Patents by Inventor Aaron L. Halpern

Aaron L. Halpern 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: 20200087723
    Abstract: Disclosed herein are systems and methods for spinal muscular atrophy (SMA) diagnosis from whole genome sequencing data. In one embodiment, a method comprises aligning whole genome sequencing (WGS) reads of a subject's sample to a modified reference sequence such as a modified reference genome sequence. After counting the reads supporting quasi-alleles at select positions of the reference sequence, the method can adjust for coverage and determine a number of functional SMN1 gene copies. The method can determine affected or carrier status of the subject based on the copy number of functional SMN1 gene copies.
    Type: Application
    Filed: December 14, 2017
    Publication date: March 19, 2020
    Inventors: Aaron L. Halpern, Semyon Kruglyak, Peter Krusche
  • Patent number: 8738296
    Abstract: Generating an index includes receiving a reference sequence and applying one or more key patterns to the reference sequence to obtain a plurality of keys in the index. Each of the one or more key patterns is derived based on a corresponding set of oligomer sequence relationships of a plurality of oligomer sequences that are expected to be generated from the reference, and the keys correspond to a plurality of candidate and/or validated locations in the reference sequence.
    Type: Grant
    Filed: February 2, 2010
    Date of Patent: May 27, 2014
    Assignee: Complete Genomics, Inc.
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Patent number: 8731843
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, modifying positions within these keys, and locating the one or more keys in an index configured to map a plurality of candidate and/or validated keys to their respective possible and/or validated locations in a reference.
    Type: Grant
    Filed: February 2, 2010
    Date of Patent: May 20, 2014
    Assignee: Complete Genomics, Inc.
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Patent number: 8615365
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.
    Type: Grant
    Filed: February 2, 2010
    Date of Patent: December 24, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Publication number: 20120197533
    Abstract: Methods, apparatuses, and systems for identification of junctions (e.g., resulting from large-scale rearrangements) of a sequenced genome with respect to a human genome reference sequence is provided. For example, false positives can be distinguished from actual junctions. Such false positives can result from many sources, including mismapping, chimeric reactions among the DNA of a sample, and problems with the reference genome. As part of the filtering processes, a base pair resolution (or near base pair resolution) of a junction can be provided. In various implementations, junctions can be identified using discordant mate pairs and/or using a statistical analysis of the length distributions of fragments for local regions of the sample genome. Clinically significant junctions can also be identified so that further analysis can be focused on genomic regions that may have more of an impact on the health of a patient.
    Type: Application
    Filed: January 28, 2011
    Publication date: August 2, 2012
    Applicant: Complete Genomics, Inc.
    Inventors: Igor Nazarenko, Aaron L. Halpern, Paolo Carnevali
  • Publication number: 20110015864
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, modifying positions within these keys, and locating the one or more keys in an index configured to map a plurality of candidate and/or validated keys to their respective possible and/or validated locations in a reference.
    Type: Application
    Filed: February 2, 2010
    Publication date: January 20, 2011
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Publication number: 20110004413
    Abstract: Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence.
    Type: Application
    Filed: April 29, 2010
    Publication date: January 6, 2011
    Applicant: COMPLETE GENOMICS, INC.
    Inventors: Paolo Carnevali, Jonathan M. Baccash, Igor Nazarenko, Aaron L. Halpern, Geoffrey Nilsen, Bruce Martin, Radoje Drmanac
  • Publication number: 20100287165
    Abstract: Generating an index includes receiving a reference sequence and applying one or more key patterns to the reference sequence to obtain a plurality of keys in the index. Each of the one or more key patterns is derived based on a corresponding set of oligomer sequence relationships of a plurality of oligomer sequences that are expected to be generated from the reference, and the keys correspond to a plurality of candidate and/or validated locations in the reference sequence.
    Type: Application
    Filed: February 2, 2010
    Publication date: November 11, 2010
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Publication number: 20100286925
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.
    Type: Application
    Filed: February 2, 2010
    Publication date: November 11, 2010
    Inventors: Aaron L. Halpern, Igor Nazarenko