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Methods and systems for determining spatial patterns of biological targets in a sample

A technology of biological targets and spatial distribution, applied in biochemical equipment and methods, microbial measurement/inspection, chemical instruments and methods, etc., can solve problems such as expensive, laborious, and low spatial resolution

Active Publication Date: 2016-08-10
PROGNOSYS BIOSCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

While these methods are useful, they cannot simultaneously measure the expression of multiple genes or the presence and / or activity of multiple proteins at multiple spatial locations in a sample
[0007] Laser capture microdissection can analyze many genes at a small number of loci, but the technique is expensive, laborious, and poorly measured
Certain 2D forms of PCR analysis preserve spatial information (see Armani et al., Lab on aChip, 9(24):3526-34 (2009) for details), but these methods have low spatial resolution because they rely on organizing tissue Physical transfer to reaction wells, which also prevents random access to (pending) tissue samples and high level doubling

Method used

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  • Methods and systems for determining spatial patterns of biological targets in a sample
  • Methods and systems for determining spatial patterns of biological targets in a sample
  • Methods and systems for determining spatial patterns of biological targets in a sample

Examples

Experimental program
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example 1

[0219] Example 1 Addressing scheme proof of concept and scalability

[0220] An analytical model system was developed using microarrays to validate multiple spatially encoded abundances of working polynucleotide targets. The basic design validates the concept of the assay and the addressing scheme, and establishes a usable assay before addressing issues associated with the analysis of more complex biological samples.

[0221] Microarrays are used as an alternative to tissue sections. The target sequence of the microarray is fully specified so that the composition of the target is known and systematically varied. Those skilled in the art will recognize from the present disclosure that similar assays can be performed on different samples, including tissue sections, and for different targets including polynucleotide or protein targets as well as other biological targets.

[0222] 16-fold × 8-locus analysis using 8-layer gene chip as artificial sample

[0223] The 16-fold × 8...

example 2

[0224] Example 2 Demonstration of Spatial Coding Using Spot Gene Chips

[0225] The scalability of the spatial processing and analysis system is demonstrated by implementing a 24-plex x 24-locus analysis using the chip model system.

[0226] The amount of the biological target, here the DNA target sequence, varies systematically at each assay site on the substrate on the gene chip. For example, in a microarray with a spot size (center to center) of 50 microns, a 1 mm2 area contains ~400 spots. The surrounding region of each site is optionally occupied by a region lacking such spots, allowing the target sequence to be resolved individually. Alternatively, 2 or more adjacent spots or spots surrounding a region lacking a target sequence can be clustered.

[0227] To confirm that the spatial addressing or encoding was accurate, the loci included different target compositions and it was shown that the detected reads for each locus matched the expected composition. 24 target se...

example 3

[0230] The analysis method of example 3 preserves sample and biological sample

[0231] Genomic DNA is examined to characterize changes in coding and regulatory sequences, such as single nucleotide polymorphisms (SNPs) or mutations, small insertions and deletions (indels), copy number variations such as deletions or amplifications of genes, and gene Rearrangements such as transposition, all of which may have significant functional significance in cancer and other diseases. Genomic sequence variation as a function of location in a sample can indicate somatic mosaicism in a sample. In cancer samples, mutations can provide prognostic or diagnostic markers, which are useful for determining optimal treatment options. Genetic mutations can identify regions of a sample that include cancer cells and can help distinguish them from normal cells or from cells in the tumor microenvironment, which is defined as cells that are affected by cancer cells in genetics Cells whose sequence le...

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Abstract

The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and / or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.

Description

[0001] related application [0002] This application claims priority to U.S. Provisional Application No. 61 / 839,320, filed June 25, 2013, entitled "Bioanalysis Employing Spatial Compilation of Microfluidic Devices," and filed June 25, 2013 , US Provisional Application No. 61 / 839,313, entitled "Method and System for Detecting the Spatial Distribution of Biological Targets in a Sample", the disclosures of which are incorporated herein by reference. In some embodiments, the application number is PCT / US2014 / ___, the filing date is June 25, 2014, the agency docket number is 699932000340, and the title is "Spatially encoded bioanalysis using a microfluidic device" , its disclosed content is incorporated into this application in its entirety by reference. [0003] This invention was made with the support of the National Institute of General Medicine, US Department of Health and Human Services under grant R43GM096706, and the National Human Genome Research Institute under grant R43HG00...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68
CPCB01L3/5027C12Q1/6853C12Q1/6841C12Q2543/101C12Q2563/179C12Q2565/514C12Q2565/629C12Q1/6809C12Q2565/513
Inventor 马克·S·朱大卫·罗腾伯格
Owner PROGNOSYS BIOSCI