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Methylation markers and targeted methylation probe panels

A technology of methylation and unmethylation, applied in biochemical equipment and methods, combinatorial chemistry, chemical library, etc., can solve the problem of no cost-effective method for accurate diagnosis of diseases

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

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Problems solved by technology

[0006] Therefore, there is no cost-effective method capable of accurately diagnosing diseases by detecting multiple differentially methylated regions

Method used

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  • Methylation markers and targeted methylation probe panels
  • Methylation markers and targeted methylation probe panels
  • Methylation markers and targeted methylation probe panels

Examples

Experimental program
Comparison scheme
Effect test

example 1

[0377]Example 1: Probe quality analysis

[0378]In order to test how much overlap between a cfDNA fragment and a probe is needed to achieve a non-negligible pull-down amount, a variety of test panels designed to contain three different types of probes (V1D3, V1D4, V1E2) are used to test different lengths of overlap. Each probe's specific 175bp target DNA fragment has a different overlap. The overlap range tested is between 0bp and 120bp. A plurality of samples containing a plurality of 175 bp target DNA fragments are applied to the test plate and washed, and then a plurality of DNA fragments bound to the plurality of probes are collected. Measure multiple numbers of multiple DNA fragments collected, and plot the multiple numbers as density and overlap size, such asPicture 9 Shown.

[0379]When the overlap is less than 45bp, multiple target DNA fragments do not bind and pull down significantly. These results indicate that a probe overlap of at least 45 bp is usually required to achieve a n...

example 2

[0384]Example 2: Annotation of target genomic regions

[0385]byFigure 4 The multiple target genomic regions identified by the procedures outlined in are used to understand multiple characteristics of multiple target regions. In particular, multiple selected target genome regions are aligned with a reference genome to determine multiple arrangement positions. Alignment position information is collected for each selected target genomic region, and the alignment position information includes the number of chromosomes, starting bases, ending bases, and genome annotations for a given genomic region. Multiple target genomic regions are located in introns, exons, intergenic regions, 5'UTRs, 3'UTRs or control regions, such as promoters or enhancers. The number of multiple target genome regions that fall within each genome annotation is counted and plotted inPicture 12 In the diagram provided in.Picture 12 The number of selected multiple target genomic regions (black bars) or the number of ran...

example 3

[0387]Example 3: Cancer Test Board (CCGA)

[0388]Use a database generated by sequencing multiple cfDNA fragments obtained from more than 1800 individuals to select multiple target genomic regions. The cfDNA sequencing database is referred to herein as the Cyclic Cell-Free Genome Atlas Study ("CCGA"). The CCGA study is described in Clinical Trial.gov, identifier: NCT02889978 (https: / / www.clinicaltrials.gov / ct2 / show / NCT02889978).

[0389]Specifically, multiple cfDNA sequences in the database are screened based on the p value using non-cancer distribution, and only multiple fragments with p<0.001 are retained. The selected multiple cfDNAs are further filtered to retain only those cfDNAs that are at least 90% methylated or 90% unmethylated. Next, for each CpG site in the selected fragment, the number of cancer samples or non-cancer samples containing multiple fragments overlapping the CpG site is counted. Specifically, the P (cancer|overlapping fragment) of each CpG is calculated, and multip...

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Abstract

The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein includes methods of designing, making, and using the cancer assay panel for diagnosis of cancer.

Description

[0001]Cross references to related applications [0002]This application claims the rights of U.S. Provisional Patent Application No. 62 / 651,643 filed on April 2, 2018 and U.S. Provisional Patent Application No. 62 / 738,271 filed on September 28, 2018, all of which are hereby incorporated by reference The content is incorporated in this article.Background technique[0003]Deoxyribonucleic acid (DNA) methylation plays an important role in regulating gene expression. Abnormal DNA methylation is associated with many disease processes, including cancer. DNA methylation analysis using methylation sequencing (e.g., whole genome bisulfite sequencing (WGBS)) is increasingly recognized as a valuable diagnostic tool for detecting, diagnosing, and / or monitoring cancer. For example, the specific patterns of different methylation regions can be used as molecular markers for various diseases.[0004]However, WGBS is not ideally suited for product testing. The reason is that most genomes are not different...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12N15/10C12N15/11C12Q1/6869
CPCC12Q1/6886C12Q2600/154C12Q1/6806C12Q1/701C12Q2537/159C12Q1/70C40B40/06C12Q2535/122
Inventor 塞缪尔·S·格罗斯哈米德·阿米尼阿拉什·詹姆席狄塞德梅迪·肖吉斯林卡·戈什祁容素M·赛勒斯·马厄亚历山大·P·菲尔兹奥利弗·克劳德·维恩
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