Abstract: Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the extended oligonucleotides include a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing the extended oligonucleotide by competition with a competitor; detecting the extended oligonucleotide, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the extended oligonucleotide.

Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.

Abstract: The presently disclosed subject matter provides devices and methods for sample extraction from a swab during biological sample processing. In particular embodiments, the devices and methods are configured for use in conjunction with microfluidic devices for sample processing.

Abstract: Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.

Abstract: The present disclosure provides an assay cartridge used in a PCR-based molecular diagnostic device. In one embodiment, the assay cartridge comprises (1) an elongated body having a proximal end, a distal end and a plurality of compartments arranged between the proximal end and the distal end, said plurality of compartments include at least a first pipette tip holder near the proximal end, and a second pipette tip holder near the distal end; and (2) a seal assembly covering the elongated body comprising a rigid frame which matches the top periphery of the elongated body, and an elastic top mounted on the rigid frame, the elastic top comprising a first sub-portion near the proximal end comprising a first ring structure that matches the first pipette holder, and a second sub-portion near the distal end comprising a second ring structure that matches the second pipette holder.

Abstract: A sample carrier may include a sample preparation module and an amplification module. A sample mixes with a lysis medium and a nucleic acid amplification medium in the sample preparation module and then flows into a plurality of microfluidic chambers in the amplification module. The microfluidic chambers have disposed therein primers configured to initiate amplification of one or more target nucleic acid sequences corresponding to one or more pathogens. The sample carrier is inserted into an apparatus that includes a plurality of Sight sources and a camera. The light sources illuminate the microfluidic chambers with excitation light, a fluorophore emits fluorescence light indicative of nucleic acid amplification in response to the excitation-light, and the camera captures images of the microfluidic chambers. A target nucleic acid sequence in the sample is indicated by the images showing an increasing fluorescence in a microfluidic chamber that has the primers for that sequence.

Abstract: The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.

Abstract: The disclosure concerns a method and a device for enriching cells, cell fragments and molecules from whole blood for a specific detection of at least one population of cells, cell fragments or molecules contained therein. The task was to detect a broad spectrum of target objects including their molecules simply, quickly and yet sensitively and specifically from whole blood. According to the disclosure, not the target objects themselves, but matrix objects are specifically enriched, but target objects are specifically analyzed and thus a specific and sensitive detection of target objects is achieved.

Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.

Abstract: The present invention relates to a low-cost, thermally reversible valve for paper-fluidic diagnostic devices. In particular, this invention demonstrates a tunable valve mechanism fabricated by wax-ink printing and localized heating via thin-film resistors to sequentially release liquids through a cellulose or nitrocellulose membrane. The wax-ink valve can obstruct fluid flow for a sustained time and are thermally actuated to release a controlled amount of liquid past the valve. This integrated paper-fluidic diagnostic assay device requires minimal user involvement, can be easily manufactured and tuned to meet various fluid delivery timing and incubation needs.

Abstract: A fluidic card assembly (1) comprises an inlet (20) for introducing a fluid to the fluidic card assembly (1), a turbulent flow portion (30) downstream of the inlet (20), the turbulent flow portion (30) comprising a widening fluid channel (31) whereby a fluid introduced via the inlet (20) channel undergoes turbulence, and a laminar flow portion (40) downstream of the turbulent flow portion (30). The laminar flow portion (40) is configured to allow fluid passing from the turbulent flow portion (30) into the laminar flow portion (40) to establish a laminar flow pattern, and is configured to house a biochip (44) such that a fluid in the laminar flow portion (40) may be in contact with the biochip (44).

Abstract: A method for direct quantification of nucleic acids in real time qPCR. The invention discloses a method for specific quantification of nucleic acids in real time qPCR. The disclosed invention can be achieved in three ways; 1) using a modified primer for qPCR quantification; 2) using strand displacement based probes for qPCR quantification; 3) using label-free endonuclease probe for qPCR quantification. The mechanism of quantification is based on the fact that, DNA, RNA or modified oligonucleotide based light-up dye-aptamer system, where dye is not fluorescent in free state but its fluorescence increases multi-fold when it binds to its specific aptamer.

Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.

Abstract: A method may include maintaining a sample comprising an ionic species and an optical indicator at an elevated temperature above 25° C. on a semi-conductive microfluidic die during an incubation period, intermittently interrogating the sample with an interrogating light during the incubation period and sensing a response of the sample to the interrogating light, wherein the sample is interrogated with the interrogating light only during those times at which the sample is being sensed.

Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.

Abstract: A gene detection method, a gene detection kit, and a gene detection device, including the following steps: providing a plurality of separation cavities on a kit, using a plunger to separate adjacent separation cavities, and respectively providing a lysate solution, a washing solution and a reaction solution in the separation cavities; when detecting a sample, pushing each plunger to align a plunger hole of the plunger with the separation cavity, thereby making the separation cavities interconnected; then, controlling magnetic beads in the kit to drive the sample to be tested to pass through the separation cavities in sequence by an electromagnetic control method, carrying out a lysing, a washing and a reaction in sequence; and finally, performing a optical detection on a gene in the reaction solution from outside.

Abstract: Disclosed herein are methods and devices for rapid assessment of whether a microorganism present in a sample is susceptible or resistant to a treatment.

Abstract: Provided are methods of detecting replication competent virus, e.g., replication competent retrovirus such as gammaretrovirus or lentivirus, in a sample containing a cell transduced with a viral vector particle encoding a recombinant and or heterologous molecule, e.g., heterologous gene product. The methods may include assessing transcription of one or more target genes, such as viral genes, that are expressed in a retrovirus but not expressed in the viral vector particle. Replication competent retrovirus may be determined to be present if the levels of RNA of the one or more target genes is higher than a reference value, which can be measured directly or indirectly, including from a positive control sample containing RNA from the respective target gene at a known level and/or at or above the limit of detection of the assay.

Abstract: Methods for human identification using polymorphisms in the Penta E short tandem repeat locus are significant in preventing allelic drop out. An exemplary method encompasses (a) contacting a first primer to a nucleic acid sample to be analyzed, (b) contacting a second primer to the nucleic acid sample, and (c) subjecting the nucleic acid sample, the first primer, and the second primer to an amplification reaction, and thereby forming an amplification product. The first primer, the second primer, or both the first and second primers can be labeled with a non-nucleic-acid label. Additionally, or alternatively, the amplification product can include an adenosine at position 14 from the 5? end of SEQ ID NO:1, a thymidine at position 21 from the 5? end of SEQ ID NO:2, or both an adenine at position 14 and a thymidine at position 21 from the 5? end of SEQ ID NO:3.

Abstract: The methods, compositions, and kits of the disclosure provide a novel approach for a whole genome, unbiased DNA analysis method that can be performed on limited amounts of DNA. can be used to analyze DNA to determine its modification status. Aspects of the disclosure relate to a method for amplifying bisulfite-treated deoxyribonucleic acid (DNA) molecules comprising: (a) ligating an adaptor to the DNA molecules, wherein the adaptor comprises a RNA polymerase promoter comprising bisulfite-protected cytosines; (b) treating the ligated DNA molecules with bisulfite; (c) hybridizing the bisulfite-treated DNA molecules with a primer; (d) extending the hybridized primer to make double stranded DNA; and (e) in vitro transcribing the double-stranded DNA to make RNA.