1
|
Nodzenski M, Shi M, Krahn JM, Wise AS, Li Y, Li L, Umbach DM, Weinberg CR. GADGETS: a genetic algorithm for detecting epistasis using nuclear families. Bioinformatics 2022; 38:1052-1058. [PMID: 34788792 PMCID: PMC10060691 DOI: 10.1093/bioinformatics/btab766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/08/2021] [Accepted: 11/03/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Epistasis may play an etiologic role in complex diseases, but research has been hindered because identification of interactions among sets of single nucleotide polymorphisms (SNPs) requires exploration of immense search spaces. Current approaches using nuclear families accommodate at most several hundred candidate SNPs. RESULTS GADGETS detects epistatic SNP-sets by applying a genetic algorithm to case-parent or case-sibling data. To allow for multiple epistatic sets, island subpopulations of SNP-sets evolve separately under selection for evident joint relevance to disease risk. The software evaluates the identified SNP-sets via permutation testing and provides graphical visualization. GADGETS correctly identified epistatic SNP-sets in realistically simulated case-parent triads with 10 000 candidate SNPs, far more SNPs than competitors can handle, and it outperformed competitors in simulations with many fewer SNPs. Applying GADGETS to family-based oral-clefting data from dbGaP identified SNP-sets with possible epistatic effects on risk. AVAILABILITY AND IMPLEMENTATION GADGETS is part of the epistasisGA package at https://github.com/mnodzenski/epistasisGA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Michael Nodzenski
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Alison S Wise
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Yuanyuan Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Leping Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| |
Collapse
|
2
|
Chirita-Emandi A, Serban CL, Paul C, Andreescu N, Velea I, Mihailescu A, Serafim V, Tiugan DA, Tutac P, Zimbru C, Puiu M, Niculescu MD. CHDH-PNPLA3 Gene-Gene Interactions Predict Insulin Resistance in Children with Obesity. Diabetes Metab Syndr Obes 2020; 13:4483-4494. [PMID: 33239899 PMCID: PMC7682614 DOI: 10.2147/dmso.s277268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 09/26/2020] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Insulin resistance plays a major role in metabolic syndrome and is recognized as the most common risk factor for non-alcoholic fatty liver disease (NAFLD). Identifying predictors for insulin resistance could optimize screening and prevention. PURPOSE To evaluate the contribution of multiple single nucleotide polymorphisms across genes related to NAFLD and choline metabolism, in predicting insulin resistance in children with obesity. METHODS One hundred fifty-three children with obesity (73 girls), aged 7-18 years, were evaluated within the NutriGen Study (ClinicalTrials.gov-NCT02837367). Insulin resistance was defined by Homeostatic Model Assessment for insulin-resistance cut-offs that accommodated pubertal and gender differences. Anthropometric, metabolic, intake-related variables, and 55 single nucleotide polymorphisms related to NAFLD and choline metabolism were evaluated. Gene-gene interaction effects were assessed using Multiple Data Reduction Software. RESULTS Sixty percent (93/153) of participants showed insulin resistance (58.7% of boys, 63% of girls). Children with insulin resistance presented significantly higher values for standardized body mass index, triglycerides, transaminases and plasma choline when compared to those without insulin resistance. Out of 52 single nucleotide polymorphisms analysed, the interaction between genotypes CHDH(rs12676) and PNPLA3(rs738409) predicted insulin resistance. The model presented a 6/10 cross-validation consistency and 0.58 testing accuracy. Plasma choline levels and alanine aminotransferase modulated the gene interaction effect, significantly improving the model. CONCLUSION The interaction between genotypes in CHDH and PNPLA3 genes, modulated by choline and alanine aminotransferase levels, predicted insulin-resistance status in children with obesity. If replicated in larger cohorts, these findings could help identify metabolic risk in children with obesity.
Collapse
Affiliation(s)
- Adela Chirita-Emandi
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
- Regional Center of Medical Genetics Timis, Clinical Emergency Hospital for Children “Louis Turcanu”, Timisoara, Romania
| | - Costela Lacrimioara Serban
- Regional Center of Medical Genetics Timis, Clinical Emergency Hospital for Children “Louis Turcanu”, Timisoara, Romania
- Department of Functional Sciences, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
| | - Corina Paul
- Pediatrics Department – Pediatrics Discipline II, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
- Pediatrics, Endocrinology and Diabetes Department, Clinic II Pediatrics, “Pius Branzeu” Clinical Emergency County Hospital, Timisoara, Romania
| | - Nicoleta Andreescu
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
- Regional Center of Medical Genetics Timis, Clinical Emergency Hospital for Children “Louis Turcanu”, Timisoara, Romania
- Correspondence: Nicoleta Andreescu Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania Email
| | - Iulian Velea
- Pediatrics Department – Pediatrics Discipline II, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
- Pediatrics, Endocrinology and Diabetes Department, Clinic II Pediatrics, “Pius Branzeu” Clinical Emergency County Hospital, Timisoara, Romania
| | - Alexandra Mihailescu
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
| | - Vlad Serafim
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
- The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Diana-Andreea Tiugan
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
| | - Paul Tutac
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
| | - Cristian Zimbru
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
- Department of Automation and Applied Informatics, Politehnica University of Timisoara, Timisoara, Romania
| | - Maria Puiu
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
- Regional Center of Medical Genetics Timis, Clinical Emergency Hospital for Children “Louis Turcanu”, Timisoara, Romania
| | - Mihai Dinu Niculescu
- Department of Microscopic Morphology - Genetics, Center of Genomic Medicine, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania
- Advanced Nutrigenomics, Cary, NC27511, USA
| |
Collapse
|