Reconstructing and counting genomic fragments through tagmentation-based haploid phasing

• DOI: 10.1038/s41598-021-97852-w
• Publication Date: 2021-09-23T10:57:49Z
• Authors: Patrick P. T. Leong; Aleksandar Mihajl...; Nadežda Bogdanović; Luka Breberina; Larry Xi
• Keywords: 0301 basic medicine; noise; Genomic Library; algorithm; DNA Copy Number Variations; Genome, Human; Science; Q; article; R; ploidy; Chromosome Mapping; Saccharomyces cerevisiae; Sequence Analysis, DNA; Haploidy; genomic fragment; Article; 03 medical and health sciences; Neoplasms; Medicine; Humans; Genome, Fungal; Single-Cell Analysis

AbstractSingle-cell sequencing provides a new level of granularity in studying the heterogeneous nature of cancer cells. For some cancers, this heterogeneity is the result of copy number changes of genes within the cellular genomes. The ability to accurately determine such copy number changes is critical in tracing and understanding tumorigenesis. Current single-cell genome sequencing methodologies infer copy numbers based on statistical approaches followed by rounding decimal numbers to integer values. Such methodologies are sample dependent, have varying calling sensitivities which heavily depend on the sample’s ploidy and are sensitive to noise in sequencing data. In this paper we have demonstrated the concept of integer-counting by using a novel bioinformatic algorithm built on our library construction chemistry in order to detect the discrete nature of the genome.