Methods for determining the presence or absence of expansion of CGG repeat sequence in the FMR1 gene presence or absence of expansion of CCG repeat sequence in the FMR2 gene are provided. The methods are useful in identifying an individual with normal/intermediate, versus premutation or full mutation allele of FMR1 gene and FMR2 gene due to the expansion of CGG repeats and CCG repeats in the 5′-untranslated region respectively. The methods are also useful for screening newborns for fragile X syndrome or for screening women to determine heterozygosity status with full premutation of the CCG repeat tract. The methods are also useful in estimating the premutation and full mutation carrier frequency and estimating the prevalence of FXTAS AND FXPOI in a population. The methods are simple, rapid and require small amount of sample.

The present disclosure provides methods and systems for personalized genetic testing of disease in a subject, in particular for identifying and tracking genetic mutations identified in an individual subject to monitor for cancer or for the spread or recurrence of the disease. In some embodiments, custom assays, including custom panels designed to target sequence data corresponding to both subject-specific loci and other loci known for cancer-causing or therapy resistance mutations, are designed based upon the sequencing of a screening biopsy sample. Such custom assays are then run on subsequently obtained tissue samples, such as tissue obtained from a surgical resection of a primary or metastatic tumor or from a lymph node biopsy. The subsequently obtained tissue samples can be taken from the subject at various time points after an initial screening biopsy to further allow for extended monitoring of the subject for spread or recurrence of the disease.

This disclosure describes an efficient method to copy all polynucleotides encoding digital data of digital files in a polynucleotide storage container while maintaining random access capabilities over a collection of files or data items in the container. The disclosure further describes a process whereby random-access and sequencing of the polynucleotides are combined in a single step.

The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein are methods of designing, making, and using the cancer assay panel for the diagnosis of cancer.

Method for identifying a subset of cells from a dataset for targeted gene expression analysis, comprising: defining an expected total recovered cell count for a barcode dataset; determining a region of interest for the total recovered cell count by calculating a lower bound for the region; and (b) calculating an upper bound for the region of interest by including an additional subset of barcodes having molecule counts below the lower bound; fitting the barcode dataset to a model; wherein the model groups barcodes as a function of molecule count; identifying a cut-off value on the model, wherein all barcodes having a molecule count above the cut-off value are called as cells; and identifying a targeted subset of cells from the called cells for conducting targeted gene expression, wherein a cell qualifies as part of the targeted subset if the cell has a molecule count above a target threshold.

The present invention relates to methods for the analysis of nucleic acids present in biological samples, and more specifically to normalize a high resolution melt curve to assist in the identification of one or more properties of the nucleic acids. The present invention provides methods and systems that incorporate a background identification algorithm according to invention principles using raw melt curve data to identify reactions that are unrelated actual DNA melt reactions. Furthermore, a web-based application for analyzing experimental data is provided. The raw experimental data obtained from a variety of instruments is processed and analyzed on a server and presented to a user through a user interface (UI).

Provided herein are methods and systems allowing for real-time measurement of cellular drug-target engagement. Use of fluorescence-based cell target engagement technology with real-time gene expression machinery provides several advantages over prior systems. Integration with real-time gene expression machinery without bias to any particular design or brand is provided. Programmability of cell target engagement methodology, such that any software in real-time gene expression machine can seamlessly be used for programming is provided. Single or multiple machine integration for the use of cell target engagement technology is provided. Compatibility with multiple multi-well plate setups is provided. Development of unique modifications of real-time (quantitative) gene expression software to detect real-time cellular drug-target engagement to work efficiently with existing gene expression machinery is provided.

Provided herein are methods and systems allowing for real-time measurement of cellular drug-target engagement. Use of fluorescence-based cell target engagement technology with real-time gene expression machinery provides several advantages over prior systems. Integration with real-time gene expression machinery without bias to any particular design or brand is provided. Programmability of cell target engagement methodology, such that any software in real-time gene expression machine can seamlessly be used for programming is provided. Single or multiple machine integration for the use of cell target engagement technology is provided. Compatibility with multiple multi-well plate setups is provided. Development of unique modifications of real-time (quantitative) gene expression software to detect real-time cellular drug-target engagement to work efficiently with existing gene expression machinery is provided.

The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.

The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein are methods of designing, making, and using the cancer assay panel for the diagnosis of cancer.