Reconstructing and counting genomic fragments through tagmentation-based haploid phasing

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 cr...

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Autores principales:	Patrick P. T. Leong, Aleksandar Mihajlović, Nadežda Bogdanović, Luka Breberina, Larry Xi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/09b5a697e27d46549e20b82bd83e072f
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spelling	oai:doaj.org-article:09b5a697e27d46549e20b82bd83e072f2021-12-02T15:15:04ZReconstructing and counting genomic fragments through tagmentation-based haploid phasing10.1038/s41598-021-97852-w2045-2322https://doaj.org/article/09b5a697e27d46549e20b82bd83e072f2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97852-whttps://doaj.org/toc/2045-2322Abstract 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.Patrick P. T. LeongAleksandar MihajlovićNadežda BogdanovićLuka BreberinaLarry XiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Patrick P. T. Leong Aleksandar Mihajlović Nadežda Bogdanović Luka Breberina Larry Xi Reconstructing and counting genomic fragments through tagmentation-based haploid phasing
description	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.
format	article
author	Patrick P. T. Leong Aleksandar Mihajlović Nadežda Bogdanović Luka Breberina Larry Xi
author_facet	Patrick P. T. Leong Aleksandar Mihajlović Nadežda Bogdanović Luka Breberina Larry Xi
author_sort	Patrick P. T. Leong
title	Reconstructing and counting genomic fragments through tagmentation-based haploid phasing
title_short	Reconstructing and counting genomic fragments through tagmentation-based haploid phasing
title_full	Reconstructing and counting genomic fragments through tagmentation-based haploid phasing
title_fullStr	Reconstructing and counting genomic fragments through tagmentation-based haploid phasing
title_full_unstemmed	Reconstructing and counting genomic fragments through tagmentation-based haploid phasing
title_sort	reconstructing and counting genomic fragments through tagmentation-based haploid phasing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/09b5a697e27d46549e20b82bd83e072f
work_keys_str_mv	AT patrickptleong reconstructingandcountinggenomicfragmentsthroughtagmentationbasedhaploidphasing AT aleksandarmihajlovic reconstructingandcountinggenomicfragmentsthroughtagmentationbasedhaploidphasing AT nadezdabogdanovic reconstructingandcountinggenomicfragmentsthroughtagmentationbasedhaploidphasing AT lukabreberina reconstructingandcountinggenomicfragmentsthroughtagmentationbasedhaploidphasing AT larryxi reconstructingandcountinggenomicfragmentsthroughtagmentationbasedhaploidphasing
_version_	1718387551748751360

Reconstructing and counting genomic fragments through tagmentation-based haploid phasing

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