DNA variants may be classified according to a rules-based scoring system into five categories that include pathogenic, likely pathogenic, variant of unknown significance, likely benign, and benign. Scores may be associated with variants in a framework that weighs evidence from prediction tools, population frequency, co-occurrence, segregation, and functional studies. A standardized scoring system for assessing pathogenicity may provide reliable, consistent pathogenicity scores for DNA variants encountered in a clinical laboratory setting.

Provided herein are methods for determining the presence of a mutant of target polynucleotides in a sample solution by contacting the sample solution and a reference solution containing the target nucleotide with identical probe sets and then comparing the hybridization intensities of corresponding probes of the probe sets. The probes provide a varying complementarity to the target sequence so that a range of hybridization intensities for the hybridization between the target polynucleotide and the probes is covered.

Embodiments of the present disclosure relate generally to the genetic analysis of intractable microbes. More particularly, the present disclosure provides materials and methods that incorporate chemical mutagenesis, phenotypic selection, suppression analysis, and genomic sequencing-based mutational mapping, to identify novel genetic regulators in previously intractable organisms, such as microbes that constitute the human microbiome. Given the paucity of experimental tools to manipulate bacterial genomes, there is a need for improved methods for determining how microbial communities assemble and influence human and environmental health.

Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).

According to one aspect, systems and processes for assaying a plurality of nucleic acid samples are provided. In an exemplary process, a matrix is generated including pools and samples using a pooling scheme with decoding capability equal to a number D. Matrix organization includes assigning one pool in a set of pools per row by one sample in a set of samples per column. Sample assignment creates a known pattern of pools, wherein each sample in the set of pools is assigned a total number of D+1 times and any two pools have at most one sample in common. Samples are pooled based on a pooling scheme, where pooled samples are assayed. Positive pools are determined and one or more positive samples are identified. The matrix is displayed as a visual pattern representing the known pattern of pools, the identified positive samples, and the determined positive pools.

A conversational and embodied Virtual Assistant (VA) with Decision Support (DS) capabilities that can simulate and improve upon information gathering sessions between clinicians, researchers, and patients. The system incorporates a conversational and embodied VA and a DS and deploys natural interaction enabled by natural language processing, automatic speech recognition, and an animation framework capable of rendering character animation performances through generated verbal and nonverbal behaviors, all supplemented by on-screen prompts.

Methods and systems for analyzing genetic variants are disclosed.

The present invention provides a method for indicating differentiation between tissues. For each tissue amongst multiple tissues, a magnetization vector corresponding to each tissue is generated on the basis of a random scan sequence; on the basis of the magnetization vector corresponding to each of the multiple tissues, a differentiation-indicating value between each pair of the multiple tissues is calculated. Thus, a physician can select a suitable random scan sequence, according to the method provided in the present invention, and generate a magnetic resonance image comprising multiple brightness curves corresponding to multiple tissues, such that the trends of the brightness curves corresponding to the multiple tissues in the magnetic resonance image differ significantly. The present invention also provides a device for indicating differentiation between tissues.

A method and system for determining interaction sites between biosequences is described herein. A dataset of contact data for a plurality of biomolecule pairs is obtained to account their frequency of occurrence. Statistical weights are determined for each frequency of occurrence. Each vector of a statistical residual vector space (SRV) is decomposed through principal component decomposition. The vectors of the SRV are re-projected back to a new SRV with a new set of coordinates. A feature vector is generated and inputted into a predictor for outputting a likelihood of an interaction site.

The disclosed methods are used to predict or assess colon tumor status in a patient. They can be used to determine nature of tumor, recurrence, or patient response to treatments. Some embodiments of the methods include generating a report for clinical management. The methodology provided herein is intended to detect technical variations and to allow for data normalization and enhance signal detection and build predictive proteins profiles of disease status and response.