来自亚利桑那州的两个土著美国人的De Novo基因组组合在非参考序列中识别了新的多态性
Çiğdem Köroğlu1, Peng Chen1, Michael Traurig1
1Diabetes Molecular Genetics Section, Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ 85004, USA.
Genome biology and evolution
|August 27, 2024
概括
为了使人类遗传研究多样化,需要改进参考基因组. 将来自美国土著人的非参考序列 (NRS) 纳入,揭示了数千个遗漏的遗传变异,增强了在代表性不足的人群中的变异检测.
科学领域:
- 基因组学就是基因组学.
- 人口遗传学 人口遗传学
- 生物信息学是一种生物信息学.
背景情况:
- 人类遗传学研究越来越多地关注人口多样化,以改善代表性.
- 目前的参考基因组,如GRCh38/hg38,主要以欧洲祖先为基础,不足以分析代表性不足的群体的DNA.
- 将DNA序列与适当的参考基因组对齐是基因分析中的关键第一步.
研究的目的:
- 使用长时间读取的测序技术,为亚利桑那州 (IAZ) 的土著美国人构建新的基因组组件.
- 开发一种修改后的参考基因组,其中包含特定种群的非参考序列 (NRS).
- 评估修改基因组对IAZ全基因组测序数据调用变异的影响.
主要方法:
- 使用两个IAZ个体的长时间读取的测序数据进行了de novo基因组组.
- 在hg38参考基因组中缺少的识别和定非参考序列 (NRSs).
- 通过整合已识别的NRSs创建了一个修改的hg38-NRS参考基因组.
- 对387个IAZ样本进行了全基因组测序 (WGS) 对齐和变异调用,使用hg38和hg38-NRS参考图.
主要成果:
- 生成的 de novo 基因组组件显示每个人大约有 17 Mb 的非参考序列 (NRS),主要是重复元素.
- 将总计240kb的40个NRS定在hg38组件上,创建了hg38-NRS参考基因组.
- hg38-NRS地图在至少5%的IAZ WGS样本中发现了大约50,000个单核酸变异 (SNV),这些变异在hg38地图中被遗漏.
- 在Exon 3下游的HCN2基因内发现了一种新的187bp NRS,它含有调节元素,在IAZ群体中被丰富 (小等位基因频率=0.45).
结论:
- 包括特定人群的非参考序列 (NRSs) 显著改善了在代表性不足的人群中的变异检测.
- 结合NRSs的修改参考基因组可以发现以前错过的常见遗传变异.
- 这种方法对于提高不同种族群体遗传研究的准确性和全面性至关重要.
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