Methods for context based compression of genomic data for immuno-oncology biomarkers

A technique for context and compressed values, applied in genomics, gene models, bioinformatics, etc.

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

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However, anticancer responses may only be observed in a subset of tumors

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  • Methods for context based compression of genomic data for immuno-oncology biomarkers
  • Methods for context based compression of genomic data for immuno-oncology biomarkers
  • Methods for context based compression of genomic data for immuno-oncology biomarkers

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Embodiment Construction

[0014] In accordance with the teachings and principles embodied in this application, novel methods, systems, and non-transitory machine-readable storage media are provided for compressing data of nucleic acid sequence reads of genes associated with immuno-oncology biomarkers and based on the compressed data Detect enrichment or loss of signatures corresponding to functional context. Novel methods, systems, and non-transitory machine-readable storage media are provided for analyzing result information from multiple assays to predict response to immuno-oncology therapy.

[0015] In various embodiments, DNA (deoxyribonucleic acid) can be referred to as a nucleotide chain composed of 4 types of nucleotides: A (adenine), T (thymine), C (cytosine), and G (guanine), and the RNA (ribonucleic acid) contains 4 types of nucleotides; A, U (uracil), G and C. Certain pairs of nucleotides bind specifically to each other in a complementary manner (known as complementary base pairing). That ...

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Abstract

The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.

Description

[0001] Cross References to Related Applications [0002] This application claims the benefit of U.S. Provisional Application No. 62 / 835,586, filed April 18, 2019, under 35 U.S.C. §119(e). The entire contents of the aforementioned applications are incorporated herein by reference. Background technique [0003] Nucleic acid sequencing data can be obtained in various ways, including using next-generation sequencing systems, such as implementing IonTorrent TM Ion PGM for Sequencing Technology TM 、Ion Proton TM and Ion S5 TM system (see, e.g., U.S. Patent No. 7,948,015 issued May 24, 2011, U.S. Patent Application Publication No. 2010 / 0137143 published June 3, 2010, U.S. Patent Application Publication No. Application Publication No. 2009 / 0026082 and US Patent Application Publication No. 2010 / 0282617, published November 11, 2010, which are hereby incorporated by reference in their entireties). Such next-generation sequencing systems can be used in conjunction with primers for t...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B25/10
CPCG16B25/10G06F16/24575G06F16/248G16B20/20G06N3/126
Inventor F·海兰A·卡玛特T·隆尼
Owner LIFE TECH CORP
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