Abstract: A method for designing test or control sequences may include identifying, using a variant caller, loci with systematic errors present in a plurality of sequencing runs included in a training set of sequencing runs obtained using sequencing-by-synthesis; and selecting a representative set of loci, including selecting from the identified loci an approximately equal number of loci involving errors in A, T, C, and G homopolymers and selecting from the identified loci an approximately equal number of loci involving homopolymers having a length of two, three, and four.

Abstract: The present disclosure relates, in some embodiments, to a system for measuring capillary electrophoresis current. The system includes a plurality of capillaries, where each capillary has a cathode end and an anode end. The system further includes a plurality of cathode buffers. Each of the cathode buffers is configured to be electrically isolated from the other cathode buffers. Further, each cathode buffer is associated with one capillary of the plurality of capillaries. The cathode end of each capillary is immersed in its associated cathode buffer. The system includes a plurality of current sensors, each current sensor associated with one capillary of the plurality of capillaries for measuring current. In some embodiments, the plurality of capillaries is four capillaries.

Abstract: A method for mixing a biological suspension includes disposing a biological suspension within a compartment of a container, the biological suspension comprising cells or microorganisms suspended within a nutrient growth medium; and rotating a first drive line and laterally spaced apart second drive line within the compartment of the container so as to cause the drive lines to twist into a helical configuration and mix the biological suspension.

Abstract: A method for filtering a gas comprises passing a gas through a compartment of a filter assembly, the filter assembly comprising: an inlet opening; a first outlet opening; a casing comprising polymeric film and bounding the compartment, the compartment communicating with the inlet opening and the first outlet opening; and a first filter at least partially disposed within the compartment. The method further comprising forming a first seal across a first section of the casing at a location between the inlet opening and the first filter to form a first sub-compartment within the casing and severing the casing at a first location.

Abstract: A carrier for holding a biological sample includes a substrate. The substrate is configured to engage a first sample chamber comprising a first opening characterized by a first opening diameter or a second sample chamber comprising a second opening characterized by a second opening diameter that is greater than the first opening diameter. The substrate includes an upper portion, a lower portion, and an intermediate portion disposed between the upper portion and the lower portion. The lower portion is disposed below the upper portion and comprises a bottom surface configured to receive a biological sample. The intermediate portion is characterized by a first substrate diameter and the lower portion is characterized by a second substrate diameter that is less than the first substrate diameter.

Abstract: A fluidic coupler to engage a plurality of flow cells of a sensor device includes a body and a plurality of fluidics interfaces formed in the body. Each fluidic interface of the plurality of fluidics interfaces includes an opening, a first port in fluid communication with the opening, a second port, and a third port in fluidic communication with the second port.

Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.

Abstract: The instant technology relates to a production system to produce AAV vectors in a serum free suspension platform and at high titers. This technology uses reagents comprising media, cells, transfection reagent, AAV enhancer, and a lysis buffer, each of which is designed to provide maximal AAV production from suspension culture of mammalian cells, e.g. HEK293 cells. With this new system we are able to deliver up to about 2×1011 viral genomes per milliliter (vg/mL) of unconcentrated AAV vectors.

Abstract: The present disclosure describes oligonucleotide-tethered nucleotides, methods of making them, and methods of using them. The oligonucleotide-tethered nucleotides comprise, in some embodiments, a nucleotide linked to an oligonucleotide of from about 3 to about 100 nucleotides in length. These oligonucleotide-tethered nucleotides can be used to label a plurality of different types of nucleic acids in a plurality of different situations with a known oligonucleotide, which can serve as a barcode in some embodiments. The resulting oligonucleotide-labeled nucleic acids oligonucleotides can be used in a variety of nucleic acid sequencing methods.

Abstract: A method of registering a location of a dispenser array in relation to a microfluidic array is provided. One of the dispenser array and the microfluidic array can be movable in relation to the frame, and the other can be fixed relative to the frame. Their relative positions can be identified by a set of coordinates. Identification of a fiducial marker can occur in a manner permitting the fiducial reference to appear in a first position of a field of view of a first camera when the dispenser array or the microfluidic array is in an alignment position. Quantities related to a vector displacement from the alignment position to a fixed position on the microfluidic array or the dispenser array can be identified. Quantities determined can be used to guide positioning of the dispenser array relative to the microfluidic array.

Abstract: Methods are provided for making bispecific antibodies and antibody conjugates comprising site-specifically cross-linking two or more antibodies, antibody fragments or Fc-fusion proteins. Also provided are compositions and uses for the bispecific antibodies and antibody conjugates. The bispecific antibodies may be used to treat a disease or condition. Also provided are methods for site-specifically conjugating a liposome, an mRNA or an siRNA to an antibody, and uses of the antibody-conjugated liposome, mRNA or siRNA.

Abstract: Compositions, assays, methods, diagnostic methods, kits, and diagnostic kits are disclosed for the specific and differential detection of SARS-CoV-2 and/or other viruses from samples, including veterinary samples, clinical samples, food samples, forensic sample, environmental samples (e.g., obtained from soil, garbage, sewage, air, water, food processing and manufacturing surfaces, or likewise), or biological sample obtained from a human or non-human animal.

Abstract: The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire. In one aspect, methods provide for determining convergence of T cell receptor and/or B cell receptor repertoires in samples prior to a treatment and predicting a subjects response to the treatment based on the measured convergence frequency. In another aspect, methods provide for an immune receptor haplotype group and predicting a subjects potential or predisposition to be protected from or vulnerable to an adverse event following a treatment.

Abstract: Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.

Abstract: Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.

Abstract: Disclosed herein is a method including one or more of amplifying a nucleic acid sequence of interest in a sample comprising genomic DNA of a subject; amplifying a reference nucleic acid sequence in the sample; quantifying the amplified sequence of interest relative to the amplified reference sequence; and determining a copy number of the sequence of interest from the relative quantified amplified sequence of interest. The reference sequence can have at least 80% sequence identity to at least one of SEQ ID NO:1-38. Also disclosed are kits, systems and compositions that can include a first probe which specifically hybridizes to at least a portion of at least one reference sequence.

Abstract: Methods, compositions and kits for detecting microorganisms and/or profiling microbiota such as for example through use of nucleic acid amplification and detection.

Abstract: A method for nucleic acid sequencing includes receiving a plurality of signals indicative of a parameter measured for a plurality of defined spaces, at least some of the defined spaces including one or more sample nucleic acids, the signals being responsive to a plurality of nucleotide flows introducing nucleotides to the defined spaces; determining, for at least some of the defined spaces, whether the defined space includes a sample nucleic acid; processing, for at least some of the defined spaces determined to include a sample nucleic acid, the received signals to improve a quality of the received signals; and predicting a plurality of nucleotide sequences corresponding to respective sample nucleic acids for the defined spaces based on the processed signals and the nucleotide flows.