Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice
Positional cloning of ENU-induced mutations has traditionally relied on analysis of polymorphic variation between two strains. In contrast, the application of whole-genome sequencing (WGS) has enabled gene discovery in mutant lines maintained on an inbred genetic background. This approach utilizes g...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2018-02-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.117.300292 |
| _version_ | 1818618879678611456 |
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| author | Krista A. Geister Andrew E. Timms David R. Beier |
| author_facet | Krista A. Geister Andrew E. Timms David R. Beier |
| author_sort | Krista A. Geister |
| collection | DOAJ |
| description | Positional cloning of ENU-induced mutations has traditionally relied on analysis of polymorphic variation between two strains. In contrast, the application of whole-genome sequencing (WGS) has enabled gene discovery in mutant lines maintained on an inbred genetic background. This approach utilizes genetic variation derived from ENU-induced variants for mapping and reduces the likelihood of phenotypic variation, making it an ideal method for genetic modifier screening. Here, we describe the results of such a screen, wherein we determined the minimal number of mutant genomic DNA samples to include in our analyses and improved the sensitivity of our screen by individually barcoding each genomic DNA library. We present several unique cases to illustrate this approach’s efficacy, including the discovery of two distinct mutations that generate essentially identical mutant phenotypes, the ascertainment of a non-ENU-induced candidate variant through homozygosity mapping, and an approach for the identification of putative dominant genetic modifiers. |
| first_indexed | 2024-12-16T17:28:36Z |
| format | Article |
| id | doaj.art-a3b72831dd454ce8b7b0edc84f8b4d2f |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-16T17:28:36Z |
| publishDate | 2018-02-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-a3b72831dd454ce8b7b0edc84f8b4d2f2022-12-21T22:22:59ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362018-02-018240140910.1534/g3.117.3002924Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred MiceKrista A. GeisterAndrew E. TimmsDavid R. BeierPositional cloning of ENU-induced mutations has traditionally relied on analysis of polymorphic variation between two strains. In contrast, the application of whole-genome sequencing (WGS) has enabled gene discovery in mutant lines maintained on an inbred genetic background. This approach utilizes genetic variation derived from ENU-induced variants for mapping and reduces the likelihood of phenotypic variation, making it an ideal method for genetic modifier screening. Here, we describe the results of such a screen, wherein we determined the minimal number of mutant genomic DNA samples to include in our analyses and improved the sensitivity of our screen by individually barcoding each genomic DNA library. We present several unique cases to illustrate this approach’s efficacy, including the discovery of two distinct mutations that generate essentially identical mutant phenotypes, the ascertainment of a non-ENU-induced candidate variant through homozygosity mapping, and an approach for the identification of putative dominant genetic modifiers.http://g3journal.org/lookup/doi/10.1534/g3.117.300292Mus musculusColgalt1Plod3Kif20bTgdsFbn2Mutant screen report |
| spellingShingle | Krista A. Geister Andrew E. Timms David R. Beier Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice G3: Genes, Genomes, Genetics Mus musculus Colgalt1 Plod3 Kif20b Tgds Fbn2 Mutant screen report |
| title | Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice |
| title_full | Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice |
| title_fullStr | Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice |
| title_full_unstemmed | Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice |
| title_short | Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice |
| title_sort | optimizing genomic methods for mapping and identification of candidate variants in enu mutagenesis screens using inbred mice |
| topic | Mus musculus Colgalt1 Plod3 Kif20b Tgds Fbn2 Mutant screen report |
| url | http://g3journal.org/lookup/doi/10.1534/g3.117.300292 |
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