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 disclosure relates to biomarkers predictive of a patient's cancer responsiveness to an immune checkpoint inhibitor therapy. The disclosure provides, in some embodiments, diagnostic and/or prognostic methods of using such biomarkers for determining whether a cancer patient would benefit from being treated with an aryl hydrocarbon receptor antagonist. In some embodiments, the biomarkers described herein may be used to inform and provide effective therapeutic methods for treating cancer comprising administering an aryl hydrocarbon receptor antagonist, optionally in combination with an immune checkpoint inhibitor therapy.

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 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 negative selection of nucleic acids. The invention provides methods and systems that remove unwanted segments of nucleic acid in a sample so that a target gene or region of interest may be analyzed without interference from the unwanted segments. A sample is obtained that includes single-stranded nucleic acid with one or more unwanted segments. Complementary nucleic acid is added to the single-stranded nucleic acid to create a double-stranded region that includes the unwanted segment. The double-stranded region is then digested, leaving single-stranded nucleic acid that includes the target gene or region of interest. This allows paralogs, pseudogenes, repetitive elements, and other segments of the genome that may be similar to the target gene or region of interest to be removed from the sample.

Abstract: The invention generally relates to a method for determining carrier or disease status with respect to a particular disease or condition. In certain embodiments, methods of the invention involve obtaining a sample including nucleic acid from a subject. The nucleic acid includes a genomic locus that is diagnostic for an autosomal recessive disease. The nucleic acid is captured and isolated from the sample and further sequenced. The method further includes analyzing sequence reads to determine a copy number of the captured nucleic acid and further determine a disease status based upon the copy number.

Abstract: The invention generally relates to negative selection of nucleic acids. The invention provides methods and systems that remove unwanted segments of nucleic acid in a sample so that a target gene or region of interest may be analyzed without interference from the unwanted segments. A sample is obtained that includes single-stranded nucleic acid with one or more unwanted segments. Complementary nucleic acid is added to the single-stranded nucleic acid to create a double-stranded region that includes the unwanted segment. The double-stranded region is then digested, leaving single-stranded nucleic acid that includes the target gene or region of interest. This allows paralogs, pseudogenes, repetitive elements, and other segments of the genome that may be similar to the target gene or region of interest to be removed from the sample.

Abstract: The invention generally relates to a method for determining carrier or disease status with respect to a particular disease or condition. In certain embodiments, methods of the invention involve obtaining a sample including nucleic acid from a subject. The nucleic acid includes a genomic locus that is diagnostic for an autosomal recessive disease. The nucleic acid is captured and isolated from the sample and further sequenced. The method further includes analyzing sequence reads to determine a copy number of the captured nucleic acid and further determine a disease status based upon the copy number.

Abstract: The invention generally relates to method for assessing a genomic region of a subject. In certain embodiments, methods of the invention involve obtaining a sample including nucleic acid from a subject. The nucleic acid includes a target sequence from a target genomic region and a paralogous sequence from a non-target genomic region. The target sequence and the paralogous sequence are isolated from the sample. The target sequence and the paralogous sequence are sequenced to obtain sequence reads that include target sequence reads and paralogous sequence reads. The paralogous sequence reads are excluded, and the genomic region of the subject are assessed based on the target sequence reads.

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 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 method for assessing a genomic region of a subject. In certain embodiments, methods of the invention involve obtaining a sample including nucleic acid from a subject. The nucleic acid includes a target sequence from a target genomic region and a paralogous sequence from a non-target genomic region. The target sequence and the paralogous sequence are isolated from the sample. The target sequence and the paralogous sequence are sequenced to obtain sequence reads that include target sequence reads and paralogous sequence reads. The paralogous sequence reads are excluded, and the genomic region of the subject are assessed based on the target sequence reads.

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 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 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 of performing a capture reaction. In certain embodiments, the method involves obtaining a nucleic acid, fragmenting the nucleic acid, and capturing a target sequence on the nucleic acid fragment using a capture moiety, such as a molecular inversion probe.

Abstract: The present invention provides methods for validating results of a pre-implantation genetic screen. Methods of the invention increase the efficacy of the common PGS assay FAST-SeqS by taking advantage of single-nucleotide polymorphisms (SNPs) generated from the assay to confirm copy number calls, detect errors, identify samples, and recognize and identify sources of contamination. Methods of the invention increase the reliability of a PGS result, thereby making embryo selection more precise and improving outcomes of in vitro fertilization.

Abstract: The present invention generally relates to determining the clinical significance of a variant nucleic acid sequence. The invention can involve sequencing a nucleic acid to generate at least one sequence read, identifying a variant sequence within the sequence read, determining the equivalent insertion/deletion region (EIR) of the variant sequence, identifying a functional region including at least a portion of the EIR, and associating the EIR with the identified functional region, thereby to determine the clinical significance of the variant.

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 of performing a capture reaction. In certain embodiments, the method involves obtaining a nucleic acid, fragmenting the nucleic acid, and capturing a target sequence on the nucleic acid fragment using a capture moiety, such as a molecular inversion probe.