Population Genetics

Doolittle, Donald P.

doi:10.1007/978-3-642-71734-5

Cited by 6 publications

(1 citation statement)

References 38 publications

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“…We have implemented operators for the encoding phase that demonstrate an additive inheritance model and alternatives [22] (e.g. dominance deviations and heterosis).…”

Section: Methodsmentioning

confidence: 99%

Automated quantitative trait locus analysis (AutoQTL)

Freda

Ghosh

Luo

et al. 2023

Preprint

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Background: Quantitative Trait Locus (QTL) analysis and Genome-Wide Association Studies (GWAS) have the power to identify variants that capture significant levels of phenotypic variance in complex traits. However, effort and time are required to select the best methods and optimize parameters and pre-processing steps. Although machine learning approaches have been shown to greatly assist in optimization and data processing, applying them to QTL analysis and GWAS is challenging due to the complexity of large, heterogenous datasets. Here, we describe proof-of-concept for an automated machine learning approach, AutoQTL, with the ability to automate many complex decisions related to analysis of complex traits and generate diverse solutions to describe relationships that exist in genetic data. Results: Using a dataset of 18 putative QTL from a large-scale GWAS of body mass index in the laboratory rat, Rattus norvegicus, AutoQTL captures the phenotypic variance explained under a standard additive model while also providing evidence of non-additive effects including deviations from additivity and 2-way epistatic interactions from simulated data via multiple optimal solutions. Additionally, feature importance metrics provide different insights into the inheritance models and predictive power of multiple GWAS-derived putative QTL. Conclusions: This proof-of-concept illustrates that automated machine learning techniques can be applied to genetic data and has the potential to detect both additive and non-additive effects via various optimal solutions and feature importance metrics. In the future, we aim to expand AutoQTL to accommodate omics-level datasets with intelligent feature selection strategies.

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“…We have implemented operators for the encoding phase that demonstrate an additive inheritance model and alternatives [22] (e.g. dominance deviations and heterosis).…”

Section: Methodsmentioning

confidence: 99%

Automated quantitative trait locus analysis (AutoQTL)

Freda

Ghosh

Luo

et al. 2023

Preprint

View full text Add to dashboard Cite

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Association of lung cancer death rates by parish with migration rate by age group

Thurmon

Ursin

Wiley

1989

American J Hum Biol

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Geographic distribution of cancer incidence, as judged from death certificates in Louisiana, shows evidence of strong epidemiological forces. Inspection of data on migration and lung cancer frequency shows them to be associated. Inmigrants account for a majority of the lung cancer deaths. Under assumptions of phenotypic complexity stemming from both genetic and environmental components, we used a multiple regression technique to test the significance of this association. Given the nature of the data and the assumptions of the analysis, there was a reasonable level of significance, suggesting that inmigration of older persons may be largely responsible for higher cancer rates in some parishes (counties) in Louisiana.

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On the principle underlying the tabular method to compute coancestry

Chang

Fernando

Grossman

1991

Theoret. Appl. Genetics

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The tabular method to compute coancestry between two individuals is based on the principle that coancestry may be computed as the average coancestry between one individual and the parents of the other, on the condition that the former individual is not a direct descendent of the latter. It follows that coancestry also may be computed as the average of the four coancestries between the parents of the two individuals, on the condition that each individual is not a direct descendent of the other. The requirement for these conditions is explained.

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Population Genetics

Cited by 6 publications

References 38 publications

Automated quantitative trait locus analysis (AutoQTL)

Automated quantitative trait locus analysis (AutoQTL)

Association of lung cancer death rates by parish with migration rate by age group

On the principle underlying the tabular method to compute coancestry

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