Palmer, Abraham A. (2024). Genotypes for CFW mice for GWAS for age-related hearing loss (Version 1). In Genotype data from Crl:CFW(SW)-US_P08 stock of outbred mice. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0ZP46BH

This object contains genotype data for 946 CFW mice for the GWAS for age-related hearing loss. The project is ongoing, and we plan to release the next version when more animals are tested and genotyped.

• 2021 to 2024

• 2024

• Palmer, Abraham A.

• Palmer, Abraham A.

The genotypes at ~4.18 million SNPs on mouse genome build GRCm38 were obtained using low-coverage (mean coverage 0.27x) whole-genome sequencing followed by imputation using STITCH. To determine the accuracy of the genotypes we sequenced 8 samples at >30x coverage and used calls from those samples to estimate the discordance rate, which was 0.45%.

DNA was extracted from mouse spleen tissue using DNAdvance kit (Beckman Coulter). Multiplexed sequencing libraries were prepared using the Twist 96-Plex Library Prep kit (TWIST Bioscience), and then sequenced on a NovaSeq 6000 or NovaSeq X (Illumina). An average of ∼3.2 million reads per sample were obtained (paired end, 150 bp). The reads were aligned to the mouse reference genome GRCm38 (GCA_000001635.2). To generate genotypes at SNPs we used STITCH software (Davies et al. 2016) without reference panel, with the “niterations” parameter set to 40 and a position file as described below, to create a reference panel; then we ran STITCH again with the “niterations” parameter set to 1, using with the above result as a reference panel, filtered resulted genotypes by INFO score > 0.9, and then performed imputation using BEAGLE (Browning and Browning, 2016) . To construct the position file we used low-coverage sequencing data from earlier generations of CFW mice (Zou et al. 2022; Davis et al, 2016). The SNPs on X, Y, and MT chromosomes were not called. After genotypes were called with STITCH, the following SNPs were removed: (1) monomorphic SNPs, (2) SNPs that violate Hardy-Weinberg equilibrium with -log10(p) > 7, and (3) SNPs that have genotype missingness rate > 0.1 based on the results generated by STITCH.

NIH NIDCD (National Institute on Deafness and Other Communication Disorders): R01DC018566

• Biological sciences
• Crl:CFW(SW)-US_P08 stock of outbred mice
• Genetics
• Imputation
• Low-Coverage Whole Genome Sequencing (lc-WGS)
• Mouse
• Swiss Webster (CFW) Mouse

• data

• English

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

Doi: https://doi.org/10.6075/J0ZP46BH

Reference

• Browning BL, Browning SR. Genotype Imputation with Millions of Reference Samples. Am J Hum Genet. 2016 Jan 7;98(1):116-26. PMID: 26748515; PMCID: PMC4716681. https://doi.org/10.1016/j.ajhg.2015.11.020
• Davies, R., Flint, J., Myers, S. et al. Rapid genotype imputation from sequence without reference panels. Nat Genet 48, 965–969 (2016). https://doi.org/10.1038/ng.3594
• Zou J, Gopalakrishnan S, Parker CC, Nicod J, Mott R, Cai N, Lionikas A, Davies RW, Palmer AA, Flint J. Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility. G3 (Bethesda). 2022 Jan 4;12(1):jkab394. PMID: 34791208; PMCID: PMC8728023. https://doi.org/10.1093/g3journal/jkab394

Other resource

• Rat Genes (ratgenes.org)

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• UC Regents

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2024-07-08