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High-throughput single nucleotide variant discovery in E14 mouse embryonic stem cells provides a new reference genome
Danny Incarnato1, Anna Krepelova2, Francesco Neri2
1Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy; Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Fiorentina 1, 53100 Siena, Italy.
Genomics
|July 9, 2014
Summary
Researchers developed a new genome reference for mouse embryonic stem cells (ESCs), identifying millions of genetic variants. This improved reference enhances genome analysis and epigenetic studies in ESCs.
Area of Science:
- Genomics
- Epigenetics
- Stem Cell Biology
Background:
- Mouse E14 embryonic stem cells (ESCs) are crucial for genome-wide studies.
- Existing genome references may limit the accuracy of next-generation sequencing analysis in ESCs.
Purpose of the Study:
- To create an improved genome assembly reference for E14 ESCs.
- To identify and catalog single nucleotide variants (SNVs) within the E14 ESC genome.
- To enhance epigenetic profiling using Reduced Representation Bisulfite Sequencing (RRBS).
Main Methods:
- Whole-genome sequencing data from E14 ESCs (over 2x10^9 sequences).
- Development of a novel E14 genome assembly.
- Reduced Representation Bisulfite Sequencing (RRBS) for DNA methylation analysis.
Main Results:
- A database of approximately 2.7x10^6 single nucleotide variants (SNVs) was generated.
- The new reference increased read mapping by approximately 5%.
- RRBS analysis identified ~120,000 additional CpGs and corrected ~20,000 erroneous CpG calls compared to the mm9 reference.
Conclusions:
- The novel E14 genome assembly reference significantly improves genome analysis accuracy for ESCs.
- The identified SNVs, including those in functional regions, offer insights into ESC molecular biology.
- Enhanced CpG calling through RRBS refines epigenetic landscape characterization in E14 ESCs.
