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- Publisher Website: 10.1016/j.csbj.2020.12.021
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- PMID: 33489004
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Article: Experimental and bioinformatics considerations in cancer application of single cell genomics
Title | Experimental and bioinformatics considerations in cancer application of single cell genomics |
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Authors | |
Keywords | Single cell genomics Whole genome amplification Single cell somatic variant caller Protocol aware bioinformatics |
Issue Date | 2021 |
Publisher | Research Network of Computational and Structural Biotechnology. The Journal's web site is located at http://journals.sfu.ca/rncsb/index.php/csbj |
Citation | Computational and Structural Biotechnology Journal, 2021, v. 19, p. 343-354 How to Cite? |
Abstract | Single cell genomics offers an unprecedented resolution to interrogate genetic heterogeneity in a patient’s tumour at the intercellular level. However, the DNA yield per cell is insufficient for today’s sequencing library preparation protocols. This necessitates DNA amplification which is a key source of experimental noise. We provide an evaluation of two protocols using micro-fluidics based amplification for whole exome sequencing, which is an experimental scenario commonly used in single cell genomics. The results highlight their respective biases and relative strengths in identification of single nucleotide variations. Towards this end, we introduce a workflow SoVaTSiC, which allows for quality evaluation and somatic variant identification of single cell data. As proof of concept, the framework was applied to study a lung adenocarcinoma tumour. The analysis provides insights into tumour phylogeny by identifying key mutational events in lung adenocarcinoma evolution. The consequence of this inference is supported by the histology of the tumour and demonstrates usefulness of the approach. |
Persistent Identifier | http://hdl.handle.net/10722/302015 |
ISSN | 2023 Impact Factor: 4.4 2023 SCImago Journal Rankings: 1.485 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Tan, JHJ | - |
dc.contributor.author | Kong, SL | - |
dc.contributor.author | Tai, JA | - |
dc.contributor.author | Poh, HM | - |
dc.contributor.author | Yao, F | - |
dc.contributor.author | Sia, YY | - |
dc.contributor.author | Lim, EKH | - |
dc.contributor.author | Takano, AM | - |
dc.contributor.author | Tan, DSW | - |
dc.contributor.author | Javed, A | - |
dc.contributor.author | Hillmer, AM | - |
dc.date.accessioned | 2021-08-21T03:30:19Z | - |
dc.date.available | 2021-08-21T03:30:19Z | - |
dc.date.issued | 2021 | - |
dc.identifier.citation | Computational and Structural Biotechnology Journal, 2021, v. 19, p. 343-354 | - |
dc.identifier.issn | 2001-0370 | - |
dc.identifier.uri | http://hdl.handle.net/10722/302015 | - |
dc.description.abstract | Single cell genomics offers an unprecedented resolution to interrogate genetic heterogeneity in a patient’s tumour at the intercellular level. However, the DNA yield per cell is insufficient for today’s sequencing library preparation protocols. This necessitates DNA amplification which is a key source of experimental noise. We provide an evaluation of two protocols using micro-fluidics based amplification for whole exome sequencing, which is an experimental scenario commonly used in single cell genomics. The results highlight their respective biases and relative strengths in identification of single nucleotide variations. Towards this end, we introduce a workflow SoVaTSiC, which allows for quality evaluation and somatic variant identification of single cell data. As proof of concept, the framework was applied to study a lung adenocarcinoma tumour. The analysis provides insights into tumour phylogeny by identifying key mutational events in lung adenocarcinoma evolution. The consequence of this inference is supported by the histology of the tumour and demonstrates usefulness of the approach. | - |
dc.language | eng | - |
dc.publisher | Research Network of Computational and Structural Biotechnology. The Journal's web site is located at http://journals.sfu.ca/rncsb/index.php/csbj | - |
dc.relation.ispartof | Computational and Structural Biotechnology Journal | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Single cell genomics | - |
dc.subject | Whole genome amplification | - |
dc.subject | Single cell somatic variant caller | - |
dc.subject | Protocol aware bioinformatics | - |
dc.title | Experimental and bioinformatics considerations in cancer application of single cell genomics | - |
dc.type | Article | - |
dc.identifier.email | Javed, A: javed@hku.hk | - |
dc.identifier.authority | Javed, A=rp02386 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1016/j.csbj.2020.12.021 | - |
dc.identifier.pmid | 33489004 | - |
dc.identifier.pmcid | PMC7788095 | - |
dc.identifier.scopus | eid_2-s2.0-85098709023 | - |
dc.identifier.hkuros | 324276 | - |
dc.identifier.volume | 19 | - |
dc.identifier.spage | 343 | - |
dc.identifier.epage | 354 | - |
dc.identifier.isi | WOS:000684869700005 | - |
dc.publisher.place | Denmark | - |