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SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains
Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with eight C57BL/6 and five C57BL/10 closely related inbred substrains. Whole-genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 ind...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205302/ https://www.ncbi.nlm.nih.gov/pubmed/35720252 http://dx.doi.org/10.1016/j.xgen.2022.100102 |
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author | Mortazavi, Milad Ren, Yangsu Saini, Shubham Antaki, Danny St. Pierre, Celine L. Williams, April Sohni, Abhishek Wilkinson, Miles F. Gymrek, Melissa Sebat, Jonathan Palmer, Abraham A. |
author_facet | Mortazavi, Milad Ren, Yangsu Saini, Shubham Antaki, Danny St. Pierre, Celine L. Williams, April Sohni, Abhishek Wilkinson, Miles F. Gymrek, Melissa Sebat, Jonathan Palmer, Abraham A. |
author_sort | Mortazavi, Milad |
collection | PubMed |
description | Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with eight C57BL/6 and five C57BL/10 closely related inbred substrains. Whole-genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 indels, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs), and 2,826 differentially expressed genes (DE genes) among these 14 strains; 312,981 SNPs (89%) distinguished the B6 and B10 lineages. These SNPs were clustered into 28 short segments that are likely due to introgressed haplotypes rather than new mutations. Outside of these introgressed regions, we identified 53 SVs, protein-truncating SNPs, and frameshifting indels that were associated with DE genes. Our results can be used for both forward and reverse genetic approaches and illustrate how introgression and mutational processes give rise to differences among these widely used inbred substrains. |
format | Online Article Text |
id | pubmed-9205302 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-92053022022-06-17 SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains Mortazavi, Milad Ren, Yangsu Saini, Shubham Antaki, Danny St. Pierre, Celine L. Williams, April Sohni, Abhishek Wilkinson, Miles F. Gymrek, Melissa Sebat, Jonathan Palmer, Abraham A. Cell Genom Article Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with eight C57BL/6 and five C57BL/10 closely related inbred substrains. Whole-genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 indels, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs), and 2,826 differentially expressed genes (DE genes) among these 14 strains; 312,981 SNPs (89%) distinguished the B6 and B10 lineages. These SNPs were clustered into 28 short segments that are likely due to introgressed haplotypes rather than new mutations. Outside of these introgressed regions, we identified 53 SVs, protein-truncating SNPs, and frameshifting indels that were associated with DE genes. Our results can be used for both forward and reverse genetic approaches and illustrate how introgression and mutational processes give rise to differences among these widely used inbred substrains. Elsevier 2022-03-09 /pmc/articles/PMC9205302/ /pubmed/35720252 http://dx.doi.org/10.1016/j.xgen.2022.100102 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Mortazavi, Milad Ren, Yangsu Saini, Shubham Antaki, Danny St. Pierre, Celine L. Williams, April Sohni, Abhishek Wilkinson, Miles F. Gymrek, Melissa Sebat, Jonathan Palmer, Abraham A. SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains |
title | SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains |
title_full | SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains |
title_fullStr | SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains |
title_full_unstemmed | SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains |
title_short | SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains |
title_sort | snps, short tandem repeats, and structural variants are responsible for differential gene expression across c57bl/6 and c57bl/10 substrains |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205302/ https://www.ncbi.nlm.nih.gov/pubmed/35720252 http://dx.doi.org/10.1016/j.xgen.2022.100102 |
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