Abstract: In certain aspects of the present disclosure, a computer-implemented method includes receiving a 3D imaging of a heart valve in a pre-operative state. The method includes generating a segmented heart valve by segmenting the heart valve of the 3D imaging. The method includes simulating a surgical procedure on the parameterized heart valve. The method includes determining at least one post-operative outcome based on simulating the surgical procedure on the parameterized heart valve. Systems and machine-readable media are also provided.

Abstract: Described herein are various systems, methods, and apparatus for identifying biomarkers for detection of a disease or condition such as advanced adenoma, colorectal cancer, or other cancers. In certain embodiments, the present invention relates to methods and/or systems for identifying one or more biomarkers related to methylation status in cell-free deoxyribonucleic acid (DNA) of a human subject and/or detecting (e.g., screening for) cancer based on one or more known biomarkers (e.g., the identified biomarkers).

Abstract: The disclosed technology generally relates to storing data, and more particularly relates to a method of storing data in a polymer, where the data comprises a sequence of bits. In one aspect, the method comprises receiving a sequence of bits to be stored and providing a group of different homo-bifunctional monomers. Each homo-bifunctional monomer comprises a core structure having identical functional groups attached at two different positions of the core structure. The group of different homo-bifunctional monomers comprises homo-bifunctional monomers having at least two different core structures. The method further comprises linking the different homo-bifunctional monomers together to form the polymer having a sequence of monomer core structures representing the sequence of bits to be stored. The different homo-bifunctional monomers are linked together using a click chemistry reaction between the functional groups of the different homo-bifunctional monomers.

Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for genotyping repeat sequences such as medically significant short tandem repeats (STRs). The methods involve aligning reads to a repeat sequence represented by a sequence graph, and using the aligned reads to genotype the repeat sequence. The sequence graph is a directed graph each including at least one self-loop representing a repeat sub-sequence. In some implementations, the reads are paired end reads, and both mates of each read pair may be used to genotype the repeat sequences. Some implementations can be used to determine degenerate codon repeats. Some implementations can be used to genotype repeat sequences each including two or more repeat sub-sequences. Some implementations can be used to genotype nucleic acid sequences each including at least one repeat sub-sequence and another genetic variant such as an insertion, deletion, or substitution.

Abstract: Computer implemented methods and computer systems are provided for estimating cancer cell fractions indicating proportions of cancer cells carrying one or more mutations of interest using one or more nucleic acid samples from a subject. The methods and systems provided herein implement processes that use a variational Bayesian mixture model to cluster initial cancer cell fractions and obtain the one or more final cancer cell fractions, the initial cancer cell fractions accounting for cancer purity and copy numbers. The disclosed methods and systems improve accuracy, validity, and reliability of tests for cancer clonality, and save time, materials, cost, and computer resources required for the tests, which can help design more affective cancer treatments.

Abstract: The current document discusses a detection system comprising a mechanical-change sensor that exhibits one or more mechanical changes when specifically interacting with entities within a target, each entity having a type, a mechanical-change-to-signal transducer that transduces the one or more mechanical changes into a signal, and an analysis subsystem that determines the types of entities within the target using the signal.

Abstract: The present invention relates to a method of diagnosing over active bladder disorder (OAB), the method comprising: measuring the concentrations of adenosine triphosphate (ATP), acetylcholine (ACh), nitrite, monocyte chemoattractant protein 1 (MCP-1) and interleukin 5 (IL-5) in a sample obtained from a subject; normalising the concentrations to the concentration of creatinine (Cr) in the sample; range standardising the normalised concentrations and subject's age to the following values: Age to 120 years old; ATP/Cr to 0.000001 mole/mg×dl?1; ACh/Cr to 0.1 mole/mg×dl?1; Nitrite to 200 nM/mg×dl?1; MCP-1/Cr to 100 pg×ml?1/mg×dl?1; IL-5/Cr 100 pg×ml-mg×dl?1; applying the normalised and range standardised concentrations to the following formula: Logit (p)=?1.738±1.404±4.985±2.914×subject's age+3315.959±5435.254×[ATP]/[Cr]+(?25204.194±20268.337)×[ACh]/[Cr]+26.799±32.967×[nitrite]/[Cr]+6.755±25.132 [MCP-1]/[Cr]+(?61.838±148.

Abstract: A command center includes at least one network communications interface configured for two-way communications with a plurality of sites remote from the command center and at least one display screen and user interface. Each of the plurality of sites includes at least one forensic field test device configured to identify individuals using DNA samples from the individuals. The display screen and user interface are configured to depict aspects of forensic field test devices of the plurality of sites, wherein the aspects include a site identifier for each of the forensic field test devices and one or more additional aspects.

Abstract: The present disclosure provides methods of identifying unreliable biological samples that may be mislabeled or contaminated, by determining the heteroplasmy and homoplasmy of mitochondrial DNA present in the biological samples.

Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.

Abstract: A method for prioritizing sequencing of nucleic acid molecules from two or more sources, comprising: (i) ligating one or more ends of each of a plurality of nucleic acid molecules to an adapter, wherein the adaptor is unique to each source and comprises a unique identifier nucleic acid sequence; (ii) pooling the nucleic acid molecules from each of the two or more sources; (iii) sequencing a plurality of nucleotides of an identifier nucleic acid sequence of an adapter; (iv) determining in real-time from which of the two or more sources the nucleic acid molecule being sequenced came; (v) determining, from a prioritization rule set and based on the determined source, a sequencing priority for the nucleic acid molecule; and (vi) allowing the sequencing process to proceed, or modifying the sequencing process, based on the determined sequencing priority.

Abstract: Provided herein are systems and methods for quantitating the HLA diversity in a solid tissue or circulating tumor DNA sample that is predictive of a patient's responsiveness to immune checkpoint inhibitory therapies.

Abstract: The present invention discloses a method of constructing a pharmacophore to determine whether a molecule is a peroxisome proliferator-activated receptor ? full agonist, partial agonist or antagonist in terms of a binding energy or a free energy surface comprising: providing a protein receptor mimicking said peroxisome proliferator-activated receptor ? and a corresponding ligand; docking the corresponding ligand and the protein receptor to form a docked conformation; performing at least two rounds of molecular dynamic simulation to obtain at least one trajectory and at least one free energy surface; inputting the trajectory to construct at least one pharmacophore and obtaining the binding energy of the corresponding ligand; comparing the molecule with the corresponding ligand in terms of the binding energy thereof to the protein receptor in order to determine whether the molecule is the peroxisome proliferator-activated receptor ? full agonist, partial agonist or antagonist.

Abstract: The present invention relates to the field of noninvasive prenatal gene testing by high-through sequencing technologies. Particularly, the present application relates to a method for determining the content of cell-free fetal DNA in maternal peripheral blood.

Abstract: A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.

Abstract: Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining a set of sequence reads. The sequence reads each include a single molecule barcode (SMB) sequence that is a non-random oligonucleotide sequence. The method further includes assigning the sequence reads to read groups according to a read group signature. The read group signature comprises an SMB sequence and a start and end position of a nucleic acid fragment from the circulating cell free sample nucleic acid. The sequence reads comprising start and end positions and an SMB sequence similar to the read group signature are assigned to a read group. The method further includes generating a consensus for each read group, and determining the presence or absence of a genetic alteration based on the consensus for each read group.

Abstract: Methods, systems and compositions that allow for treating a patient according to a patient customized therapeutic regimen are provided. Embodiments of the invention include obtaining dosage administration information from a patient and using the same to tailor a therapeutic regimen for the patient. Embodiments of the invention further include preparing and forwarding to the patient physical pharmaceutical dosages based on the customized therapeutic regimen.

Abstract: Disclosed herein are methods, systems, and apparatus for detecting microamplifications or microdeletions in the genome of a fetus. In some embodiments, the method comprises receiving sequence tags for each of a plurality of DNA fragments in a biological sample; determining genomic positions for the sequence tags; determining whether the density of DNA in each of a plurality of genomic regions is aberrantly high or low; identifying as a microamplification a set of consecutive genomic regions having aberrantly high density; and identifying as a microdeletion a set of consecutive genomic regions having aberrantly low density. The biological sample may be a blood sample obtained noninvasively from a female subject pregnant with the fetus.

Abstract: A method for storage of an item of information (210) is disclosed. The method comprises encoding bytes (720) in the item of information (210), and representing using a schema the encoded bytes by a DNA nucleotide to produce a DNA sequence (230). The DNA sequence (230) is broken into a plurality of overlapping DNA segments (240) and indexing information (250) added to the plurality of DNA segments. Finally, the plurality of DNA segments (240) is synthesized (790) and stored (795).

Abstract: Provided are methods of treating a patient diagnosed with Fabry disease and methods of enhancing ?-galactosidase A in a patient diagnosed with or suspected of having Fabry disease. Certain methods comprise administering to a patient a therapeutically effective dose of a pharmacological chaperone for ?-galactosidase A, wherein the patient has a mutation in the nucleic acid sequence encoding ?-galactosidase A. Also described are uses of pharmacological chaperones for the treatment of Fabry disease and compositions for use in the treatment of Fabry disease.