The present invention relates to methods of detecting differentially expressed protein expression indicative of COPD in a test sample. The detection of circulating levels of proteins within an identified COPD biomarker signature can aid in COPD diagnosis and disease monitoring, as well as in the prediction of responses to therapeutics. Evaluation of the biomarker signatures disclosed, or a subset of biomarkers thereof, provides a level of discrimination not found with individual markers.

The lack of clear predictors of prostate cancer progression leads to subjective decision-making regarding courses of treatment. The identification of new biomarkers that are predictive of recurrence after radical prostatectomy would advance the field of prostate cancer treatment. Disclosed are miRNAs that can be used as molecular biomarkers to detect or predict the progression of prostate cancer and to adjust a treatment plan accordingly. Furthermore, kits are included for the detection of these miRNAs.

A log of molecular events experienced by a cell and timing indicators for those events are stored in existing polynucleotides through a process of creating a double strand break (“DSB”) in a polynucleotide and inserting a new polynucleotide sequence by repairing the DSB with homology directed repair (“HDR”). The presence, order, and number of new polynucleotide sequences provides a log of events and timing of those events. Cellular mechanisms for creating the DSB and/or repairing with HDR are regulated by intra- or extra-cellular signals. When the log is created in the DNA of a cell, the changes may be heritably passed to subsequent generations of the cell. A correlation between the cellular signals and sequence of inserted HDR templates allows for identification of events and the timing experienced by the cell.

The present invention relates to methods and systems for the analysis of nucleic acids present in biological samples, and more specifically, relates to clustering melt curves derived from high resolution thermal melt analysis performed on a sample of nucleic acids, the resulting clusters being usable, in one embodiment, for analyzing the sequences of nucleic acids and to classify their genotypes that are useful for determining the identity of the genotype of a nucleic acid that is present in a biological sample.

Methods for improving clinical diagnostic tests are provided, along with associated diagnostic techniques.

Methods and kits for diagnosing and/or treating a lower respiratory infection in a subject include obtaining a biological sample from the subject; detecting RNA expression levels of one or more biomarkers in the biological sample and comparing the expression levels of the one or more three biomarkers to at least one invariant control marker wherein an increase or decrease in the level of expression of the one or more biomarkers as compared to the at least one invariant control marker is indicative of a lower respiratory infection.

According to one embodiment, a genotype estimation device includes: an acquirer configured to acquire a clustering strength of genotype data of a plurality of specimens including an unknown specimen whose genotype is not known and known specimens whose genotypes are known; and an estimator configured to estimate the genotype of the unknown specimen on the basis of the genotype data in response to the clustering strength being larger than a first threshold, and output an estimation result.

A genotyping device includes a representative value calculator, a first labeler, a model creator, a second labeler. The representative value calculator calculates a representative value for each of one or more clusters with respect to each of a plurality of SNPs. The representative value being calculated based on signal intensities of specimens included in each of the clusters. The first labeler assigns genotypes to clusters of an SNP pertaining to three clusters among the SNPs on basis of the representative values of the clusters. The model creator creates a model indicative of a relationship between the genotypes of the clusters of the SNP pertaining to the three clusters among the SNPs and the representative values of the clusters. The second labeler assigns genotypes to clusters of an SNP pertaining to one or two clusters among the SNPs on basis of the representative values of the clusters and the model.

A computer-implemented drug evaluation method and system provides for evaluating safety of a drug or a drug group by performing certain computations associated with gene sequence variation information of individuals within a population. The system calculates various scores for individual within a population and ultimately combines the scores in determining safety of the drug across the population. The drug evaluation method and a system can further be configured for identifying individuals having a high-risk of side effects to a drug or a drug group. The drug evaluation provides universal drug safety information based on gene sequence variation information without the need to identify specific genetic markers for each drug.

The techniques and/or systems described herein are directed to improvements in genomic prediction using homomorphic encryption. For example, a genomic model can be generated by a prediction service provider to predict a risk of a disease or a presence of genetic traits. Genomic data corresponding to a genetic profile of an individual can be batch encoded into a plurality of polynomials, homomorphically encrypted, and provided to a service provider for evaluation. The genomic model can be batch encoded as well, and the genetic prediction may be determined by evaluating a dot product of the genomic model data the genomic data. A genomic prediction result value can be provided to a computing device associated with a user for subsequent decrypting and decoding. Homomorphic encoding and encryption can be used such that the genomic data may be applied to the prediction model and a result can be obtained without revealing any information about the model, the genomic data, or any genomic prediction.