseases and human disorders; software as a service (SAAS) services and platform as a service (PAAS) featuring software and computer software platforms featuring software in the field of genomics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data; product research and development and consulting services for others in the fields of genomic bioinformatics and data analysis; genomic data analysis services for scientific, clinical, and medical research purposes Genomic mapping, genomic imaging, genomic analysis, and genomic data analysis services for medical diagnostic purposes; providing medical analysis services in the nature of relationships between genetic variants and neurodevelopmental disorders for identifying, testing, and developing diagnostic tools and treatments for such disorders; medical testing services, namely, molecular and genetic testing for disorders of childhood development; providing an internet website for medical professionals and medical patients featuring information in the field of medical testing services for diagnostic or treatment purposes; providing medical information, namely, reporting of molecular and genetic medical testing results to patients via the internet
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
downloadable and recorded software in the field of genomic bioinformatics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data; downloadable and recorded software for genomic analysis used for medical diagnostic purposes, and in scientific, clinical, or medical research; downloadable and recorded genomic data analysis software software as a service (SAAS) services and platform as a service (PAAS) featuring software and computer software platforms in the field of genomics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data; product research and development and consulting services for others in the fields of genomic bioinformatics and data analysis; genomic data analysis services for scientific, clinical, and medical research purposes genomic data analysis services for medical diagnostic purposes
42 - Scientific, technological and industrial services, research and design
Goods & Services
software as a service (SAAS) services and platform as a service (PAAS) featuring software and computer software platforms in the field of genomics for processing, storing, analyzing, presenting, interpreting, and sharing genomic data; product research and development and consulting services for others in the fields of genomic bioinformatics and data analysis; genomic data analysis services for scientific, clinical, and medical research purposes
33.
PHOTOCLEAVAGE METHOD AND APPARATUS TO CLEAN FLUIDIC DEVICES
A method and system for improving throughput of a fluidic system such as a biopolymer analysis system by cleaning accumulated or clogging biopolymer from the fluidic system is disclosed. The method and system utilize a light energy source to photocleave the biopolymer molecules that may accumulate or aggregate in the fluidic system or clog a passageway. The accumulated biopolymer may be exposed to a light energy source for a sufficient period of time such that the biopolymer molecule is dosed with sufficient energy to photocleave the biopolymer molecules, thereby restoring the efficiency of and flow through the system.
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Medical specimen collection and transportation kit comprised
of blood collection tubes, foam container for tubes,
absorbent pad, biohazard bag, and medical indicator marker
and labels, for molecular and genetic testing for disorders
of childhood development. Medical testing services, namely, molecular and genetic
testing for disorders of childhood development; providing
information related to medical testing services via an
internet website for medical professionals and medical
patients; providing molecular and genetic medical testing
results via the internet; genomic mapping, genomic imaging,
and genomic analysis services for medical diagnostic
purposes.
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Medical specimen collection and transportation kit comprised
of blood collection tubes, foam container for tubes,
absorbent pad, biohazard bag, marker, labels, mail
packaging, forms and instructions, for molecular and genetic
testing for disorders of childhood development. Medical testing services, namely, molecular and genetic
testing for disorders of childhood development; providing an
internet website for medical professionals and medical
patients featuring information related to medical testing
services; providing molecular and genetic medical testing
results via the internet; genomic mapping, genomic imaging,
and genomic analysis services for medical diagnostic
purposes.
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
(1) Medical specimen collection and transportation kit comprised of blood collection tubes, foam container for tubes, absorbent pad, biohazard bag, and medical indicator marker and labels, for molecular and genetic testing for disorders of childhood development. (1) Medical testing services, namely, molecular and genetic testing for disorders of childhood development; providing information related to medical testing services via an internet website for medical professionals and medical patients; providing molecular and genetic medical testing results via the internet; genomic mapping, genomic imaging, and genomic analysis services for medical diagnostic purposes.
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
(1) Medical specimen collection and transportation kit comprised of blood collection tubes, foam container for tubes, absorbent pad, biohazard bag, marker, labels, mail packaging, forms and instructions, for molecular and genetic testing for disorders of childhood development. (1) Medical testing services, namely, molecular and genetic testing for disorders of childhood development; providing an internet website for medical professionals and medical patients featuring information related to medical testing services; providing molecular and genetic medical testing results via the internet; genomic mapping, genomic imaging, and genomic analysis services for medical diagnostic purposes.
38.
Methods and devices for single-molecule whole genome analysis
Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g. determining structural variations and copy number variations between individuals.
Methods of labeling DNA molecules comprising the use of one or more dCas proteins and one or more labeled guide RNAs (gRNAs) are described herein. In some embodiments, the labeled DNA molecules are elongated in fluidic nanochannels, where they can be analyzed.
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Medical specimen collection and transportation kit comprised of blood collection tubes, foam container for tubes, absorbent pad, biohazard bag, marker, labels, mail packaging, forms and instructions, for molecular and genetic testing for disorders of childhood development Medical testing services, namely, molecular and genetic testing for disorders of childhood development; providing an internet website for medical professionals and medical patients featuring information related to medical testing services; providing molecular and genetic medical testing results via the internet; genomic mapping, genomic imaging, and genomic analysis services for medical diagnostic purposes
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Medical specimen collection and transportation kit comprised of blood collection tubes, foam container for tubes, absorbent pad, biohazard bag, marker, labels, mail packaging, forms and instructions, for molecular and genetic testing for disorders of childhood development Medical testing services, namely, molecular and genetic testing for disorders of childhood development; providing an internet website for medical professionals and medical patients featuring information related to medical testing services; providing molecular and genetic medical testing results via the internet; genomic mapping, genomic imaging, and genomic analysis services for medical diagnostic purposes
42.
Reduction of bias in genomic coverage measurements
Methods are provided for detecting and quantitating molecules using fluidics. In some embodiments, the methods comprise minimizing or eliminating biases caused by label density, or minimizing or eliminated biases caused by factors other than label density. In some embodiments, the methods comprise automated identification of genetic structural variation. In some embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.
Provided are integrated analysis devices having features of macroscale and nanoscale dimensions, and devices that have reduced background signals and that reduce quenching of fluorophores disposed within the devices. Related methods of manufacturing these devices and of using these devices are also provided.
Constricted nanochannel devices suitable for use in analysis of macromolecular structure, including DNA sequencing, are disclosed. Also disclosed are methods for fabricating such devices and for analyzing macromolecules using such devices.
Methods of double-stranded nucleic acid sequence determination and assembly that are able to identify insertions, deletions, repeat region sizes and genomic rearrangements, for example, are disclosed herein, which can use relatively large labeled nucleic acid fragments to analyze the structure of even larger genetic regions. In some embodiments these methods involve the use of certain parameters which unexpectedly improve overall method performance. In some embodiments these methods involve sample labeling that does not result in the formation of single-stranded nucleic acid fragment labeling intermediaries.
Methods are provided for detecting and quantitating molecules using fluidics. In preferred embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g. determining structural variations and copy number variations between individuals.
09 - Scientific and electric apparatus and instruments
Goods & Services
Genomic data analysis software; software for interpreting
and analyzing data generated by an imaging apparatus for the
purpose of studying biopolymer samples.
Methods of labeling DNA molecules comprising the use of one or more dCas proteins and one or more labeled guide RNAs (gRNAs) are described herein. In some embodiments, the labeled DNA molecules are elongated in fluidic nanochannels, where they can be analyzed.
09 - Scientific and electric apparatus and instruments
Goods & Services
Nucleic acid extraction and purification system, for scientific research purposes, the aforementioned system comprised of laboratory equipment, namely, a laboratory apparatus that utilizes isotachophoresis to extract, purify, isolate and concentrate nucleic acid from biological samples incorporating a touchscreen, downloadable software, and nucleic acid fluidics chips
51.
Nanonozzle device arrays: their preparation and use for macromolecular analysis
Constricted nanochannel devices suitable for use in analysis of macromolecular structure, including DNA sequencing, are disclosed. Also disclosed are methods for fabricating such devices and for analyzing macromolecules using such devices.
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
Goods & Services
Polynucleotide isolation, purification, and labeling kit
including enzymes, color reagents, buffers, and other
reagents or combinations thereof, used for scientific or
medical research purposes; kits for extracting and labeling
polynucleotide molecules for research purposes, containing
enzymes, color reagents, buffers, and other reagents, or
combinations thereof; reagents for use in preparing
polynucleotide molecules for genomic research; diagnostic
kits containing enzymes, color reagents, buffers, and other
reagents, or combinations thereof, for extracting and
labeling polynucleotide molecules. Reagents for use in clinical medicine for preparing
polynucleotide molecules for genomic analysis. Reaction preparation device and slides for polynucleotide
isolation, purification and labeling; reaction preparation
device and slides for extracting and labeling polynucleotide
molecules for research purposes; reaction preparation device
and slides for use in preparing polynucleotide molecules for
genomic research; reaction preparation device and slides for
extracting and labeling polynucleotide molecules for
scientific research purposes; reaction preparation device
and slides for use in clinical medicine research for
preparing polynucleotide molecules for genomic analysis.
54.
Integrated analysis devices and related fabrication methods and analysis techniques
Provided are integrated analysis devices having features of macroscale and nanoscale dimensions, and devices that have reduced background signals and that reduce quenching of fluorophores disposed within the devices. Related methods of manufacturing these devices and of using these devices are also provided.
A method and system for improving throughput of a fluidic system such as a biopolymer analysis system by cleaning accumulated or clogging biopolymer from the fluidic system is disclosed. The method and system utilize a light energy source to photocleave the biopolymer molecules that may accumulate or aggregate in the fluidic system or clog a passageway. The accumulated biopolymer may be exposed to a light energy source for a sufficient period of time such that the biopolymer molecule is dosed with sufficient energy to photocleave the biopolymer molecules, thereby restoring the efficiency of and flow through the system.
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
Solid state substrates, namely, plates, chips, and wafers
for use in scientific or medical research, having a pattern
of channels for confining and linearizing biopolymer
samples; disposable substrates, namely, plates, chips, and
wafers for use in scientific or medical research, having a
pattern of channels to facilitate genomic imaging and
analysis. Solid state substrates, namely, plates, chips, and wafers
for use in clinical medicine, having a pattern of channels
for confining and linearizing biopolymer samples; disposable
substrates, namely, plates, chips, and wafers for use in
clinical medicine, having a pattern of channels to
facilitate genomic imaging and analysis.
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
An imaging apparatus and software for genomic analysis in
scientific or medical research; an imaging system, namely,
an imaging apparatus and software sold as a unit, for
genomic analysis in scientific or medical research; software
for genomic analysis used for medical diagnostic purposes. A medical diagnostic imaging system, namely, an imaging
apparatus and software sold as a unit for genomic analysis;
a medical imaging apparatus for genomic analysis.
58.
Methods and devices for single-molecule whole genome analysis
Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g. determining structural variations and copy number variations between individuals.
09 - Scientific and electric apparatus and instruments
Goods & Services
genomic data analysis software; software for interpreting and analyzing data generated by an imaging apparatus for the purpose of studying biopolymer samples
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
SOLID STATE SUBSTRATES, NAMELY, PLATES, CHIPS, AND WAFERS FOR USE IN SCIENTIFIC OR MEDICAL RESEARCH, HAVING A PATTERN OF CHANNELS FOR CONFINING AND LINEARIZING BIOPOLYMER SAMPLES; DISPOSABLE SUBSTRATES, NAMELY, PLATES, CHIPS, AND WAFERS FOR USE IN SCIENTIFIC OR MEDICAL RESEARCH, HAVING A PATTERN OF CHANNELS TO FACILITATE GENOMIC IMAGING AND ANALYSIS SOLID STATE SUBSTRATES, NAMELY, PLATES, CHIPS, AND WAFERS FOR USE IN CLINICAL MEDICINE, HAVING A PATTERN OF CHANNELS FOR CONFINING AND LINEARIZING BIOPOLYMER SAMPLES; DISPOSABLE SUBSTRATES, NAMELY, PLATES, CHIPS, AND WAFERS FOR USE IN CLINICAL MEDICINE, HAVING A PATTERN OF CHANNELS TO FACILITATE GENOMIC IMAGING AND ANALYSIS
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
Goods & Services
AN IMAGING APPARATUS AND SOFTWARE FOR GENOMIC ANALYSIS IN SCIENTIFIC OR MEDICAL RESEARCH; AN IMAGING SYSTEM, NAMELY, AN IMAGING APPARATUS AND SOFTWARE SOLD AS A UNIT, FOR GENOMIC ANALYSIS IN SCIENTIFIC OR MEDICAL RESEARCH; SOFTWARE FOR GENOMIC ANALYSIS USED FOR MEDICAL DIAGNOSTIC PURPOSES A MEDICAL DIAGNOSTIC IMAGING SYSTEM, NAMELY, AN IMAGING APPARATUS AND SOFTWARE SOLD AS A UNIT FOR GENOMIC ANALYSIS; A MEDICAL IMAGING APPARATUS FOR GENOMIC ANALYSIS
62.
Methods of determining nucleic acid structural information
Methods of double-stranded nucleic acid sequence determination and assembly that are able to identify insertions, deletions, repeat region sizes and genomic rearrangements, for example, are disclosed herein, which can use relatively large labeled nucleic acid fragments to analyze the structure of even larger genetic regions. In some embodiments these methods involve the use of certain parameters which unexpectedly improve overall method performance. In some embodiments these methods involve sample labeling that does not result in the formation of single-stranded nucleic acid fragment labeling intermediaries.
Methods are provided for detecting and quantitating molecules using fluidics. In some embodiments, the methods comprise minimizing or eliminating biases caused by label density, or minimizing or eliminated biases caused by factors other than label density. In some embodiments, the methods comprise automated identification of genetic structural variation. In some embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.
Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as wen as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed.
The present invention provides methods of obtaining structural information about a biopolymer sample. The methods include labeling portions of a biopolymer, such as DNA or RNA, linearizing the biopolymer in some cases, and determining the distance between the labels. The user can then compare different samples' between-label distances to qualitatively compare different samples and to assay a given sample for additions or deletions of nucleotides in the regions flanked by the labels. The methods also permit sequencing of biopolymers.
A method and system for improving throughput of a fluidic system such as a biopolymer analysis system by cleaning accumulated or clogging biopolymer from the fluidic system is disclosed. The method and system utilize a light energy source to photocleave the biopolymer molecules that may accumulate or aggregate in the fluidic system or clog a passageway. The accumulated biopolymer may be exposed to a light energy source for a sufficient period of time such that the biopolymer molecule is dosed with sufficient energy to photocleave the biopolymer molecules, thereby restoring the efficiency of and flow through the system.
Methods are provided for characterizing a sample comprising polynucleotide sequences. The methods can comprise labeling nucleic acid molecules of the sample, translocating the plurality of labeled sample nucleic acid molecules though one or more fluidic nanochannels, detecting physical counts of signals from the labeled sample nucleic acid molecule, and determining a copy number of a genome or a fragment or fragments thereof in the sample.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C40B 40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof
G01N 31/22 - Investigating or analysing non-biological materials by the use of the chemical methods specified in the subgroupsApparatus specially adapted for such methods using chemical indicators
G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
Methods for single-molecule preparation and analysis are disclosed herein. The methods can, for example, be used for isolating and analyzing DNA from various biological samples.
C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
C12N 9/00 - Enzymes, e.g. ligases (6.)ProenzymesCompositions thereofProcesses for preparing, activating, inhibiting, separating, or purifying enzymes
69.
Nanonozzle device arrays: their preparation and use for macromolecular analysis
Constricted nanochannel devices suitable for use in analysis of macromolecular structure, including DNA sequencing, are disclosed. Also disclosed are methods for fabricating such devices and for analyzing macromolecules using such devices.
Methods and compositions for processing polynucleotides are provided according to some embodiments herein. In some embodiments, a sample is immobilized in a porous matrix, and non-polynucleotides are removed from the sample. In some embodiments, polynucleotides are labeled or enzymatically modified the matrix. In some embodiments, labeled or enzymatically modified polynucleotides are removed from the matrix for analysis.
Methods are provided for detecting and quantitating molecules using fluidics. In some embodiments, the methods comprise minimizing or eliminating biases caused by label density, or minimizing or eliminated biases caused by factors other than label density. In some embodiments, the methods comprise automated identification of genetic structural variation. In some embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.
Methods of double-stranded nucleic acid sequence determination and assembly that are able to identify insertions, deletions, repeat region sizes and genomic rearrangements, for example, are disclosed herein, which can use relatively large labeled nucleic acid fragments to analyze the structure of even larger genetic regions. In some embodiments these methods involve the use of certain parameters which unexpectedly improve overall method performance. In some embodiments these methods involve sample labeling that does not result in the formation of single-stranded nucleic acid fragment labeling intermediaries.
09 - Scientific and electric apparatus and instruments
Goods & Services
Genomic data analysis software; software for interpreting
and analyzing data generated by an imaging apparatus for the
purpose of studying biopolymer samples.
Disclosed herein are cartridges and systems for nanoanalysis, and methods for using the cartridges and systems. For example, a cartridge can have a chip forming one or more sample wells, with a plurality of nanotubes running between a pair of adjacent sample wells, the nanotubes configured to receive linearized molecules. Upon linearization, the molecules in the nanochannels are imaged through a transparent substrate on which the chip is located. The movement of molecules through the nanochannels can be started and stopped, and cartridge can be moved to facilitate imaging of the molecules.
According to some embodiments herein, methods and kits for labeling and analyzing nucleic acids are provided, In some embodiments, sequence-specific labeling is performed on polynucleotide sequences associated with a host genome, and the presence or absence of patterns characteristic of extragenomic sequences are determined.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
09 - Scientific and electric apparatus and instruments
Goods & Services
Genomic data analysis software; software for interpreting and analyzing data generated by an imaging apparatus for the purpose of studying biopolymer samples
77.
Methods of macromolecular analysis using nanochannel arrays
Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as wen as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
Methods are provided for detecting and quantitating molecules using fluidics. In preferred embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.
Methods for single-molecule preparation and analysis are disclosed herein. The methods can, for example, be used for isolating and analyzing DNA from various biological samples.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
80.
Methods and devices for single-molecule whole genome analysis
Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g. determining structural variations and copy number variations between individuals.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
10 - Medical apparatus and instruments
42 - Scientific, technological and industrial services, research and design
Goods & Services
Reagents for use in preparing molecules for genomic research and analysis; a kit for extracting and labeling biopolymers for research purposes, containing enzymes, color reagents, buffers, and other reagents Reagents for use in clinical medicine for preparing molecules for genomic analysis; a medical diagnostic kit containing enzymes, color reagents, buffers, and other reagents for extracting and labeling biopolymers An imaging system, namely, an imaging apparatus and software, for the analysis of biopolymer samples in scientific or medical research; software used in the analysis of biopolymer samples for medical diagnostic purposes; software used in the analysis of biopolymer samples for scientific or medical research; an imaging apparatus for use in the analysis of biopolymer samples in scientific or medical research A medical diagnostic imaging system, namely, an imaging apparatus and software sold as a unit and used in the analysis of biopolymer samples; a medical diagnostic imaging apparatus used in the analysis of biopolymer samples Product research and development and consulting services for others in the fields of biopolymer imaging and analysis; genomic mapping, genomic imaging, and genomic analysis services for scientific research purposes
82.
PHYSICAL MAP CONSTRUCTION OF WHOLE GENOME AND POOLED CLONE MAPPING IN NANOCHANNEL ARRAY
Methods for generating physical maps for polynucleotides, such as genomic DNA, are disclosed herein. Also disclosed are methods for identifying the source of polynucleotides. The methods can, for example, be used in physical map construction of whole genome. In addition, methods and systems capable of performing high throughput characterization of macromolecules using nanofludic devices are enclosed.
09 - Scientific and electric apparatus and instruments
Goods & Services
An imaging system, imaging apparatus, or software for use in
the analysis of polymer samples in scientific or medical
research; an imaging system, namely, an imaging apparatus
and software, for genomic analysis in scientific or medical
research.
Provided are devices and methods for polymer analysis, in which labeled polymers are translocated along nanochannels that have illuminated detection regions within. As a labeled polymer translocates along the nanochannel and the labels pass over the illuminated detection regions, the labels become detectable (e.g., where different labels fluoresce in response to different wavelengths present at different illumination regions), and the user generates a spatial map of the location of the various labels along the length of the polymer. The location of the labels is then correlated to one or more structural characteristics of the polymer.
09 - Scientific and electric apparatus and instruments
Goods & Services
Nanofluidic devices, namely, solid state substrates in the nature of plates, chips and wafers, and software, both of the foregoing for genomic imaging and analysis
87.
SYSTEMS AND METHODS FOR ASSESSING BIOMOLECULE CHARACTERISTICS
Provided are methods and systems for assessing the presence and extent of damage on a polynucleotide. The methods include incorporating a label at the site of the damage and imaging the label to determine the presence and extent of the damage. The systems include devices capable of performing damage assessment on single molecules.
The present invention provides methods of obtaining structural information about a biopolymer sample. The methods include labeling portions of a biopolymer, such as DNA or RNA, linearizing the biopolymer in some cases, and determining the distance between the labels. The user can then compare different samples' between-label distances to qualitatively compare different samples and to assay a given sample for additions or deletions of nucleotides in the regions flanked by the labels. The methods also permit sequencing of biopolymers.
Provided are integrated analysis devices having features of macroscale and nanoscale dimensions, and devices that have reduced background signals and that reduce quenching of fluorophores disposed within the devices. Related methods of manufacturing these devices and of using these devices are also provided.
Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g., determining structural variations and copy number variations between individuals.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C12M 3/00 - Tissue, human, animal or plant cell, or virus culture apparatus
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
91.
METHODS AND RELATED DEVICES FOR SINGLE MOLECULE WHOLE GENOME ANALYSIS
Provided are methods of labeling and analyzing features along at least one macro molecule such as a linear biopolymer, including methods of mapping the distribution and frequency of specific sequence motifs or the chemical or proteomic modification state of such sequence motifs along individual unfolded nucleic acid molecules. The present invention also provides methods of identifying signature patterns of sequence or epigenetic variations along such labeled macro molecules for direct massive parallel single molecule level analysis. The present invention also provides systems suitable for high throughput analysis of such labeled macro mo lecules.
Provided are devices and methods for polymer analysis, in which labeled polymers are translocated along nanochannels that have illuminated detection regions within. As a labeled polymer translocates along the nanochannel and the labels pass over the illuminated detection regions, the labels become detectable (e.g., where different labels fluoresce in response to different wavelengths present at different illumination regions), and the user generates a spatial map of the location of the various labels along the length of the polymer. The location of the labels is then correlated to one or more structural characteristics of the polymer.
C40B 60/12 - Apparatus specially adapted for use in combinatorial chemistry or with libraries for screening libraries
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
93.
DEVICES AND METHODS FOR DYNAMIC DETERMINATION OF SAMPLE SPATIAL ORIENTATION AND DYNAMIC REPOSITIONING
Provided are devices and methods for determining the spatial orientation of a target sample, which devices and methods are useful in auto focus systems. The devices and methods function by correlating (a) the location of radiation on a radiation detector of radiation reflected by the sample with (b) the position of the sample, and in some embodiments, adjusting the position of the sample, the position of an optical device, or both, in accordance with the location of radiation reflected by the sample onto the detector so as to maintain the sample in focus.
Constricted nanochannel devices suitable for use in analysis of macromolecular structure, including DNA sequencing, are disclosed. Also disclosed are methods for fabricating such devices and for analyzing macromolecules using such devices.
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
G01N 15/06 - Investigating concentration of particle suspensions
G01N 21/00 - Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
B82Y 30/00 - Nanotechnology for materials or surface science, e.g. nanocomposites
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glasswareDroppers
G01N 33/487 - Physical analysis of biological material of liquid biological material
G01N 35/10 - Devices for transferring samples to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
95.
Methods of macromolecular analysis using nanochannel arrays
Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as well as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
96.
METHODS OF MACROMOLECULAR ANALYSIS USING NANOCHANNEL ARRAYS
Abstract Provided herein, in some embodiments, are devices that address the need for efficient determination of the sizes and composition of DNA or other macromolecules by linearizing and analyzing such molecules. Devices for analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules are disclosed. In some embodiments, the devices can perform such high throughput analysis in a massively parallel fashion. In some embodiments, the devices disclosed herein advantageously enable a minimal amount of sample to be used. Date Recue/Date Received 2020-06-15
Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as well as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed. The sample embodiment shown in the figure illustrates detection of a macromolecule flowing through a nanochannel device where passage of the macromolecule through the nanochannel is recorded by exciting features of interest to fluoresce with an excitation source, and then sensing the fluorescence with a photon detection device, the resulting fluorescent signal being correlated along the length of the macromolecule.
Methods for single-molecule preparation and analysis are disclosed herein. The methods can, for example, be used for isolating and analyzing DNA from various biological samples.
C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
Provided are integrated analysis devices having features of macroscale and nanoscale dimensions, and devices that have re-duced background signals and that reduce quench-ing of fluorophores disposed within the devices. Related methods of manufacturing these devices and of using these devices are also provided.
Constricted nanochannel devices suitable for use in analysis of macromolecular structure, including DNA sequencing, are disclosed. Also disclosed are methods for fabricating such devices and for analyzing macromolecules using such devices.
