Abstract: Methods are described which enable nucleic acid sample standardization prior to anchoring to a surface, especially useful in single molecule nucleic acid sequencing applications when sample is limiting or unamplified.

Abstract: A method, flow cell and/or device for increasing the recovery of a limiting analyte in a sample, e.g., for single molecule analysis is disclosed. Methods for preparing a nucleic acid sample from a single cell and capturing nucleic acids on a surface configured for use in or with single molecule analysis are also provided.

Abstract: Methods of the invention comprise methods and devices for nucleic acid sequence determination.

Abstract: The disclosure provides methods of reducing the range of representation levels of nucleic acid targets. The methods are particularly useful for multi-target analyses benefiting from a low variance of target representations, such as, e.g., single molecule sequencing and/or heterozygous genotyping, and pathogen diagnosis. Two general methods are provided. In Method 1, starting concentrations of probes are adjusted. In Method 2, target-specific probes are “binned,” i.e., several subsets of probes are selected based on similar representation levels. Thereafter, each subset of corresponding targets is extracted, with or without amplification, using a separate portion of the sample (i.e., separate vessels).

Abstract: The invention generally relates to methods for detecting fetal nucleic acids and methods for diagnosing fetal abnormalities. In certain embodiments, the invention provides methods for determining whether fetal nucleic acid is present in a maternal sample including obtaining a maternal sample suspected to include fetal nucleic acids, and performing a sequencing reaction on the sample to determine presence of at least a portion of a Y chromosome in the sample, thereby determining that fetal nucleic acid is present in the sample. In other embodiments, the invention provides methods for quantitative or qualitative analysis to detect fetal nucleic acid in a maternal sample, regardless of the ability to detect the Y chromosome, particularly for samples including normal nucleic acids from a female fetus.

Abstract: The invention generally relates to methods for detecting fetal nucleic acids and methods for diagnosing fetal abnormalities. In certain embodiments, the invention provides methods for determining whether fetal nucleic acid is present in a maternal sample including obtaining a maternal sample suspected to include fetal nucleic acids, and performing a sequencing reaction on the sample to determine presence of at least a portion of a Y chromosome in the sample, thereby determining that fetal nucleic acid is present in the sample. In other embodiments, the invention provides methods for quantitative or qualitative analysis to detect fetal nucleic acid in a maternal sample, regardless of the ability to detect the Y chromosome, particularly for samples including normal nucleic acids from a female fetus.

Abstract: The disclosure provides nucleotide analogs and methods of their use. Analogs of the invention comprise a reporter molecule (label) attached via the N4, N6, O4, or O6 position of the nitrogenous base portion of the analog. In a preferred embodiment, nucleotide analogs of the invention comprise a label attached to the nitrogenous base portion of the analog via a cleavable linker at the N4, O4, N6 or O6 position.

Abstract: The invention generally relates to polymerases for efficient and controlled sequencing-by-synthesis reactions. In certain embodiments, the invention provides a polymerase enzyme including at least one mutation that enhances ability of the polymerase as compared to a wild-type polymerase to incorporate a nucleotide into a nascent strand of DNA or cDNA including at least one modified nucleotide.

Abstract: The invention provides nucleotide analogs and methods of using them in sequencing reactions.

Abstract: The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.

Abstract: Methods are described which enable higher signal/noise when performing surface measurements at the single molecule level. Methods are particularly useful in the field of molecular biology when performing single molecule nucleic acid sequencing by synthesis using dye labeled nucleotides. The method employs using a competitor molecule which blocks nonspecific binding of analog molecules to the surface.

Abstract: The invention provides methods and compositions for sequencing DNA or RNA samples that would be impossible to do via standard means. Samples that are part of mixtures or are degraded or modified may be sequenced so that the individual from whom the sample originated can be determined or useful biological information can be associated with the sample. Methods are described that allow high efficiency sequencing of degraded nucleic acid samples such as are typically found with FFPE. Samples from severely degraded sources or that have been treated with preservatives such as formalin may be sequenced. In addition to permitting identification of samples, information about disease or treatment status may also be determined.

Abstract: A liquid storage apparatus provides a safe and easy to use device for efficiently managing liquid reagents used in a variety of laboratory equipment. The liquid storage apparatus helps reduce the likelihood of accidental sticks to laboratory personnel, allows for flexibility of experimental design, and helps maximize the use of chemical regents to prevent waste. The apparatus includes a plurality of containers of liquid with a pierceable septum interface at each end. The apparatus also includes a lower array of needles with each of the lower needles in the lower array of needles arranged to penetrate the bottom pierceable septum of a different one of the containers. Each of the needles includes a passage so the liquid can flow out of the pierced container. The apparatus further includes an upper array of needles with each of the upper needles in the upper array of needles arranged to penetrate the top pierceable septum of a different one of the containers.

Abstract: The invention provides methods for stabilizing a nucleic acid sequencing reaction. Generally, methods of the invention include exposing a target nucleic acid to a single-stranded nucleic acid binding protein and performing a sequencing reaction.

Abstract: Methods and kits for selective preparing cDNA relatively free of sequences found in rRNA and subcellular RNAs are disclosed. The methods and kits utilize approximately 200 hexamer sequences which target messenger RNA. The methods and kits are useful in preparing samples for sequencing analysis, especially when performing single molecule sequencing by synthesis.

Abstract: The invention provides methods and devices for detecting, enumerating or identifying target nucleic acid molecules using immobilized capture probes and single molecule sequencing techniques.

Abstract: Methods for preparing fragments for nucleic acids sequence analysis that demonstrates uniform coverage across the full fragment length. The methods disclosed herein are useful for candidate gene re-sequencing wherein the detailed analysis is performed on selected, amplified regions of the genome.

Abstract: The present invention relates to apparatus, systems, and methods for analyzing biological samples. The apparatus, systems, and methods can involve using a vacuum source to pull microfluidic volumes through analytical equipment, such as flow cells and the like. Additionally, the invention involves using optical equipment in conjunction with the analytical equipment to analyze samples and control the operation thereof.

Abstract: The disclosure provides nucleotide analogs and methods of their use. Analogs of the invention comprise a reporter molecule (label) attached via the N4, N6, O4, or O6 position of the nitrogenous base portion of the analog. In a preferred embodiment, nucleotide analogs of the invention comprise a label attached to the nitrogenous base portion of the analog via a cleavable linker at the N4, O4, N6 or O6 position.

Abstract: The invention provides methods and devices for detecting, enumerating or identifying target nucleic acid molecules using immobilized capture probes and single molecule sequencing techniques.