The present disclosure provides, in some aspects, nucleic acid-based molecular tools that enable the recording of molecular structure and soluble signals as well as the programmed assembly of molecular structures.

Methods for detecting cancer that include hybridizing a set of chromosomal probes to a biological sample obtained from a patient, and identifying if aneusomic cells are present in a selected subset of cells obtained from the biological sample are described. A set of chromosomal probes and kits for detecting cancer that include sets of chromosomal probes, are also described.

Provided herein are compositions and methods for isolating cell-free nucleic acid, e.g., cell-free DNA, from a sample. In particular embodiments, provided herein are compositions and methods using anti-dsDNA antibodies for isolating cell-free DNA from a sample, and for providing a sample of isolated cell-free DNA, e.g., for a nucleic acid assay. In particular embodiments, the technology relates to providing cell-free DNA from a maternal sample that is enriched for fetal cell-free fetal DNA.

Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter. In some implementations, information from fragments of different sizes are used to evaluate copy number variations. In some implementations, one or more t-statistics obtained from coverage information of the sequence of interest is used to evaluate copy number variations. In some implementations, one or more fetal fraction estimates are combined with one or more t-statistics to determine copy number variations.

Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter. In some implementations, information from fragments of different sizes are used to evaluate copy number variations. In some implementations, one or more t-statistics obtained from coverage information of the sequence of interest is used to evaluate copy number variations. In some implementations, one or more fetal fraction estimates are combined with one or more t-statistics to determine copy number variations.

Provided herein is the use of measurements of cell-free DNA, protein, and/or metabolite found in biofluid (e.g., urine) for identifying and treating organ injury. Provided herein are methods and compositions for monitoring, detecting, quantifying, and treating kidney injury in subjects suffering from or suspected of having an altered renal status by measuring amounts of cfDNA and one or more other markers, such as inflammation markers, apoptosis markers, protein, and DNA methylation.

Provided herein is the use of measurements of cell-free DNA, protein, and/or metabolite found in biofluid (e.g., urine) for identifying and treating organ injury. Provided herein are methods and compositions for monitoring, detecting, quantifying, and treating kidney injury in subjects suffering from or suspected of having an altered renal status by measuring amounts of cfDNA and one or more other markers, such as inflammation markers, apoptosis markers, protein, and DNA methylation.

A high throughput method for detecting chromosomal aberrations and/or telomere aberrations using a biological sample of 150 μL to 200 μL including preparing a cytogenetic slide from the sample in a microplate, the mitotic index in the cytogenetic slide being 3 times higher on average than the conventional procedure of culturing cells in flasks with 10 to 20 mL of medium, simultaneously labeling the telomeres and centromeres with peptide nucleic acid probes with a hybridisation time from 30 minutes to 1.5 hours, flow image quantifying the fluorescence intensity of telomeres on interphase nuclei using a 10× magnification objective for overall telomere quantification, and automatically capturing the metaphase chromosomes to detect chromosomal aberrations and/or telomere aberrations in each chromosome. Also a high-throughput detection kit for quantifying telomeres and detecting chromosomal aberrations and/or telomere aberrations.

A high throughput method for detecting chromosomal aberrations and/or telomere aberrations using a biological sample of 150 μL to 200 μL including preparing a cytogenetic slide from the sample in a microplate, the mitotic index in the cytogenetic slide being 3 times higher on average than the conventional procedure of culturing cells in flasks with 10 to 20 mL of medium, simultaneously labeling the telomeres and centromeres with peptide nucleic acid probes with a hybridisation time from 30 minutes to 1.5 hours, flow image quantifying the fluorescence intensity of telomeres on interphase nuclei using a 10× magnification objective for overall telomere quantification, and automatically capturing the metaphase chromosomes to detect chromosomal aberrations and/or telomere aberrations in each chromosome. Also a high-throughput detection kit for quantifying telomeres and detecting chromosomal aberrations and/or telomere aberrations.

The present invention relates to a method for determining the statistical noise level in the calculation of a subject's genetic copy number value in massively parallel nucleic acid sequencing data derived from a sample, as well as a method for determining a subject's genetic copy number value in massively parallel nucleic acid sequencing data derived from a sample and a method to determine a subject's genetic copy number value for stratifying the subject for cancer therapy.