Palmer, Abraham A. (2023). Heterogeneous Stock (HS) Rat Genotypes, Version 1. In Genotype Data from: NIDA Center for GWAS in Outbred Rats. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0028RR4

This collection contains genotype data collected as part of the NIDA Center for GWAS in Outbred rats and more than 10 additional research projects that use N/NIH heterogeneous stock (HS) outbred rats. We obtain genotypes for DNA samples derived from rats that are phenotyped by different research projects. We use these genotypes to perform genome wide association studies (GWAS) and a number of related analyses.

We release updated data every 2-3 months, and provide detailed information on our genotyping pipeline in the Readme file associated with the object.

• Date of data collection: 2014 to 2019. Date of version: 2019-08-15.

• 2023

• Palmer, Abraham A.

• Palmer, Abraham A.

Rat Genome assembly: Rnor_6.0

All software versions used to generate the data in this object are noted below and in the Methods section of the associated publication:
• fastx_toolkit-0.0.14
• Cutadapt v1.9.1
• bwa-0.7.12
• picard-tools-1.141
• GATK IndelRealginer v3.5
• Beagle v4.1
• impute-2.3.2
• java openjdk version “1.8.0_191”
• python 2

Demultiplexing was performed using fastx_toolkit. Barcode, adapter and quality trimming was performed using Cutadapt. The Rattus norvegicus genome assembly rn6 was used as the reference genome for read alignment with the BWA software. We then used GATK IndelRealginer to improve alignment quality by locally realigning reads around a reference set of known indels in 42 whole-genome sequenced inbred rat strains, including the eight HS progenitor strains. Variants were called, and genotype likelihoods were computed at variant sites using ANGSD, under the SAMtools model for genotype likelihoods (ANGSD-SAMtools). Beagle was used to improve the genotyping within the samples without the use of an external reference panel. We used a combination of existing sequencing and array genotyping data from the HS rat founder and other inbred laboratory rat strains (Hermsen et al. 2015) as reference panel for imputation. Imputation by IMPUTE2 was performed in 5Mb windows using the aforementioned reference panels and genetic maps.

NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844).

• Rattus norvegicus

• Biological sciences
• Genetics
• Genotyping-by-sequencing (GBS)
• Heterogeneous stock (HS) rats
• Imputation
• Low-Coverage Whole Genome Sequencing (lc-WGS)
• Rat

• data
• text

• English

Identifier: Abraham A. Palmer: https://orcid.org/0000-0003-3634-0747

Primary associated publication

• Alexander F Gileta, Jianjun Gao, Apurva S Chitre, Hannah V Bimschleger, Celine L St. Pierre, Shyam Gopalakrishnan, Abraham A Palmer, Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats, G3 Genes | Genomes | Genetics, Volume 10, Issue 7, 1 July 2020, Pages 2195–2205. https://doi.org/10.1534/g3.120.401325
• Gunturkun, Mustafa Hakan; Wang, Tengfei; Chitre, Apurva S.; Garcia, Martinez Angel; Holl, Katie; St. Pierre, Celine; Bimschleger, Hannah; Gao, Jianjun; Cheng, Riyan; Polesskaya, Oksana; Solberg Woods, Leah C.; Palmer, Abraham A.; Chen, Hao (2022). Genome-Wide Association Study on Three Behaviors Tested in an Open Field in Heterogeneous Stock Rats Identifies Multiple Loci Implicated in Psychiatric Disorders. Frontiers in Psychiatry. https://doi.org/10.3389/fpsyt.2022.790566

Related data

• Rat Genome Database -- Strain: NMcwi:HS, RRID:RGD_2314009 https://scicrunch.org/resolver/RGD_2314009

Reference

• Hermsen R, de Ligt J, Spee W, Blokzijl F, Schäfer S, Adami E, Boymans S, Flink S, van Boxtel R, van der Weide RH, Aitman T, Hübner N, Simonis M, Tabakoff B, Guryev V, Cuppen E. Genomic landscape of rat strain and substrain variation. BMC Genomics. 2015 May 6; 16(1):357. PMID: 25943489; PMCID: PMC4422378. https://doi.org/10.1186/s12864-015-1594-1

Other resource

• Rat Genes (ratgenes.org)

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• UC Regents

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2024-06-20