Abstract: An example device includes processing circuitry and a memory. The memory includes instructions that cause the device to perform various functions. The functions include receiving datastreams from a plurality of sensors of a high performance computing system, classifying each datastream of the each sensor to one of a plurality of datastream models, selecting an anomaly detection algorithm from a plurality of anomaly detection algorithms for each datastream, determining parameters of the each anomaly detection algorithm, determining an anomaly threshold for each datastream, and generating an indication that the sensor associated with the datastream is acting anomalously.

Abstract: A system and related method exchange medical information with a medical management system. The method comprises receiving, using a processor of a code point resolver, from the medical management system, medical text via a network interface. A code point is a single standardized medical terminology code (SMTC) that corresponds to a medical concept contained within the medical text. The method further applies rule-based logic to process the medical text to form a localized mapping of a text portion of the medical text to a plurality of candidate SMTCs (CSMTCs) that are related to at least one metathesaurus concept entity (MCE) in a metathesaurus, and to determines the code point from the CSMTCs. The method transmits, via the network interface, to the medical management system, the code point.

Abstract: A method, software, database and system for attribute partner identification and social network based attribute analysis are presented in which attribute profiles associated with individuals can be compared and potential partners identified. Connections can be formed within social networks based on analysis of genetic and non-genetic data. Degrees of attribute separation (genetic and non-genetic) can be utilized to analyze relationships and to identify individuals who might benefit from being connected.

Abstract: Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.

Abstract: Methods and computer apparatuses are disclosed for processing genomic data in at least partially automated workflows of modules. A method comprises: specifying a source from which nucleic acid sequence(s) are to be obtained; selecting module(s) for processing data, including at least one module for processing the one or more nucleic acid sequences; presenting, in a graphical user interface, graphical components representing the source and the module(s) as nodes within a workspace; receiving, via the graphical user interface, inputs arranging the source and the module(s) as a workflow comprising a series of nodes, the series indicating, for each particular module, that output from one of the source or another particular module is to be input into the particular module; generating an output for the workflow based upon the nucleic acid sequence(s) by processing each module in an order indicated by the series.

Abstract: Disclosed herein are systems and methods for performing secondary analyses of nucleotide sequencing data in a time-efficient manner. Some embodiments include performing a secondary analysis iteratively while sequence reads are generated by a sequencing system. Secondary analyses can encompass both alignment of sequence reads to a reference sequence (e.g., the human reference genome sequence) and utilization of this alignment to detect differences between a sample and the reference. Secondary analysis can enable detection of genetic differences, variant detection and genotyping, identification of single nucleotide polymorphisms (SNPs), small insertions and deletion (indels) and structural changes in the DNA, such as copy number variants (CNVs) and chromosomal rearrangements.

Abstract: A method for global mapping between a first sequence Xp and a second sequence Xg.

Abstract: The present systems and methods are directed to de novo identification of peptide sequences from tandem mass spectrometry data. The systems and methods uses unconverted mass spectrometry data from which features are extracted. Using unconverted mass spectrometry data reduces the loss of information and provides more accurate sequencing of peptides. The systems and methods combine deep learning and neural networks to sequencing of peptides.

Abstract: A method of measuring body fluid content, the method comprising computer executed steps, the steps comprising: receiving a value of a temperature of a body part of a subject, and generating corrective data based on the received measured temperature value and on previously gathered data, the corrective data being usable for correcting a measurement of content of a fluid sample taken from the body part.

Abstract: A method of compressive read mapping. A high-resolution homology table is created for the reference genomic sequence, preferably by mapping the reference to itself. Once the homology table is created, the reads are compressed to eliminate full or partial redundancies across reads in the dataset. Preferably, compression is achieved through self-mapping of the read dataset. Next, a coarse mapping from the compressed read data to the reference is performed. Each read link generated represents a cluster of substrings from one or more reads in the dataset and stores their differences from a locus in the reference. Preferably, read links are further expanded to obtain final mapping results through traversal of the homology table, and final mapping results are reported. As compared to prior techniques, substantial speed-up gains are achieved through the compressive read mapping technique due to efficient utilization of redundancy within read sequences as well as the reference.

Abstract: The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.

Abstract: There is a need for more effective and efficient predictive data analysis solutions for processing genetic sequencing data. This need can be addressed by, for example, techniques for performing predictive data analysis based on genetic sequences that utilize at least one of cross-variant polygenic risk modeling using genetic risk profiles, cross-variant polygenic risk modeling using functional genetic risk profiles, per-condition polygenic clustering operations, cross-condition polygenic predictive inferences, and cross-condition polygenic diagnoses.

Abstract: Polynucleotide sequencing generates multiple reads of a polynucleotide molecule. Many or all of the reads contain errors. Trace reconstruction takes multiple reads generated by a polynucleotide sequencer and uses those multiple reads to reconstruct accurately the nucleotide sequence of the polynucleotide molecule. Some reads may contain errors that cannot be corrected. Thus, there may be reads that can be used throughout their entire length and other reads that have indeterminant errors which cannot be corrected. Rather than discarding the entire read when an indeterminant error is found, the portion of the read with the error is skipped and the sequence of the read following the error is used to reconstruct the trace. The amount of the read skipped is determined by the location of subsequence after the error that matches a consensus sequence of the other reads. Analysis resumes at a location determined by the location of the match.

Abstract: In one embodiment, a sample surface of a biosensor includes pixel areas and holds a plurality of clusters during a sequence of sampling events such that the clusters are distributed unevenly over the pixel areas. In another embodiment, a biosensor has a sample surface that includes pixel areas and an array of wells overlying the pixel areas, the biosensor including two wells and two clusters per pixel area. The two wells per pixel area include a dominant well and a subordinate well. The dominant well has a larger cross section over the pixel area than the subordinate well. In yet another embodiment, an illumination system is coupled to a biosensor that illuminates the pixel areas with different angles of illumination during a sequence of sampling events, including, for a sampling event, illuminating each of the wells with off-axis illumination to produce asymmetrically illuminated well regions in each of the wells.

Abstract: A nervous system emulator engine includes working computational models of the vertebrate nervous system to generate lifelike animal behavior in a robot. These models include functions representing several anatomical features of the vertebrate nervous system, such as spinal cord, brainstem, basal ganglia, thalamus and cortex. The emulator engine includes a hierarchy of controllers in which controllers at higher levels accomplish goals by continuously specifying desired goals for lower-level controllers. The lowest levels of the hierarchy reflect spinal cord circuits that control muscle tension and length. Moving up the hierarchy into the brainstem and midbrain/cortex, progressively more abstract perceptual variables are controlled. The nervous system emulator engine may be used to build a robot that generates the majority of animal behavior, including human behavior. The nervous system emulator engine may also be used to build working models of nervous system functions for clinical experimentation.

Abstract: Particles such as blood cells can be categorized and counted by a digital image processor. A digital microscope camera can be directed into a flowcell defining a symmetrically narrowing flowpath in which the sample stream flows in a ribbon flattened by flow and viscosity parameters between layers of sheath fluid. A contrast pattern for autofocusing is provided on the flowcell, for example at an edge of a rear illumination opening. The image processor assesses focus accuracy from pixel data contrast. A positioning motor moves the microscope and/or flowcell along the optical axis for autofocusing on the contrast pattern target. The processor then displaces microscope and flowcell by a known distance between the contrast pattern and the sample stream, thus focusing on the sample stream. Blood cell images are collected from that position until autofocus is reinitiated, periodically, by input signal, or when detecting temperature changes or focus inaccuracy in the image data.

Abstract: Platelet cell data may be obtained from analysis of a blood sample by a hematology analyzer or like device. Systems and apparatus may process the platelet cell data in accordance with platelet parameter thresholds selected by a user. The platelet cell data may then be categorized and displayed in one or more useful forms for medical diagnostic and/or research purposes. The platelet cell data may be categorized and displayed in, e.g., tabular and/or graphical form based on the user-selected platelet parameter thresholds. Methods of processing platelet cell data for categorizing and displaying the platelet cell data in one or more useful forms are also provided, as are other aspects.

Abstract: The present disclosure provides methods of estimating a degree of ancestral relatedness between individuals. In an aspect, a method comprises receiving haplotype data comprising genetic markers shared among a population of individuals; dividing the haplotype data into segments based on the genetic markers; for each of the population of test individuals: (i) based on the genetic markers, matching segments of the haplotype data that are identical-by-descent between two individuals, (ii) for each of the matched segments: dividing the matched segment into discrete genomic intervals, scoring each of the discrete genomic intervals based on a degree of matching within or between the individuals, correcting the scores for consistency, and (iii) calculating a weighted sum over the discrete genomic intervals of the matched segment, based on the corrected scores and assigned weights; and (d) estimating the degree of ancestral relatedness between the individuals based on the weighted sums of the matched segments.

Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

Abstract: An object classification system for classifying objects is described. The system comprises an imaging region adapted for irradiating an object of interest, an arrayed detector, and a mixing unit configured for mixing the irradiation stemming from the object of interest by reflecting or scattering on average at least three times the irradiation after its interaction with the object of interest and prior to said detection.

Abstract: The technology disclosed processes a first input through a first neural network and produces a first output. The first input comprises first image data derived from images of analytes and their surrounding background captured by a sequencing system for a sequencing run. The technology disclosed processes the first output through a post-processor and produces metadata about the analytes and their surrounding background. The technology disclosed processes a second input through a second neural network and produces a second output. The second input comprises third image data derived by modifying second image data based on the metadata. The second image data is derived from the images of the analytes and their surrounding background. The second output identifies base calls for one or more of the analytes at one or more sequencing cycles of the sequencing run.

Abstract: The present disclosure describes a method of foreground segmentation and nucleus ranking for scoring dual ISH images. The method has been developed to better identify those nuclei, within a selected field of view, that meet the criteria for dual ISH scoring.

Abstract: A cartridge for digital real-time Polymerase chain reaction (PCR) includes a microfluidic chamber, a well array, a CMOS photo sensor array and a PCB. The microfluidic chamber includes an inlet formed for injection of a liquid sample, the microfluidic chamber being capable of injection molding. The well array includes a plurality of microwells through which upper and lower portions are perforated and being attached to a lower surface of the microfluidic chamber. The CMOS photo sensor array is disposed below the well array to capture a response image of a sample filled in microwells of the well array. The PCB has a vent formed for vacuum processing of micro flow path formed in the microfluidic chamber, a space formed between the well array and the microfluidic chamber, and a microwell formed in the well array as the liquid sample is injected through the inlet.

Abstract: Techniques are described that facilitate determining potential cancer gene therapy targets by joint modeling of cancer survival events. In one embodiment, a computer-implemented comprises employing, by a device operatively coupled to a processor, a multi-task learning model to determine active genetic factors respectively associated with different types of cancer based on cancer survival data and patient genomic data for groups of patients that respectively survived the different types of cancer. The computer-implemented method further comprises, determining, by the device, common active genetic factors of the active genetic factors that are shared between two or more types of cancer of the different types of cancer.

Abstract: The disclosure provides for methods, compositions, systems, devices, and kits for whole transcriptome amplification using stochastic barcodes.

Abstract: A biosensor for base calling is provided. The biosensor comprises a sampling device, which includes a sample surface that has an array of pixel areas and a solid-state imager that has an array of sensors. Each sensor generates pixel signals in each base calling cycle. Each pixel signal represents light gathered in one base calling cycle from one or more clusters in a corresponding pixel area of the sample surface. The biosensor further comprises a signal processor configured for connection to the sampling device. The signal processor receives and processes the pixel signals from the sensors for base calling in a base calling cycle, and uses the pixel signals from fewer sensors than a number of clusters base called in the base calling cycle. The pixel signals from the fewer sensors include at least one pixel signal representing light gathered from at least two clusters in the corresponding pixel area.

Abstract: Techniques are provided for detecting copy number variations. Each sequence read of a set of sequence reads is aligned with a portion of a reference sequence. A coverage vector is generated that includes a plurality of elements, each element in the plurality of elements indicating a number of the set of sequence reads that were aligned to a particular position within the reference sequence. A normalization vector is accessed that was generated based on performance of a component analysis on a set of other coverage vectors corresponding to a set of other subjects. An adjusted coverage vector is generated using the coverage vector and normalization vector. One or more subject-specific normalization values are generated based on the coverage vector. One or more copy number variations are identified that corresponding to the sample using the adjusted coverage vector and the subject-specific normalization values.

Abstract: Provided is a method for detecting chromosomal Robertsonian translocation and the SNP (single nucleotide polymorphism) site and primer composition for use therein. The method is practical, simple, convenient and high in universality; moreover, a high-throughput sequencing technology is combined, so that the method has the advantages of low cost, and high sensitivity, specificity and accuracy.

Abstract: The present invention relates to a compound of formula (I), wherein X is C?O, C?S or B—OH; Y is an electrophile and Z is a leaving group, or Y?Z is an electrophile; R1 comprises or consists of (a) (i) a first group binding to a proteolytic site of a proteasome, the first group being bound to X; and (ii) optionally a second group enhancing delivery; or (b) a group binding between subunits ?1 and ?2 of a proteasome; R2 and R3 are independently selected from H, methyl, methoxy, ethyl, ethenyl, ethynyl and cyano, wherein methyl and ethyl may be substituted with OH or halogen.

Abstract: The technology disclosed relates to generating ground truth training data to train a neural network-based template generator for cluster metadata determination task. In particular, it relates to accessing sequencing images, obtaining, from a base caller, a base call classifying each subpixel in the sequencing images as one of four bases (A, C, T, and G), generating a cluster map that identifies clusters as disjointed regions of contiguous subpixels which share a substantially matching base call sequence, determining cluster metadata based on the disjointed regions in the cluster map, and using the cluster metadata to generate the ground truth training data for training the neural network-based template generator for the cluster metadata determination task.

Abstract: A computer-based genomic annotation system, including a database configured to store genomic data, non-transitory memory configured to store instructions, and at least one processor coupled with the memory, the processor configured to implement the instructions in order to implement an annotation pipeline and at least one module filtering or analysis of the genomic data.

Abstract: A data processing system 2 supporting vector processing operations uses scaling vector length querying instructions. The scaling vector length querying instructions return a result which is dependent upon a number of elements in a vector for a variable vector element size specified by the instruction and multiplied by a scaling value specified by the instruction. The scaling vector length querying instructions may be in the form of count instructions, increment instructions or decrement instructions. The instructions may include a pattern constraint applying a constraint, such as modulo(M) or power of 2 to the partial result value representing the number of vector elements provided for the register element size specified for the instruction.

Abstract: The current invention concerns a computer-implemented method, a computer system and a tangible non-transitory computer-readable data carrier comprising a computer program product for aligning a query nucleic acid sequence against a reference nucleic acid sequence. An optimal alignment score of the query sequence against the reference sequence is determined by a dynamic programming algorithm. The algorithm is configured for locally optimizing a partial alignment score based on a nucleotide substitution cost, a gap insertion cost, an amino acid substitution cost, as well as a frameshift penalty.

Abstract: A method for nucleic acid sequencing includes receiving a plurality of signals indicative of a parameter measured for a plurality of defined spaces, at least some of the defined spaces including one or more sample nucleic acids, the signals being responsive to a plurality of nucleotide flows introducing nucleotides to the defined spaces; determining, for at least some of the defined spaces, whether the defined space includes a sample nucleic acid; processing, for at least some of the defined spaces determined to include a sample nucleic acid, the received signals to improve a quality of the received signals; and predicting a plurality of nucleotide sequences corresponding to respective sample nucleic acids for the defined spaces based on the processed signals and the nucleotide flows.

Abstract: Disclosed herein are methods of identifying infections, such as methods of identifying bacterial infections which utilize whole metagenome sequence analysis to sequence the entire wound microbiome of clinical samples. The disclosed methods use fast k-mer based sequence analysis, predictive modeling, and Bayesian network analysis, to analyze bacterial metagenomic sequence compositions in conjunction with clinical factors to stratify communities of bacteria into healing versus non-healing clusters. The methods of identifying infections can include performing molecular analysis of a patient wound sample, preparing the data obtained from the molecular analysis, diagnosing the wound sample and/or prognosing the wound sample. The disclosed methods can also be used to identify protein function as well as novel biomarkers.

Abstract: Determination of a frequency distribution of nucleotide sequence variants—differing from a nucleotide reference by at least one intermediate part—of a sample is disclosed. A reference set of sequence read data is generated by performing a plurality of reference sequence reads (each having a read start site, RSS) for each sequence reference variant of a reference variant list. It is determined (for each RSS and for the intermediate part of each sequence reference variant) whether the intermediate part is detectable by corresponding reference sequence read. A sample set of sequence read data is generated by performing sample sequence reads for the sample, and a total number of occurrences in the sample set is determined for each RSS and for the intermediate part of each sequence reference variant. The frequency distribution of the plurality of nucleotide sequence variants is determined based on the number of occurrences determined for an RSS where the intermediate part is detectable.

Abstract: Techniques are disclosed relating to fluorescence-based flow cytometry. A flow cytometer may include a partially-reflective surface configured to reflect a first portion of fluorescent emissions from a sample to a first optical sensor and direct a second, greater portion of fluorescent emissions from the sample to a second optical sensor and a controller configured to determine a value representing the intensity of the fluorescent emissions based on a first measurement taken by the first optical sensor, a second measurement taken by the second optical sensor, or both. A flow cytometer may include a baseplate with a first side and a second, opposing side with a flow cell, a laser, and a reflective surface disposed above the first side and an optical sensor and isolating material disposed below the second side. The reflective surface receives fluorescent emissions and reflects at least a portion through the baseplate to the optical sensor.

Abstract: Values for tumor mutation burden from different samples can be made more comparable to each other or control standards by a normalization regime that takes into account the minor allele fraction of highly rated mutations in a sample. Such analysis can provide an indication where the tumor mutation burden of a test sample lies on a distribution of tumor mutation burdens in a control population, and thus, whether the individual providing the test sample is likely to be amenable to immunotherapy to treat cancer.

Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

Abstract: Embodiments include methods, systems, and computer program products for analyzing genomic data. Aspects include receiving genomic data for an organism, sample phenotypes, and a plurality of gene sets. Aspects include, for each of the gene sets, determining a set of genes G corresponding to genes in the gene set and a set of genes G? corresponding to genes outside the gene set for the phenotypes R and R?. Aspects also include determining a set of mutated genes M and a set of non-mutated genes M? for R and R? and a mutation enrichment score. Aspects also include determining a set of differentiated genes D a set of non-differentiated genes D? for R and R?. Aspects also include identifying an enriched gene set GE based at least in part upon the mutation enrichment score and the differentiation enrichment score.

Abstract: Methods are provided for analyzing one or more genetic samples, comprising procuring one or more genetic samples comprising genetic material from one or more individuals and sequencing the genetic material using non-targeted, ultra-low coverage sequencing to obtain genetic information for individual associated with the one or more genetic samples. Personal and genetic information associated with the individuals is stored in a database for retrieval and manipulation.

Abstract: Techniques for securely encoding, communicating, and comparing genomic information using probabilistic data structures are provided. In some embodiments, genomic information in a secure computing environment may be encoded and/or anonymized by building a probabilistic data structure that represents sub-strings of the genomic information as members of a set; the probabilistic data structure may then be securely transmitted outside the secure computing environment. In some embodiments, a probabilistic data structure representing sub-strings of sensitive genomic information as members of a set may be received in an unsecure computing environment and may be queried to generate output data indicating whether reference sub-strings are probable members of the set.

Abstract: Provided herein and methods and apparatuses for sequencing nucleic acids. For example, provided is an analytical detection apparatus, including (a) a stage configured to support a flow cell; (b) a detector configured to observe a detection channel of the flow cell when the flow cell is supported by the stage; (c) a plurality of fluid delivery channels, wherein each of the fluid delivery channels fluidically connects a reservoir to the detection channel of the flow cell; and (d) a first heater configured to heat the plurality of fluid delivery channels.

Abstract: Various embodiments are described herein related to an assay, method and apparatus for performing an RNA Disruption Assay (RDA) for cellular RNA optionally in response to a cytotoxic treatment such as chemotherapy and/or radiation treatment. The method comprises obtaining at least one electropherogram dataset corresponding to a unique biological sample comprising the cellular RNA at a time point, optionally during or after the treatment; determining values for features from at least two shifted regions of the at least one electropherogram dataset, the shifting being due to the treatment; and optionally determining an RDA score based on a combination of the values of the features.

Abstract: A computer-implemented method, computer program product, and computer processing system are provided for metagenomic pattern classification. The method includes pre-processing, by a processor, a taxonomy tree associated with a genome database to extract taxonomy related information therefrom. The genome database includes a plurality of genome sequences. The method further includes building, by the processor, a suffix tree on the genome database. The method also includes annotating, by the processor, nodes in the suffix tree, using a plurality of right maximal patterns derived from the extracted taxonomy related information as annotations, such that each of the plurality of right maximal patterns in the suffix tree points to a respective one of a plurality of nodes in the taxonomy tree and such that a leaf node in the taxonomy tree represents a respective sample organism. The annotations are configured to function as classifications for the plurality of genome sequences.

Abstract: The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes, or their co-expressed genes, from a biological sample obtained from a prostate cancer patient. The genes may be grouped into functional gene subsets for calculating a quantitative score useful to predict a likelihood of a clinical outcome for a prostate cancer patient.

Abstract: A sequencing data analysis method, a device and a computer-readable medium for microsatellite instability. The present invention can use NGS sequencing results to determine whether the microsatellite instability is present. The sequencing data analysis method can significantly improve detection sensitivity without reducing specificity, and can quickly and automatically evaluate a stable or unstable status of each MSI locus with high throughput, high sensitivity, and high specificity. By combining the statuses for all MSI loci in each sample, the samples can be comprehensively evaluated as MSS, MSI-L, or MSI-H.

Abstract: Embodiments in the present disclosure relate generally to computer network architectures for machine learning, artificial intelligence, and automated improvement and regularization of forecasting models, providing rapid improvement of the models. Embodiments may generate such rapid improvement of the models either occasionally on demand, or periodically, or as triggered by events such as an update of available data for such forecasts. Embodiments may indicate, after the improvement of the models, that various web applications using the models may be rerun to seek improved results for the web applications. Embodiments may include a combination of third-party databases to drive the forecasting models, including social media data, financial data, socio-economic data, medical data, search engine data, e-commerce site data, and other databases.

Abstract: A system for personalized depression disorder treatment is disclosed herein. The system includes a server configured to communicate with existing healthcare resources and to receive patient data corresponding to a patient, the server including an analytics module. The system further includes a first database configured to store empirical patient outcomes, and further configured to communicate with the analytics module. Additionally, the system includes a user device having a graphical user interface (GUI) configured to communicate with the server and to display at least one output generated by the analytics module. The analytics module is configured to determine at least one of a personalized depression treatment and a personalized depression state prediction based on the empirical patient outcomes and the patient data.

Abstract: Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences.