Abstract: The invention relates to integrated DNA and RNA library preparations and methods of making and uses thereof, wherein the DNA molecules are labelled with a tag identifying the molecule as being a DNA molecule and the RNA molecules are labelled with a tag identifying the molecule as being a RNA molecule. The methods do not require physical separation of DNA and RNA. The methods output two separate libraries from DNA and RNA, respectively, which helps flexible manipulation on downstream sequencing platforms. The application also claims the DNA library and the cDNA library produced by the method and the DNA tag and the RNA tag used in the method.

Abstract: Compositions and methods are provided for detection, diagnosis and prognosis of Lyme disease (LD), including a method for confirming Borrelia spp. infection by contacting, in vitro, whole blood samples from subjects suspected of having LD with synthetic peptides comprising T-cell epitope-containing regions derived from Borrelia proteins that are expressed at different stages of Lyme disease, and indirectly detecting LD-specific activated T-cells by determining production of a T-cell immune response indicator (e.g., interferon-Y) in response to stimulation by the peptides.

Abstract: A microfluidic device with a microfluidic circuit including an array of fluidly coupled microchambers. Each microchamber includes a reaction chamber and an associated vent chamber. The microfluidic circuit may be arranged so that a fluid sample introduced to microfluidic device flows into the reaction chamber and air or other gas present in the reaction chamber is vented from the microchamber through the vent chamber. The microchamber may be configured to allow only the flow of air into the vent chamber from the reaction chamber until the air has been displaced from the reaction chamber by the fluid sample and/or a predefined volume of the fluid sample has been received in the reaction chamber. The microchamber may be further configured to release the fluid sample to thereafter flow from the reaction chamber into the vent chamber.

Abstract: Provided are methods for isolating biomolecules, such as nucleic acids and proteins, from a sample using a silica-containing surface and/or a high salt, low pH buffer.

Abstract: Provided are methods and compositions for negatively and positively selecting for different size nucleic acid (e.g., DNA or RNA) fragments on borosilicate glass fiber membranes, silica and metal oxide surfaces such that only those fragments falling within a desired size range are obtained.

Abstract: The present disclosure provides primers, primer sets, kits and methods for multiple displacement amplification, especially in combination with nucleic acid sequencing. The primers comprise self-complementary sequences at their 5? termini and random or semi-random sequences at their 3? termini. Use of such primers facilitates handling of multiple samples, increases sequence coverage uniformity, and improves sequencing error corrections.

Abstract: An imaging system for exciting and measuring fluorescence on or in samples comprising fluorescent materials (e.g. fluorescent labels, dyes or pigments). In one embodiment, a device is used to detect fluorescent labels on nucleic acid. In a preferred embodiment, the device is configured such that fluorescent labels in a plurality of different DNA templates are simultaneously detected.

Abstract: Modular flow cells, devices with modular flow cells, and methods of sequencing using modular flow cells, as well as systems and kits including modular flow cells, are described, permitting sequencing wherein less than the full capacity for sequencing is desired.

Abstract: The present disclosure relates to methods for predicting time-to-delivery in pregnant women. The methods include predicting that a pregnant woman will deliver within a predetermined time frame if PAMG-1 is determined to be present at a level above a predetermined detection threshold in a vaginal fluid sample obtained from the pregnant woman. Also provided are methods for determining a patient's risk of preterm labor and/or spontaneous rupture of the chorioamniotic membrane.

Abstract: A microfluidic device with a microfluidic circuit including an array of fluidly coupled microchambers. Each microchamber includes a reaction chamber and an associated vent chamber. The microfluidic circuit may be arranged so that a fluid sample introduced to microfluidic device flows into the reaction chamber and air or other gas present in the reaction chamber is vented from the microchamber through the vent chamber. The microchamber may be configured to allow only the flow of air into the vent chamber from the reaction chamber until the air has been displaced from the reaction chamber by the fluid sample and/or a predefined volume of the fluid sample has been received in the reaction chamber. The microchamber may be further configured to release the fluid sample to thereafter flow from the reaction chamber into the vent chamber.

Abstract: The present disclosure provides oligonucleotides that comprise semi-random barcode sequences. Such oligonucleotides may be incorporated into reverse transcription primers, PCR primers, or portions of sequencing adapters in preparing sequencing libraries. The resulting sequencing libraries can be used for accurate sequencing, including DNA or RNA counting and mutation detection. Methods and kits for preparing sequencing adapters and sequencing libraries are also provided.

Abstract: The present invention provides methods, compositions, mixtures and kits utilizing deoxynucleoside triphosphates comprising a 3?-O position capped by a group comprising methylenedisulfide as a cleavable protecting group and a detectable label reversibly connected to the nucleobase of said deoxynucleoside. Such compounds provide new possibilities for future sequencing technologies, including but not limited to Sequencing by Synthesis.

Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. A plurality of smaller flow cells is employed, each with a relatively small area to be imaged, in order to provide greater flexibility and efficiency.

Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.

Abstract: Compositions and methods are provided for detection, diagnosis and prognosis of Lyme disease (LD), including a method for confirming Borrelia spp. infection by contacting, in vitro, whole blood samples from subjects suspected of having LD with synthetic peptides comprising T-cell epitope-containing regions derived from Borrelia proteins that are expressed at different stages of Lyme disease, and indirectly detecting LD-specific activated T-cells by determining production of a T-cell immune response indicator (e.g., interferon-Y) in response to stimulation by the peptides.

Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.

Abstract: A flowcell device for a sequencing by synthesis instrument. The flowcell device has a fluid inlet configured to receive one or more liquid reagents, a fluid outlet configured to pass the one or more liquid reagents, and a channel extending between and fluidly connecting the fluid inlet and the fluid outlet. At least a portion of the channel comprises a reflective structure configured to retain a plurality of sequencing targets thereon. The reflective structure includes at least a metal oxide layer and a film having a first surface and a second surface opposed the first surface. The first surface of the film is disposed on the metal oxide layer and the second surface of the film is configured to receive a plurality of sequencing targets immobilized thereon.

Abstract: The present disclosure provides methods and kits for highly multiplex single primer extensions using a MutS protein and Mg2+ at a concentration higher than that in a typical PCR reaction. Also disclosed is the use of such methods and kits in next generation sequencing.

Abstract: A method of determining suitability of a pregnant woman to be a candidate for induction of labor can include: obtaining a vaginal fluid sample from a pregnant woman; contacting the vaginal fluid sample with a PAMG-1 antibody that binds with PAMG-1; detecting whether the PAMG-1 antibody binds with PAMG-1 in the vaginal fluid sample to form a PAMG-1-antibody complex; and providing the determination of suitability for induction of labor to the pregnant woman. When the PAMG-1-antibody complex forms, the pregnant woman is determined to be in a condition that is not suitable for induction of labor because PAMG-1 is detected in the vaginal sample. When the PAMG-1-antibody complex does not form, the pregnant woman is determined to be in a condition that is suitable to be a candidate for induction of labor because the PAMG-1 is not detected in the vaginal sample.

Abstract: Provided are methods and compositions for negatively and positively selecting for different size nucleic acid (e.g., DNA or RNA) fragments on borosilicate glass fiber membranes, silica and metal oxide surfaces such that only those fragments falling within a desired size range are obtained.