Reconstructing and counting genomic fragments through tagmentation-based haploid phasing
Authors
Leong, Patrick P. T.Mihajlović, Aleksandar
Bogdanović, Nadežda
Breberina, Luka M.
Xi, Larry
Article (Published version)
Metadata
Show full item recordAbstract
Single-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.
Keywords:
algorithm / article / genomic fragment / noise / ploidySource:
Scientific Reports, 2021, 11, 1, 18907-Publisher:
- Nature Research
Note:
- Supplementary material: https://cherry.chem.bg.ac.rs/handle/123456789/4686
Related info:
- Referenced by
https://cherry.chem.bg.ac.rs/handle/123456789/4686
DOI: 10.1038/s41598-021-97852-w
ISSN: 2045-2322
WoS: 000698791600115
Scopus: 2-s2.0-85115350298
Collections
Institution/Community
Hemijski fakultet / Faculty of ChemistryTY - JOUR AU - Leong, Patrick P. T. AU - Mihajlović, Aleksandar AU - Bogdanović, Nadežda AU - Breberina, Luka M. AU - Xi, Larry PY - 2021 UR - https://cherry.chem.bg.ac.rs/handle/123456789/4685 AB - Single-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. PB - Nature Research T2 - Scientific Reports T1 - Reconstructing and counting genomic fragments through tagmentation-based haploid phasing VL - 11 IS - 1 SP - 18907 DO - 10.1038/s41598-021-97852-w ER -
@article{ author = "Leong, Patrick P. T. and Mihajlović, Aleksandar and Bogdanović, Nadežda and Breberina, Luka M. and Xi, Larry", year = "2021", abstract = "Single-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.", publisher = "Nature Research", journal = "Scientific Reports", title = "Reconstructing and counting genomic fragments through tagmentation-based haploid phasing", volume = "11", number = "1", pages = "18907", doi = "10.1038/s41598-021-97852-w" }
Leong, P. P. T., Mihajlović, A., Bogdanović, N., Breberina, L. M.,& Xi, L.. (2021). Reconstructing and counting genomic fragments through tagmentation-based haploid phasing. in Scientific Reports Nature Research., 11(1), 18907. https://doi.org/10.1038/s41598-021-97852-w
Leong PPT, Mihajlović A, Bogdanović N, Breberina LM, Xi L. Reconstructing and counting genomic fragments through tagmentation-based haploid phasing. in Scientific Reports. 2021;11(1):18907. doi:10.1038/s41598-021-97852-w .
Leong, Patrick P. T., Mihajlović, Aleksandar, Bogdanović, Nadežda, Breberina, Luka M., Xi, Larry, "Reconstructing and counting genomic fragments through tagmentation-based haploid phasing" in Scientific Reports, 11, no. 1 (2021):18907, https://doi.org/10.1038/s41598-021-97852-w . .