SYSTEM, METHOD, AND COMPUTER SOFTWARE PRODUCT FOR GENOTYPE DETERMINATION USING PROBE ARRAY DATA
Granted: June 10, 2021
Application Number:
20210174232
An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster…
METHODS AND DEVICES FOR READING MICROARRAYS
Granted: August 20, 2020
Application Number:
20200265213
In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.
SYSTEMS AND METHODS FOR PROBE DESIGN TO DETECT THE PRESENCE OF SIMPLE AND COMPLEX INDELS
Granted: July 23, 2020
Application Number:
20200234791
Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.
ANALYSIS OF DATA OBTAINED FROM MICROARRAYS
Granted: May 28, 2020
Application Number:
20200167916
Disclosed are methods and software for biological data analysis. Specifically, provided are methods, computer programs and systems for analyzing data in the form of various intensity measurements obtained from an oligonucleotides microarray experiment. Such data may be microarray data obtained from an experiment conducted to determine copy number of a human genetic sample. The data are corrected by application of one or more covariate adjusters which may be applied simultaneously and…
METHODS AND COMPUTER SOFTWARE FOR DETECTING SPLICE VARIANTS
Granted: October 10, 2019
Application Number:
20190311780
Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.
METHODS AND DEVICES FOR READING MICROARRAYS
Granted: October 10, 2019
Application Number:
20190311178
In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.
METHODS FOR IDENTIFYING DNA COPY NUMBER CHANGES USING HIDDEN MARKOV MODEL BASED ESTIMATIONS
Granted: September 19, 2019
Application Number:
20190287650
Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
SYSTEMS AND METHODS FOR SNP CHARACTERIZATION AND IDENTIFYING OFF TARGET VARIANTS
Granted: June 27, 2019
Application Number:
20190198134
Methods for processing data using information gained from examining biological materials identifies and characterized probes for Single Nucleotide Polymorphisms and identifies Off Target Variants.
METHODS AND DEVICES FOR READING MICROARRAYS
Granted: November 29, 2018
Application Number:
20180341802
In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.
METHODS AND DEVICES FOR READING MICROARRAYS
Granted: April 5, 2018
Application Number:
20180096190
In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.
SYSTEM, METHOD, AND COMPUTER SOFTWARE PRODUCT FOR GENOTYPE DETERMINATION USING PROBE ARRAY DATA
Granted: February 8, 2018
Application Number:
20180039727
An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster…
DIFFERENTIAL FILTERING OF GENETIC DATA
Granted: January 11, 2018
Application Number:
20180011970
Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and…
SYSTEM, METHOD, AND PRODUCT FOR IMAGING PROBE ARRAYS WITH SMALL FEATURE SIZES
Granted: February 26, 2015
Application Number:
20150057167
An embodiment of a method for resolving features on a probe array is described that, comprises acquiring a plurality of micro-shifted images of a region of a probe array; reconstructing an image of the probe array using the micro-shifted images; and deriving intensity values for one or more probe features disposed on the probe array from the reconstructed image.
ANALYSIS OF METHYLATION USING NUCLEIC ACID ARRAYS
Granted: February 5, 2015
Application Number:
20150038352
Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.
Complexity Management of Genomic DNA
Granted: January 15, 2015
Application Number:
20150017632
The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for…
METHODS FOR SYNTHESIZING POOLS OF PROBES
Granted: January 1, 2015
Application Number:
20150004600
Compositions, methods and kits are disclosed for synthesizing and amplifying pools of probes using precursor oligonucleotides. In some aspects the precursor is amplified and nicking enzymes are used to separate the full length probes from the amplification products. The methods enable the preparation of single stranded DNA probes of defined sequence and length that are suitable for use in target detection assays.
Detection of Nucleic Acids
Granted: September 18, 2014
Application Number:
20140274756
This invention provides compositions, methods, and systems for characterizing, resolving, and quantitating single stranded and double stranded DNA and RNA in-situ. Paired sense and anti-sense probes can signal the presence of double stranded nucleic acids. DNA and RNA can be distinguished in cell and tissue samples by hybridizing with probe sets adapted to highlight differences in these targets in-situ.
Systems and Methods For Probe Design to Detect the Presence of Simple and Complex Indels
Granted: September 18, 2014
Application Number:
20140274728
Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.
Multiplex Capture of Nucleic Acids
Granted: July 10, 2014
Application Number:
20140194296
Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Methods of capturing one or more long nucleic acids and methods of capturing one or more nucleic acid for sequencing are also provided. Compositions, kits, and systems related to the methods are also…
Nucleic Acid Labeling Compounds
Granted: July 3, 2014
Application Number:
20140187434
Nucleic acid labeling compounds are disclosed. The compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
