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- W4283373048 abstract "Abstract In fragmented DNA, PCR-based methods quantify the number of intact regions at a specific amplicon length. However, the relationship between the population of DNA fragments within a sample and the likelihood they will amplify has not been fully described. To address this, we have derived a mathematical equation that relates the distribution profile of a stochastically fragmented DNA sample to the probability that a DNA fragment within that sample can be amplified by any PCR assay of arbitrary length. Two panels of multiplex PCR assays for quantifying fragmented DNA were then developed: a four-plex panel that can be applied to any human DNA sample and used to estimate the percentage of regions that are intact at any length; and a two-plex panel optimized for quantifying circulating cell-free DNA (cfDNA). For these assays, regions of the human genome least affected by copy number aberration were identified and selected; within these copy-neutral regions, each PCR assay was designed to amplify both genomic and bisulfite-converted DNA; and all assays were validated for use in both conventional qPCR and droplet-digital PCR. Finally, using the cfDNA-optimized assays we find evidence of universally conserved nucleosome positioning among individuals." @default.
- W4283373048 created "2022-06-25" @default.
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- W4283373048 date "2022-06-22" @default.
- W4283373048 modified "2023-09-25" @default.
- W4283373048 title "Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite, FFPE and cfDNA sample analysis" @default.
- W4283373048 doi "https://doi.org/10.21203/rs.3.rs-1728412/v1" @default.
- W4283373048 hasPublicationYear "2022" @default.
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