April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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撰写可完全复现的论文
｜
455
14.3.2
变异效果预测、排序和变异负荷分析
我们用几分钟时间扼要重述问题，并回顾这部分的实验设计，因为讲到这里我们几
乎忘记之前细节。首先，我们手头上有什么，我们尝试达成什么？我们从一个群体
层级的
VCF
文件开始。其内容是群体的变异列表，该列表很长。我们希望识别导致
法洛四联症这种先天性疾病形成的有害基因。需说明的是，我们并不是尝试找到一
种与这种疾病相关的特定变异，而是寻找与跟疾病有关的基因，因为我们理解不同
病人可能在同一基因中含有不同变异。这个问题的难点在于变异天然存在于所有基
因中，如在足够多的样本探究足够多的变异，你可以轻松发现毫无意义的假关联。
解决该问题的第一步是缩小变异列表，根据它们有多普遍，消除尽可能多的变异，
不管它们是否在
control
样本，不管它们是否具有以及可能具有什么生物学效应。变
异识别结果集绝大多数变异确实都是普通、枯燥和（或）不可能具有任何生物学效
应的。我们想为变异排序，例如，只关注仅
case
样本含有且可能对基因功能产生有
害影响的变异。
变异列表经大幅削减之后，接着分析变异负荷，如图
14-9
所示。分析过程，需寻找
的是基因大小给定的情况下，发生变异的可能性高于偶然的那些基因。
长度为X的基因
在一个群体而非单个个体中观察到的变异
参考
预计变异数
过量变异
（特别是有害变异）
图
14
-
9
：比较多个样本中同一基因的变异负荷
原研究采用
SnpEff
工具预测变异效应，然后用
GEMINI
的
vt
工具根据基因的预测
效应、基因在群体数据库的频次和只在
case
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.