This invention provides methods for identifying genes associated with cognitive impairment and for identifying compounds useful in the treatment of cognitive impairment. The methods can in particular be used to identify genes associated with, and compounds useful in treating, cognitive impairment in aging.

Disclosed are methods related to identifying an essential gene which serves as an antibiotic target in a bacterium.

Disclosed is a registry system, including member institutions, in which transfusion donors and recipients are registered following genotyping, which would typically take place in a member institution, or a member institution would have access to the genotyping information, if performed outside. The registry database can be accessed and searched by members seeking samples of particular type(s). Systems are disclosed for maintaining economic viability of genotyping in connection with transfusions, by maximizing the number of units placed with the minimal number of candidate donors typed. Genotyping of potential donors, and product supply, is matched to forecasted demand. Genotyping can also be limited to the more clinically relevant markers. The registry system can also be integrated with one format of assay which generates an image for analysis, whereby the imaged results can be analyzed and redacted by experts in a central location, and then transmitted back to the patient or their representative.

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

Systems and methods for processing sequence data are disclosed herein. In an embodiment, the system is comprised of a computing device that is configured for receiving, storing, and processing sequence data utilizing object-oriented functions. Sequencing is disclosed herein which provides for the customization of sequencing and analysis processing for next generation sequence processing and analysis. The system may be characterized as a bioinformatics system, which uses object oriented functions to process and store sequencing data efficiently and without the need for extensive programming knowledge. Object instances configured as part of the system may be manipulated, transformed, probed, and shared in memory, yet still saved to the disk. Due to the nature of sequence representation within the system, the required disk space needed is much less than existing bioinformatics programs. In another embodiment, MATLAB is utilized as part of the configuration of the system. Due to its object-oriented approach it may be adapted to more complex development functions and processing. This provides for much needed flexibility and ease of use.

There is provided a genome analysis device configured to analyze genome data including a large quantity of fragmented genome base sequences, and transmit output data concerning the genome data in response to an output request from a client device connected via a network, the genome analysis device including; a storage unit for storing data for visualization of multiple different layers, for the genome data; a request receiving unit for receiving an output request from the client device; and an output data generating unit for selecting data for visualization of a layer corresponding to the output request from the storage when the request receiving unit receives the output request, and generating output data based on the data for visualization of the selected layer.

A method of identifying co-expressed coding and noncoding genes is disclosed. The method may include receiving genetic sequences, mapping the genetic sequences to known coding and noncoding genes, correlating the mapped genes, and generating a co-expression network. A system for generating a co-expression network and providing the co-expression network to a user on a display is disclosed. The system may include a memory, one or more processors, one or more databases, and a display.

Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation (CNV) of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter, such as a size-weighted coverage or a fraction of fragments in a size range. In some embodiments, the fragment size parameter is adjusted to remove 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. Also disclosed are systems and computer program products for evaluation of CNV of sequences of interest.

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 Bayesian multilevel whole-genome regression model is disclosed and its prediction performance compared to that of the popular BayesA model applied to each population separately (no pooling) and to the joined data set (complete pooling). For small population sizes (e.g., <50), partial pooling increased prediction accuracy over no or complete pooling for populations represented in the estimation set. Partial pooling with multilevel models can make optimal use of information in multi-population estimation sets.