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    • 2. 发明申请
      US20160298185A1 POLYMORPHIC GENE TYPING AND SOMATIC CHANGE DETECTION USING SEQUENCING DATA 审中-公开
    • POLYMORPHIC GENE TYPING AND SOMATIC CHANGE DETECTION USING SEQUENCING DATA
    • 使用序列数据进行多态基因型和自变量检测
    • US20160298185A1
    • 2016-10-13
    • US15037394
    • 2014-12-05
    • The Broad Institute Inc. , Dana-Farber Cancer Institute, Inc. , The General Hospital Corporation
    • Sachet Ashok Shukla , Catherine Ju-Ying Wu , Gad Getz
    • C12Q1/68 , G06F19/18 , G06F19/22
    • C12Q1/6874 , C12Q1/6827 , C12Q1/6881 , C12Q1/6886 , C12Q2600/156 , G16B20/00 , G16B30/00 , C12Q2537/165
    • A system and method for determining the exact pair of alleles corresponding to polymorphic genes from sequencing data and for using the polymorphic gene information in formulating an immunogenic composition. Reads from a sequencing data set mapping to the target polymorphic genes in a canonical reference genome sequence, and reads mapping within a defined threshold of the target gene sequence locations are extracted from the sequencing data set. Additionally, all reads from the set data set are matched against a probe reference set, and those reads that match with a high degree of similarity are extracted. Either one, or a union of both these sets of extracted reads are included in a final extracted set for further analysis. Ethnicity of the individual may be inferred based on the available sequencing data which may then serve as a basis for assigning prior probabilities to the allele variants. The extracted reads are aligned to a gene reference set of all known allele variants. The allele variant that maximizes a first posterior probability or posterior probability derived score is selected as the first allele variant. A second posterior probability or posterior probability derived score is calculated for reads that map to one or more other allele variants and the first allele variant using a weighting factor. The allele that maximizes the second posterior probability or posterior probability score is selected as the second allele variant.A system and method for identifying somatic changes in polymorphic loci using WES data. The exact pair of alleles corresponding to the polymorphic gene are determined as described using a normal or germline sample from an individual. A tumor or otherwise diseased sample is also retrieved from the individual and the corresponding WES data is generated. Reads corresponding to the polymorphic gene are extracted as described in the paragraph above. These reads are then aligned to the inferred pair of allele sequences. The alignment of the germline or normal reads to the inferred pair of alleles, along with the alignment of the tumor or diseased reads to the inferred pair of alleles are simultaneously used as inputs to somatic change detection algorithms to identify somatic changes with greater precision and sensitivity.
    • 使用WES数据识别多态性位点体细胞变化的系统和方法。 如使用来自个体的正常或种系样品所描述的，确定对应于多形性基因的精确对等位基因。 还从个体检索肿瘤或其他患病样本，并生成相应的WES数据。 如上段所述提取对应于多形性基因的读数。 然后将这些读数与推断的等位基因序列对齐。 种系或正常读数与推断的等位基因对的一致性以及肿瘤或病变读数对推断的等位基因对的同时被同时用作体细胞变化检测算法的输入，以更精确和灵敏地鉴定体细胞变化 。
    • 基本信息 添加关注 加入工作空间 PDF全文 PDF下载 全文下载 相似专利 双屏查看 权利要求书 说明书全文 Global Dossier Espacenet 法律信息 同族专利 专利引用
    • 6. 发明授权
      US11725237B2 Polymorphic gene typing and somatic change detection using sequencing data 有权
    • Polymorphic gene typing and somatic change detection using sequencing data
    • US11725237B2
    • 2023-08-15
    • US15037394
    • 2014-12-05
    • The Broad Institute Inc. , Dana-Farber Cancer Institute, Inc. , The General Hospital Corporation
    • Sachet Ashok Shukla , Catherine Ju-Ying Wu , Gad Getz
    • C12Q1/6874 , G16B20/00 , G16B30/00 , C12Q1/6827 , C12Q1/6886 , G16B30/10 , G16B20/20 , G16B20/40 , C12Q1/6881
    • C12Q1/6874 , C12Q1/6827 , C12Q1/6881 , C12Q1/6886 , G16B20/00 , G16B20/20 , G16B20/40 , G16B30/00 , G16B30/10 , C12Q2600/156 , C12Q1/6827 , C12Q2537/165
    • A system and method for determining the exact pair of alleles corresponding to polymorphic genes from sequencing data and for using the polymorphic gene information in formulating an immunogenic composition. Reads from a sequencing data set mapping to the target polymorphic genes in a canonical reference genome sequence, and reads mapping within a defined threshold of the target gene sequence locations are extracted from the sequencing data set. Additionally, all reads from the set data set are matched against a probe reference set, and those reads that match with a high degree of similarity are extracted. Either one, or a union of both these sets of extracted reads are included in a final extracted set for further analysis. Ethnicity of the individual may be inferred based on the available sequencing data which may then serve as a basis for assigning prior probabilities to the allele variants. The extracted reads are aligned to a gene reference set of all known allele variants. The allele variant that maximizes a first posterior probability or posterior probability derived score is selected as the first allele variant. A second posterior probability or posterior probability derived score is calculated for reads that map to one or more other allele variants and the first allele variant using a weighting factor. The allele that maximizes the second posterior probability or posterior probability score is selected as the second allele variant.
      A system and method for identifying somatic changes in polymorphic loci using WES data. The exact pair of alleles corresponding to the polymorphic gene are determined as described using a normal or germline sample from an individual. A tumor or otherwise diseased sample is also retrieved from the individual and the corresponding WES data is generated. Reads corresponding to the polymorphic gene are extracted as described in the paragraph above. These reads are then aligned to the inferred pair of allele sequences. The alignment of the germline or normal reads to the inferred pair of alleles, along with the alignment of the tumor or diseased reads to the inferred pair of alleles are simultaneously used as inputs to somatic change detection algorithms to identify somatic changes with greater precision and sensitivity.
    • 基本信息 添加关注 加入工作空间 PDF全文 PDF下载 全文下载 相似专利 双屏查看 权利要求书 说明书全文 Espacenet 法律信息 同族专利 专利引用
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