Genome-wide association study of delay discounting in Heterogenous Stock rats DOI Creative Commons
Montana Kay Lara, Apurva S. Chitre, Denghui Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 13, 2023

Delay discounting refers to the behavioral tendency devalue rewards as a function of their delay in receipt. Heightened has been associated with substance use disorders, well multiple co-occurring psychopathologies. Genetic studies humans and animal models have established that is heritable trait, but only few specific genes discounting. Here, we aimed identify novel genetic loci through genome-wide association study (GWAS) using Heterogenous Stock rats, genetically diverse outbred population derived from eight inbred founder strains. We assessed 650 male female rats an adjusting amount procedure which chose between smaller immediate sucrose or larger reward at variable delays. Preference switch points were calculated for each rat both exponential hyperbolic functions fitted these indifference points. Area under curve (AUC) parameter

Language: Английский

Development of a single‐nucleotide polymorphism panel genotyping system for genetic analysis of Chinese hamsters DOI Creative Commons

Minghe Sun,

Yafang Guo,

Zhaorui Ren

et al.

Animal Models and Experimental Medicine, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Abstract Chinese hamster with characteristics is used in experiments, and it of great value the field medical biology research. However, at present, there no high‐efficiency method for evaluating genetic quality hamsters. Here, we developed a novel detection system using single‐nucleotide polymorphism (SNP) markers. To find SNP loci, conducted whole genome sequencing on 24 Then, employed an locus screening criterion that set up previously initially screened 214 loci wide distribution high level. Subsequently, multitarget region capture technique based second‐generation sequencing, 55 panel evaluation populations was developed. PopGen.32. analysis results showed average effective allele number, Shannon index, observed heterozygosity, expected information, other parameters population A were higher than those B. Using scientific optimization, successfully can efficiently accurately analyze population.

Language: Английский

Citations

0
Versatile functions of methyl-CpG-binding domain 2 (MBD2) in cellular characteristics and differentiation DOI

Rabia Tuana Lekesiz,

Kerim Koca,

Gizem Kugu

et al.

Molecular Biology Reports, Journal Year: 2025, Volume and Issue: 52(1)

Published: March 15, 2025

Language: Английский

Citations

0
Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils DOI Open Access

Yafang Guo,

Yutong Cui,

Minghe Sun

et al.

Genes, Journal Year: 2024, Volume and Issue: 15(6), P. 817 - 817

Published: June 20, 2024

The Mongolian gerbil is a distinctive experimental animal in China, as its genetic qualities possess significant value the field of medical biology research. Here, we aimed to establish an economical and efficient panel for quality detection gerbils using single-nucleotide polymorphism (SNP) markers. To search SNPs, conducted whole-genome sequencing (WGS) 40 from outbred populations. Reliable screening criteria were established preliminarily select SNPs with wide genome distribution high levels polymorphism. Subsequently, multiple-target regional capture system based on second-generation was developed SNP genotyping. Based results WGS, 219 selected, they optimized multiple-amplification that included 206 loci by genotyping three PopGen.32 analysis revealed average effective allele number, Shannon index, observed heterozygosity, expected information content, other population parameters Capital Medical University (CMU) highest, followed those Zhejiang Dalian gerbils. Through scientific optimization, successfully novel, robust, cost-effective utilizing markers first time.

Language: Английский

Citations

1
A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations DOI
Denghui Chen, Apurva S. Chitre, Khai-Minh H Nguyen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 18, 2024

Affordable sequencing and genotyping methods are essential for large scale genome-wide association studies. While microarrays reference panels imputation available human subjects, non-human model systems often lack such options. Our lab previously demonstrated an efficient cost-effective method to genotype heterogeneous stock rats using double-digest genotyping-by-sequencing. However, low-coverage whole-genome offers alternative that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy N/NIH can use combination of data generated by genotyping-by-sequencing more recently whole-genome-sequencing data. Using from 5,745 (mean 0.21x coverage) 8,760 0.27x coverage), impute 7.32 million bi-allelic single-nucleotide polymorphisms with concordance rate >99.76% compared high-coverage 33.26x subset the same individuals. results demonstrate feasibility or accurate genotyping, techniques may also be useful other genetic studies in subjects.

Language: Английский

Citations

1
Genome‐wide association study of delay discounting in Heterogeneous Stock rats DOI Creative Commons
Montana Kay Lara, Apurva S. Chitre, Denghui Chen

et al.

Genes Brain & Behavior, Journal Year: 2024, Volume and Issue: 23(4)

Published: Aug. 1, 2024

Delay discounting refers to the behavioral tendency devalue rewards as a function of their delay in receipt. Heightened has been associated with substance use disorders and multiple co-occurring psychopathologies. Human animal genetic studies have established that is heritable, but only few genes identified. We aimed identify novel loci through genome-wide association study (GWAS) using Heterogeneous Stock (HS) rats, genetically diverse outbred population derived from eight inbred founder strains. assessed 650 male female HS rats an adjusting amount procedure which chose between smaller immediate sucrose or larger reward at various delays. Preference switch points were calculated both exponential hyperbolic functions fitted these indifference points. Area under curve (AUC) parameter k used measures. GWAS for AUC, k, one point identified significant on chromosomes 20 14. The gene Slc35f1, encodes member solute carrier family, was sole within chromosome locus. That locus also contained eQTL suggesting heritable differences expression might be responsible behavior. Adgrl3, latrophilin subfamily G-protein coupled receptor, 14 These findings implicate highlight need further exploration.

Language: Английский

Citations

0
A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations DOI Creative Commons
Denghui Chen, Apurva S. Chitre, Khai-Minh H Nguyen

et al.

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 13, 2024

Abstract Affordable sequencing and genotyping methods are essential for large scale genome-wide association studies. While microarrays reference panels imputation available human subjects, non-human model systems often lack such options. Our lab previously demonstrated an efficient cost-effective method to genotype heterogeneous stock rats using double-digest genotyping-by-sequencing. However, low-coverage whole-genome offers alternative that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy N/NIH can use combination of data generated by genotyping-by-sequencing more recently whole-genome-sequencing data. Using from 5,745 (mean 0.21x coverage) 8,760 0.27x coverage), impute 7.32 million bi-allelic single-nucleotide polymorphisms with concordance rate >99.76% compared high-coverage 33.26x subset the same individuals. results demonstrate feasibility or accurate genotyping, techniques may also be useful other genetic studies in subjects.

Language: Английский

Citations

0
Genome-wide association study of delay discounting in Heterogenous Stock rats DOI Creative Commons
Montana Kay Lara, Apurva S. Chitre, Denghui Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 13, 2023

Delay discounting refers to the behavioral tendency devalue rewards as a function of their delay in receipt. Heightened has been associated with substance use disorders, well multiple co-occurring psychopathologies. Genetic studies humans and animal models have established that is heritable trait, but only few specific genes discounting. Here, we aimed identify novel genetic loci through genome-wide association study (GWAS) using Heterogenous Stock rats, genetically diverse outbred population derived from eight inbred founder strains. We assessed 650 male female rats an adjusting amount procedure which chose between smaller immediate sucrose or larger reward at variable delays. Preference switch points were calculated for each rat both exponential hyperbolic functions fitted these indifference points. Area under curve (AUC) parameter

Language: Английский

Citations

1