Abstract: An array-based system of assembled DNA for computer data storage is described. An array surface contains immobilized seed DNA initially having with blunt (or blocked) ends with a photocleavable optical linker at a forward end thereof holding the last few base pairs. A light source is light is applied to break the linker, generating a sticky end which allows for hybridization. Data-bearing DNA cassettes are introduced to the array and attach via their sticky ends to the unblock sites on the array surface. The attachment is made permanent via ligase.

Abstract: The present invention relates to methods to detect an amount of DNA that originates from cells of a given type, where the sample comprising such DNA in admixture with DNA that does not originate from such cells. Such methods are based on differential methylation, at certain regions, of the DNA that originates from the given type of cells compared to the admixed DNA. Such methods have particular application in the detection, from a biological fluid from a pregnant female, of cell free DNA that originates from a foetus or the placenta of a foetus, or the detection, from a biological fluid from an individual, of cell free DNA that originates from cells of a tumour.

Abstract: Methods and associated apparatus involving designing a ligand ab initio that will bind to a binding site of a macromolecular target, or of identifying a modification to a ligand for improving the affinity of the ligand to a binding site of a macromolecular target, comprising using information about non-bonding, intra-molecular or inter-molecular atom to atom contacts extracted from a database of biological macromolecules to identify favoured regions adjacent to the binding site for particular atom types and modifying a candidate ligand to increase the intersection between atoms of the candidate ligand and the favoured regions. One or more steps of the methods may be performed by a computer.

Abstract: Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of copy number alterations. In particular, a method is provided for determining presence or absence of a copy number alteration for a test subject. The method includes providing a set of sequence reads. The sequence reads may be obtained from circulating cell free sample nucleic acid from a test sample obtained from the test subject, and the circulating cell free sample nucleic acid may be captured by probe oligonucleotides under hybridization conditions. The method further includes determining a probe coverage quantification of the sequence reads for the probe oligonucleotides and determining the presence or absence of a copy number alteration in the circulating cell free sample nucleic acid based on the probe coverage quantification of the sequence reads for the probe oligonucleotides for the test sample.

Abstract: Methods described herein include receiving data from flowing a plurality of aptamers over a sample of tumor cells randomly affixed to a surface of a microfluidic device. The tumor cells may include one or more unknown tumor subtypes of cells. The plurality of aptamers may include a plurality of aptamer families. Each aptamer family of the plurality of aptamer families may be determined to bind to at least one possible subtype of the tumor cells. The data may include a measure of binding affinity of each aptamer family to the tumor cells. The method may include analyzing the measure of the binding affinity of each aptamer family to the tumor cells. The analyzing may include classifying the binding affinity. The method may also include determining one or more aptamer families that characterize the one or more unknown tumor subtypes of cells based on the classifying.

Abstract: Systems and methods for communicating, storing, and/or analyzing data that may include genomic data are described herein. In various embodiments, unaligned genomic sequence read data and/or portions thereof may be stored and/or communicated as a list of variants relative to a particular reference associated with a reference motif identified in the genomic sequence read data. In further embodiments, quality score information associated with a genomic dataset may be analyzed and/or communicated as quality score parameter information. Additional embodiments may facilitate relatively efficient analysis of unaligned genomic sequence read data using metadata associated with reference motifs identified in the unaligned genomic sequence read data.

Abstract: Systems, methods, and computer-readable media are disclosed for patient-specific modeling of hemodynamic parameters in coronary arteries. Example methods may include performing computational fluid dynamics simulations using a patient-specific coronary artery anatomical model derived from medical imaging data and patient-specific boundary conditions derived from a continuously recorded blood pressure waveform to determine patient-specific hemodynamic parameters in a patient's coronary arteries.

Abstract: A method is disclosed for calculating and recalculating protein confidence values by recalculating peptide confidence values in proteomic analysis. A plurality of scans are performed of a sample that is proteolytically digested into surrogate peptide analytes. A plurality of spectra are obtained, and a plurality of peptides are identified. A protein database is searched for proteins matching peptides from the plurality of peptides. Peptide confidence values are determined for the set of peptides. A protein confidence value is calculated for each protein in the set of proteins. A protein from the set of proteins with a largest protein confidence value is selected, the largest protein confidence value for the protein is saved, the protein from the set of proteins is removed, and peptides corresponding to the protein is removed from the set of peptides. The protein confidence value is recalculated for each protein in the set of proteins.

Abstract: Systems and methods are disclosed for predicting the location, onset, or change of coronary lesions from factors like vessel geometry, physiology, and hemodynamics. One method includes: acquiring, for each of a plurality of individuals, a geometric model, blood flow characteristics, and plaque information for part of the individual's vascular system; training a machine learning algorithm based on the geometric models and blood flow characteristics for each of the plurality of individuals, and features predictive of the presence of plaque within the geometric models and blood flow characteristics of the plurality of individuals; acquiring, for a patient, a geometric model and blood flow characteristics for part of the patient's vascular system; and executing the machine learning algorithm on the patient's geometric model and blood flow characteristics to determine, based on the predictive features, plaque information of the patient for at least one point in the patient's geometric model.

Abstract: A large collection of sample genomes containing misclassified k-mers and metadata errors from a reference taxonomy was converted to a self-consistent k-mer database comprising a self-consistent taxonomy. The self-consistent taxonomy was based on genetic distances calculated using the MinHash method or the Meier-Koltoff method. An agglomerative clustering algorithm was used to calculate the self-consistent taxonomy. Each k-mer of the sample genomes was assigned to only one node of the self-consistent taxonomy. In another step, each node of the self-consistent taxonomy was mapped to the reference taxonomy, thereby preserving in the self-consistent taxonomy links to the reference taxonomy while correcting for the misclassification errors therein. The self-consistent k-mer database can be used to taxonomically profile sequenced nucleic acids with greater specificity compared to systems relying on the reference taxonomy.

Abstract: Systems and methods for multi-dimensional mapping of binary data DNA sequences are described. In one embodiment, the method may include determining a current level of a first DNA base from a sequence of DNA bases based at least in part on a read process of the sequence, determining a current level of a second DNA base after the first DNA base and a current level of a third DNA base after the second DNA base, and decoding binary data from the sequence based at least in part on the determined current level of the first DNA base, the determined current level of the second DNA base, and/or the determined current level of the third DNA base.

Abstract: Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.

Abstract: The invention provides biomarkers and combinations of biomarkers useful in diagnosing non-small cell lung cancer. Measurements of these biomarkers are inputted into a classification system such as Random Forest to assist in determining the likelihood that an individual has non-small cell lung cancer. Kits comprising agents for detecting the biomarkers and combination of biomarkers, as well as systems that assist in diagnosing non-small cell lung cancer are also provided.

Abstract: Among other things, motility of at least one individual microorganism or a change in motility of at least one individual microorganism or both is or are characterized. The characterized motility or change in motility is used to detect the presence or count of the at least one individual microorganism, or determine the identity of a species or strain of the at least one individual microorganism, or determine a susceptibility of the at least one individual microorganism to one or more antibiotics or other antimicrobials.

Abstract: [PROBLEM] It is an object to provide a biological tissue fabrication information generating device that generates biological tissue fabrication information for fabrication of tissue imitative of the structure of the biological tissue of a patient, a biological tissue fabrication system that fabricates biological tissue based on biological tissue fabrication information, and a medical expense calculation system that calculates the medical expense of a patient receiving therapeutic graft of biological tissue.

Abstract: Disclosed herein are methods in which an individual with multiple sclerosis (MS) can be classified into one of six subject groups, each subject group predictive for the patient's responsiveness to an interferon-? (IFN-?) therapy. The individual with MS can be classified according to the individual's serum marker levels, e.g., at baseline or following treatment with therapy. Depending on the classification, the individual with MS can be treated with standard therapies (e.g. IFN-?) or one or more alternative therapies with or without IFN-?.

Abstract: Embodiments include methods and systems for determining a sensitivity of a patient's blood flow characteristic to anatomical or geometrical uncertainty. For each of one or more of individuals, a sensitivity of a blood flow characteristic may be obtained for one or more uncertain parameters. An algorithm may be trained based on the sensitivities of the blood flow characteristic and one or more of the uncertain parameters for each of the plurality of individuals. A geometric model, a blood flow characteristic, and one or more of the uncertain parameters of at least part of the patient's vascular system may be obtained for a patient. The sensitivity of the patient's blood flow characteristic to one or more of the uncertain parameters may be calculated by executing the algorithm on the blood flow characteristic of at least part of the patient's vascular system, and one or more of the uncertain parameters.

Abstract: A system and method for determining the exact pair of alleles corresponding to polymorphic genes from sequencing data and for using the polymorphic gene information in formulating an immunogenic composition. Reads from a sequencing data set mapping to the target polymorphic genes in a canonical reference genome sequence, and reads mapping within a defined threshold of the target gene sequence locations are extracted from the sequencing data set. Additionally, all reads from the set data set are matched against a probe reference set, and those reads that match with a high degree of similarity are extracted. Either one, or a union of both these sets of extracted reads are included in a final extracted set for further analysis. Ethnicity of the individual may be inferred based on the available sequencing data which may then serve as a basis for assigning prior probabilities to the allele variants. The extracted reads are aligned to a gene reference set of all known allele variants.

Abstract: A system and method are provided for training and using a machine learning model to analyze hematoxylin and eosin (H&E) slide images, where the machine learning model is trained using a training data set comprising a plurality of unmarked H&E images and a plurality of marked H&E images, each marked H&E image being associated with one unmarked H&E image and each marked H&E image including a location of one or more molecules determined by analyzing a multiplex IHC image having at least two IHC stains, each IHC stain having a unique color and a unique target molecule. Predicted molecules and locations identified with the machine learning model result in an immunotherapy response class being assigned to the H&E slide image.

Abstract: Contemplated cancer treatments comprise recursive analysis of patient-, cancer-, and location-specific neoepitopes from various biopsy sites of a patient after treatment or between successive rounds of immunotherapy and/or chemotherapy to inform further immunotherapy. Recursive analysis preferably includes various neoepitope attributes to so identify treatment relevant neoepitopes.