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: 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: The invention generally relates to methods for determining carrier status with respect to a condition or disease. In certain embodiments, the method involves exposing a sample to a plurality of molecular inversion probes capable of capturing DNA from at least one genomic region suspected of having an altered copy number and at least one internal control DNA known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the molecular inversion probes, and determining a copy number state of the at least one genomic region based on the sequence results.

Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.

Abstract: The invention generally relates to devices and systems for individually barcoding sample vessels. In certain embodiments, the devices comprise an attachment member and an extension member, where the extension member can accommodate an identifier, such as a barcode. When loaded into a substrate, the barcoded vials are scanned by a barcode reader.

Abstract: The present disclosure describes a method of processing a biological sample. The method includes contacting the sample with a pH indicator that changes color in response to changes in pH. The presence of a pH indicator such as cresol red provides the benefit of improved visualization of the sample, verification that the sample is properly frozen and thawed, and increased precision in pH adjustments during the assay, among other benefits.

Abstract: The invention relates to carrier screening and methods for describing a structural variant, such as a large rearrangement or chromosomal abnormality, in a person's genome using probes that are designed to determine the person's genetic sequence and reveal substitution mutations and small structural variants. Identifying a structural variant may include exposing a nucleic acid to a plurality of probes. Each probe has a linked pair of targeting arms designed to hybridize upstream and downstream of a target in a genome. The method includes hybridizing two of the probes to the nucleic acid and attaching the two probes together to create an inter-probe product as well as detecting the inter-probe product and reporting a structural variant of the genome in the nucleic acid.

Abstract: The invention generally relates to devices and systems for individually barcoding sample vessels. In certain embodiments, the devices comprise an attachment member and an extension member, where the extension member can accommodate an identifier, such as a barcode. When loaded into a substrate, the barcoded vials are scanned by a barcode reader.

Abstract: The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.

Abstract: The invention generally relates to methods for analyzing nucleic acids. In certain aspects, methods of the invention involve obtaining a sample including a nucleic acid template. A plurality of molecular inversion probes are tiled across a portion of the template. The probes are designed such that immediately adjacent probes hybridize to opposite strands of the nucleic acid template and probes on the same strand hybridize to the template in an overlapping manner. A region between targeting arms of a plurality of the molecular inversion probes is filled-in with nucleotides, and the filled-in region of a plurality of the probes is analyzed to obtain sequence information about the nucleic acid template.

Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.

Abstract: The invention provides a system and method for describing polymorphisms or genetic variants based on information about mutations and relationships among them. The invention uses object-oriented concepts to describe variants as variant objects and relations among those variants as variant relation object, each object being an instance of an abstract class of genomic feature and able to contain any number of other objects. Information about genetic disorders is stored in association with the object that represents the pathogenic variant. Genetic test results are used to access corresponding objects to provide a report based on variants or polymorphisms in a patient's genetic material.

Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.

Abstract: The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.

Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.

Abstract: The invention generally relates to methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. In certain embodiments, methods of the invention involve obtaining a template nucleic acid, incorporating a pair of sequence identifiers into the template, and sequencing the template.

Abstract: The invention generally relates to methods for analyzing nucleic acids. In certain aspects, methods of the invention involve obtaining a sample including a nucleic acid template. A plurality of molecular inversion probes are tiled across a portion of the template. The probes are designed such that immediately adjacent probes hybridize to opposite strands of the nucleic acid template and probes on the same strand hybridize to the template in an overlapping manner. A region between targeting arms of a plurality of the molecular inversion probes is filled-in with nucleotides, and the filled-in region of a plurality of the probes is analyzed to obtain sequence information about the nucleic acid template.

Abstract: The invention generally relates to methods for determining carrier status with respect to a condition or disease. In certain embodiments, the method involves exposing a sample to a plurality of molecular inversion probes capable of capturing DNA from at least one genomic region suspected of having an altered copy number and at least one internal control DNA known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the molecular inversion probes, and determining a copy number state of the at least one genomic region based on the sequence results.

Abstract: The invention generally relates to methods for determining carrier status with respect to a condition or disease. In certain embodiments, the method involves exposing a sample to a plurality of molecular inversion probes capable of capturing DNA from at least one genomic region suspected of having an altered copy number and at least one internal control DNA known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the molecular inversion probes, and determining a copy number state of the at least one genomic region based on the sequence results.