ddRAD-seq的变异调用和基因型准确性:与20X WGS在层中的比较
Mathilde Doublet1, Fabien Degalez1, Sandrine Lagarrigue1
1PEGASE, INRAE, Institut Agro, Saint Gilles, France.
PloS one
|July 26, 2024
概括
双消化限制位点关联DNA测序 (ddRAD-seq) 提供了一个具有成本效益的替代方案,用于识别和基因型单核酸多态 (SNP) 产母,证明适合常规使用.
科学领域:
- 动物基因组学 动物基因组学
- 分子生物学分子生物学
- 量化遗传学 量化遗传学
背景情况:
- 全基因组测序 (WGS) 目前对于常规的产卵母基因型定型来说太昂贵了.
- 通常使用SNP芯片,但需要替代的,具有成本效益的测序方法.
- 减少代表性测序方法通过针对特定的基因组区域来平衡质量和成本.
研究的目的:
- 评估双消化限制点关联DNA测序 (ddRAD-seq) 用于SNP识别和产母的基因定型.
- 将ddRAD-seq性能与全基因组测序 (WGS) 进行比较.
- 评估数据过门对基因型确定可靠性和SNP数量的影响.
主要方法:
- ddRAD-seq在母上进行,并与WGS数据进行比较.
- 确定了变异调用灵敏度,精度和基因型确定可靠性.
- 分析了SNP呼叫率 (CRSNP) 和每个SNP的平均序列深度 (DPSNP).
主要成果:
- 原始ddRAD-seq识别了349,497个SNP,平均基因型确定可靠性为80%.
- 预期片段内SNP的灵敏度和精度分别为32.4%和96.4%.
- 预期碎片之外的SNP显示CRSNP和DPSNP明显较低,影响了整体可靠性.
结论:
- ddRAD-seq是一种适合于SNP变异呼叫和产母的基因定型的方法.
- 确定CRSNP和DPSNP的过门对于优化基因型确定可靠性和SNP产量至关重要.
- 严格的ddRAD-seq数据质量控制可以产生至少40%的SNP,可靠性为98%.
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