Somatic Mosaicism across Human Tissues Program: Genome Characterization Centers (GCC SMaHT)

摘要： 作为我们提案的补充，“人类组织中的嵌合体，从端粒到端粒”，我们将帮助 使用高度突变的癌细胞系（COLO 829）和配对的 来源于同一个体的正常淋巴母细胞系（COLO 829 BL）。COLO 829的优点 作为体细胞参考标准系统包括大量（> 20，000）确定的体细胞变体， 变异类型的多样性（单核苷酸变异和结构变异），最重要的是， 体细胞变体在其天然单倍型背景下的存在。最后一点对于验证 长读段测序鉴定变异的能力，特别是在传统上“不可映射”的基因片段中， 这些基因组恰恰是可能包含一些最高率的体细胞突变的区域。最后， COLO 829系统已经得到了很好表征，并可立即购买（ATCC）， 不需要任何专门的方法来产生或维持细胞。具体来说，我们将创建 以下三个资源将有助于推进SMaHT网络的使命： 1.我们将建立近端粒到端粒（T2 T）基因组组装的COLO 829和 COLO 829 BL细胞系，这将使我们有一个金标准参考真阳性遗传学 用于随后的混合实验。 2.我们将应用我们的基因组表征中心（GCC）测序方法对COLO 829 和COLO 829 BL细胞系，以及这些细胞系的体外和计算机模拟混合物， 可用于验证用于识别体细胞变异的计算方法的数据集， 变异等位基因频率范围为0.1%-10%。 3.我们将产生可提供给本领域技术人员的预混合形式的COLO 829和COLO 829 BL细胞系。 无限期作为可再生的“假阳性”材料，用于检测低水平的体细胞 所有SMaHT网络中心的变体。

ABSTRACT: As a supplement to our proposal, “Mosaicism in Human Tissues, from Telomere to Telomere,” we will help establish a benchmarking approach using to a hypermutated cancer cell line (COLO829) and the paired normal lymphoblastoid line (COLO829BL) derived from the same individual. Advantages of the COLO829 system as a somatic reference standard include a large (>20,000) number of defined somatic variants, diversity of variant types (single nucleotide variants and structural variants), and, most importantly, the presence of somatic variants in their native haplotype context. This last point is essential for validating the ability of long-read sequencing to identify variants, particularly in the traditionally “unmappable” segments of the genome that are precisely the areas likely to contain some of the highest rates of somatic mutation. Lastly, the COLO829 system is already well-characterized and immediately available for purchase (ATCC) and does not require any specialized methods for generating or maintaining cells. Specifically, we will create the following three resources that will be useful for furthering the mission of the SMaHT network: 1. We will establish near telomere-to-telomere (T2T) genome assemblies of both the COLO829 and COLO829BL cell lines, which will enable us to have a gold standard reference of true positive genetic variants across the entire genome for subsequent mixing experiments. 2. We will apply our Genome Characterization Center’s (GCCs) sequencing approach to the COLO829 and COLO829BL cell lines, as well as in vitro and in silico mixtures of these cell lines, providing datasets that can be used to validate computational approaches for identifying somatic variants at variant allele frequencies ranging from 0.1% to 10%. 3. We will generate pre-mixed versions of the COLO829 and COLO829BL cell lines that can be provided indefinitely as renewable “pseudomosaic” material for benchmarking the detection of low-level somatic variants across all of the SMaHT network centers.