Natural genetic variation caused by transposable elements in humans
Natural genetic variation caused by transposable elements in humans
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DOI：
10.1534/genetics.104.031757
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发表时间：
2004-10-01
期刊：
影响因子：
3.3
通讯作者：
Devine, SE
中科院分区：
文献类型：
--
作者：
Bennettt, EA;Coleman, LE;Devine, SE
转座子和转座子样重复元件共同占据了人类基因组序列的44%。为了测量人类转座子引起的遗传变异水平，我们开发了一种新方法来广泛检测人类各种转座子插入多态性。我们首先在不同人类的基因组中鉴定了606，093个插入和缺失（indel）多态性。然后我们筛选这些多态性来检测由从头转座子插入引起的indel。我们的方法是非常有效的，并导致605个非冗余转座子插入多态性在36个不同的人的鉴定。我们估计这代表了人类群体中25-35%的2075种常见转座子多态性。因为我们用一种方法鉴定了所有转座子插入多态性，所以我们可以评估每种转座子引起的相对变异水平。在我们的研究中，平均人类估计有1283个Alu插入多态性，180个L1多态性，56个SVA多态性，和17个与其他形式的动员DNA相关的多态性。总的来说，我们的研究为（i）测量人类转座子插入引起的遗传变异和（ii）鉴定产生这种变异的转座子拷贝提供了重要步骤。
Transposons and transposon-like repetitive elements collectively occupy 44% of the human genome sequence. In an effort to measure the levels of genetic variation that are caused by human transposons, we have developed a new method to broadly detect transposon insertion polymorphisms of all kinds in humans. We began by identifying 606,093 insertion and deletion (indel) polymorphisms in the genomes of diverse humans. We then screened these polymorphisms to detect indels that were caused by de novo transposon insertions. Our method was highly efficient and led to the identification of 605 nonredundant transposon insertion polymorphisms in 36 diverse humans. We estimate that this represents 25-35% of similar to2075 common transposon polymorphisms in human populations. Because we identified all transposon insertion polymorphisms with a single method, we could evaluate the relative levels of variation that were caused by each transposon class. The average human in our study was estimated to harbor 1283 Alu insertion polymorphisms, 180 L1 polymorphisms, 56 SVA polymorphisms, and 17 polymorphisms related to other forms of mobilized DNA. Overall, our study provides significant steps toward (i) measuring the genetic variation that is caused by transposon insertions in humans and (ii) identifying the transposon copies that produce this variation.