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    Array-based methods for analysing mixed samples using differently labelled allele-specific probes
    2.
    发明授权
    Array-based methods for analysing mixed samples using differently labelled allele-specific probes 有权

    公开(公告)号：US11441174B2

    公开(公告)日：2022-09-13

    申请号：US16616741

    申请日：2018-06-01

    申请人： AFFYMETRIX, INC.

    发明人： Michael Shapero ,  Ronald Sapolsky ,  Eric Fung ,  Jeanette Schmidt ,  Monica Chadha ,  Anju Shukla

    IPC分类号： C12Q1/6837 ,  C12Q1/6827

    摘要： This disclosure provides methods and kits useful in analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The method is based on the hybridisation of amplified fragments obtained from the sample, e.g. using molecular inversion probes (MIP) to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.

    ARRAY-BASED METHODS FOR ANALYSING MIXED SAMPLES USING DIFFERENTLY LABELLED ALLELE-SPECIFIC PROBES
    3.
    发明申请
    ARRAY-BASED METHODS FOR ANALYSING MIXED SAMPLES USING DIFFERENTLY LABELLED ALLELE-SPECIFIC PROBES 有权

    公开(公告)号：US20210147920A1

    公开(公告)日：2021-05-20

    申请号：US16616741

    申请日：2018-06-01

    申请人： AFFYMETRIX, INC.

    发明人： Michael SHAPERO ,  Ronald SAPOLSKY ,  Eric FUNG ,  Jeanette SCHMIDT ,  Monica CHADHA ,  Anju SHUKLA

    IPC分类号： C12Q1/6837 ,  C12Q1/6827

    摘要： This disclosure provides methods and kits useful in analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The method is based on the hybridisation of amplified fragments obtained from the sample, e.g. using molecular inversion probes (MIP) to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.

    ARRAY-BASED METHODS FOR ANALYSING MIXED SAMPLES USING DIFFERENTLY LABELLED ALLELE-SPECIFIC PROBES
    4.
    发明申请
    ARRAY-BASED METHODS FOR ANALYSING MIXED SAMPLES USING DIFFERENTLY LABELLED ALLELE-SPECIFIC PROBES 有权

    公开(公告)号：US20210147919A1

    公开(公告)日：2021-05-20

    申请号：US16616735

    申请日：2018-06-01

    申请人： AFFYMETRIX, INC.

    发明人： Ronald SAPOLSKY ,  Michael SHAPERO ,  Jeanette SCHMIDT ,  Eric FUNG ,  Orna MIZRAHI MAN ,  Jiang LI ,  Monica CHADHA ,  Anju SHUKLA

    IPC分类号： C12Q1/6837 ,  C12Q1/6827

    摘要： This disclosure provides methods and systems useful in array-based analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The disclosure is based on the hybridisation of amplified fragments from the sample, e.g. a maternal sample, which may employ molecular inversion probes MIP to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP. The disclosure also discloses how the determination of the allele ratio may be used in the determination of fetal and maternal CNVs, e.g. aneuploidies.

    DNA ligation on RNA template
    7.
    发明授权
    DNA ligation on RNA template 有权

    公开(公告)号：US10648021B2

    公开(公告)日：2020-05-12

    申请号：US15798238

    申请日：2017-10-30

    申请人： AFFYMETRIX, INC.

    发明人： Eugeni A. Namsaraev ,  Xin Miao ,  John E. Blume

    IPC分类号： C12Q1/68 ,  C12Q1/6837

    摘要： Disclosed are methods and compositions for detection and amplification of nucleic acids, wherein two DNA strands hybridized to an RNA strand are ligated. In one aspect, the disclosed methods include removal of an energy source, such as ATP, upon charging a ligase to form an enzyme-AMP intermediate, and then adding substrate, which results in one complete round of RNA-templated DNA ligation. In another aspect, the ligation reaction is accomplished by use of a mixture of at least two different ligase enzymes. The disclosed methods and compositions for RNA-templated DNA ligation may be particularly useful for detection of RNA sequence variants, for example RNA splice variants, and for quantitative expression analysis.

    Analysis of data obtained from microarrays
    8.
    发明授权
    Analysis of data obtained from microarrays 有权

    公开(公告)号：US10515447B2

    公开(公告)日：2019-12-24

    申请号：US13689027

    申请日：2012-11-29

    申请人： Affymetrix, Inc.

    发明人： Benjamin M. Bolstad ,  Harry Zuzan

    IPC分类号： G06F19/00 ,  G06T7/00

    摘要： 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 which may be selected by a user. Further, the present application provides methods of filtering image data and signal restoration of image data using log2 ratio data.

    Methods of analysis of methylation
    10.
    发明授权
    Methods of analysis of methylation 有权

    公开(公告)号：US10407717B2

    公开(公告)日：2019-09-10

    申请号：US15281721

    申请日：2016-09-30

    申请人： Affymetrix, Inc.

    发明人： Shivani Nautiyal ,  Malek Faham

    IPC分类号： C12Q1/683 ,  C12Q1/6813 ,  C12Q1/6806

    摘要： Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.