Patents by Inventor Srinka Ghosh

Srinka Ghosh has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20190338343
    Abstract: In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.
    Type: Application
    Filed: July 17, 2019
    Publication date: November 7, 2019
    Inventors: David JOUN, Chieh-Yuan LI, Brian REED, Craig OBERGFELL, Devin DRESSMAN, Abraham ROSENBAUM, Scott BENSON, Andi BROKA, Srinka GHOSH
  • Publication number: 20190287650
    Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
    Type: Application
    Filed: January 10, 2019
    Publication date: September 19, 2019
    Applicant: Affymetrix, Inc.
    Inventor: Srinka Ghosh
  • Publication number: 20190172550
    Abstract: Methods of identifying changes in genomic DNA copy number are disclosed. This disclosure provides methods for detecting chromosomal aberrations in a subject using Hidden Markov modeling. In some cases, methods provided herein use de novo sequence assembly to detect chromosomal aberrations in a subject. The methods can be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods can be used to diagnose cancer and other diseases associated with chromosomal anomalies.
    Type: Application
    Filed: November 30, 2018
    Publication date: June 6, 2019
    Inventor: Srinka GHOSH
  • Patent number: 10229244
    Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
    Type: Grant
    Filed: June 20, 2008
    Date of Patent: March 12, 2019
    Assignee: Affymetrix, Inc.
    Inventor: Srinka Ghosh
  • Publication number: 20150361481
    Abstract: In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.
    Type: Application
    Filed: June 11, 2015
    Publication date: December 17, 2015
    Inventors: David JOUN, Chieh-Yuan LI, Brian REED, Craig OBERGFELL, Devin DRESSMAN, Abraham ROSENBAUM, Scott BENSON, Andi BROKA, Srinka GHOSH
  • Publication number: 20090098547
    Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
    Type: Application
    Filed: June 23, 2008
    Publication date: April 16, 2009
    Applicant: Affymetrix, Inc.
    Inventor: Srinka Ghosh
  • Publication number: 20080161206
    Abstract: Biopolymeric array scanners that are capable of automatically selecting a dye specific scale factor to employ for a plurality of different dyes, as wells as methods for making and using the same, are provided. In many embodiments, the actual dye specific scale factor automatically selected by the scanner is one that is equal to a preset “master” scale factor, so that the scanner reads any supported dye using the same constant scale factor. The dye specific scale factor selection is typically made by reference to a collection of nominal scale factors for each member of the plurality of dyes. In using the subject scanners, a user simply inputs the one or more dyes being used in a given array assay, and the scanner automatically reads the array using an automatically chosen dye specific scale factor for the selected dyes. Also provided are methods of obtaining collections of nominal scale factors and computer readable mediums comprising the same.
    Type: Application
    Filed: December 26, 2007
    Publication date: July 3, 2008
    Inventors: John F. Corson, Scott D. Connell, Srinka Ghosh
  • Patent number: 7331511
    Abstract: Biopolymeric array scanners that are capable of automatically selecting a dye specific scale factor to employ for a plurality of different dyes, as wells as methods for making and using the same, are provided. In many embodiments, the actual dye specific scale factor automatically selected by the scanner is one that is equal to a preset “master” scale factor, so that the scanner reads any supported dye using the same constant scale factor. The dye specific scale factor selection is typically made by reference to a collection of nominal scale factors for each member of the plurality of dyes. In using the subject scanners, a user simply inputs the one or more dyes being used in a given array assay, and the scanner automatically reads the array using an automatically chosen dye specific scale factor for the selected dyes. Also provided are methods of obtaining collections of nominal scale factors and computer readable mediums comprising the same.
    Type: Grant
    Filed: December 23, 2002
    Date of Patent: February 19, 2008
    Assignee: Agilent Technologies, Inc.
    Inventors: John F. Corson, Scott D. Connell, Srinka Ghosh
  • Patent number: 7221785
    Abstract: A method and system for estimating the background signal over an arbitrarily-sized region of a scanned image of a molecular array, including a background region surrounding the ROI corresponding to the feature. A bit mask is generated, based on a molecular-array, feature-based data set that includes pixel-based intensities and a list of features, including feature coordinates and feature ROI radii, to indicate those pixels in the scanned image of the molecular array corresponding to background, and those pixels in the scanned image of the molecular array corresponding to features and ROIs. An integrated intensity for a background region of arbitrary size and shape can be efficiently determined by selecting pixels within the background region that are indicated to be background pixels in the bit mask.
    Type: Grant
    Filed: May 21, 2002
    Date of Patent: May 22, 2007
    Assignee: Agilent Technologies, Inc.
    Inventors: Bo U. Curry, Herbert F. Cattell, Srinka Ghosh
  • Publication number: 20060046252
    Abstract: A method and system for determining a set of dye-normalization microarray probes that consistently hybridize to approximately the same number of target molecules in a wide range of sample solutions. The method of one embodiment of the method of the present invention generates a set of candidate probe molecules. The set of candidate probe molecules are arrayed on one or more replicate microarrays. Sample solutions are made from one or more tissues of one or more species. Microarray-base hybridization assays are conducted by using the replicate microarrays and different sample solutions. A subset of the candidate probe molecules that are functional for the microarray-base hybridization assays are determined.
    Type: Application
    Filed: August 30, 2004
    Publication date: March 2, 2006
    Inventors: Srinka Ghosh, Patrick Collins
  • Publication number: 20060036373
    Abstract: A method and system for cropping a digital image of multiple individual microarrays. Various embodiments of the present invention include, a digital image of multiple individual microarrays projected along a first coordinate axis by summing columns of pixel intensity values. A transformation maps the projected pixel intensity values to a transform in a frequency domain. A filter function is constructed from a power spectrum of the transform and multiplied by the transform to obtain a filtered transform. The filtered transform is mapped back to the spatial domain to give the filtered, spatial-domain image. The filtered, spatial-domain image is used to determine the coordinates of boundaries separating the individual microarrays along the first coordinate axis. The multi-pack of microarrays is rotated, and the method may be repeated for a second coordinate axis that is perpendicular to the first coordinate axis. The boundaries are used to identify the boundaries separating individual microarrays.
    Type: Application
    Filed: August 11, 2004
    Publication date: February 16, 2006
    Inventors: Srinka Ghosh, Peter Webb
  • Publication number: 20050226535
    Abstract: A method and system for rectilinearizing an image of a double-density, microarray having a non-rectilinear, outermost feature-position arrangement. In a disclosed embodiment, an image of a microarray having a non-rectilinear, outermost, feature-position arrangement is obtained from the signal intensity data of a microarray of features. A coordinate scheme of horizontal and vertical grid lines is superimposed on the image in order to assign a coordinate location to each feature of the microarray. Three corner features of the microarray are selected and used to determine one or more feature positions to add to the non-rectilinear, outermost, feature-position arrangement to form a rectilinear, outermost, feature-position arrangement of the microarray features.
    Type: Application
    Filed: April 13, 2004
    Publication date: October 13, 2005
    Inventor: Srinka Ghosh
  • Publication number: 20050208504
    Abstract: A method and system for monitoring the feature-extractability of microarrays by integrating control-feature blocks, or reference pattern blocks within a microarrray. The embedded control features comprise an array of pattern blocks, or reference pattern, in which each pattern block is composed of a set of microarray features arranged in a specific pattern of low-intensity and high-intensity features. Positive control features are designed to generate high-intensity signals following exposure of the microarray to a sample solution, and negative control features are designed to generate no signal or a low-intensity signal. The pattern blocks may be visually inspected to determine the feature extractability of a microarray prior to undertaking full, automated feature extraction, or may select a feature-extraction method based on an analysis of the reference pattern.
    Type: Application
    Filed: March 17, 2004
    Publication date: September 22, 2005
    Inventors: Srinka Ghosh, Eric Leproust
  • Publication number: 20050203708
    Abstract: A method and system for detecting and optionally characterizing background intensity gradients is disclosed. Various embodiments of the present invention employ metrics computed for a number of features within an image of a microarray that provide an indication of background intensity gradients within the image of the microarray. In one embodiment of the present invention, a metric is computed for a feature by determining the size of a region surrounding the feature for which the difference between the mean and median pixel intensities is large.
    Type: Application
    Filed: March 11, 2004
    Publication date: September 15, 2005
    Inventor: Srinka Ghosh
  • Publication number: 20050177315
    Abstract: A microarray processing system provides to a user an ability to draw one or more contour lines around portions of the microarray considered by the user to be undamaged, non-defective, and otherwise not compromised and therefore suitable for feature extraction. The microarray processing system then constructs one or more rectangular regions of feature extractability based on the user-indicated subregions of feature extractability, and proceeds to extract data from the one or more rectangular regions of feature extractability.
    Type: Application
    Filed: February 6, 2004
    Publication date: August 11, 2005
    Inventor: Srinka Ghosh
  • Publication number: 20050049797
    Abstract: A method and system for detecting block and zone misalignment of feature positions within a microarray-data set and for correcting feature positions for block or zone misalignment. In one embodiment of the present invention, displacement vectors representing the vector differences between observed positions of features and expected positions for the features of a microarray are calculated, based on an initially determined coordinate system. Features within a microarray data set are then partitioned with respect to the calculated vector displacements, so that features misaligned by a common rotation or translation are partitioned into a separate partition. A correction for each common misalignment can then be calculated and applied to the features of each partition.
    Type: Application
    Filed: August 27, 2003
    Publication date: March 3, 2005
    Inventors: Srinka Ghosh, Nicholas Sampas
  • Publication number: 20050038839
    Abstract: A method and system for evaluating the quality of normalizing feature sets used in normalizing two or more data sets obtained from microarrays, and for iteratively normalizing two or more data sets. In a described implementation, a rank-consistency threshold employed in selection and/or refinement of invariant features from the one or more data sets varied, as needed, during each iteration of an iterative normalization method, so that the iterative normalization converges on a set of invariant features for which a metric ? falls below a threshold value. The metric ? may be calculated as the percentage of selected invariant features, or normalizing features, that are differentially expressed in one or more data sets, to a specified level of significance. For a perfect set of invariant, or normalizing, features, the metric ? has the value of 0. ?-metric values of increasing magnitude correspond to normalizing feature sets of decreasing utility for normalization.
    Type: Application
    Filed: August 11, 2003
    Publication date: February 17, 2005
    Inventors: Srinka Ghosh, Mark Hartnett
  • Publication number: 20040241670
    Abstract: Method and system for partitioning pixels of a region within a scanned, digital image of a microarray into a set of feature pixels and a set of background pixels based on a difference between the intensity variance or noise within a subregion of pixels corresponding to a feature and the variance of background pixels. In one embodiment of the present invention, a standard deviation and mean for the pixel intensities within a microarray-image region are computed, assuming a normal distribution for the noise, and are used to compute a one-dimensional computed probability distribution function for the pixels in the microarray-image region. The one-dimensional, computed probability distribution is generally bimodal, with pixels within a first peak at a lower-probability region of the computed probability distribution corresponding to feature pixels and pixels within a second, larger peak at a relatively larger computed probability corresponding to background pixels.
    Type: Application
    Filed: June 2, 2003
    Publication date: December 2, 2004
    Inventors: Srinka Ghosh, Michael P. Caren
  • Publication number: 20040241669
    Abstract: A method and system for computing or using a larger region of interest (“ROI”) for each feature in the digital image of a microarray, in order to facilitate an analysis of the pixel-intensity distribution in or surrounding each feature, without incorporating pixels of adjacent features into the ROI. A cross-shaped ROI is computed for each feature. The cross-shaped ROI can be efficiently computed, and can in some embodiments at least double the number of pixels contained within the ROI with respect to standard, square or rectangular ROIs, without suffering centroid-displacement artifacts arising from differences in the intensities or adjacent features, irregularities of adjacent feature sizes, misalignment of adjacent feature positions, and other such phenomena.
    Type: Application
    Filed: June 2, 2003
    Publication date: December 2, 2004
    Inventor: Srinka Ghosh
  • Publication number: 20040121483
    Abstract: Biopolymeric array scanners that are capable of automatically selecting a dye specific scale factor to employ for a plurality of different dyes, as wells as methods for making and using the same, are provided. In many embodiments, the actual dye specific scale factor automatically selected by the scanner is one that is equal to a preset “master” scale factor, so that the scanner reads any supported dye using the same constant scale factor. The dye, specific scale factor selection is typically made by reference to a collection of nominal scale factors for each member of the plurality of dyes. In using the subject scanners, a user simply inputs the one or more dyes being used in a given array assay, and the scanner automatically reads the array using an automatically chosen dye specific scale factor for the selected dyes. Also provided are methods of obtaining collections of nominal scale factors and computer readable mediums comprising the same.
    Type: Application
    Filed: December 23, 2002
    Publication date: June 24, 2004
    Inventors: John F. Corson, Scott D. Connell, Srinka Ghosh