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Leveraging sequence-based fecal microbial community survey data to identify composite biomarker for colorectal cancer

A colorectal cancer and microbiological technology, applied in the field of markers for the diagnosis of CRC and CRA, and detection of transition from adenoma to cancer, can solve problems such as expensive, lack of comparability, and limited compliance rate of screening recommendations

Pending Publication Date: 2019-12-31
SECOND GENOME +1
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[2-4] Despite this, adherence to screening recommendations remains limited
[0007] Colonoscopy is invasive, expensive and does not detect interval cancers (ie, CRC diagnosed within 6-36 months of colonoscopy), but it represents the most commonly used screening method
[5,6] At-home fecal occult blood testing (FOBT) is used infrequently because it is not considered effective in reducing cancer-related mortality
[5] Moreover, FOBT has low sensitivity for detection of precancerous lesions and colorectal adenomas (CRA)
However, there is a lack of direct comparability between different experimental methods, 16S rRNA gene target regions, sequencing platforms, informatics techniques, and demographics

Method used

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  • Leveraging sequence-based fecal microbial community survey data to identify composite biomarker for colorectal cancer
  • Leveraging sequence-based fecal microbial community survey data to identify composite biomarker for colorectal cancer
  • Leveraging sequence-based fecal microbial community survey data to identify composite biomarker for colorectal cancer

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Embodiment 1

[0123] To determine whether universal microbial markers for CRC and CRA could be identified, we obtained raw 16S rRNA gene sequence data from multiple faecal microbiome studies published between 2006 and 2016. We analyzed the data using two bioinformatics pipelines, (1) de novo QIIME (QIIME-CR), a de novo (closed-reference ) OTU assignment method, and (2) Strain Select-UPARSE (SS-UP), a strain-specific method that in some cases uses more raw sequence data to give strain-level resolution. In addition, we compared our panel of microbial markers with the take-home guaiac-based fecal occult blood test (FOBT), a non-invasive but less precise test, where data were available. test. [23,24]

[0124] Research search, selection and adoption

[0125]We performed a systematic PubMed search for studies with colorectal cancer, colon cancer, or colorectal adenocarcinoma in the title, including human subjects, published between 2006 and 2016. The specific search terms that ended up using ...

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Abstract

The present disclosure provides fecal microbial markers for diagnosing colorectal cancer and colorectal adenoma. The present disclosure also provides methods for diagnosing colorectal cancer and colorectal adenoma using these intestinal microbial markers.

Description

[0001] Cross References to Related Applications [0002] This application claims priority to US Provisional Application 62 / 472,863, filed March 17, 2017, the contents of which are incorporated herein by reference in their entirety. technical field [0003] This article relates to the use of the fecal microbiome as a non-invasive biomarker for the diagnosis of colorectal cancer (CRC) and colorectal adenoma (CRA) and for the detection of adenoma-to-carcinoma transition. In particular, it relates to the use of 16S rRNA sequences of excreted microorganisms as markers for the diagnosis of CRC and CRA. [0004] Electronic Submission Text Instructions [0005] The content of the submitted text in electronic form is hereby incorporated into this article as a whole: computer-readable sequence listing (file name: SEGE_002_01WO_SeqList_ST25, date of entry on February 18, 2018, file size 315K bytes). Background technique [0006] Colorectal cancer (CRC) is the third most common cancer...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/689C12Q1/6888C12Q1/04
CPCC12Q1/6886C12Q1/6888C12Q1/689C12Q2600/158G01N33/57407G01N33/57419C12Q1/6816G01N33/57446G16B25/00G16B30/00G16B50/00
Inventor T·Z·德桑蒂斯T·威迈尔M·S·沙阿E·B·霍利斯特布莱登
Owner SECOND GENOME
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