Patent Application
20240038327
In recent years, biotechnology firms and research institutions have improved hardware and software for (i) sequencing nucleotides that indicate gene expression, accessible chromatin, and methylation for a sample's individual cells and (ii) determining metrics measuring cell-specific gene expression, accessible chromatin, etc. For instance, some existing sequencing machines and sequencing-data-analysis software (together “existing sequencing systems”) synthesize oligonucleotides that have been extracted from a sample and placed into library fragments to determine nucleobase calls for nucleotide reads. Such reads may include genomic reads corresponding to deoxyribonucleic acid (DNA) from open chromatin, ribonucleic acid (RNA)-based reads corresponding to a transcriptome, or other nucleotide reads. To illustrate one such genomic read, some existing sequencing systems synthesize Assay for Transposase-Accessible Chromatin (ATAC) reads based on genomic DNA from accessible chromatin that a transposase has identified by inserting adapters into open gDNA regions of a cell.
In some cases, assays for ATAC reads and RNA-based reads can be combined into a multiomics assay that generate metrics corresponding to DNA-based and RNA-based reads. Based on cell barcodes embedded in nucleotide reads, for instance, some existing sequencing systems run a multiomics assay to determine counts of RNA-based reads and ATAC reads for genes and selected genomic regions corresponding read-coverage peaks, respectively, for various cells as indicators of cell-specific gene expression and cell-specific accessible chromatin.
Despite these recent advances, existing sequencing systems that use state-of-the-art technology for multiomics assays still consume excessive computer-processing time and memory to determine cell-specific gene-expression and accessible chromatin metrics respectively using RNA-based reads and ATAC reads. For example, some existing sequencing systems run individual scripts for approximately two hours (or more) to execute a multiomics assay with approximately 50 million RNA-based reads and 200 million ATAC reads and generate the relevant cell-specific metrics. To illustrate, some existing sequencing systems run individual Python scripts for a collection of multiomics software that consumes about two hours to process RNA-based reads and ATAC reads associated with cellular barcodes and unique molecular identifiers (UMIs), correct errors in such barcodes and UMIs, align ATAC and transcriptomic reads, count such reads per feature, and filter cells based on counts, respectively, among other such tasks. Accordingly, the individual scripts for various pipelines within such a collection of multiomics software unnecessarily prolong computer processing.
In addition to consuming excessing computing-processing time, existing sequencing systems consume unnecessary memory to run such multiomics assays using RNA-based reads and ATAC reads. For instance, as one pipeline runs using RNA-based reads or another pipeline runs using ATAC reads, some existing sequencing systems store counts for ATAC reads or RNA-based reads, respectively, on a hard drive or disc. When a multiomics assays includes approximately 50 million RNA-based reads and 200 million ATAC reads, corresponding read counts per feature per cell consume considerable memory. By storing on and accessing read counts from a hard drive, existing sequencing systems not only consume unnecessary and slow-accessible memory, but slow down either gene-expression assays or ATAC assays, but also combined multiomics assays.
These, along with additional problems and issues exist in existing sequencing systems.
This disclosure describes one or more embodiments of systems, methods, and non-transitory computer readable storage media that solve one or more of the problems described above or provide other advantages over the art. In particular, the disclosed systems can use a single executable file to efficiently run a single-cell multiomics analysis that (i) aligns transcriptomic reads and genomic reads with a reference genome and (ii) jointly filters cellular barcode sequences for cells based on feature-specific, single-cell read counts. To run such an assay using a single executable file, the disclosed systems identify transcriptomic reads and genomic reads for a sample, where such reads comprise different sets of cellular barcode sequences. In some cases, the disclosed systems further use separate invocations of a configurable processor to align the transcriptomic reads and genomics reads with a reference genome. Based on single-cell counts of aligned transcriptomic reads and single-cell counts of aligned genomic reads for target nucleotide sequences within cells of the sample, the disclosed systems select a subset of candidate cells corresponding to a subset of cellular barcode sequences. The disclosed systems further generate, for the sample, single-cell multiomics outputs for individual cells of the selected subset of candidate cells based on the counts of aligned reads.
Additional features and advantages of one or more embodiments of the present disclosure will be set forth in the description which follows, and in part will be obvious from the description, or may be learned by the practice of such example embodiments.
The detailed description refers to the drawings briefly described below.
This disclosure describes one or more embodiments of a multiomics sequencing system that can use a single executable file to efficiently run a single-cell multiomics analysis that (i) aligns transcriptomic reads and genomic reads with a reference genome and (ii) jointly filters cellular barcode sequences for cells based on feature-specific, single-cell read counts. To run such a single-cell multiomics assay using a single executable file, the multiomics sequencing system identifies transcriptomic reads and genomic reads for a sample, where such reads comprise different sets of cellular barcode sequences representing candidate cells of the sample. In some cases, the multiomics sequencing system further uses separate configurations of a Field Programmable Gate Array (FPGA) or other configurable processor to align the transcriptomic reads and genomics reads with a reference genome. Based on single-cell counts of aligned transcriptomic reads for genes and single-cell counts of aligned genomic reads for accessible genomic regions corresponding to read-coverage peaks, the multiomics sequencing system selects a subset of candidate cells corresponding to a subset of cellular barcode sequences. The multiomics sequencing system further generates, for the sample, single-cell multiomics outputs for individual cells of the selected subset of candidate cells based on the counts of aligned transcriptomic reads and aligned genomic reads.
As just noted, in some embodiments, the multiomics sequencing system identifies transcriptomic reads and genomic reads that each include different sets of cellular barcode sequences. While the represented cells of the sample are the same or substantially overlap, in some embodiments, the set of cellular barcode sequences incorporated into the transcriptomic reads for a gene-expression assay differ from the set of cellular barcode sequences incorporated into the genomic reads for an ATAC assay or methylation assay. But such different sets can nevertheless be mapped to the same overlapping cells from the sample. Similarly, the multiomics sequencing system can identify transcriptomic and genomic reads generated by a same or different sequencing run or same or different sequencing machine.
Having identified or received such reads, in some embodiments, the multiomics sequencing system invokes a single FPGA or other configurable processor to perform separate alignment of transcriptomic reads and genomic reads with a reference genome. In a first invocation, for instance, the multiomics sequencing system configures a configurable processor to execute a first alignment model (e.g., DNA aligner model) that aligns the genomic reads with the reference genome. In a second invocation, the multiomics sequencing system configures the same configurable processor to execute a second alignment model (e.g., RNA aligner model) that aligns the transcriptomic reads with the reference genome. The type of reads aligned in each configurable-processor invocation can be programmed for any order.
After aligning transcriptomic and genomic reads, as suggested above, the multiomics sequencing system can jointly filter cells of the sample represented by cellular barcode sequences. For instance, the multiomics sequencing system can determine single-cell counts of aligned transcriptomic reads for each gene and single-cell counts of genomic reads for each accessible genomic region corresponding to a read-coverage peak. In some cases, the single-cell counts of aligned transcriptomic reads comprise single-cell counts of unique molecular identifier (UMI) sequences within (or corresponding to) aligned transcriptomic reads. The multiomics sequencing system can further determine summed single-cell counts for aligned transcriptomic reads and summed single-cell counts of aligned genomic reads for each candidate cell. Based on such summed single-cell counts of aligned transcriptomic reads and aligned genomic reads, in some embodiments, the multiomics sequencing system clusters cellular barcode sequences representing candidate cells and selects a subset of candidate cells as more likely representing real biological cells (or valid cells) of the sample.
Having jointly filtered cells, in some embodiments, the multiomics sequencing system generates, for the sample, single-cell multiomics outputs for the selected subset of candidate cells. The single-cell multiomics outputs can include a subset of single-cell counts of aligned transcriptomic reads and a subset of single-cell counts of aligned genomic reads corresponding to the selected subset of candidate cells. As part of an expedited multiomics assay, for instance, the multiomics sequencing system can generate single-cell multiomics outputs for multiple different “omes,” such as metrics for a transcriptome indicating gene expression for each candidate cell and metrics for a genome indicating accessible genomic deoxyribonucleic acid (DNA) corresponding to open chromatin.
As indicated above, the multiomics sequencing system provides several technical advantages relative to existing sequencing systems by, for example, improving the computer-processing time and memory consumed to perform a multiomics assays. For example, the multiomics sequencing system expedites the computer-processing time used to perform a multiomics assay using transcriptomic and genomic reads. Unlike existing sequencing systems that use individual scripts to perform separate tasks of a multiomics assay, in some embodiments, the multiomics sequencing system uses a single multiomics executable file to run a single-cell multiomics assay that can (i) align transcriptomic reads and genomic reads with a reference genome and (ii) jointly filter cellular barcode sequences for cells based on feature-specific, single-cell counts for transcriptomic and genomic reads. In some such cases, the multiomics sequencing system runs two separate invocations or configurations of a same configurable processor to align the transcriptomic reads and genomics reads. In part due to running a single multiomics executable file and jointly filtering cells to select a subset of candidate cells, the disclosed multiomics sequencing system reduces the computer-processing time to execute a multiomics assay processing approximately 50 million RNA-based reads and 200 million ATAC reads from over 2 hours by the state-of-the-art systems to approximately 12 minutes.
In addition to or as part of expedited computer processing, in some embodiments, the multiomics sequencing system also improves the memory usage and memory accessibility for performing a multiomics assay using transcriptomic and genomic reads. Unlike existing sequencing systems that run separate scripts and further store and access reads counts on and from a hard drive or disc, in some embodiments, the multiomics sequencing system uses a single multiomics executable file that facilitates storing counts for transcriptomic reads and genomic reads and other data on high-speed storage media, such as random-access memory (RAM). Because some multiomics assays often includes approximately 50 million RNA-based reads and 200 million DNA-based reads, the multiomics sequencing system significantly expedites speed and memory accessibility by running a multiomics executable file that can store and access corresponding read counts per feature per candidate cell from RAM or other high-speed storage media.
As illustrated by the foregoing discussion, the present disclosure utilizes a variety of terms to describe features and advantages of the multiomics sequencing system. As used herein, for example, the term “nucleotide read” (or simply “read”) refers to an inferred sequence of one or more nucleobases (or nucleobase pairs) from all or part of a sample nucleotide sequence. Such a sample nucleotide sequence may take the form of a sample genomic sequence from genomic DNA (gDNA), a transcriptomic sequence from complementary DNA (cDNA), a transcriptomic sequence from RNA, or other nucleotide sequence. In particular, a nucleotide read includes a determined or predicted sequence of nucleobase calls for a nucleotide sequence (or group of monoclonal nucleotide sequences) from a sample library fragment corresponding to a sample. For example, in some cases, a sequencing device determines a nucleotide read by generating nucleobase calls for nucleobases passed through a nanopore of a nucleotide-sample slide, determined via fluorescent tagging, or determined from a cluster in a flow cell. A nucleotide read may comprise one or more of a read primer sequence, an indexing sequence, a binding adapter sequence, or a cellular barcode sequence.
Relatedly, as used herein, the term “genomic read” refers to a nucleotide read representing an inferred sequence of nucleobases (or nucleobase pairs) derived from genomic DNA (gDNA) extracted from a sample. For example, a genomic read includes a read comprising gDNA that is (i) extracted from or derived from gDNA extracted from a sample and (ii) part of a sample library fragment corresponding to the sample. In some cases, a genomic read includes reads comprising adapter sequences for Assay for Transposase-Accessible Chromatin (ATAC) reads, which are also called ATAC reads. In some embodiments, genomic reads may include, but are not limited to, DNase 1 hypersensitive sites (DNase) sequencing reads, Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) sequencing reads, or Tet-Assisted Bisulfite (TAB) sequencing reads.
Conversely, as used herein, the term “transcriptomic read” refers to a nucleotide read representing an inferred sequence of nucleobases (or nucleobase pairs) that either complement or represent RNA extracted from a sample. For example, a transcriptomic read includes a read comprising cDNA that is (i) synthesized from single-stranded messenger RNA (mRNA) or microRNA (miRNA) or derived from RNA extracted from a sample and (ii) part of a sample library fragment corresponding to the sample. As a further example, a transcriptomic read includes a read comprising RNA (e.g., mRNA, miRNA, transfer RNA (tRNA)) that is (i) extracted from or derived from RNA extracted from a sample and (ii) part of a sample library fragment corresponding to the sample.
As further used herein, the term “cellular barcode sequence” refers to a unique and artificial nucleotide sequence that identifies (or corresponds to) a cell of a sample. In some cases, a cellular barcode sequence includes a unique nucleotide sequence that represents a cell of a sample and that is ligated to a sample's nucleotide sequence (e.g., a gDNA fragment or cDNA fragment) or to another sequence within a sample library fragment. Accordingly, a cellular barcode sequence can be part of a sample library fragment. Similarly, a cellular barcode sequence can be used to sort reads by cell or into different files, among other things.
To illustrate but a few examples, a cellular barcode sequence for an ATAC read may be sixteen nucleobases in length and be represented in single-letter codes for nucleobases as AAACAGCCAAACAACA, AAACAGCCAAACATAG, AAACAGCCAAACCCTA, AAACAGCCAAACCTAT, etc. Further, a cellular barcode sequence for a transcriptomic read may be sixteen nucleobases in length and be represented in single-letter codes for nucleobases as ACAGCGGGTGTGTTAC, ACAGCGGGTTGTTCTT, ACAGCGGGTAACAGGC, ACAGCGGGTGCGCGAA, etc.
As further used herein, the term “multiomics executable file” refers to a file comprising instructions in a programming language that a computing device can directly execute to analyze reads for a multiomics assay. In some cases, a multiomics executable file comprises machine instructions that have been translated from source code by a compiler and that can be executed by a native computing device to analyze reads for a multiomics assay. To illustrate, in some embodiments, a multiomics executable file comprises a compiled binary file deployed on a computing device, such as a remote server or a local server. In some such cases, a multiomics executable file constitutes or is part of a DRAGEN executable software program by Illumina, Inc. As suggested above, a multiomics executable file is not a script or a collection of individual scripts. A script is typically written in a different language (e.g., Python, VBA, Perl) than an executable file and is interpreted from source code or bytecode.
A suggested above, the term “target nucleotide sequence” refers to a nucleotide sequence that is from a sample and that is targeted for detection, measurement, sequencing, or quantification. In particular, a target nucleotide sequence includes a nucleotide sequence from a sample's genome or transcriptome for which an assay is designed to detect, measure, sequence, or quantify. For example, a target nucleotide sequence can include a gene targeted by a gene-expression assay or an accessible genomic region corresponding to a read-coverage peak by an ATAC or by another accessible-chromatin assay.
As indicated above, in some embodiments, the multiomics sequencing system determines a count of genomic reads for an accessible genomic region corresponding to a read-coverage peak. As used herein, the term “read-coverage peak” refers to a set of aligned nucleotide reads that resemble a crest or a pile-up of reads covering or overlapping with a genomic region of a reference genome. In particular, a read-coverage peak refers to a set of genomic reads forming a pile-up of reads aligned with or mapped to an accessible genomic region identified by ATAC as part of a peak-calling process.
Relatedly, the term “accessible genomic region” refers to a genomic region of DNA that is part of accessible chromatin. In particular, an accessible genomic region includes a genomic region from accessible chromatin that a transposase has identified by inserting adapters into open gDNA regions. Accordingly, in some cases, an accessible genomic region comprising a genomic region that corresponds to a read-coverage peak and that is identified by ATAC as part of a peak-calling process.
As further used herein, the term “single-cell multiomics outputs” refers to files, matrices, metrics, or other generated outputs indicating counts or measurements of nucleotide reads (or other biological samples or markers) for a single cell of a sample. For example, a single-cell multiomics output may include counts of aligned transcriptomic reads and/or counts of genomic reads for specific target nucleotide sequences (e.g., genes, accessible genomic regions corresponding to read-cover peaks) in a given cell. As a further example, single-cell multiomics outputs may include metrics for median number of accessible genomic regions corresponding to read-cover peaks (sometimes called median “peaks”) per candidate cell, which can be reported in a metrics.csv file. As yet a further example, single-cell multiomics outputs may include a joint cell-by-feature matrix comprising both single-cell counts of aligned transcriptomic reads and single-cell counts of aligned genomic reads for target nucleotide sequences organized by each candidate cell.
As also used herein, the term “reference genome” refers to a digital nucleic acid sequence assembled as a representative example (or representative examples) of genes and other genetic sequences of an organism. Regardless of the sequence length, in some cases, a reference genome represents an example set of genes or a set of nucleic acid sequences in a digital nucleic acid sequence determined as representative of an organism. For example, a linear human reference genome may be GRCh38 (or other versions of reference genomes) from the Genome Reference Consortium. GRCh38 may include alternate contiguous sequences representing alternate haplotypes, such as SNPs and small indels (e.g., 10 or fewer base pairs, 50 or fewer base pairs).
Additionally, as used herein, the term “genomic coordinate” refers to a particular location or position of a nucleotide base within a genome (e.g., an organism's genome or a reference genome). In some cases, a genomic coordinate includes an identifier for a particular chromosome of a genome and an identifier for a position of a nucleotide base within the particular chromosome. For instance, a genomic coordinate or coordinates may include a number, name, or other identifier for a chromosome (e.g., chr1 or chrX) and a particular position or positions, such as numbered positions following the identifier for a chromosome (e.g., chr1:1234570 or chr1:1234570-1234870). Further, in certain implementations, a genomic coordinate refers to a source of a reference genome (e.g., mt for a mitochondrial DNA reference genome or SARS-CoV-2 for a reference genome for the SARS-CoV-2 virus) and a position of a nucleotide-base within the source for the reference genome (e.g., mt:16568 or SARS-CoV-2:29001). By contrast, in certain cases, a genomic coordinate refers to a position of a nucleotide-base within a reference genome without reference to a chromosome or source (e.g., 29727).
As used herein, a “genomic region” refers to a range of genomic coordinates. Like genomic coordinates, in certain implementations, a genomic region may be identified by an identifier for a chromosome and a particular position or positions, such as numbered positions following the identifier for a chromosome (e.g., chr1:1234570-1234870). In various implementations, a genomic coordinate includes a position within a reference genome. In some cases, a genomic coordinate is specific to a particular reference genome.
As used herein, for example, the term “configurable processor” refers to a circuit or chip that can be configured or customized to perform a specific application. For instance, a configurable processor includes an integrated circuit chip that is designed to be configured or customized on site by an end user's computing device to perform a specific application. Configurable processors include, but are not limited to, an application-specific integrated circuit (ASIC), an application-specific standard product (ASSP), a coarse-grained reconfigurable array (CGRA), or an FPGA. By contrast, configurable processors do not include a CPU or GPU. In some embodiments, the multiomics sequencing system uses a configurable processor (e.g., FPGA) or a processor (e.g., CPU) to perform the various embodiments described herein.
Also, as used herein, the term “sample” refers to a target genome or transcriptome (or portion of a genome) from an organism undergoing sequencing. For example, a sample includes a sequence of nucleotides isolated or extracted from a sample organism (or a copy of such an isolated or extracted sequence). In particular, a sample includes a full genome that is isolated or extracted (in whole or in part) from a sample organism and composed of nitrogenous heterocyclic bases. A sample can include a segment of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or other polymeric forms of nucleic acids or chimeric or hybrid forms of nucleic acids noted below. In some cases, the sample is found in a sample prepared or isolated by a kit and received by a sequencing device. In some cases, the sample is a genomic sample and/or a transcriptomic sample corresponding to a same sample organism.
The following paragraphs describe the multiomics sequencing system with respect to illustrative figures that portray example embodiments and implementations. For example,
As indicated by
In one or more embodiments, the sequencing device 102 utilizes SBS to sequence nucleotide fragments into nucleotide reads and determine nucleobase calls for the nucleotide reads. In addition or in the alternative to communicating across the network 118, in some embodiments, the sequencing device 102 bypasses the network 118 and communicates directly with the local device 108 or the client device 114. By executing the sequencing device system 104, the sequencing device 102 can further store the nucleobase calls as part of base-call data that is formatted as a binary base call (BCL) file and send the BCL file to the local device 108 and/or the server device(s) 110.
As further indicated by
As further indicated by
In some embodiments, the server device(s) 110 comprise a distributed collection of servers, where the server device(s) 110 include a number of server devices distributed across the network 118 and located in the same or different physical locations. Further, the server device(s) 110 can comprise a content server, an application server, a communication server, a web-hosting server, or another type of server.
As indicated above, as part of the server device(s) 110 or the local device 108, the multiomics sequencing system 106 can run a single-cell multiomics assay that (i) aligns transcriptomic reads and genomic reads with a reference genome and (ii) jointly filters cellular barcode sequences for cells based on feature-specific, single-cell read counts. For instance, the multiomics sequencing system 106 can identify transcriptomic reads and genomic reads corresponding to a sample, where the transcriptomic reads comprise a first set of cellular barcode sequences and the genomic reads comprise a second set of cellular barcode sequences. The multiomics sequencing system 106 further configures a configurable processor to (i) align the transcriptomic reads with a reference genome as part of a first configurable-processor invocation and (ii) align genomics reads with the reference genome as part of a second configurable-processor invocation. Based on single-cell counts of aligned transcriptomic reads and single-cell counts of aligned genomic reads for target nucleotide sequences within cells of the sample, the multiomics sequencing system 106 jointly filters cells by selecting a subset of candidate cells corresponding to a subset of cellular barcode sequences. Based on the counts of aligned transcriptomic reads and aligned genomic reads, the multiomics sequencing system 106 generates single-cell multiomics outputs for individual cells of the selected subset of candidate cells.
As further illustrated and indicated in
Although
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As indicated above, some existing sequencing systems perform multiomics assays. As shown in
As part of the gene-expression pipeline 200a, for instance, the existing sequencing system determines RNA-based reads from sample library fragments 202a and generates an RNA-based-read sequencing file comprising read data. In particular, the existing sequencing system includes a sequencing device that receives a nucleotide-sample slide (e.g., flow cell) comprising the sample library fragments 202a corresponding to RNA extracted from one or more samples used to detect gene expression. The existing sequencing system further performs a sequencing run 204a to determine nucleobase calls from the sample library fragments 202a and generate RNA-based reads. After the sequencing run 204a, the existing sequencing system sends a BCL file 206a from the sequencing device to a computing device for processing. In particular, the computing device runs a demultiplexing script 208a to demultiplex the BCL file 206a into a sequencing file, such as a FAST-ALL Q (FASTQ) file.
As further part of the gene-expression pipeline 200a in
By contrast, as part of the ATAC pipeline 200b, the existing sequencing system determines ATAC reads from sample library fragments 202b and generates an ATAC-read sequencing file comprising read data. In particular, the sequencing device receives a nucleotide-sample slide comprising the sample library fragments 202b corresponding to accessible-chromatin DNA used to assess genome-wide chromatin accessibility in individual cells. The existing sequencing system further performs a sequencing run 204b to determine nucleobase calls from the sample library fragments 202b to generate ATAC reads. After the sequencing run 204b, the existing sequencing system sends a BCL file 206b from the sequencing device to a computing device for processing. In particular, the computing device again runs a demultiplexing script 208b to demultiplex the BCL file 206b into a sequencing file, such as a FASTQ file.
As further part of the ATAC pipeline 200b in
By running separate demultiplexing scripts, read-counting scripts, analysis scripts, or other scripts, the existing sequencing system consumes approximately two hours (or more) of computer-processing time to execute a multiomics assay with approximately 50 million RNA-based reads and 200 million ATAC reads. The separate scripts accordingly prolong analysis, isolate similar processes, and sometimes force the existing sequencing system to store data, such as read counts, on a hard drive for later and slower access for analysis.
Unlike the separate scripts of existing sequencing systems, in some embodiments, the multiomics sequencing system 106 executes a multiomics executable file to perform a multiomics analysis on reads representing a sample's genome and transcriptome. In accordance with one or more embodiments,
As shown in
After identifying the transcriptomic reads 302a and genomic reads 302b, as further shown in
Having aligned the transcriptomic reads 302a and the genomic reads 302b, as further shown in
As depicted in
After determining single-cell counts of transcriptomic reads and genomic reads, in some embodiments, the multiomics sequencing system 106 selects a subset of candidate cells 312 based on the single-cell counts of aligned transcriptomic reads and aligned genomic reads per target nucleotide sequence. For example, in some embodiments, the multiomics sequencing system 106 sums such single-cell counts to determine summed counts of aligned transcriptomic reads for each candidate cell and summed counts of aligned genomic reads for each candidate cell. As noted above, in some cases, the summed single-cell counts of aligned transcriptomic reads comprise summed single-cell counts of UMI sequences within (or corresponding to) aligned transcriptomic reads.
While this disclosure refers to counts of UMI sequences and a UMI-sequence-count threshold below with respect to
Based on such summed single-cell counts, the multiomics sequencing system 106 clusters cellular barcode sequences representing candidate cells into a selected cluster of candidate cells 314a and a non-selected cluster of candidate cells 314b. Accordingly, in certain embodiments, the multiomics sequencing system 106 selects a subset of candidate cells as more likely representing real biological cells (or valid cells) of the sample when the selected subset of candidate cells satisfies one or both of a threshold summed count of aligned transcriptomic reads (e.g., UMI sequences) per candidate cell and a threshold summed count of aligned genomic reads relative to a non-selected cluster of candidate cells.
Having selected a subset of candidate cells, as further shown in
As indicated above, the multiomics sequencing system 106 can integrate analyses for a sample's transcriptome and genome into a single pipeline. In accordance with one or more embodiments,
As shown in
After identifying cellular barcode sequences from transcriptomic reads, as further shown in
In addition to correcting cellular barcode sequences of transcriptomic reads, as further shown in
After aligning transcriptomic sequences from transcriptomic reads, as further shown in
As further suggested above, in some embodiments, the multiomics sequencing system 106 also performs read counting per UMI sequence for each candidate cell represented by a cellular barcode sequence. For each cellular barcode sequence representing a candidate cell, for instance, the multiomics sequencing system 106 determines single-cell counts of aligned transcriptomic sequences from transcriptomic reads for each gene. In some cases, for instance, the multiomics sequencing system 106 determines such single-cell counts of aligned transcriptomic reads using an intermediate matrix comprising columns for genes, rows for cellular barcode sequences, and a number of aligned transcriptomic reads in each matrix cell.
After UMI correction and reading counting, as further shown in
Having filtered cells based on transcriptomic-read counts, in some embodiments, the multiomics sequencing system 106 further generates single-cell metrics 422 for transcriptomic reads. As shown in
In addition to analyzing transcriptomic reads for the gene-expression assay, as further shown in
After identifying cellular barcode sequences from genomic reads, as further shown in
In addition to correcting cellular barcode sequences of genomic reads, as further shown in
After aligning genomic sequences from genomic reads, as further shown in
As suggested above, the multiomics sequencing system 106 also performs read counting per cellular barcode sequence for each candidate cell. For each cellular barcode sequence representing a candidate cell, for instance, the multiomics sequencing system 106 determines single-cell counts of aligned genomic sequences from genomic reads for each accessible genomic region corresponding to a read-coverage peak. In some cases, for instance, the multiomics sequencing system 106 determines such single-cell counts of aligned genomic reads using an intermediate matrix comprising columns for accessible genomic regions or “peaks,” rows for cellular barcode sequences, and a number of aligned genomic reads in each matrix cell.
After peak calling and reading counting, as further shown in
Having filtered cells based on genomic-read counts, in some embodiments, the multiomics sequencing system 106 further generates the single-cell metrics 422 for genomic reads in addition to transcriptomic reads. As shown in
In contrast to the multiomics analysis with separate cell filtering depicted in
After receiving and identifying different sequences in one or both of the transcriptomic-read sequencing file 402a and genomic-read sequencing file 402b, as shown in
As part of the first FPGA invocation 432a to perform the RNA alignment 410, for instance, the multiomics sequencing system 106 (i) sends a bit stream encoding for a first alignment model to the FPGA to reconfigure the FPGA to perform the RNA alignment 410 and (ii) sends data representing the reference genome to the FPGA that is saved on D-RAM of the FPGA board or other high-speed storage media. Unlike the second FPGA invocation 432b to perform the DNA alignment 416, the multiomics sequencing system 106 sends data for the reference genome unique to the RNA alignment 410, such as a General Transfer Format (GTF) file comprising data representing nucleotide sequences encoding genes or exons, a Browser Extensible Data (BED) file that comprises a homology table that identifies paralogous genomic regions or otherwise boosts certain genomic regions comprising paralogous genes (e.g., for gene fusion), or a masking file that masks non-coding regions of the reference genome. As part of the second FPGA invocation 432b to perform the DNA alignment 416, by contrast, the multiomics sequencing system 106 (i) sends a bit stream encoding for a second alignment model to the FPGA to reconfigure the FPGA to perform the DNA alignment 416 and (ii) again sends data representing the reference genome to the FPGA that is saved on D-RAM of the FPGA board or other high-speed storage media. Unlike the first FPGA invocation 432a to perform the RNA alignment 410, in some embodiments, the multiomics sequencing system 106 sends data for the reference genome unique to the DNA alignment 416, such as a different masking file that masks targeted sequences of alternate haplotypes. As noted above, in some embodiments, the multiomics sequencing system 106 performs such FPGA invocations in a different order, such as by aligning genomic sequences with a reference genome in a first FPGA invocation and aligning transcriptomic sequences with the reference genome in a second FPGA invocation.
In addition to different configurable-processor invocations to align reads, as further shown in
Having determined summed single-cell counts of target nucleotide sequences for each candidate cell, the multiomics sequencing system 106 clusters candidate cells based on respective combined single-cell counts of target nucleotide sequences. Based on a summed count of aligned transcriptomic reads (e.g., UMI sequences) per candidate cell and a summed count of aligned genomic reads, in some embodiments, the multiomics sequencing system 106 identifies a selected cluster of candidate cells and a non-selected cluster of candidate cells. As further explained below with respect to
As suggested above, by performing the joint cell filtering 434 and using a single multiomics executable file, the multiomics sequencing system 106 facilitates storing single-cell counts for aligned transcriptomic reads and aligned genomic reads per target nucleotide sequence, one or more intermediate matrices of summed single-cell counts, and other data on high-speed storage media, such as RAM of an FPGA board. As the multiomics sequencing system 106 determines either transcriptomic-read counts or genomic-read counts, the multiomics sequencing system 106 can retain such counts on RAM as it progresses to the joint cell filtering 434 without waiting for a separate cell-filtering process to conclude.
As further shown in
As just suggested, the multiomics sequencing system 106 can jointly filter candidate cells based on single-cell UMI-sequence counts and single-cell genomic-read counts. In accordance with one or more embodiments,
As shown in
While this disclosure frequently refers to counts of UMI sequences and a UMI-sequence-count threshold and counts of genomic reads and a genomic-read-count threshold, in some embodiments, the multiomics sequencing system 106 may determine and use counts of aligned transcriptomic reads and a transcriptomic-read-count threshold and/or counts of nucleotide “read fragments” overlapping “peaks” or read-coverage peaks and a peak-fragment-count threshold.
In addition to determining the threshold 504a for single-cell UMI-sequence counts and the threshold 504b for single-cell genomic-read counts, the multiomics sequencing system 106 further determines UMI-sequence counts and genomic-read counts per candidate cell 506. For each candidate cell, for example, the multiomics sequencing system 106 determines a single-cell count of UMI sequences per gene and a single-cell count of genomic reads per accessible genomic region corresponding to a read-coverage peak. Based on such single-cell counts per gene and per accessible genomic region, the multiomics sequencing system 106 determines summed single-cell counts of UMI sequences for a set of genes within a candidate cell and summed single-cell counts of genomic reads for a set of accessible genomic regions within a candidate cell corresponding to read-coverage peaks.
As further shown in
In addition to clustering, as further shown in
The following paragraphs describing
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As further suggested by
As noted above, in some embodiments, the multiomics sequencing system 106 identifies candidate cells that satisfies both the UMI-sequence-count threshold 606a and the genomic-read-count threshold 606b. By identifying candidate cells that satisfy one or both thresholds, the multiomics sequencing system 106 identifies cellular barcode sequences that more likely represent real biological cells (or valid cells) of a sample. In some cases, sample library fragments from which transcriptomic reads and genomic reads are synthesized are placed in droplets into some (but not all) wells of a nucleotide-sample slide (e.g., flow cell) to avoid cross contamination. Accordingly, some wells include droplets without target RNA or DNA from a sample, but may nevertheless include nucleotides with cellular barcode sequences or other non-targeted biomaterial. The UMI-sequence-count threshold 606a and the genomic-read-count threshold 606b provide bases upon which the multiomics sequencing system 106 distinguishes between empty droplets in wells or noise and wells comprising RNA or DNA from a sample.
In addition to or after identifying candidate cells satisfying such count thresholds, in some embodiments, the multiomics sequencing system 106 determines UMI-sequence counts and genomic-read counts per candidate cell. In accordance with one or more embodiments,
As shown in the consolidated intermediate matrix 702 of
As further shown in the consolidated intermediate matrix 702, the multiomics sequencing system 106 determines, for each candidate cell, single-cell counts 710 of genomic reads per accessible genomic region corresponding to a read-coverage peak. In the consolidated intermediate matrix 702, for instance, the multiomics sequencing system 106 determines candidate cell C comprises one genomic read overlapping with a first accessible genomic region corresponding to a read-coverage peak (P1), zero genomic reads overlapping with a second accessible genomic region corresponding to a read-coverage peak (P2), and one genomic read overlapping with a third accessible genomic region corresponding to a read-coverage peak (P3).
While
After determining target-nucleotide-sequence-specific single-cell counts, as further shown in
After determining summed single-cell counts, as further indicated by
As shown by a transition from the consolidated intermediate matrix 704 to the consolidated intermediate matrix 706, for instance, the multiomics sequencing system 106 deduplicates candidate cell A and candidate cell B. Because both candidate cells A and B exhibit (i) a sum total of five UMI sequences for transcriptomic reads overlapping with G1-G4 and (ii) a sum total of two genomic reads overlapping with P1-P3, the multiomics sequencing system 106 removes candidate cell B. As shown in the consolidated intermediate matrix 706, the multiomics sequencing system 106 filters down the candidate cells A, B, and C to candidate cells A and C.
After determining summed single-cell counts of UMI sequences and genomic reads and deduplicating candidate cells, in some cases, the multiomics sequencing system 106 clusters candidate cells into a selected cluster and a non-selected cluster. In accordance with one or more embodiments,
As shown in the cluster graph 800a in
As further indicated by the cluster graph 800a, the multiomics sequencing system 106 optionally clusters the data points corresponding to cellular barcode sequences based on a UMI-sequence-count threshold 802a and a genomic-read-count threshold 802b. The multiomics sequencing system 106 determines the UMI-sequence-count threshold 802a and the genomic-read-count threshold 802b by a performing knee-plot algorithm to identify a precipitous decline or threshold difference in UMI-sequence counts and genomic-read counts, respectively. Indeed, in some embodiments, the UMI-sequence-count threshold 802a and the genomic-read-count threshold 802b constitute the UMI-sequence-count threshold 606a and the genomic-read-count threshold 606b, respectively, described above with respect to
Based on the UMI-sequence-count threshold 802a and the genomic-read-count threshold 802b, the multiomics sequencing system 106 clusters the data points corresponding to cellular barcode sequences into an initially selected cluster of candidate cells 808a and an initially non-selected cluster of candidate cells 810a. In particular, the multiomics sequencing system 106 clusters cellular barcode sequences satisfying only the UMI-sequence-count threshold 802a in a bottom-right quadrant of the cluster graph 800a, cellular barcode sequences that satisfy neither the UMI-sequence-count threshold 802a nor the genomic-read-count threshold 802b in a bottom-left quadrant of the cluster graph 800a, cellular barcode sequences that satisfy only the genomic-read-count threshold 802b in the top-left quadrant of the cluster graph 800a, and cellular barcode sequences that satisfy both the UMI-sequence-count threshold 802a and the genomic-read-count threshold 802b in the top-right quadrant of the cluster graph 800a. Indeed the cellular barcode sequences in the top-right quadrant constitute the initially selected cluster of candidate cells 808a, and the cellular barcode sequences in the other quadrants of the cluster graph 800a constitute the initially non-selected cluster of candidate cells 810a.
In addition or in the alternative to clustering based on thresholds for summed single-cell counts, as shown in
In the alternative to K-means clustering, the multiomics sequencing system 106 can use other suitable clustering models to cluster candidate cells into a selected cluster of candidate cells and a non-selected cluster of candidate cells based on summed single-cell counts. For instance, the multiomics sequencing system 106 can apply X-means clustering, Akaike information criterion, Bayesian information criterion, or another suitable method of determining clusters.
As indicated above, the multiomics sequencing system 106 can generate single-cell multiomics outputs for the selected cluster of candidate cells and/or the non-selected cluster of candidate cells. For example, in some embodiments, the multiomics sequencing system 106 generates a joint cell-by-feature matrix comprising both single-cell counts of UMI sequences and single-cell counts of aligned genomic reads for target nucleotide sequences organized by each candidate cell within the selected subset or cluster of candidate cells. Alternatively, the multiomics sequencing system 106 generates a joint cell-by-feature matrix comprising both single-cell counts of UMI sequences and single-cell counts of aligned genomic reads for target nucleotide sequences organized by each candidate cell within both the selected subset or cluster of candidate cells and the non-selected subset or cluster of candidate cells.
Turning now to
As shown in
As suggested above, in some cases, the first set of cellular barcode sequences differs from the second set of cellular barcode sequences, and the first set of cellular barcode sequences and the second set of cellular barcode sequences correspond to a same set of candidate cells. Further, in certain embodiments, the transcriptomic reads comprise a sequence of complementary DNA synthesized from single-stranded ribonucleic acid (RNA) from the sample; and the genomic reads comprise a nucleotide sequence of genomic deoxyribonucleic acid (DNA) complementing a genomic sequence from the sample. Additionally, or alternatively, in certain cases, the genomic reads comprise Assay for Transposase-Accessible Chromatin (ATAC) reads for the sample.
As further shown in
For example, in some cases, aligning the transcriptomic reads and the genomic reads with the reference genome comprises: configuring a configurable processor to execute a first alignment model that aligns the transcriptomic reads with the reference genome; and configuring the configurable processor to execute a second alignment model that aligns the genomic reads with the reference genome. Similarly, in certain cases, aligning the transcriptomic reads and the genomic reads with the reference genome comprises: configuring a configurable processor to execute a first alignment model that aligns the genomic reads with the reference genome; and configuring the configurable processor to execute a second alignment model that aligns the transcriptomic reads with the reference genome.
As further shown in
For example, in some cases, selecting the subset of candidate cells corresponding to the subset of cellular barcode sequences comprises: determining, for each target nucleotide sequence within each candidate cell, a first count of aligned transcriptomic reads and a second count of aligned genomic reads; and clustering, from the first set of cellular barcode sequences and the second set of cellular barcode sequences, cellular barcode sequences in a selected cluster of candidate cells and a non-selected cluster of candidate cells based on the first count of aligned transcriptomic reads and the second count of aligned genomic reads for each target nucleotide sequence within each candidate cell.
Relatedly, in certain embodiments, determining the first count of aligned transcriptomic reads comprises determining, for each gene encoded by a nucleotide sequence within each candidate cell, a count of unique molecular identifier (UMI) sequences corresponding to aligned genomic reads; and determining the second count of aligned genomic reads comprises determining, for each accessible genomic region corresponding to a read-coverage peak within each candidate cell, a count of read fragments from aligned genomic reads.
Further, in some implementations, clustering the cellular barcode sequences comprises clustering the cellular barcode sequences into the selected cluster of candidate cells and a non-selected cluster of candidate cells based on a first dimension for summed counts of aligned transcriptomic reads for each candidate cell and a second dimension for summed counts of aligned genomic reads for each candidate cell.
Additionally, or alternatively, in certain embodiments, determining that an initial subset of candidate cells satisfies a threshold for counts of aligned transcriptomic reads and a threshold for counts of aligned genomic reads; determining the first count of aligned transcriptomic reads for each threshold-passing candidate cell from the initial subset of candidate cells and the second count of aligned genomic reads for each threshold-passing candidate cell from the initial subset of candidate cells; and clustering the cellular barcode sequences corresponding to the initial subset of candidate cells in the selected cluster of candidate cells and the non-selected cluster of candidate cells.
As noted above, in some cases, selecting the subset of candidate cells corresponding to the subset of cellular barcode sequences comprises: storing, on random-access memory, the counts of aligned transcriptomic reads and the counts of aligned genomic reads for the target nucleotide sequences; and selecting the subset of candidate cells corresponding to the subset of cellular barcode sequences based on the counts of aligned transcriptomic reads and the counts of aligned genomic reads stored on the random-access memory.
As further shown in
As suggested above, in some cases, generating the single-cell multiomics outputs for individual cells comprises generating a joint cell-by-feature matrix comprising both single-cell counts of aligned transcriptomic reads and single-cell counts of aligned genomic reads for target nucleotide sequences organized by each candidate cell within the selected subset of candidate cells. Additionally, or alternatively, in certain embodiments, generating the single-cell multiomics outputs for individual cells comprises: generating a first set of single-cell metrics indicating gene expression for each candidate cell of the selected subset of candidate cells based on the counts of aligned transcriptomic reads; and generating a second set of single-cell metrics indicating accessible genomic deoxyribonucleic acid (DNA) corresponding to open chromatin for each candidate cell of the selected subset of candidate cells based on the counts of aligned genomic reads.
The methods described herein can be used in conjunction with a variety of nucleic acid sequencing techniques. Particularly applicable techniques are those wherein nucleic acids are attached at fixed locations in an array such that their relative positions do not change and wherein the array is repeatedly imaged. Embodiments in which images are obtained in different color channels, for example, coinciding with different labels used to distinguish one nucleobase type from another are particularly applicable. In some embodiments, the process to determine the nucleotide sequence of a target nucleic acid (i.e., a nucleic-acid polymer) can be an automated process. Preferred embodiments include sequencing-by-synthesis (SBS) techniques.
SBS techniques generally involve the enzymatic extension of a nascent nucleic acid strand through the iterative addition of nucleotides against a template strand. In traditional methods of SBS, a single nucleotide monomer may be provided to a target nucleotide in the presence of a polymerase in each delivery. However, in the methods described herein, more than one type of nucleotide monomer can be provided to a target nucleic acid in the presence of a polymerase in a delivery.
SBS can utilize nucleotide monomers that have a terminator moiety or those that lack any terminator moieties. Methods utilizing nucleotide monomers lacking terminators include, for example, pyrosequencing and sequencing using γ-phosphate-labeled nucleotides, as set forth in further detail below. In methods using nucleotide monomers lacking terminators, the number of nucleotides added in each cycle is generally variable and dependent upon the template sequence and the mode of nucleotide delivery. For SBS techniques that utilize nucleotide monomers having a terminator moiety, the terminator can be effectively irreversible under the sequencing conditions used as is the case for traditional Sanger sequencing which utilizes dideoxynucleotides, or the terminator can be reversible as is the case for sequencing methods developed by Solexa (now Illumina, Inc.).
SBS techniques can utilize nucleotide monomers that have a label moiety or those that lack a label moiety. Accordingly, incorporation events can be detected based on a characteristic of the label, such as fluorescence of the label; a characteristic of the nucleotide monomer such as molecular weight or charge; a byproduct of incorporation of the nucleotide, such as release of pyrophosphate; or the like. In embodiments, where two or more different nucleotides are present in a sequencing reagent, the different nucleotides can be distinguishable from each other, or alternatively, the two or more different labels can be the indistinguishable under the detection techniques being used. For example, the different nucleotides present in a sequencing reagent can have different labels and they can be distinguished using appropriate optics as exemplified by the sequencing methods developed by Solexa (now Illumina, Inc.).
Preferred embodiments include pyrosequencing techniques. Pyrosequencing detects the release of inorganic pyrophosphate (PPi) as particular nucleotides are incorporated into the nascent strand (Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlen, M. and Nyren, P. (1996) “Real-time DNA sequencing using detection of pyrophosphate release.” Analytical Biochemistry 242(1), 84-9; Ronaghi, M. (2001) “Pyrosequencing sheds light on DNA sequencing.” Genome Res. 11(1), 3-11; Ronaghi, M., Uhlen, M. and Nyren, P. (1998) “A sequencing method based on real-time pyrophosphate.” Science 281(5375), 363; U.S. Pat. Nos. 6,210,891; 6,258,568 and 6,274,320, the disclosures of which are incorporated herein by reference in their entireties). In pyrosequencing, released PPi can be detected by being immediately converted to adenosine triphosphate (ATP) by ATP sulfurylase, and the level of ATP generated is detected via luciferase-produced photons. The nucleic acids to be sequenced can be attached to features in an array and the array can be imaged to capture the chemiluminescent signals that are produced due to incorporation of a nucleotides at the features of the array. An image can be obtained after the array is treated with a particular nucleotide type (e.g., A, T, C or G). Images obtained after addition of each nucleotide type will differ with regard to which features in the array are detected. These differences in the image reflect the different sequence content of the features on the array. However, the relative locations of each feature will remain unchanged in the images. The images can be stored, processed and analyzed using the methods set forth herein. For example, images obtained after treatment of the array with each different nucleotide type can be handled in the same way as exemplified herein for images obtained from different detection channels for reversible terminator-based sequencing methods.
In another exemplary type of SBS, cycle sequencing is accomplished by stepwise addition of reversible terminator nucleotides containing, for example, a cleavable or photobleachable dye label as described, for example, in WO 04/018497 and U.S. Pat. No. 7,057,026, the disclosures of which are incorporated herein by reference. This approach is being commercialized by Solexa (now Illumina Inc.), and is also described in WO 91/06678 and WO 07/123,744, each of which is incorporated herein by reference. The availability of fluorescently-labeled terminators in which both the termination can be reversed and the fluorescent label cleaved facilitates efficient cyclic reversible termination (CRT) sequencing. Polymerases can also be co-engineered to efficiently incorporate and extend from these modified nucleotides.
Preferably in reversible terminator-based sequencing embodiments, the labels do not substantially inhibit extension under SBS reaction conditions. However, the detection labels can be removable, for example, by cleavage or degradation. Images can be captured following incorporation of labels into arrayed nucleic acid features. In particular embodiments, each cycle involves simultaneous delivery of four different nucleotide types to the array and each nucleotide type has a spectrally distinct label. Four images can then be obtained, each using a detection channel that is selective for one of the four different labels. Alternatively, different nucleotide types can be added sequentially and an image of the array can be obtained between each addition step. In such embodiments, each image will show nucleic acid features that have incorporated nucleotides of a particular type. Different features are present or absent in the different images due the different sequence content of each feature. However, the relative position of the features will remain unchanged in the images. Images obtained from such reversible terminator-SBS methods can be stored, processed and analyzed as set forth herein. Following the image capture step, labels can be removed and reversible terminator moieties can be removed for subsequent cycles of nucleotide addition and detection. Removal of the labels after they have been detected in a particular cycle and prior to a subsequent cycle can provide the advantage of reducing background signal and crosstalk between cycles. Examples of useful labels and removal methods are set forth below.
In particular embodiments some or all of the nucleotide monomers can include reversible terminators. In such embodiments, reversible terminators/cleavable fluors can include fluor linked to the ribose moiety via a 3′ ester linkage (Metzker, Genome Res. 15:1767-1776 (2005), which is incorporated herein by reference). Other approaches have separated the terminator chemistry from the cleavage of the fluorescence label (Ruparel et al., Proc Natl Acad Sci USA 102: 5932-7 (2005), which is incorporated herein by reference in its entirety). Ruparel et al described the development of reversible terminators that used a small 3′ allyl group to block extension, but could easily be deblocked by a short treatment with a palladium catalyst. The fluorophore was attached to the base via a photocleavable linker that could easily be cleaved by a 30 second exposure to long wavelength UV light. Thus, either disulfide reduction or photocleavage can be used as a cleavable linker. Another approach to reversible termination is the use of natural termination that ensues after placement of a bulky dye on a dNTP. The presence of a charged bulky dye on the dNTP can act as an effective terminator through steric and/or electrostatic hindrance. The presence of one incorporation event prevents further incorporations unless the dye is removed. Cleavage of the dye removes the fluor and effectively reverses the termination. Examples of modified nucleotides are also described in U.S. Pat. Nos. 7,427,673, and 7,057,026, the disclosures of which are incorporated herein by reference in their entireties.
Additional exemplary SBS systems and methods which can be utilized with the methods and systems described herein are described in U.S. Patent Application Publication No. 2007/0166705, U.S. Patent Application Publication No. 2006/0188901, U.S. Pat. No. 7,057,026, U.S. Patent Application Publication No. 2006/0240439, U.S. Patent Application Publication No. 2006/0281109, PCT Publication No. WO 05/065814, U.S. Patent Application Publication No. 2005/0100900, PCT Publication No. WO 06/064199, PCT Publication No. WO 07/010,251, U.S. Patent Application Publication No. 2012/0270305 and U.S. Patent Application Publication No. 2013/0260372, the disclosures of which are incorporated herein by reference in their entireties.
Some embodiments can utilize detection of four different nucleotides using fewer than four different labels. For example, SBS can be performed utilizing methods and systems described in the incorporated materials of U.S. Patent Application Publication No. 2013/0079232. As a first example, a pair of nucleotide types can be detected at the same wavelength, but distinguished based on a difference in intensity for one member of the pair compared to the other, or based on a change to one member of the pair (e.g. via chemical modification, photochemical modification or physical modification) that causes apparent signal to appear or disappear compared to the signal detected for the other member of the pair. As a second example, three of four different nucleotide types can be detected under particular conditions while a fourth nucleotide type lacks a label that is detectable under those conditions, or is minimally detected under those conditions (e.g., minimal detection due to background fluorescence, etc.). Incorporation of the first three nucleotide types into a nucleic acid can be determined based on presence of their respective signals and incorporation of the fourth nucleotide type into the nucleic acid can be determined based on absence or minimal detection of any signal. As a third example, one nucleotide type can include label(s) that are detected in two different channels, whereas other nucleotide types are detected in no more than one of the channels. The aforementioned three exemplary configurations are not considered mutually exclusive and can be used in various combinations. An exemplary embodiment that combines all three examples, is a fluorescent-based SBS method that uses a first nucleotide type that is detected in a first channel (e.g. dATP having a label that is detected in the first channel when excited by a first excitation wavelength), a second nucleotide type that is detected in a second channel (e.g. dCTP having a label that is detected in the second channel when excited by a second excitation wavelength), a third nucleotide type that is detected in both the first and the second channel (e.g. dTTP having at least one label that is detected in both channels when excited by the first and/or second excitation wavelength) and a fourth nucleotide type that lacks a label that is not, or minimally, detected in either channel (e.g. dGTP having no label).
Further, as described in the incorporated materials of U.S. Patent Application Publication No. 2013/0079232, sequencing data can be obtained using a single channel. In such so-called one-dye sequencing approaches, the first nucleotide type is labeled but the label is removed after the first image is generated, and the second nucleotide type is labeled only after a first image is generated. The third nucleotide type retains its label in both the first and second images, and the fourth nucleotide type remains unlabeled in both images.
Some embodiments can utilize sequencing by ligation techniques. Such techniques utilize DNA ligase to incorporate oligonucleotides and identify the incorporation of such oligonucleotides. The oligonucleotides typically have different labels that are correlated with the identity of a particular nucleotide in a sequence to which the oligonucleotides hybridize. As with other SBS methods, images can be obtained following treatment of an array of nucleic acid features with the labeled sequencing reagents. Each image will show nucleic acid features that have incorporated labels of a particular type. Different features are present or absent in the different images due the different sequence content of each feature, but the relative position of the features will remain unchanged in the images. Images obtained from ligation-based sequencing methods can be stored, processed and analyzed as set forth herein. Exemplary SBS systems and methods which can be utilized with the methods and systems described herein are described in U.S. Pat. Nos. 6,969,488, 6,172,218, and 6,306,597, the disclosures of which are incorporated herein by reference in their entireties.
Some embodiments can utilize nanopore sequencing (Deamer, D. W. & Akeson, M. “Nanopores and nucleic acids: prospects for ultrarapid sequencing.” Trends Biotechnol. 18, 147-151 (2000); Deamer, D. and D. Branton, “Characterization of nucleic acids by nanopore analysis”. Acc. Chem. Res. 35:817-825 (2002); Li, J., M. Gershow, D. Stein, E. Brandin, and J. A. Golovchenko, “DNA molecules and configurations in a solid-state nanopore microscope” Nat. Mater. 2:611-615 (2003), the disclosures of which are incorporated herein by reference in their entireties). In such embodiments, the target nucleic acid passes through a nanopore. The nanopore can be a synthetic pore or biological membrane protein, such as α-hemolysin. As the target nucleic acid passes through the nanopore, each base-pair can be identified by measuring fluctuations in the electrical conductance of the pore. (U.S. Pat. No. 7,001,792; Soni, G. V. & Meller, “A. Progress toward ultrafast DNA sequencing using solid-state nanopores.” Clin. Chem. 53, 1996-2001 (2007); Healy, K. “Nanopore-based single-molecule DNA analysis.” Nanomed. 2, 459-481 (2007); Cockroft, S. L., Chu, J., Amorin, M. & Ghadiri, M. R. “A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution.” J. Am. Chem. Soc. 130, 818-820 (2008), the disclosures of which are incorporated herein by reference in their entireties). Data obtained from nanopore sequencing can be stored, processed and analyzed as set forth herein. In particular, the data can be treated as an image in accordance with the exemplary treatment of optical images and other images that is set forth herein.
Some embodiments can utilize methods involving the real-time monitoring of DNA polymerase activity. Nucleotide incorporations can be detected through fluorescence resonance energy transfer (FRET) interactions between a fluorophore-bearing polymerase and 7-phosphate-labeled nucleotides as described, for example, in U.S. Pat. Nos. 7,329,492 and 7,211,414 (each of which is incorporated herein by reference) or nucleotide incorporations can be detected with zero-mode waveguides as described, for example, in U.S. Pat. No. 7,315,019 (which is incorporated herein by reference) and using fluorescent nucleotide analogs and engineered polymerases as described, for example, in U.S. Pat. No. 7,405,281 and U.S. Patent Application Publication No. 2008/0108082 (each of which is incorporated herein by reference). The illumination can be restricted to a zeptoliter-scale volume around a surface-tethered polymerase such that incorporation of fluorescently labeled nucleotides can be observed with low background (Levene, M. J. et al. “Zero-mode waveguides for single-molecule analysis at high concentrations.” Science 299, 682-686 (2003); Lundquist, P. M. et al. “Parallel confocal detection of single molecules in real time.” Opt. Lett. 33, 1026-1028 (2008); Korlach, J. et al. “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nano structures.” Proc. Natl. Acad. Sci. USA 105, 1176-1181 (2008), the disclosures of which are incorporated herein by reference in their entireties). Images obtained from such methods can be stored, processed and analyzed as set forth herein.
Some SBS embodiments include detection of a proton released upon incorporation of a nucleotide into an extension product. For example, sequencing based on detection of released protons can use an electrical detector and associated techniques that are commercially available from Ion Torrent (Guilford, C T, a Life Technologies subsidiary) or sequencing methods and systems described in US 2009/0026082 A1; US 2009/0127589 A1; US 2010/0137143 A1; or US 2010/0282617 A1, each of which is incorporated herein by reference. Methods set forth herein for amplifying target nucleic acids using kinetic exclusion can be readily applied to substrates used for detecting protons. More specifically, methods set forth herein can be used to produce clonal populations of amplicons that are used to detect protons.
The above SBS methods can be advantageously carried out in multiplex formats such that multiple different target nucleic acids are manipulated simultaneously. In particular embodiments, different target nucleic acids can be treated in a common reaction vessel or on a surface of a particular substrate. This allows convenient delivery of sequencing reagents, removal of unreacted reagents and detection of incorporation events in a multiplex manner. In embodiments using surface-bound target nucleic acids, the target nucleic acids can be in an array format. In an array format, the target nucleic acids can be typically bound to a surface in a spatially distinguishable manner. The target nucleic acids can be bound by direct covalent attachment, attachment to a bead or other particle or binding to a polymerase or other molecule that is attached to the surface. The array can include a single copy of a target nucleic acid at each site (also referred to as a feature) or multiple copies having the same sequence can be present at each site or feature. Multiple copies can be produced by amplification methods such as, bridge amplification or emulsion PCR as described in further detail below.
The methods set forth herein can use arrays having features at any of a variety of densities including, for example, at least about 10 features/cm2, 100 features/cm2, 500 features/cm2, 1,000 features/cm2, 5,000 features/cm2, 10,000 features/cm2, 50,000 features/cm2, 100,000 features/cm2, 1,000,000 features/cm2, 5,000,000 features/cm2, or higher.
An advantage of the methods set forth herein is that they provide for rapid and efficient detection of a plurality of target nucleic acid in parallel. Accordingly the present disclosure provides integrated systems capable of preparing and detecting nucleic acids using techniques known in the art such as those exemplified above. Thus, an integrated system of the present disclosure can include fluidic components capable of delivering amplification reagents and/or sequencing reagents to one or more immobilized DNA fragments, the system comprising components such as pumps, valves, reservoirs, fluidic lines and the like. A flow cell can be configured and/or used in an integrated system for detection of target nucleic acids. Exemplary flow cells are described, for example, in US 2010/0111768 A1 and U.S. Ser. No. 13/273,666, each of which is incorporated herein by reference. As exemplified for flow cells, one or more of the fluidic components of an integrated system can be used for an amplification method and for a detection method. Taking a nucleic acid sequencing embodiment as an example, one or more of the fluidic components of an integrated system can be used for an amplification method set forth herein and for the delivery of sequencing reagents in a sequencing method such as those exemplified above. Alternatively, an integrated system can include separate fluidic systems to carry out amplification methods and to carry out detection methods. Examples of integrated sequencing systems that are capable of creating amplified nucleic acids and also determining the sequence of the nucleic acids include, without limitation, the MiSeq™ platform (Illumina, Inc., San Diego, CA) and devices described in U.S. Ser. No. 13/273,666, which is incorporated herein by reference.
The sequencing system described above sequences nucleic-acid polymers present in samples received by a sequencing device. As described herein and defined above, a “sample” and its derivatives, is used in its broadest sense and includes any specimen, culture and the like that is suspected of including a target. In some embodiments, the sample comprises DNA, RNA, PNA, LNA, chimeric or hybrid forms of nucleic acids. The sample can include any biological, clinical, surgical, agricultural, atmospheric or aquatic-based specimen containing one or more nucleic acids. The term also includes any isolated nucleic acid sample such a genomic DNA, fresh-frozen or formalin-fixed paraffin-embedded nucleic acid specimen. It is also envisioned that the sample can be from a single individual, a collection of nucleic acid samples from genetically related members, nucleic acid samples from genetically unrelated members, nucleic acid samples (matched) from a single individual such as a tumor sample and normal tissue sample, or sample from a single source that contains two distinct forms of genetic material such as maternal and fetal DNA obtained from a maternal subject, or the presence of contaminating bacterial DNA in a sample that contains plant or animal DNA. In some embodiments, the source of nucleic acid material can include nucleic acids obtained from a newborn, for example as typically used for newborn screening.
The nucleic acid sample can include high molecular weight material such as genomic DNA (gDNA). The sample can include low molecular weight material such as nucleic acid molecules obtained from FFPE or archived DNA samples. In another embodiment, low molecular weight material includes enzymatically or mechanically fragmented DNA. The sample can include cell-free circulating DNA. In some embodiments, the sample can include nucleic acid molecules obtained from biopsies, tumors, scrapings, swabs, blood, mucus, urine, plasma, semen, hair, laser capture micro-dissections, surgical resections, and other clinical or laboratory obtained samples. In some embodiments, the sample can be an epidemiological, agricultural, forensic or pathogenic sample. In some embodiments, the sample can include nucleic acid molecules obtained from an animal such as a human or mammalian source. In another embodiment, the sample can include nucleic acid molecules obtained from a non-mammalian source such as a plant, bacteria, virus or fungus. In some embodiments, the source of the nucleic acid molecules may be an archived or extinct sample or species.
Further, the methods and compositions disclosed herein may be useful to amplify a nucleic acid sample having low-quality nucleic acid molecules, such as degraded and/or fragmented genomic DNA from a forensic sample. In one embodiment, forensic samples can include nucleic acids obtained from a crime scene, nucleic acids obtained from a missing persons DNA database, nucleic acids obtained from a laboratory associated with a forensic investigation or include forensic samples obtained by law enforcement agencies, one or more military services or any such personnel. The nucleic acid sample may be a purified sample or a crude DNA containing lysate, for example derived from a buccal swab, paper, fabric or other substrate that may be impregnated with saliva, blood, or other bodily fluids. As such, in some embodiments, the nucleic acid sample may comprise low amounts of, or fragmented portions of DNA, such as genomic DNA. In some embodiments, target sequences can be present in one or more bodily fluids including but not limited to, blood, sputum, plasma, semen, urine and serum. In some embodiments, target sequences can be obtained from hair, skin, tissue samples, autopsy or remains of a victim. In some embodiments, nucleic acids including one or more target sequences can be obtained from a deceased animal or human. In some embodiments, target sequences can include nucleic acids obtained from non-human DNA such a microbial, plant or entomological DNA. In some embodiments, target sequences or amplified target sequences are directed to purposes of human identification. In some embodiments, the disclosure relates generally to methods for identifying characteristics of a forensic sample. In some embodiments, the disclosure relates generally to human identification methods using one or more target specific primers disclosed herein or one or more target specific primers designed using the primer design criteria outlined herein. In one embodiment, a forensic or human identification sample containing at least one target sequence can be amplified using any one or more of the target-specific primers disclosed herein or using the primer criteria outlined herein.
The components of the multiomics sequencing system 106 can include software, hardware, or both. For example, the components of the multiomics sequencing system 106 can include one or more instructions stored on a computer-readable storage medium and executable by processors of one or more computing devices (e.g., the client device 114). When executed by the one or more processors, the computer-executable instructions of the multiomics sequencing system 106 can cause the computing devices to perform the bubble detection methods described herein. Alternatively, the components of the multiomics sequencing system 106 can comprise hardware, such as special purpose processing devices to perform a certain function or group of functions. Additionally, or alternatively, the components of the multiomics sequencing system 106 can include a combination of computer-executable instructions and hardware.
Furthermore, the components of the multiomics sequencing system 106 performing the functions described herein with respect to the multiomics sequencing system 106 may, for example, be implemented as part of a stand-alone application, as a module of an application, as a plug-in for applications, as a library function or functions that may be called by other applications, and/or as a cloud-computing model. Thus, components of the multiomics sequencing system 106 may be implemented as part of a stand-alone application on a personal computing device or a mobile device. Additionally, or alternatively, the components of the multiomics sequencing system 106 may be implemented in any application that provides sequencing services including, but not limited to Illumina BaseSpace, Illumina DRAGEN, Illumina NextSeq, Illumina TruSeq, or Illumina TruSight software. “Illumina,” “BaseSpace,” “DRAGEN,” “NextSeq,” “TruSeq,” and “TruSight,” are either registered trademarks or trademarks of Illumina, Inc. in the United States and/or other countries.
Embodiments of the present disclosure may comprise or utilize a special purpose or general-purpose computer including computer hardware, such as, for example, one or more processors and system memory, as discussed in greater detail below. Embodiments within the scope of the present disclosure also include physical and other computer-readable media for carrying or storing computer-executable instructions and/or data structures. In particular, one or more of the processes described herein may be implemented at least in part as instructions embodied in a non-transitory computer-readable medium and executable by one or more computing devices (e.g., any of the media content access devices described herein). In general, a processor (e.g., a microprocessor) receives instructions, from a non-transitory computer-readable medium, (e.g., a memory, etc.), and executes those instructions, thereby performing one or more processes, including one or more of the processes described herein.
Computer-readable media can be any available media that can be accessed by a general purpose or special purpose computer system. Computer-readable media that store computer-executable instructions are non-transitory computer-readable storage media (devices). Computer-readable media that carry computer-executable instructions are transmission media. Thus, by way of example, and not limitation, embodiments of the disclosure can comprise at least two distinctly different kinds of computer-readable media: non-transitory computer-readable storage media (devices) and transmission media.
Non-transitory computer-readable storage media (devices) includes RAM, ROM, EEPROM, CD-ROM, solid state drives (SSDs) (e.g., based on RAM), Flash memory, phase-change memory (PCM), other types of memory, other optical disk storage, magnetic disk storage or other magnetic storage devices, or any other medium which can be used to store desired program code means in the form of computer-executable instructions or data structures and which can be accessed by a general purpose or special purpose computer.
A “network” is defined as one or more data links that enable the transport of electronic data between computer systems and/or modules and/or other electronic devices. When information is transferred or provided over a network or another communications connection (either hardwired, wireless, or a combination of hardwired or wireless) to a computer, the computer properly views the connection as a transmission medium. Transmissions media can include a network and/or data links which can be used to carry desired program code means in the form of computer-executable instructions or data structures and which can be accessed by a general purpose or special purpose computer. Combinations of the above should also be included within the scope of computer-readable media.
Further, upon reaching various computer system components, program code means in the form of computer-executable instructions or data structures can be transferred automatically from transmission media to non-transitory computer-readable storage media (devices) (or vice versa). For example, computer-executable instructions or data structures received over a network or data link can be buffered in RAM within a network interface module (e.g., a NIC), and then eventually transferred to computer system RAM and/or to less volatile computer storage media (devices) at a computer system. Thus, it should be understood that non-transitory computer-readable storage media (devices) can be included in computer system components that also (or even primarily) utilize transmission media.
Computer-executable instructions comprise, for example, instructions and data which, when executed at a processor, cause a general-purpose computer, special purpose computer, or special purpose processing device to perform a certain function or group of functions. In some embodiments, computer-executable instructions are executed on a general-purpose computer to turn the general-purpose computer into a special purpose computer implementing elements of the disclosure. The computer executable instructions may be, for example, binaries, intermediate format instructions such as assembly language, or even source code. Although the subject matter has been described in language specific to structural features and/or methodological acts, it is to be understood that the subject matter defined in the appended claims is not necessarily limited to the described features or acts described above. Rather, the described features and acts are disclosed as example forms of implementing the claims.
Those skilled in the art will appreciate that the disclosure may be practiced in network computing environments with many types of computer system configurations, including, personal computers, desktop computers, laptop computers, message processors, hand-held devices, multi-processor systems, microprocessor-based or programmable consumer electronics, network PCs, minicomputers, mainframe computers, mobile telephones, PDAs, tablets, pagers, routers, switches, and the like. The disclosure may also be practiced in distributed system environments where local and remote computer systems, which are linked (either by hardwired data links, wireless data links, or by a combination of hardwired and wireless data links) through a network, both perform tasks. In a distributed system environment, program modules may be located in both local and remote memory storage devices.
Embodiments of the present disclosure can also be implemented in cloud computing environments. In this description, “cloud computing” is defined as a model for enabling on-demand network access to a shared pool of configurable computing resources. For example, cloud computing can be employed in the marketplace to offer ubiquitous and convenient on-demand access to the shared pool of configurable computing resources. The shared pool of configurable computing resources can be rapidly provisioned via virtualization and released with low management effort or service provider interaction, and then scaled accordingly.
A cloud-computing model can be composed of various characteristics such as, for example, on-demand self-service, broad network access, resource pooling, rapid elasticity, measured service, and so forth. A cloud-computing model can also expose various service models, such as, for example, Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS). A cloud-computing model can also be deployed using different deployment models such as private cloud, community cloud, public cloud, hybrid cloud, and so forth. In this description and in the claims, a “cloud-computing environment” is an environment in which cloud computing is employed.
In one or more embodiments, the processor 1002 includes hardware for executing instructions, such as those making up a computer program. As an example, and not by way of limitation, to execute instructions for dynamically modifying workflows, the processor 1002 may retrieve (or fetch) the instructions from an internal register, an internal cache, the memory 1004, or the storage device 1006 and decode and execute them. The memory 1004 may be a volatile or non-volatile memory used for storing data, metadata, and programs for execution by the processor(s). The storage device 1006 includes storage, such as a hard disk, flash disk drive, or other digital storage device, for storing data or instructions for performing the methods described herein.
The I/O interface 1008 allows a user to provide input to, receive output from, and otherwise transfer data to and receive data from computing device 1000. The I/O interface 1008 may include a mouse, a keypad or a keyboard, a touch screen, a camera, an optical scanner, network interface, modem, other known I/O devices or a combination of such I/O interfaces. The I/O interface 1008 may include one or more devices for presenting output to a user, including, but not limited to, a graphics engine, a display (e.g., a display screen), one or more output drivers (e.g., display drivers), one or more audio speakers, and one or more audio drivers. In certain embodiments, the I/O interface 1008 is configured to provide graphical data to a display for presentation to a user. The graphical data may be representative of one or more graphical user interfaces and/or any other graphical content as may serve a particular implementation.
The communication interface 1010 can include hardware, software, or both. In any event, the communication interface 1010 can provide one or more interfaces for communication (such as, for example, packet-based communication) between the computing device 1000 and one or more other computing devices or networks. As an example, and not by way of limitation, the communication interface 1010 may include a network interface controller (NIC) or network adapter for communicating with an Ethernet or other wire-based network or a wireless NIC (WNIC) or wireless adapter for communicating with a wireless network, such as a WI-FI.
Additionally, the communication interface 1010 may facilitate communications with various types of wired or wireless networks. The communication interface 1010 may also facilitate communications using various communication protocols. The communication infrastructure 1012 may also include hardware, software, or both that couples components of the computing device 1000 to each other. For example, the communication interface 1010 may use one or more networks and/or protocols to enable a plurality of computing devices connected by a particular infrastructure to communicate with each other to perform one or more aspects of the processes described herein. To illustrate, the sequencing process can allow a plurality of devices (e.g., a client device, sequencing device, and server device(s)) to exchange information such as sequencing data and error notifications.
In the foregoing specification, the present disclosure has been described with reference to specific exemplary embodiments thereof. Various embodiments and aspects of the present disclosure(s) are described with reference to details discussed herein, and the accompanying drawings illustrate the various embodiments. The description above and drawings are illustrative of the disclosure and are not to be construed as limiting the disclosure. Numerous specific details are described to provide a thorough understanding of various embodiments of the present disclosure.
The present disclosure may be embodied in other specific forms without departing from its spirit or essential characteristics. The described embodiments are to be considered in all respects only as illustrative and not restrictive. For example, the methods described herein may be performed with less or more steps/acts or the steps/acts may be performed in differing orders. Additionally, the steps/acts described herein may be repeated or performed in parallel with one another or in parallel with different instances of the same or similar steps/acts. The scope of the present application is, therefore, indicated by the appended claims rather than by the foregoing description. All changes that come within the meaning and range of equivalency of the claims are to be embraced within their scope.
The present application claims the benefit of, and priority to, U.S. Provisional Application No. 63/369,482, entitled “RAPID SINGLE-CELL MULTIOMICS PROCESSING USING AN EXECUTABLE FILE,” filed on Jul. 26, 2022. The aforementioned application is hereby incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 63369482 | Jul 2022 | US |
