Genotypes for CFW mice for GWAS for age-related hearing loss (Version 1)
Genotyping data in Variant Call Format (VCF)
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- Collection
- Cite This Work
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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
- Description
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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.
- Date Collected
- 2021 to 2024
- Date Issued
- 2024
- Director
- Principal Investigator
- Methods
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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%.
- Technical Details
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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.
- Funding
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NIH NIDCD (National Institute on Deafness and Other Communication Disorders): R01DC018566
- Topics
Format
View formats within this collection
- Language
- English
- Identifier
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Identifier: Abraham A. Palmer: https://orcid.org/0000-0003-3634-0747
- Related Resources
- 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
Reference
Other resource
- License
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Creative Commons Attribution 4.0 International Public License
- Rights Holder
- UC Regents
- Copyright
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Under copyright (US)
Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.
Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.
- Digital Object Made Available By
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Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)
- Last Modified
2024-07-08