Scrnaseq analysis systems
AssigneeFluent Biosciences Inc.
InventorKristina Fontanez
Life of this patent
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Abstract
The invention provides a system for evaluating gene expression levels from scRNA-Seq experiments. The system uses in silico cell calling tools for distinguishing between partitions that contain cells and background partitions that did not fully capture a cell. The system also provides barcode processing tools that tests barcodes from at least cellular and UMI tiers against a whitelist and optionally converts those to a compact index format. Further, the system can implement multimapping tools to preserve information for reads that map to multiple locations in a reference.
Claims15
A system for expression analysis with cell calling, the system comprising a processor coupled to a memory subsystem comprising instructions executable by the processor to cause the system to:
- receive sequence data produced by sequencing RNA from a plurality of partitions;
- correlate, for each partition, counts of barcode sequences in the sequence data to a probability that the partition contained one entire isolated cell;
- receive a user selection for a sensitivity for the probability that the partition contained one entire isolated cell;
- and
- analyze mRNA levels among the partitions that meet the user-selected sensitivity.
A system for expression analysis with multimapping, the system comprising a processor coupled to a memory subsystem comprising instructions executable by the processor to cause the system to:
- receive sequence data produced by sequencing RNA from a single-cell;
- map at least one sequence read from the sequence data to a reference comprising reference gene information;
- identify at least a first location and a second location in the reference where the sequence read maps with at least a threshold matching score;
- store the sequence read in the memory subsystem with markup identifying the read as mapping to at least the first or the second location in the reference.
A system for expression analysis with barcode processing, the system comprising a processor coupled to a memory subsystem comprising instructions executable by the processor to cause the system to:
- receive sequence data produced by sequencing RNA from a single-cell;
- compare barcodes from sequence reads in the sequence data to a barcode whitelist;
- when a barcode in one sequence read fails to match a whitelist barcode with a predetermined Hamming distance value, omit the one sequence read from further analysis, wherein for each sequence read, a barcode from a first tier is compared to a cellular barcode whitelist and a barcode from a second tier is compared to a UMI whitelist;
- deduplicate reads for which first tier and second tier barcodes match the whitelist within the predetermined Hamming distance value;
- and
- provide a measure of mRNA levels from the deduplicated reads.
Dependencies are inferred from the claim text.