10X Genomics has filed a patent for a method of detecting nucleic acid molecules using a signal code sequence and labeled detection probes. The invention includes a sequential barcoding and decoding scheme that utilizes a sequencing-by-hybridization strategy to sequence and differentiate nucleotide barcode sequences. The patent also introduces a coding scheme for providing a detectable “color” or signal-based code for target nucleic acids. GlobalData’s report on 10X Genomics gives a 360-degree view of the company including its patenting strategy. Buy the report here.
According to GlobalData’s company profile on 10X Genomics, ChIP-seq sequencing was a key innovation area identified from patents. 10X Genomics's grant share as of September 2023 was 23%. Grant share is based on the ratio of number of grants to total number of patents.
Methods for detecting nucleic acid molecules using signal code sequences
A recently filed patent (Publication Number: US20230313290A1) describes a system for detecting a nucleic acid barcode sequence. The system includes a padlock probe with target binding sites that can hybridize to a target sequence in a target nucleic acid molecule. The padlock probe also contains a nucleotide barcode sequence that identifies it. The barcode sequence consists of a first domain sequence and a second domain sequence, with some overlap between the two.
The system also includes a universal pool of reporter probes, which contains at least two different species of reporter probes. These reporter probes have optically detectable moieties, such as fluorophores. The system further includes a first detection probe and a second detection probe. The first detection probe has a recognition sequence that matches the first domain sequence of the padlock probe and a reporter probe binding site that is complementary to a reporter probe from the universal pool. The second detection probe has a recognition sequence that matches the second domain sequence of the padlock probe and a reporter probe binding site that is also complementary to a reporter probe from the universal pool.
The second detection probe is capable of initiating a strand displacement reaction to displace the first detection probe that is hybridized to the first domain sequence.
The system can be used to detect a target sequence in various types of nucleic acid molecules, including native genomic DNA, naturally occurring RNA, cDNA, or amplification products generated from these molecules. The target nucleic acid molecule can also be linked to an antibody.
The universal pool of reporter probes can contain multiple different species, and the system can be used to detect multiple different nucleic acid molecules present in a sample. Each different nucleic acid molecule can be assigned a specific padlock probe with a different nucleotide barcode sequence and a different series of signal codes.
The system can be used with a variety of biological samples, including cells or tissue samples on a solid substrate. The first and second overhang sequences of the detection probes can be the same or different. The nucleotide barcode sequence can have a first domain that is either 5' or 3' to the second domain.
Overall, this patent describes a system for detecting nucleic acid barcode sequences using padlock probes, reporter probes, and detection probes. The system has applications in various fields, including genomics and molecular biology research.