Overview of frequent pattern mining

Ott, Jürg; Park, Taesung

doi:10.5808/gi.22074

Cited by 4 publications

(5 citation statements)

References 77 publications

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“…Cheng et al [23] reported polymorphism of HABP2 and PPARA were signi cantly associated with ischemic stroke, and polymorphism of C807T in ITGA2 increased the risk of ischemic stroke [31]. However, our current and other studies did not nd the associations [5][6][7]30]. The differences in ndings may be attributable to the diverse genetic backgrounds of the subject populations, as genetic polymorphisms vary considerably across ethnic groups.…”

Section: Discussioncontrasting

confidence: 71%

“…These results indicate that the effect of single nucleotide polymorphisms (SNPs) may be weak or restricted to speci c stroke populations or stroke subtypes. Stroke does not follow a Mendelian pattern of inheritance [4], the effect of individual locus alone may be too small to be observed [7], and it is possible the effect of interaction between gene-variant and other gene-variant [8,9]. Thus, single-gene linkage analysis may not effectively reveal the genetic etiology of stroke.…”

Section: Introductionmentioning

confidence: 99%

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Polymorphisms in genes related to inflammation and endothelial function are associated with ischemic stroke and other vascular events in populations at high risk of stroke Short title: A community-based survey and cohort study in southwestern China

Chen,

Luo,

Zhou

et al. 2024

Preprint

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Background To investigate the incidence of ischemic stroke and other vascular events in a population at high risk of stroke and to identify associations of the 19 single nucleotide polymorphisms (SNPs) in genes related to inflammation and endothelial function and interaction among these SNPs with outcomes. Methods According to the China National Stroke Screening Survey program, we performed this multi-center community-based sectional survey and prospective cohort study in the Sichuan of southwestern China from May 2015 to January 2020. The residents from 8 randomly selected communities volunteered to participate in a face-to-face survey. The 19 SNPs in endothelial function and inflammation genes were measured in the high-risk stroke population. A longitudinal study was conducted to assess the outcomes of recruited people who were at high risk for stroke. These patients were followed up for 4.7 years following a face-to-face survey. The primary outcome was a new ischemic stroke, and the secondary outcome was a composite of new vascular events. Results In the cohort of 2698 individuals who were followed up for 4.7 years, 192 subjects (7.1%) experienced various outcomes. Among them, 118 subjects (4.4%) suffered from new ischemic stroke, 24 subjects (0.9%) experienced hemorrhagic stroke, 53 subjects (2.0%) developed myocardial infarction, and 33 subjects (1.2%) passed away. There were significant differences in genotype distribution of TNF rs3093662, IL6Rrs4845625, and TLR4 rs752998 between subjects with and without outcomes by univariate analyses. Generalized multifactor dimensionality reduction (GMDR) analysis showed a significant SNP-SNP interaction among the 19 SNPs. The best outcome model was interaction among IL6R rs4845625, TLR4 rs1927911, and HABP2 rs932650 (P = 0.004). The high-risk interactive genotypes among the 3 SNPs were independently associated with a higher risk for new ischemic stroke (OR = 2.187, 95%CI: 1.256–5.374, P<0.001) and total vascular events (OR = 2.382, 95%CI: 1.423–5.894, P<0.001) after adjustment with covariates. Conclusion Subjects within the high-risk stroke group exhibited a substantially higher occurrence of ischemic stroke and other vascular events. There were associations of specific SNPs in genes related to inflammation and endothelial function with outcomes. The high-risk interactive genotypes among IL6R rs4845625, TLR4 rs1927911, and HABP2 rs932650 were independently associated with a higher risk for new ischemic stroke and other vascular events.

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Section: Discussioncontrasting

confidence: 71%

Section: Introductionmentioning

confidence: 99%

Polymorphisms in genes related to inflammation and endothelial function are associated with ischemic stroke and other vascular events in populations at high risk of stroke Short title: A community-based survey and cohort study in southwestern China

Chen,

Luo,

Zhou

et al. 2024

Preprint

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“…In one of our previous publications 16 , we discussed the rationale for working with patterns rather than single variants and also outlined applications to individual identification. Here, based on large numbers of genotype pairs (and associated variant pairs), we developed an approach to building significant networks of variants that are related to the discrimination between cases and controls.…”

Section: Discussionmentioning

confidence: 99%

“…We want to evaluate all possible genotype pairs in a given dataset and list, for each genotype pair (called a genotype pattern), its frequency in cases and controls. This is accomplished by the Gpairs program 11 , which will, for each genotype pair, create a 2 × 2 table of individuals (see Table 1 in Ott & Park 16 ), with rows representing cases and controls, and columns referring to presence and absence of the given genotype pattern in an individual. We generally disregard genotype patterns occurring in fewer than s individuals (socalled support for the pattern), and the two SNPs furnishing genotype patterns are required to reside on different chromosomes so as to avoid any potential interference with linkage disequilibrium 11 .…”

Section: Methodsmentioning

confidence: 99%

Digenic Analysis Finds Highly Interactive Genetic Variants Underlying Polygenic Traits

Ott,

Wang

2023

MRAJ

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We briefly review our recently published approach to mining digenic genotype patterns, which consist of two genotypes each originating in a different DNA variant. We do this for a genetic case-control study by evaluating all possible pairs of genotypes, distributing the workload over numerous CPUs (threads) in a high-performance computing environment and apply our methods to two known datasets, age-related macular degeneration (AMD) and Parkinson Disease (PD). Based on a list of (e.g., 100,000) genotype pairs with largest genotype pair frequency differences between cases and controls, we determine the number Nu of unique variants occurring in this list. For each unique variant, we find the number of genotype pairs it participates in, which identifies a set of variants “connected” with the given unique variant. Among the total of variants “connected” with all unique variants, only a subset of variants is unique. The ratio of all connected variants divided by that subset of variants is a measure for the overall density or connectedness of variants interacting with each other. We find that variants for the AMD data are much more interconnected than those for PD, at least based on the 100,000 genotype pairs with largest chi-square we investigated. Further, for each of the Nu unique variants, we use the number of variants connected with it as a test statistic, weighted by the inverse of the rank at which the unique variant first occurred in the original list of genotype patterns. This weighing scheme ties the number of connections to the genetics of the trait and allows us to obtain, for each of the Nu unique variants, an empirical significance level by permuting ranks. We find 12 and 8 significant, highly connected variants for AMD and PD, respectively, some of which have previously been identified by other machine learning methods, thus providing credence to our approach. Among the 100,000 genotype pairs investigated for each of AMD and PD, significant variants showed connections with up to 7,093 and 3,777 other variants, respectively. Our approach has been implemented in a freely available piece of software, the Digenic Network Test. Thus, our statistical genetics method can provide important information on the genetic architecture of polygenic traits.

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“…Various statistical and machine learning approaches have been applied to find pairs of genes or of DNA variants underlying digenic traits ( Papadimitriou et al, 2019 ; Okazaki and Ott, 2022 ; Ott and Park, 2022 ). Methods based on market-basket analysis (frequent pattern mining, FPM) apply some form of the Apriori principle ( Agrawal and Srikant, 1994 ), which focuses on common patterns and allows skipping large numbers of infrequent patterns.…”

Section: Introductionmentioning

confidence: 99%

A multi-threaded approach to genotype pattern mining for detecting digenic disease genes

Zhang,

Bhatia,

Park

et al. 2023

Front. Genet.

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To locate disease-causing DNA variants on the human gene map, the customary approach has been to carry out a genome-wide association study for one variant after another by testing for genotype frequency differences between individuals affected and unaffected with disease. So-called digenic traits are due to the combined effects of two variants, often on different chromosomes, while individual variants may have little or no effect on disease. Machine learning approaches have been developed to find variant pairs underlying digenic traits. However, many of these methods have large memory requirements so that only small datasets can be analyzed. The increasing availability of desktop computers with large numbers of processors and suitable programming to distribute the workload evenly over all processors in a machine make a new and relatively straightforward approach possible, that is, to evaluate all existing variant and genotype pairs for disease association. We present a prototype of such a method with two components, Vpairs and Gpairs, and demonstrate its advantages over existing implementations of such well-known algorithms as Apriori and FP-growth. We apply these methods to published case-control datasets on age-related macular degeneration and Parkinson disease and construct an ROC curve for a large set of genotype patterns.

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Overview of frequent pattern mining

Cited by 4 publications

References 77 publications

Polymorphisms in genes related to inflammation and endothelial function are associated with ischemic stroke and other vascular events in populations at high risk of stroke Short title: A community-based survey and cohort study in southwestern China

Polymorphisms in genes related to inflammation and endothelial function are associated with ischemic stroke and other vascular events in populations at high risk of stroke Short title: A community-based survey and cohort study in southwestern China

Digenic Analysis Finds Highly Interactive Genetic Variants Underlying Polygenic Traits

A multi-threaded approach to genotype pattern mining for detecting digenic disease genes

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