Systems and methods for tumor clonality analysis

A clonality and tumor technology, applied in the field of computational analysis of genomic data, can solve the problems of inability to identify tumors, inability to identify the relationship between clonality and cell population clones, inability to gain insight into clonality and potential therapeutic efficacy, etc.

Inactive Publication Date: 2015-09-02
FIVE3 GENOMICS
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  • Description
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Problems solved by technology

Most notably, methods known to date fail to allow the identification of tumor progression at the molecular level, giving insight into clonality and potential therapeutic efficacy
From another point of view, the hitherto known methods do not allow identification of clonality and clonal relationships of cell populations in samples containing multiple heterogeneous cells

Method used

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  • Systems and methods for tumor clonality analysis
  • Systems and methods for tumor clonality analysis
  • Systems and methods for tumor clonality analysis

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Embodiment

[0103] GBM (glioblastoma): Twelve genome-wide GBM samples were processed as described above for the determination of normal contamination levels and clonality present in each tumor biopsy. For the other 5 genome-wide GBM samples discussed in the previous section, the relative coverage and allele ratios generated by BamBam would have too much variability to be analyzed by these methods. Table 1 summarizes the results of the clonality analysis.

[0104]

[0105] Surprisingly, only 3 GBM tumor samples were found to be monoclonal, while the other 9 samples included at least two predominant clones. For 7 GBM tumors, the exact mixture of clones was determined, while the remaining 5 tumors were visually inspected to determine their clonality.

[0106] The results of two clones GBM-06-0145 and GBM-06-0185 are as follows Figure 7A with 7B shown. Relative coverage and allele ratio data for the two samples transformed by the best fit parameters described above showed a close fit ...

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Abstract

Systems and methods of genomic analysis are presented that provide a framework to determine a tumor's clonality, the number and proportion of all major clones, and the variants that distinguish them. Contemplated systems and methods also allow phasing mutations to parental alleles to so time their emergence within the population of tumor cells, and provide an accurate estimate of the amount of contaminating normal tissue that was present in the tumor biopsy.

Description

[0001] This application claims priority to our co-pending US Provisional Application Serial No. 61 / 711467, filed October 9, 2012, which is hereby incorporated by reference in its entirety. technical field [0002] The field of the invention is the computational analysis of genomic data, in particular it relates to the identification of the clonality status of mixed cell populations. Background technique [0003] With the increasing availability of whole genome data and the continuous acceleration of whole genome sequencing, large quantities of data are now available, which requires meaningful analysis to provide information to clinicians or scientists for more effective treatment or drug development. [0004] For example, multiple tumor and matched normal whole genome sequences are now available from projects like The Cancer Genome Atlas (TCGA), where it is difficult to extract relevant information. The problem is further complicated by the need for high coverage (eg, greate...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/10G16B20/20G16B20/10G16B30/10G16B45/00
CPCC12Q1/6809C12Q2600/156C12Q1/6886G06F19/18G06F19/24G16B40/00G16B20/00G16B30/00G16B30/10G16B20/10G16B20/20C12Q2537/165
Inventor J·Z·桑伯恩
Owner FIVE3 GENOMICS
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