IP Verse

Spatial Mapping Of Nucleic Acid Sequence Information

Patent No. US10913975 (titled "Spatial Mapping Of Nucleic Acid Sequence Information") was filed by Illumina Inc on Jul 21, 2016.

What is this patent about?

’975 is related to the field of spatial transcriptomics and genomics , specifically methods and compositions for analyzing nucleic acids (DNA and RNA) within tissue samples while preserving spatial information. Existing techniques often lack the ability to simultaneously characterize transcriptomes or genomic variations and maintain positional context within the tissue, which is crucial for understanding biological processes and disease states.

The underlying idea behind ’975 is to encode spatial information directly into nucleic acids derived from a tissue sample during library preparation for sequencing. This is achieved by using capture probes that incorporate location-specific sequence tags (spatial addresses). By sequencing these tagged nucleic acids in bulk, the origin of each molecule within the tissue can be determined based on its spatial address, enabling the creation of spatially resolved transcriptomic or genomic maps.

The claims of ’975 focus on a capture array design where each capture site contains a pair of probes. One probe has a primer binding region and a unique spatial address, while the other has a different primer binding region and a poly-T capture sequence. The poly-T sequence is designed to hybridize to the poly-A tail of mRNA molecules. This design allows for capturing mRNA from a tissue sample and tagging it with a spatial address for subsequent sequencing and spatial mapping.

In practice, the tissue sample is placed in contact with the capture array, allowing mRNA molecules to hybridize to the poly-T capture sequences. Reverse transcription is then performed to create cDNA, which is linked to the spatial address sequence of the first probe. This creates a spatially tagged cDNA library that can be sequenced. The resulting sequence data is then analyzed to determine the expression levels of genes at different locations within the tissue.

This approach differentiates itself from prior methods by separating the spatial address and capture functions onto two different probes . This design increases the flexibility of sequencing library designs and preparation protocols. By encoding spatial information directly into the nucleic acids, the method enables high-throughput sequencing while preserving the crucial spatial context of the tissue sample, leading to more detailed and informative analyses.

How does this patent fit in bigger picture?

Technical landscape at the time

In the mid-2010s when ’975 was filed, nucleic acid analysis at a time when spatial information was typically implemented using methods that provided either localized information for a limited number of genes or comprehensive information without positional context. At this time, techniques that could characterize transcriptomes or genomic variations in tissues while preserving spatial information were needed. Hardware and software constraints made high-throughput spatial analysis of nucleic acids non-trivial.

Novelty and Inventive Step

The examiner approved the application because the prior art neither teaches nor suggests the claimed method. Specifically, the prior art fails to disclose using an array of probe/primer pairs to capture poly-A targets from a tissue sample, where the first probe/primer has a unique sequence defining the spatial address of the array capture site, and the second probe/primer has a poly-T sequence that is the same at each site on the array. Furthermore, the prior art does not teach capturing poly-A targets, extending the second probe/primer to form a complement of the captured targets, and linking the end of the complements to the first probe/primer, whereby the linked complements comprise the spatial address sequence of the first probe/primer.

Claims

This patent contains 7 claims, with claim 1 being the only independent claim. Independent claim 1 focuses on a method for capturing and analyzing target nucleic acids from a tissue sample using a capture array with spatially addressable probes. The dependent claims generally elaborate on and refine the steps and components described in the independent claim, such as specific linking methods, amplification steps, and the composition of the complementary strands.

Key Claim Terms New

Definitions of key terms used in the patent claims.

Term (Source)Support for SpecificationInterpretation
Capture array comprising a plurality of capture sites
(Claim 1)		“The present disclosure provides a capture array for spatial detection and analysis of nucleic acids in a tissue sample, comprising a capture site comprising a pair of capture probes immobilized on a surface, wherein a first capture probe of the pair of capture probes comprises a first primer binding region and a spatial address region, and wherein a second capture probe of the pair of capture probes comprises a second primer binding region and a capture region.”An array with multiple locations where target nucleic acids can be captured, each site having a unique spatial address.
First primer binding region sequence
(Claim 1)		“Described herein are a variety of methods and compositions that allow for the characterization of analytes in tissues while preserving spatial information related to the origin of target analyte in the tissue. In various embodiments, an array includes a substrate on which a plurality of capture probes are immobilized such that each capture probe occupies a distinct position on the array.”A nucleotide sequence on the first probe that allows for primers to bind and initiate amplification or sequencing reactions.
Poly-T capture sequence
(Claim 1)		“In some embodiments, a nucleic acid in a tissue section (e.g., a formalin-fixed paraffin-embedded (FFPE) tissue section) is transferred to an array and captured onto the array by hybridization to a capture probe. In some embodiments, a capture probe can be a universal capture probe hybridizing, e.g., to an adaptor region in a nucleic acid sequencing library, or to the poly-A tail of an mRNA.”A sequence of thymine nucleotides designed to hybridize with the poly-A tail of a target nucleic acid, enabling capture of mRNA.
Second primer binding region sequence
(Claim 1)		“Described herein are a variety of methods and compositions that allow for the characterization of analytes in tissues while preserving spatial information related to the origin of target analyte in the tissue. In various embodiments, an array includes a substrate on which a plurality of capture probes are immobilized such that each capture probe occupies a distinct position on the array.”A nucleotide sequence on the second probe that allows for primers to bind and initiate amplification or sequencing reactions.
Spatial address region sequence
(Claim 1)		“Each capture probe includes, among other sequences and/or molecules, a unique positional nucleic acid tag (i.e., a spatial address or indexing sequence). Each spatial address corresponds to the position of the capture probe on the array. The position of the capture probe on the array may be correlated with a position in the tissue sample.”A sequence of nucleic acids unique to each capture site on the capture array, allowing the location of the captured nucleic acid to be determined.

Litigation Cases New

US Latest litigation cases involving this patent.

Case NumberFiling DateTitle
1:25-cv-01286Oct 21, 202510X Genomics, Inc. v. Illumina, Inc.

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US10913975

ILLUMINA INC
Application Number
US15747670
Filing Date
Jul 21, 2016
Status
Granted
Expiry Date
Jul 21, 2036
External Links
Slate, USPTO, Google Patents