Relatedness Detection Research Articles

A computational approach for positive genetic identification and relatedness detection from low-coverage shotgun sequencing data.

Several methods exist for detecting genetic relatedness or identity by comparing DNA information. These methods generally require genotype calls, either single-nucleotide polymorphisms or short tandem repeats, at the sites used for comparison. For some DNA samples, like those obtained from bone fragments or single rootless hairs, there is often not enough DNA present to generate genotype calls that are accurate and complete enough for these comparisons. Here, we describe IBDGem, a fast and robust computational procedure for detecting genomic regions of identity-by-descent by comparing low-coverage shotgun sequence data against genotype calls from a known query individual. At less than 1× genome coverage, IBDGem reliably detects segments of relatedness and can make high-confidence identity detections with as little as 0.01× genome coverage.

GRAPE: genomic relatedness detection pipeline.

Classifying the degree of relatedness between pairs of individuals has both scientific and commercial applications. As an example, genome-wide association studies (GWAS) may suffer from high rates of false positive results due to unrecognized population structure. This problem becomes especially relevant with recent increases in large-cohort studies. Accurate relationship classification is also required for genetic linkage analysis to identify disease-associated loci. Additionally, DNA relatives matching service is one of the leading drivers for the direct-to-consumer genetic testing market. Despite the availability of scientific and research information on the methods for determining kinship and the accessibility of relevant tools, the assembly of the pipeline, which stably operates on a real-world genotypic data, requires significant research and development resources. Currently, there is no open source end-to-end solution for relatedness detection in genomic data, that is fast, reliable and accurate for both close and distant degrees of kinship, combines all the necessary processing steps to work on a real data, and is ready for production integration. To address this, we developed GRAPE: Genomic RelAtedness detection PipelinE. It combines data preprocessing, identity-by-descent (IBD) segments detection, and accurate relationship estimation. The project uses software development best practices, as well as Global Alliance for Genomics and Health (GA4GH) standards and tools. Pipeline efficiency is demonstrated on both simulated and real-world datasets. GRAPE is available from: https://github.com/genxnetwork/grape.

User Experience Quantification Model from Online User Reviews

Due to the advancement in information technology and the boom of micro-blogging platforms, a growing number of online reviews are posted daily on product distributed platforms in the form of spontaneous and insightful user feedback, and these can be used as a significant data source to understand user experience (UX) and satisfaction. However, despite the vast amount of online reviews, the existing literature focuses on online ratings and ignores the real textual context in reviews. We proposed a three-step UX quantification model from online reviews to understand customer satisfaction using the effect-based Kano model. First, the relevant online reviews are selected using various filter mechanisms. Second, UX dimensions (UXDs) are extracted using a proposed method called UX word embedding Latent Dirichlet allocation (UXWE-LDA) and sentiment orientation using a transformer-based pipeline. Then, the casual relationships are identified for the extracted UXDs. Third, the UXDs are mapped on the customer satisfaction model (effect-based Kano) to understand the user perspective about the system, product, or services. Finally, the different parts of the proposed quantification model are evaluated to examine the performance of this method. We present different results of the proposed method in terms of accuracy, topic coherence (TC), Topic-wise performance, and expert-based evaluation for the proposed framework validation. For review quality filters, we achieved 98.49% accuracy for the spam detection classifier and 95% accuracy for the relatedness detection classifier. The results show that the proposed method for the topic extractor module always gives a higher TC value than other models such as WE-LDA and LDA. Regarding topic-wise performance measures, UXWE-LDA achieves a 3% improvement on average compared to LDA due to the incorporation of semantic domain knowledge. We also compute the Jaccard coefficient similarity between the extracted dimensions using UXWE-LDA and UX experts-based analysis for checking the mutual agreement, which is 0.3, 0.5, and 0.4, respectively. Based on the Kano model, the presented study has potential implications concerning issues and knowing the product’s strengths and weaknesses in product design.

GRAPE: genomic relatedness detection pipeline

Classifying the degree of relatedness between pairs of individuals has both scientific and commercial applications. As an example, genome-wide association studies (GWAS) may suffer from high rates of false positive results due to unrecognized population structure. This problem becomes especially relevant with recent increases in large-cohort studies. Accurate relationship classification is also required for genetic linkage analysis to identify disease-associated loci. Additionally, DNA relatives matching service is one of the leading drivers for the direct-to-consumer genetic testing market. Despite the availability of scientific and research information on the methods for determining kinship and the accessibility of relevant tools, the assembly of the pipeline, that stably operates on a real-world genotypic data, requires significant research and development resources. Currently, there is no open source end-to-end solution for relatedness detection in genomic data, that is fast, reliable and accurate for both close and distant degrees of kinship, combines all the necessary processing steps to work on real data, and is ready for production integration. To address this, we developed GRAPE: Genomic RelAtedness detection PipelinE. It combines data preprocessing, identity-by-descent (IBD) segments detection, and accurate relationship estimation. The project uses software development best practices, as well as Global Alliance for Genomics and Health (GA4GH) standards and tools. Pipeline efficiency is demonstrated on both simulated and real-world datasets. GRAPE is available from: https://github.com/genxnetwork/grape.

Detecting Human Diseases Relatedness

Due to the ubiquitous availability of the information on the web, there is a great need for a standardized representation of this information. Therefore, developing an efficient algorithm for retrieving information from knowledge graphs is a key challenge for many semantic web applications. This article presents spreading activation over ontology (SAOO) approach in order to detect the relatedness between two human diseases by applying spreading activation algorithm based on bidirectional search technique. The proposed approach detects two diseases relatedness by considering semantic domain knowledge. The methodology of the proposed work is divided into two phases: Semantic Matching and Diseases Relatedness Detection. In semantic matching, diseases within the user-submitted query are semantically identified in the ontology graph. In diseases relatedness detection, the relatedness between the two diseases is detected by using bidirectional-based spreading activation on the ontology graph. The classification of these diseases is provided as well.

Bidirectional Spreading Activation Method for Finding Human Diseases Relatedness Using Well-Formed Disease Ontology

The successful application of semantic web in medical informatics and the fast expanding of biomedical knowledge have prompted to the requirement for a standardized representation of knowledge and an efficient algorithm for querying this extensive information. Spreading activation algorithm is suitable to work on incomplete and large datasets. This article presents a method called SAOO (Spreading Activation over Ontology) which identifies the relatedness between two human diseases by applying spreading activation algorithm based on bidirectional search technique over large disease ontology. The proposed methodology is divided into two phases: Semantic matching and Disease relatedness detection. In Semantic Matching, semantically identify diseases in user's query in the ontology. In the Disease Relatedness Detection, URIs of the diseases are passed to the relatedness detector which returns the set of diseases that may connect them. The proposed method improves the non-semantic medical systems by considering semantic domain knowledge to infer diseases relatedness.

Learning Non-Taxonomic Relations on Demand for Ontology Extension

Learning non-taxonomic relations becomes an important research topic in ontology extension. Most of the existing learning approaches are mainly based on expert crafted corpora. These approaches are normally domain-specific and the corpora acquisition is laborious and costly. On the other hand, based on the static corpora, it is not able to meet personalized needs of semantic relations discovery for various taxonomies. In this paper, we propose a novel approach for learning non-taxonomic relations on demand. For any supplied taxonomy, it can focus on the segment of the taxonomy and collect information dynamically about the taxonomic concepts by using Wikipedia as a learning source. Based on the newly generated corpus, non-taxonomic relations are acquired through three steps: a) semantic relatedness detection; b) relations extraction between concepts; and c) relations generalization within a hierarchy. The proposed approach is evaluated on three different predefined taxonomies and the experimental results show that it is effective in capturing non-taxonomic relations as needed and has good potential for the ontology extension on demand.

Using identity by descent estimation with dense genotype data to detect positive selection

Identification of genomic loci and segments that are identical by descent (IBD) allows inference on problems such as relatedness detection, IBD disease mapping, heritability estimation and detection of recent or ongoing positive selection. Here, employing a novel statistical method, we use IBD to find signals of selection in the Maasai from Kinyawa, Kenya (MKK). In doing so, we demonstrate the advantage of statistical tools that can probabilistically estimate IBD sharing without having to thin genotype data because of linkage disequilibrium (LD), and that allow for both inbreeding and more than one allele to be shared IBD. We use our novel method, GIBDLD, to estimate IBD sharing between all pairs of individuals at all genotyped SNPs in the MKK, and, by looking for genomic regions showing excess IBD sharing in unrelated pairs, find loci that are known to have undergone recent selection (eg, the LCT gene and the HLA region) as well as many novel loci. Intriguingly, those loci that show the highest amount of excess IBD, with the exception of HLA, also show a substantial number of unrelated pairs sharing all four of their alleles IBD. In contrast to other IBD detection methods, GIBDLD provides accurate probabilistic estimates at each locus for all nine possible IBD sharing states between a pair of individuals, thus allowing for consanguinity, while also modeling LD, thus removing the need to thin SNPs. These characteristics will prove valuable for those doing genetic studies, and estimating IBD, in the wide variety of human populations.