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Methods for cancer detection and monitoring by means of personalized detection of circulating tumor DNA

A technology for cancer and breast cancer, applied in the direction of biochemical equipment and methods, microbial measurement/testing, etc., can solve problems such as insufficient sensitivity

Pending Publication Date: 2021-01-15
NATERA
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Biopsy of tumor tissue is aggressive and carries risks that may contribute to metastasis or surgical complications, while imaging-based tests are not sensitive enough to detect recurrence or metastasis at an early stage

Method used

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  • Methods for cancer detection and monitoring by means of personalized detection of circulating tumor DNA
  • Methods for cancer detection and monitoring by means of personalized detection of circulating tumor DNA
  • Methods for cancer detection and monitoring by means of personalized detection of circulating tumor DNA

Examples

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example 1

[0821] Example 1. Personalized circulating tumor DNA analysis for monitoring colorectal cancer

[0822] Early detection of disease recurrence has been shown to improve survival in colorectal cancer (CRC) patients. The detection of circulating tumor DNA (ctDNA) after surgery defines a subset of CRC patients at very high risk of recurrence. Previous studies have used small gene panel sequencing or digital droplet PCR for ctDNA analysis to monitor tumor burden in early CRC.

[0823] The aim of this example is to use a personalized multiplex PCR NGS platform targeting 16 tumor-specific mutations per patient to assess postoperative minimal residual disease and monitor treatment response in CRC.

[0824] 130 stage I-IV CRC patients treated with curative surgery and (optionally) adjuvant chemotherapy were included (see Table 1). Plasma samples were collected longitudinally at baseline before surgery and at planned control visits after surgery ( Figure 20A ). Whole-exome sequenci...

example 2

[0833] Example 2. Sequencing of plasma cfDNA from locally advanced bladder cancer patients for surveillance and efficacy monitoring

[0834] Studies of different cancer types have shown that circulating tumor DNA (ctDNA) content can be effectively used to monitor treatment response to neoadjuvant therapy and / or detect disease recurrence earlier than clinical and radiological detection. In bladder cancer, mutations in plasma have previously been used to monitor response during therapy and identify early signs of metastatic disease. Recently, longitudinal ctDNA testing in NSCLC patients was described and a personalized circulating tumor DNA (ctDNA) assay was developed (Signatera TM RUO).

[0835] The study goals were to detect metastatic recurrence, assess prognosis, and monitor treatment response in ctDNA from longitudinally collected plasma samples using patient-specific mutations identified in primary tumors.

[0836] Clinical protocol. Patients diagnosed with locally adva...

example 3

[0852] Example 3. Noninvasive Cancer Recurrence Detection and Therapy Monitoring Assay Based on Highly Sensitive Patient-Specific Multiplex PCR NGS

[0853] Identification of tumor mutations in circulating cell-free DNA has great potential for non-invasive detection of cancer recurrence prior to clinical manifestation, detection of minimal residual disease following curative-intent therapy, and detection of therapeutically relevant mutations. Review and report results of analytical validation of tumor-specific variant detection performed by the current version of the assay.

[0854] Customized monitoring technology RUO.Signatera for patients with solid tumors TM The (RUO) approach begins with the identification and prioritization of somatic mutations from whole-exome sequencing of tumor and matched normal samples. Patient-specific multiplex PCR assays targeting 16 somatic single-nucleotide and indel variants were then analyzed by massively parallel sequencing of plasma sample...

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Abstract

The invention provides methods for detecting single nucleotide variants in breast cancer, bladder cancer, or colorectal cancer. Additional methods and compositions, such as reaction mixtures and solidsupports comprising clonal populations of nucleic acids, are provided. For example, provided here is a method for monitoring and detection of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer, comprising generating a set of amplicons by performing a multiplex amplification reaction on nucleic acids isolated from a sample of blood or urine or a fraction thereof from a patient who has been treated for a breast cancer, bladder cancer, or colorectal cancer, wherein each amplicon of the set of amplicons spans at least one single nucleotide variant locus of a set ofpatient-specific single nucleotide variant loci associated with the breast cancer, bladder cancer, or colorectal cancer; and determining the sequence of at least a segment of each amplicon of the setof amplicons that comprises a patient-specific single nucleotide variant locus, wherein detection of one or more patient-specific single nucleotide variants is indicative of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer.

Description

[0001] Citations to related applications [0002] This application claims priority to: U.S. Provisional Application No. 62 / 657,727, filed April 14, 2018; U.S. Provisional Application No. 62 / 669,330, filed May 9, 2018; U.S. Provisional Application No. 62 / 693,843 filed on August 6, 2018; U.S. Provisional Application No. 62 / 715,143 filed on August 6, 2018; U.S. Provisional Application No. 62 / 746,210 filed on October 16, 2018; 2018 U.S. Provisional Application No. 62 / 777,973, filed December 11, 2019; and U.S. Provisional Application No. 62 / 804,566, filed February 12, 2019. Each of these applications cited above is incorporated herein by reference in its entirety. Background technique [0003] Detection of early recurrence or metastasis of cancer has traditionally relied on imaging and tissue biopsy. Biopsy of tumor tissue is invasive and carries risks that may contribute to metastasis or surgical complications, while imaging-based tests are not sensitive enough to detect recurre...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886
CPCC12Q1/6886C12Q2600/106C12Q2600/118C12Q2600/156C12Q1/6827C12Q2600/158C12Q2600/112
Inventor 伯恩哈德·齐默尔曼拉埃莱·萨拉里瑞安·斯韦纳顿吴欣达希曼舒·塞西
Owner NATERA
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