Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: Methods, systems, and computer-readable media are disclosed for calculating corrected amplicon coverages. One method includes: mapping a plurality of reads of a plurality of amplicons based on amplified target regions of a sample suspected of having one or more genetic abnormalities to a reference sequence that includes one or more nucleic acid sequences corresponding to the amplified target regions; calculating amplicon coverages and total reads, wherein amplicon coverages is a number of reads mapped to an amplicon, and total reads is a number of mapped reads; and calculating corrected amplicon coverages based on the calculated amplicon coverages and calculated total reads by applying a batch effect correction.

Abstract: Embodiments of the invention herein described relate to multiplex polynucleotide sequence analysis without the use of size separation methods or blotting. In certain particulars the invention relates to multiplex sequencing using massively parallel sequencing methods, such as pyrosequencing methods and sequencing by synthesis. The invention provides increased throughput, increased accuracy of enumerating sample components, and the ability to analyze greater numbers of samples simultaneously or serially on presently available systems, as well as others yet to be developed. In certain of its embodiments the invention relates to the analysis of complex microbial communities, particularly to in-depth analysis thereof in large numbers of samples.

Abstract: The invention generally relates to methods for determining aneuploidy of cells with respect to a control sample. In certain embodiments, the method involves exposing a sample to a plurality of probes capable of capturing DNA from at least one chromosome suspected of having an altered copy number, and at least one control DNA sample known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the probes, calculating a chromosomal read fraction; determining a sample specific scaling factor; scaling the chromosomal read fractions, normalizing the scaled read fractions, and determining a copy number state of at least one chromosome.

Abstract: There are provided methods, systems and processes for the utilization of microbial and related genetic information for use in the exploration, determination, production and recovery of natural resources, including energy sources, and the monitoring, control and analysis of processes and activities.

Abstract: The present invention relates to methods for generating sequences of template nucleic acid molecules, methods for determining sequences of at least two template nucleic acid molecules, computer programs adapted to perform the methods and computer readable media storing the computer programs.

Abstract: The invention generally relates to method for assessing a genomic region of a subject. In certain embodiments, methods of the invention involve obtaining a sample including nucleic acid from a subject. The nucleic acid includes a target sequence from a target genomic region and a paralogous sequence from a non-target genomic region. The target sequence and the paralogous sequence are isolated from the sample. The target sequence and the paralogous sequence are sequenced to obtain sequence reads that include target sequence reads and paralogous sequence reads. The paralogous sequence reads are excluded, and the genomic region of the subject are assessed based on the target sequence reads.

Abstract: There are provided methods, systems and processes for the utilization of microbial and related genetic information for use in industrial settings, such as the exploration, determination, and recovery of natural resources, minerals, and energy sources, the monitoring and analysis of processes, activities, and materials transmission.

Abstract: Representative embodiments are disclosed for a rapid and highly parallel configuration process for field programmable gate arrays (FPGAs). In a representative method embodiment, using a host processor, a first configuration bit image for an application is stored in a host memory; one of more FPGAs are configured with a communication functionality such as PCIe using a second configuration bit image stored in a nonvolatile memory; a message is transmitted by the host processor to the FPGAs, usually via PCIe lines, with the message comprising a memory address and also a file size of the first configuration bit image in the host memory; using a DMA engine, each FPGA obtains the first configuration bit image from the host memory and is then configured using the first configuration bit image. Primary FPGAs may further transmit the first configuration bit image to additional, secondary FPGAs, such as via JTAG lines, for their configuration.

Abstract: A scalable FPGA-based solution to the short read mapping problem in DNA sequencing is disclosed which greatly accelerates the task of aligning short length reads to a known reference genome. A representative system comprises one or more memory circuits storing a plurality of short reads and a reference genome sequence; and one or more field programmable gate arrays configured to select a short read; to extract a plurality of seeds from the short read, each seed comprising a genetic subsequence of the short read; for each seed, to determine at least one candidate alignment location (CAL) in the reference genome sequence to form a plurality of CALs; for each CAL, to determine a likelihood of the short read matching the reference genome sequence in the vicinity of the CAL; and to select one or more CALs having the currently greater likelihood of the short read matching the reference genome sequence.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.

Abstract: Representative embodiments are disclosed for data transfer between field programmable gate arrays (FPGAs). A representative system includes: a PCIe communication network comprising a PCIe switch and a plurality of PCIe communication lines; a host computing system coupled to the PCIe communication network; a nonblocking crossbar switch; a plurality of memory circuits; and a plurality of field programmable gate arrays, each field programmable gate array configurable for a plurality of data transfers to and from the host computing system and any other field programmable gate array of the plurality of field programmable gate arrays, with each data transfer including a designation of a first memory address, a file size, and a stream number. Once base DMA registers have been initialized for a selected application, no further involvement by the host computing system is involved for the duration of the selected application.

Abstract: There are provided methods, systems and processes for the utilization of microbial and related genetic information for use in the exploration, determination, production and recovery of natural resources, including energy sources, and the monitoring, control and analysis of processes and activities.

Abstract: A system and method are disclosed for inexact search acceleration using reference data. A representative system includes one or more memory circuits storing a plurality of queries and a FM-index of the reference data; and one or more FPGAs configured to select a query; select a substring of the selected query; read a section of the FM-index and calculate a plurality of suffix array intervals for the sub string with a corresponding plurality of prepended characters in a first or next position; read a first or next character in the first or next position of the query and select a suffix array interval for the read first character; determine whether the suffix array interval is valid and whether a beginning of the query has been reached; returning a first search result when the suffix array interval is valid and the beginning of the query has been reached; and returning a second search result that no match of the query with the reference data was found when the suffix array interval is not valid.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: A computer-implemented method, computer system and computer-readable medium for identifying off-target matches from a set of candidate primer sequences on a genome reference sequence can include: receiving onto a data storage unit a plurality of candidate primer sequences; for each candidate primer sequence, calculating, using a processor, a plurality of candidate matches on the genome reference sequence for the candidate primer sequences; calculating, using the processor, verified matches on the genome reference sequence based on the candidate matching locations satisfying a plurality of matching verification rules; performing matching calculations of the verified matches to determine whether the verified matches form a match condition on the genome reference sequence; and generating a location profile on the genome reference sequence based on the match condition from the verified matches that meet a predetermined threshold.

Abstract: A method and system for analyzing circulating cell-free nucleic acids from a pregnant female with reduced bias, Counts of sequence reads mapped to portions of a reference genome are obtained. A regression model is generated that models the relationship between the counts and the GC content. The read counts are normalized according to the regression model to remove the GC bias. The normalized counts are used for further analysis, such as the detection of fetal aneuploidy.

Abstract: Disclosed are thermodynamic and multiplication methods concerning CRISPR-Cas systems, and apparatus therefor.

Abstract: There is provided an apparatus and a processor-implemented method. The method includes aligning a reference genome with a plurality of DNA sequences. Each of the plurality of DNA sequences has a respective plurality of bases. The method further includes classifying and sorting the plurality of read sequences based on respective numbers of mismatched bases within the plurality of read sequences to obtain a plurality of re-arranged DNA sequences. The method also includes building a histogram based on respective positions of mismatched bases within the plurality of re-arranged DNA sequences. The method additionally includes coding at least some of the plurality of re-arranged DNA sequences based on the histogram.