The present disclosure provides methods of determining the susceptibility of a dog to liver copper accumulation, comprising detecting in a biological sample obtained from the dog the presence or absence in the genome of the dog of one or more polymorphisms, and methods of treating or breeding the dog based on such determination.

The present invention relates to methods of screening in vitro fertilization (IVF) embryos for pathogenic genetic variations, such as single nucleotide polymorphisms. In particular, the present invention relates to methods of screening IVF embryos using whole genome sequencing (WGS) data. The present invention also relates to methods of screening in vitro fertilization (IVF) embryos for phenotypic traits.

The present invention relates to methods of screening in vitro fertilization (IVF) embryos for pathogenic genetic variations, such as single nucleotide polymorphisms. In particular, the present invention relates to methods of screening IVF embryos using whole genome sequencing (WGS) data. The present invention also relates to methods of screening in vitro fertilization (IVF) embryos for phenotypic traits.

The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Embodiments of a method and/or system can include generating a co-amplified mixture based on co-amplifying a set of nucleic acid molecules (e.g., cell-free nucleic acids, etc.) from the biological sample, wherein the set of nucleic acid molecules includes a genomic region of interest associated with the medical condition; and a homologous native genomic region with partial sequence similarity to the genomic region of interest; sequencing the co-amplified mixture; determining an abundance metric for the genomic region of interest and an abundance metric for the homologous native genomic region; and/or facilitating the characterization of the medical condition based on the abundance metric for the genomic region of interest and the abundance metric for the homologous native genomic region.

Embodiments of a method and/or system can include generating a co-amplified mixture based on co-amplifying a set of nucleic acid molecules (e.g., cell-free nucleic acids, etc.) from the biological sample, wherein the set of nucleic acid molecules includes a genomic region of interest associated with the medical condition; and a homologous native genomic region with partial sequence similarity to the genomic region of interest; sequencing the co-amplified mixture; determining an abundance metric for the genomic region of interest and an abundance metric for the homologous native genomic region; and/or facilitating the characterization of the medical condition based on the abundance metric for the genomic region of interest and the abundance metric for the homologous native genomic region.

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genomic nucleic acid instability and genomic nucleic acid stability. The method comprises providing a set of genomic portions each coupled to a copy number alteration quantification for a test sample, wherein the genomic portions comprises portions of a reference genome to which sequence reads obtained for nucleic acid from a test sample obtained from the subject have been mapped, and the copy number alteration quantification coupled to each genomic portion has been determined from a quantification of sequence reads mapped to the genomic portion; and determining, by a computing device, presence or absence of genomic instability for the subject according to the copy number alteration quantifications coupled to the genomic portions.

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genomic nucleic acid instability and genomic nucleic acid stability. The method comprises providing a set of genomic portions each coupled to a copy number alteration quantification for a test sample, wherein the genomic portions comprises portions of a reference genome to which sequence reads obtained for nucleic acid from a test sample obtained from the subject have been mapped, and the copy number alteration quantification coupled to each genomic portion has been determined from a quantification of sequence reads mapped to the genomic portion; and determining, by a computing device, presence or absence of genomic instability for the subject according to the copy number alteration quantifications coupled to the genomic portions.

A kit for use in an apparatus for a genetic screening, where the kit when in operation, performs a wet-lab assay. The assay includes processing genetic material that is derived from one or more cell exomes, and detecting single nucleotide variants (SNVs), indels and copy number variations (CNVs) in genetic DNA readout from genetic material. The kit is executable as single assay that processes the genetic material. The kit includes a software product that is executable on a computing hardware to cause the computing hardware to invoke algorithms to process the genetic DNA readout by comparing portions of the genetic DNA readout against DNA sequence transcripts, to determine a probability of occurrence of the DNA sequence transcripts in the DNA readout data. The algorithms are used to detect both SNVs and CNVs concurrently in the genetic DNA readout from the genetic material and annotate clinically relevant CNVs.

A kit for use in an apparatus for a genetic screening, where the kit when in operation, performs a wet-lab assay. The assay includes processing genetic material that is derived from one or more cell exomes, and detecting single nucleotide variants (SNVs), indels and copy number variations (CNVs) in genetic DNA readout from genetic material. The kit is executable as single assay that processes the genetic material. The kit includes a software product that is executable on a computing hardware to cause the computing hardware to invoke algorithms to process the genetic DNA readout by comparing portions of the genetic DNA readout against DNA sequence transcripts, to determine a probability of occurrence of the DNA sequence transcripts in the DNA readout data. The algorithms are used to detect both SNVs and CNVs concurrently in the genetic DNA readout from the genetic material and annotate clinically relevant CNVs.