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Detecting cancer, cancer tissue of origin, and/or cancer cell type

A cancer, type of technology, applied in the detection of cancer, cancer-derived tissue and/or cancer cell types, can solve problems such as difference, loss of confidence in small control groups, and difficulty in interpretation

Pending Publication Date: 2021-11-30
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0007] Furthermore, various challenges exist in identifying differentially methylated regions in various diseases
First, calling differentially methylated regions in a disease group is only significant compared to a set of control subjects, so if the number of controls is small, the call loses confidence in a small control group
In addition, methylation status may vary within a group of control subjects, which is difficult to interpret when identifying regions of differential methylation in disease groups

Method used

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  • Detecting cancer, cancer tissue of origin, and/or cancer cell type
  • Detecting cancer, cancer tissue of origin, and/or cancer cell type
  • Detecting cancer, cancer tissue of origin, and/or cancer cell type

Examples

Experimental program
Comparison scheme
Effect test

example 1

[0297] Example 1: Analysis of Probe Quantities

[0298] To test how much overlap is needed between a cfDNA fragment and a probe to achieve a non-negligible amount of pulldown, various lengths of overlap were used designed to include three different types of probes (VID3, VID4, VIE2). Detection combinations are tested. The three different types of probes had various overlaps with several 175 bp target DNA fragments specific for each probe. The overlap range tested was between 0bp and 120bp. Several samples including 175bp target DNA fragments were applied to the detection assembly and washed, and then several DNA fragments linked to the several probes were collected. The amount of several DNA fragments collected was measured, and the amount was plotted as density versus size of the overlap, as in Figure 10 provided in .

[0299] When less than 45 bp overlap, there is no significant binding and pull-down of the target DNA fragment. These results show that a fragment-probe ...

example 2

[0303] Example 2: Annotation of genomic regions of interest

[0304] right through Figure 4 Genomic regions of interest identified by the process outlined in . Specifically, selected genomic regions of interest are aligned to a reference genome to determine a number of alignment positions. The alignment position information of each selected target genome region is collected, and the alignment position information includes: chromosome number, start nucleotide base, end nucleotide base and genome annotation of the given genome region. 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 genomic regions of interest within each genome annotation was counted and plotted in the graph provided in Figure 11. Figure 11 also compares the number of selected genomic regions of interest (black bars) or randomly selected genomic regions (gray bars) within each genome annotation.

[030...

example 3

[0306] Example 3: Cancer assay panel for detection of cancer and cancer type

[0307] Samples used for genomic region selection: DNA samples for this work were obtained from various sources.

[0308] The Circulating Cell-Free Genome Atlas study (CCGA; Clinical Trial.gov identifier (NCT02889978)) was a prospective, multicenter, case-control, observational study with longitudinal follow-up. Unidentified individuals were collected from approximately 15,000 participants at 142 sites. Identified biological samples. Samples were selected to ensure a pre-specified distribution of cancer types and non-cancer in each population, and cancer and non-cancer samples were frequency-age-matched by sex.

[0309] The Cancer Genome Atlas ("TCGA"; Clinical Trial.gov identifier NCT02889978) is a public resource developed by the National Cancer Institute (NCI) in collaboration with the National Human Genome Research Institute (NHGRI).

[0310] Isolated tumor cells (DTC) were obtained from Convers...

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Abstract

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

Description

[0001] cross reference [0002] This application is from U.S. Provisional Patent Application No. 62 / 797,176 filed on January 25, 2019 and U.S. Provisional Patent Application No. 62 / 797,174 filed on January 25, 2019 and filed in 2019 Priority is claimed in US Provisional Patent Application No. 62 / 797,170, filed January 25, which is hereby incorporated by reference in its entirety. [0003] sequence listing [0004] This application includes a "lengthy" sequence listing filed on CD-R in lieu of a printed paper copy, and is hereby incorporated by reference in its entirety. Said CD-Rs were recorded on January 23, 2020 and are labeled "CRF", "Copy 1", "Copy 2" and "Copy 3", and each CD-R contains only one identical 243821056 byte file (50251-849_601_SL.txt). Said CD-R and identical copies are hereby incorporated by reference in their entirety. Background technique [0005] DNA methylation plays an important role in regulating gene expression. Aberrant DNA methylation is ass...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886C12Q1/6832C12Q1/6827C12N15/11G16B40/00A61K45/00A61P35/00
CPCC12Q1/6886C12Q1/6832C12Q1/6827G16B40/00A61K45/00A61P35/00C12Q2600/154C12Q2600/112C12Q2523/125C12Q2531/113C12Q2525/204C12Q2535/122C12Q2521/539C12Q2537/164G16B20/20G16B40/20C12Q1/6809C12Q1/6874
Inventor 奥利弗·克劳德·维恩亚历山大·P·菲尔兹萨缪尔·S·格罗斯刘勤文简·施伦伯格約格·布登諾约翰·F·博桑塞德梅迪·肖吉奥努尔·萨卡里亚M·赛勒斯·马厄阿拉什·詹姆席狄
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