Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity in a plurality of first entities for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters. Differences in the discrete attribute values for the first entity across the second entities of a given cluster relative to the discrete attribute value for the same first entity across the other clusters are computed thereby deriving differential values. A heat map of these differential values for each first entity for each cluster is displayed to reveal the pattern in the dataset.

Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.

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: Techniques for construction of internal controls for improved accuracy and sensitivity of DNA testing include obtaining first data and determining weights over real numbers for a normalization function in less than a day. The first data indicates a measured amount of reference sequences for nucleic acids from training samples. The reference sequences include a target, for which an abundance is indicative of a condition of interest, and covariates not correlated with the condition of interest. The normalization function involves a sum of abundances of the covariates, as internal controls, each multiplied by a corresponding one of the weights. The weights are determined based on minimizing variance of a Taylor expansion of a ratio of a measured amount of the target divided by a value of the normalization function evaluated with measured amounts of the covariates over a portion of the first data in which the condition is absent.

Abstract: Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

Abstract: The invention encompasses methods for increasing genetic progress in livestock, and for genetic dissemination, including the use of amniocentesis to obtain fetal amniocytes for use in genomic evaluation and cloning.

Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions, including syndromes related to CNV of subchromosomal regions. In some embodiments, methods are provided for determining CNV of fetuses using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. In some embodiments, syndrome related biases in sample data are also removed to increase signal to noise ratio. Also disclosed are systems for evaluation of CNV of sequences of interest.

Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for biological samples; determining a respective plurality of molecular-functional (MF) profiles for a plurality of subjects; clustering the plurality of MF profiles to obtain MF profile clusters; determining a molecular-functional (MF) profile for an additional subject; and identifying, from among the MF profile clusters, a particular MF profile cluster with which to associate the MF profile for the subject.

Abstract: The invention discloses methods and apparatuses for the detection and diagnostics of genetic alterations/mutations in a target sample, which may be a solid tissue or a bodily fluid. A reference sample is also acquired, and the target and reference samples are replicated into multiple target and reference replicates. The replicates are sequenced, and the sequence data is analyzed based on a statistical test. The statistical test compares the measurements between the target and reference replicates at respective allelic indices. True positive calls are then made based on the results of the statistical testing, and the desired genetic alterations/mutations are identified at the base-pair level. The invention may be used for diagnostics related to cancer, auto-immune disease, organ transplant rejection, genetic fetal abnormalities and pathogens.

Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.

Abstract: A method of estimating a parameter related to sequencing of a sample nucleic acid template includes: receiving signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells; determining sequence information for the sample nucleic acid template using signal data from the first well; and constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells.

Abstract: Methods are described herein for small molecule biochemical profiling of an individual subject for diagnosis of a disease or disorder, facilitating diagnosis of a disease or disorder, and/or identifying an increased risk of developing a disease or disorder in the individual subject. Aberrant levels of small molecules present in a sample from an individual subject are identified and diagnostic information relevant to the individual subject is obtained based on the identified aberrant levels. The obtained diagnostic information includes one or more of an identification of at least one biochemical pathway associated with the identified subset of the small molecules having aberrant levels, an identification at least one disease or disorder associated with the identified subset of the small molecules having aberrant levels, and an identification of at least one recommended follow up test associated with the identified subset of the small molecules having aberrant levels.

Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.

Abstract: Methods, system and device are provided for detection and quantitative and qualitative analysis of components in a gaseous mixture distinguished by high selectivity and high resolution. The influence of individual gases may be distinguished through detection of changes associated with a sensor's sensitive layer that interacts with the components of the gaseous mixture. Through periodic variations of parameters or conditions of the sensor, the characteristics of the gas components may be derived. For example, the concentration of a gas or multiple gases in a mixture may be determined with a high degree of accuracy. Non-invasive detection of biological off-gases may be implemented. Other uses abound.

Abstract: The present invention provides a computer program for determining the optimum diet of an animal, determining what nutritional deficiencies exist in that diet, and formulating a supplement to correct those deficiencies. It allows the creation of a nutritionally complete and balanced diet with a sufficient but not excessive quantity of water, energy, protein, fat, carbohydrate, amino acids, fatty acids, vitamins, minerals, and vitamin-like nutrients. The specific compositions of supplements generated using the computer program are also claimed.

Abstract: Provided herein are methods, processes and apparatuses for determining the fraction of fetal nucleic acid in a test sample derived from a pregnant female with improved accuracy and/or precision. Also, provided herein are methods, processes and apparatuses for determining the presence or absence of a genetic variation in a fetus with improved accuracy and/or precision. Certain methods include using fetal fraction measurements for the determination of a fetal genetic variation.

Abstract: The present invention relates to a new diagnosis method in the field of hepatology, combining measurement of serum markers and of liver elasticity.

Abstract: Contemplated systems and methods integrate genomic/exomic data with transcriptomic data by correlating a cancer associated mutation in the genome/exome with the transcription level of the affected gene carrying the mutation, particularly where the mutation is a 3-terminal nonsense mutation.

Abstract: A determination device for enabling a computer to carry out a process including the steps of: obtaining an analysis result on methylation status of a CpG site located in a promoter region of at least one gene selected from HOXB4 (Homeobox B4) and ZSCAN31 (zinc finger and SCAN domain containing 31) in a DNA sample derived from a subject; and outputting a determination result as information on lung cancer in the subject based on the resulting analysis result is provided. A computer readable medium and a marker for obtaining information on lung cancer are also provided.

Abstract: A genetic surveillance system comprises a communications network and at least one reader-analyzer instrument. The reader-analyzer instrument has a communication interface to communicate over the network. The reader-analyzer instrument is adapted to perform genetic assay analysis of a sample obtained from a member of a population and to generate detection-related data based upon the analysis. The reader-analyzer instrument is adapted to associate qualifying information with the detection-related data and to communicate the associated qualifying information and detection-related data over the network.