Method and system for determining cancer status

A cancer and methylation technology, applied in biochemical equipment and methods, biostatistics, microbial measurement/testing, etc., can solve problems such as high procedure cost, hindrance to accurate diagnosis, high cancer incidence and mortality

Active Publication Date: 2018-05-22
RGT UNIV OF CALIFORNIA +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

In some cases, diagnostic procedures are initiated only after the patient has shown symptoms, making the procedure costly, invasive, and time-consuming
A...

Method used

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  • Method and system for determining cancer status
  • Method and system for determining cancer status
  • Method and system for determining cancer status

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0403] Example 1 - Extraction of cell-free DNA from urine for non-invasive diagnostics

[0404] Stability and Reserves

[0405] approve

[0406] This project was approved by the IRB of SYSU and Sichuan University. Informed consent was obtained from all patients. Tumor and normal tissues were obtained after patients signed informed consent.

[0407] 3 steps: Urine Stabilization Buffer - Centrifugation - Freeze Supernatant

[0408] urine stabilization buffer

[0409] Prepare urine stabilization buffer for urine DNA stabilization and cell-free DNA protection. The preservative stabilizes the cells in the urine and prevents the release of genomic DNA, allowing the isolation of high-quality cell-free DNA. Samples collected in urine stabilization buffer are stable at room temperature for up to 14 days, allowing for convenient sample collection, transport, and storage.

[0410] The formula of urine stabilizing buffer:

[0411] 2.2% sodium citrate

[0412] 0.8% citric acid

...

Embodiment 2

[0440] Example 2 - Isolation of free circulating cell-free DNA from urine.

[0441] The QIAamp Circulating Nucleic Acid Kit from 4 ml of urine was used, which was the supernatant treated with the urine stabilizing buffer mixture and centrifuged as described above. Urine samples were either fresh or frozen and then equilibrated against room temperature.

[0442] program

[0443] 1. Pipet 500 μl QIAGEN Proteinase K into a 50 ml tube (not provided).

[0444] 2. Add 4ml of urine to the 50ml tube.

[0445] 3. Add 4ml Buffer ACL (with carrier RNA if needed) and 1.0ml Buffer ATL; cap tightly and mix by pulse vortexing for 30 seconds.

[0446] 4. Incubate at 60°C for 30 minutes.

[0447] 5. Return the tube to the bench and unscrew the cap.

[0448] 6. Add 9.0ml Buffer ACB to the lysate, cap tightly and mix well by pulse vortexing for 15-30 seconds.

[0449] 7. The lysate-buffer ACB mixture was incubated on ice for 5 minutes.

[0450] 8. Insert the QIAamp Mini Column into the Va...

Embodiment 3

[0460] Example 3 - Generation of Methylation Markers

[0461] data source

[0462]DNA methylation data were obtained from various sources, including The Cancer Genome Atlas (TCGA). The methylation status of 485,000 sites was generated using the Infinium 450K Methylation Array. Other data come from the following GSE datasets: GSE46306, GSE50192, GSE58298 and GSE41826. Methylation profiles were analyzed for tumors and their corresponding normal tissues (Table 1).

[0463] Methylation data files were obtained in IDAT format with the ratio values ​​scanned for each bead. These data files were converted into scores, called beta values, using the minfi package from Bioconductor.

[0464] After obtaining beta values ​​for all samples, any markers not present in all 20 data sets were removed.

[0465] Table 1. Sample counts by sample type from The Cancer Genome Atlas (TCGA)

[0466]

[0467]

[0468] Identify high scoring markers in each comparison

[0469] Specific marke...

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Abstract

Disclosed herein are methods, systems, platforms, non-transitory computer-readable medium, services, and kits for determining a cancer type in an individual. Also described herein include methods, systems, platforms, non-transitory computer-readable medium, and compositions for generating a CpG methylation profile database.

Description

[0001] cross reference [0002] This application claims the benefit of U.S. Provisional Application No. 62 / 104,785, filed January 18, 2015, and U.S. Application No. 14 / 986,520, filed December 31, 2015, which are incorporated herein by reference. [0003] sequence listing [0004] This application contains a Sequence Listing which has been submitted in ASCII format via EFS Web and is hereby incorporated by reference in its entirety. This ASCII copy, created on January 12, 2016, is named 49697-701.601_SL.txt and is 846 kilobytes in size. Background technique [0005] Cancer is the leading cause of death worldwide, with annual cases expected to increase from 14 million in 2012 to 22 million during the next two decades (WHO). In some cases, diagnostic procedures are initiated only after the patient has developed symptoms, making the procedure costly, invasive, and time-consuming. Additionally, inaccessible areas can sometimes prevent accurate diagnosis. In addition, higher ...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886G06F19/22G06F19/24G06F19/28G06F19/20G16B50/30G16B25/10G16B30/00G16B40/20G16B40/30
CPCG16B40/00G16B25/00G16B30/00G16B50/00C12Q1/6886C12Q2600/154G16B40/30G16B40/20G16B25/10G16B50/30
Inventor 张康侯睿郑良宏
Owner RGT UNIV OF CALIFORNIA
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