Dissecting the mechanisms and timing of de novo mutations in primates

项目摘要 每代的从头突变率跨越一个数量级以上， 真核生物和至少两倍的范围之间的灵长类动物。虽然许多研究都集中在这些 在配子发生过程中出现的突变，实验表明，突变率 在胚胎发生过程中，基因突变的比例更高，并且所有突变中有一半已经存在于胚胎发育过程中。 在青春期的生殖细胞。在这个提议中，我们使用来自以下的谱系进行了多个实验： 非人灵长类动物模型恒河猴（Macaca mulatta）来量化数量 以及在胚胎发生和配子发生期间产生的突变类型。一是 通过对多个基因组的基因组进行测序来检测亲本中的胚胎发生突变， 他们的后代。在亲本胚胎发生过程中产生的传递突变将出现 马赛克，使我们能够在一些（但不是所有）后代中检测到它们。通过测序多个 在一个家庭中的兄弟姐妹，我们将能够测量胚胎发生突变率在一个家庭中， 公正的方式。第二，我们将量化男性生殖系嵌合体， 精子测序嵌合突变的频率揭示了它们在人类中发生的时间。 发展通过对从同一品种的个体父系收集的精子进行深度测序， 家系，我们将量化胚胎发生突变的频率，他们的阶段， 他们站了起来。此外，对后代精子的合并测序将有助于估计 胚胎发生突变的分数错过了系谱研究。这两个实验 一起将导致胚胎发生期间突变率的更准确估计。 第三，我们将通过配对的方法发现后代的早期胚胎发生突变， 与胎盘比较在个体发育早期出现的突变 几乎出现在所有细胞中。为了量化这些早期胚胎发生突变，我们将测序 来自同一个测序后代的胎盘。胎盘与血统分离 导致受精后不久的胚胎。比较胎盘中发现的突变 与已发育胚胎的血液样本进行比对， 的突变。这个实验有许多同卵性研究相同的优点 双胞胎，但组织很容易从一个单胞胎出生。

Project Summary The per-generation de novo mutation rate spans more than an order of magnitude among eukaryotes and at least a two-fold range among primates. While many studies focus on those mutations that arise during gametogenesis, experiments have shown that the rate of mutation is higher during embryogenesis, and that half of all mutations are already present in the germline at puberty. In this proposal we carry out multiple experiments using pedigrees from the model nonhuman primate, rhesus macaques (Macaca mulatta), to quantify the number and types of mutations produced during embryogenesis and gametogenesis. First, we detect embryogenic mutations in parents by sequencing the genomes of multiple of their offspring. Transmitted mutations produced during parental embryogenesis will appear mosaically, enabling us to detect them in some, but not all, offspring. By sequencing multiple siblings within a family, we will be able to measure the embryogenic mutation rate in an unbiased manner. Second, we will quantify male germline mosaicism with pooled sperm sequencing. The frequency of mosaic mutations reveals the timing of their genesis in development. By deeply sequencing sperm collected from individual sires of the same pedigrees, we will quantify the frequency of embryogenic mutations and they stage in which they arose. In addition, pooled sequencing of sperm from offspring will help to estimate the fraction of embryogenic mutations missed by pedigree studies. Both of these experiments together will lead to more accurate estimates of the mutation rate during embryogenesis. Third, we will uncover early embryogenic mutations in the offspring via paired comparisons with placenta. Mutations arising very early in an individual's development will appear in almost all cells. To quantify these early embryogenic mutations, we will sequence placentas from the same sequenced offspring. The placenta separates from the lineage leading to the embryo shortly after fertilization. Comparing mutations found in the placenta with those from blood samples of the developed embryo will allow us to delineate the timing of mutations. This experiment has many of the same advantages as studies of monozygotic twins, but with tissues that are readily available from a singleton birth.