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

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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.