Abstract: A biological sample collection system can include a sample collection vessel having a sample collection chamber with an opening configured to receive a biological sample into the sample collection chamber. The biological sample collection system can additionally include a selectively movable sleeve valve configured to associate with the opening of the sample collection chamber. The biological sample collection system can additionally include a sealing cap that is configured to associate with the selectively movable sleeve valve and with the sample collection vessel. The sealing cap can include a reagent chamber having reagent(s) stored therein, and when the sealing cap is associated with the sample collection vessel, the selectively movable sleeve valve opens, dispensing the reagent(s) into the sample collection chamber.

Abstract: A user may select one or more potential common ancestors with a DNA match to view the target individual's relationship with them. The process may include identifying, from a first genealogical profile of the target individual. A first individual has a first linkage that connects the target individual towards the selected potential common ancestor. The process may also include identifying, from a second genealogical profile of the DNA match, a second individual who has a second linkage that connects the DNA match towards the selected potential common ancestor. The process may further include connecting the first linkage and the second linkage with the selected potential common ancestor by adding one or more individuals whose profiles are retrieved from other searchable genealogical profiles stored in the online system. With the nodes and connections available, the process may generate a map of visual connections between the target individual and the DNA match.

Abstract: The disclosed system links an individual dataset to a database. The system receives a target individual dataset associated with a target individual and identifies candidate individual datasets that are potentially related to the target individual dataset. The system identifies a related individual dataset that has data bits that match some data bits in the target individual dataset. The system then identifies a parent node that is a common parent node to both the target individual dataset and the related individual dataset. The system retrieves a data tree that the parent node belongs to with the data tree containing information describing inter-relationships among datasets in the data tree. A node in the data tree is identified to assign the target individual dataset based on strings of matched data bits and number of the matched strings between the target individual dataset and the datasets in the data tree.

Abstract: A sample collection system can include a sample collection vessel having a sample collection chamber with an opening configured to receive a sample into the sample collection chamber. The sample collection system can additionally include a selectively movable sleeve valve configured to associate with the opening of the sample collection chamber. The sample collection system can include a sealing cap that is configured to associate with the selectively movable sleeve valve and with the sample collection vessel. The sealing cap can include a reagent chamber having reagent(s) stored therein, and when the sealing cap is associated with the sample collection vessel, the selectively movable sleeve valve opens, dispensing the reagent(s) into the sample collection chamber. When the selectively moveable sleeve associates with the sample collection chamber, an outer sleeve slides relative to an inner vessel, opening the sleeve and dispensing reagent into the sample collection chamber.

Abstract: Identification of inheritance-by-descent haplotype matches between individuals is described. A set of tables including word match, haplotypes and segment match tables are populated. DNA samples are received and stored. A word identification module extracts haplotype values from each sample. The word match table is indexed according to the unique combination of position and haplotype. Each column represents a different sample, and each cell indicates whether that sample includes that haplotype at that position. The haplotypes table includes the raw haplotype data for each sample. The segment match table is indexed by sample identifier, and columns represent other samples. Each cell is populated to indicate for each identified sample pair which position range(s) include matching haplotypes for both samples. The tables are persistently stored in databases of the matching system. As new sample data is received, each table is updated to include the newly received samples, and additional matching takes place.

Abstract: A biological sample collection system can include a sample collection vessel having a sample collection chamber with an opening configured to receive a biological sample into the sample collection chamber. The biological sample collection system can additionally include a selectively movable sleeve valve configured to associate with the opening of the sample collection chamber. The biological sample collection system can additionally include a sealing cap that is configured to associate with the selectively movable sleeve valve and with the sample collection vessel. The sealing cap can include a reagent chamber having reagent(s) stored therein, and when the sealing cap is associated with the sample collection vessel, the selectively movable sleeve valve opens, dispensing the reagent(s) into the sample collection chamber.

Abstract: Disclosed are techniques for characterizing variants of interest and predicting assignments of individuals to communities based on obtained genetic information. To characterize a variant, DNA datasets of reference individuals are accessed and used to generate a cluster with additional individuals. Reference individuals carry a variant at a genetic locus and the additional individuals share IBD with reference individuals. Statistics of genealogical data of the cluster are generated. A result summarizing the characterization of the variant is generated based on the statistics. To determine if an individual belongs to a community, a subset of the individual's haplotypes are inputted into a community-specific model. The model is trained using the training samples that each include haplotypes of reference individuals and a label identifying whether the reference individual belongs to the community. Based on the output of the model, it is determined whether the individual is a member of the community.

Abstract: Described are techniques for determining population structure from identity-by-descent (IBD) of individuals. The techniques may be used to predict that an individual belongs to zero, one or more of a number of communities identified within an IBD network. Additional data may be used to annotate the communities with birth location, surname, and ethnicity information. In turn, these data may be used to provide to an individual a prediction of membership to zero, one or more communities, accompanied by a summary of the information annotated to those communities. Ethnicity heterogeneity and age information may be tabulated and provided based on community membership information.

Abstract: A computing server generates a graph such as an identity-by-descent (IBD) network. The graph includes a plurality of nodes. Each node represents one of the individuals. Two or more nodes are connected through edges. Each edge connecting two nodes and associated with a weight that is derived from affinity between the genetic data of the two individuals represented by the two nodes. The computing system filters the graph based on features that are associated with the edges or the nodes. The filtered graph includes a subset of nodes. The computing system divides the filtered graph into a plurality of clusters to identify genetic communities that may not be discoverable without filtering. The computing server may also perform a multi-path hierarchical community detection process to assign an individual represented by a node to more than one communities.

Abstract: Provided herein are systems, devices, and methods for sample collection. A sample collection device may comprise a vessel, a lid, and pre-loaded liquid solutions. The sample collection device may collect a liquid sample, such as a biological sample. The liquid solutions may comprise reagents for preserving and/or stabilizing biological samples, such as saliva, collected in the vessel. A chamber comprising the liquid solutions may be located in the vessel and/or the lid. In some instances, the liquid solution may be released from the chamber upon closure of the vessel with the lid. In some instances, the liquid solution may be released from the chamber upon actuation of an implement, such as a plunger. In some instances, the liquid solution may be released upon compression of an absorbent member. The sample collecting device may be delivered to a remote location for further processing and/or analysis.

Abstract: A system identifies ancestral birth locations or surnames estimated to be associated with an individual's ancestors using an individual's genetic sample. The system identifies users who are genetic matches to the individual and determines whether and how often a birth location or surname appears in the pedigrees of those users. Birth locations or surnames that appear frequently throughout the pedigrees of genetically matching users may represent birth locations or surnames that are affiliated with the individual's ancestors. The system determines whether the frequency of appearance of a birth location or surname is statistically significant to eliminate biases for certain birth locations or surnames that appear more frequently than others. The birth location or surname may be provided to the individual based on an also-determined enrichment score.

Abstract: Methods and systems for assessing the probabilities of the expression of one or more traits in progeny are described.

Abstract: A computing server may use one or more recommender systems to predict phenotypes of individuals based on survey responses, other phenotypes, environmental factors, and genetic data of the individuals. The computing server may retrieve survey responses of a set of individuals regarding a set of phenotypes of the individuals. The computing server may construct a matrix that includes the values of the phenotypes. The computing server may predict an undetermined phenotype of a target individual using collaborative filtering, which provides the prediction based on other phenotypes of the target individuals and based on at least another individual's phenotypes. The computing server may also predict a target phenotype based on the phenotype of other individuals who are similar to the target individual. The computing server may determine another individual is similar to the target individual based on the length of identity-by-descent (IBD) segments between the two individuals.

Abstract: Disclosed are techniques for predicting a trait of an individual and identifying a set of enriched record collections of a genetic community. To predict a trait of an individual, DNA features and non-DNA features of the individual are accessed to generate a feature vector that is inputted into a machine learning model. The machine learning model generates a prediction of the trait. The prediction may be based on an inheritance prediction and/or a community prediction. To identify a set of enriched record collections, individuals belonging to a genetic community are identified and a set of candidate record collections are accessed. A community count and a background count is determined for each candidate record collection. The set of enriched record collections are identified based on a comparison of the community count and the background count. The genetic community may be annotated using the set of enriched record collections.

Abstract: System, computer program products, and methods are disclosed for estimating a degree of ancestral relatedness between two individuals. The haplotype data for a population of individuals is divided into segment windows based on genetic markers, and matched segments for the haplotype data are generated. Each matched segment having a first cM width that exceeds a threshold cM width is included in counting the matched segments in each segment window. A weight associated with each segment window is estimated based on the count of matched segments in the associated segment window. A weighted sum of per-window cM widths for each matched segment is calculated based on the first cM width and the weights associated with the segment windows of the matched segment. The weighted sum of per-window cM widths are used to estimate a degree of ancestral relatedness between two individuals.

Abstract: An input genotype is divided into a plurality of windows, each including a sequence of SNPs. For each window, a diploid HMM is computed based on genotypes and/or phased haplotypes to determine a probability of a haplotype sequence being associated with a particular label. For example, the diploid HMM for a window is used to determine the emission probability that the window corresponds to a set of labels. An inter-window HMM, with a set of states for each window, is computed. Labels are assigned to the input genotype based on the inter-window HMM. Upper and lower bounds are estimated to produce a range of likely percentage values an input can be assigned to a given label. Confidence values are determined indicating a likelihood that an individual inherits DNA from a certain population. Maps are generated with polygons representing regions where a measure of ethnicity of population falls within specific ranges.

Abstract: Novel haplotype cluster Markov models are used to phase genomic samples. After the models are built, they rapidly and accurately phase new samples without requiring that the new samples be used to re-build the models. The models set transition probabilities such that the probability for an appearance of any allele within any haplotype is a non-zero number. Furthermore, the most unlikely pairs of haplotypes are discarded from each model at each level until c of the likelihood mass at each level is discarded. The models are also constructed such that contributing windows of SNPs partially overlap so that phasing decisions near one of the extreme ends of any model is are not significantly determinative of the phase. Additionally, the models are configured such that two or more nodes can be merged during the building/updating procedure to consolidate haplotype clusters having similar distributions.

Abstract: A system, device and method for receiving multiple aligned genetic sequences obtained from genetic samples of multiple organisms of one or more different species. A measure of evolutionary variation may be computed for one or more alleles at each of one or more aligned genetic loci. The aligned genetic loci in the multiple organisms may be derived from one or more common ancestral genetic loci or may be otherwise related. The measure of evolutionary variation may be a function of variation in alleles at corresponding aligned genetic loci in the multiple aligned genetic sequences. One or more likelihoods may be computed that an allele mutation at each of the one or more genetic loci in a simulated virtual progeny will be deleterious based on the measure of evolutionary variation of alleles at the corresponding aligned genetic loci for the multiple organisms.