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Literature DB >> 28159966

DNA copy number profiling using single-cell sequencing.

Xuefeng Wang¹, Hao Chen², Nancy R Zhang³.

Abstract

Currently, there is a lack of software for detecting copy number variations and constructing copy number profile for the whole genome from single-cell DNA sequencing data, which are often of low coverage and high technical noises. Here we introduce a new toolkit, SCNV, which features an efficient bin-free segmentation approach and provides the highest resolution possible for breakpoint detection and the subsequent copy number calling. SCNV can auto-tune parameters based on a set of normal cells from the same batch to adjust for the technical noise level of the data, facilitating its application to data gathered from different platforms and different studies.

Mesh：

Substances：
DNA, Neoplasm

Year: 2018 PMID： 28159966 PMCID： PMC6171490 DOI： 10.1093/bib/bbx004

Source DB: PubMed Journal: Brief Bioinform ISSN： 1467-5463 Impact factor: 11.622

19 in total

1. A faster circular binary segmentation algorithm for the analysis of array CGH data.

Authors: E S Venkatraman; Adam B Olshen
Journal: Bioinformatics Date: 2007-01-18 Impact factor: 6.937

2. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.

Authors: Kai Wang; Mingyao Li; Dexter Hadley; Rui Liu; Joseph Glessner; Struan F A Grant; Hakon Hakonarson; Maja Bucan
Journal: Genome Res Date: 2007-10-05 Impact factor: 9.043

Review 3. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications.

Authors: Lei Huang; Fei Ma; Alec Chapman; Sijia Lu; Xiaoliang Sunney Xie
Journal: Annu Rev Genomics Hum Genet Date: 2015-06-11 Impact factor: 8.929

4. Genome-wide copy number analysis of single cells.

Authors: Timour Baslan; Jude Kendall; Linda Rodgers; Hilary Cox; Mike Riggs; Asya Stepansky; Jennifer Troge; Kandasamy Ravi; Diane Esposito; B Lakshmi; Michael Wigler; Nicholas Navin; James Hicks
Journal: Nat Protoc Date: 2012-05-03 Impact factor: 13.491

5. Allele-specific copy number profiling by next-generation DNA sequencing.

Authors: Hao Chen; John M Bell; Nicolas A Zavala; Hanlee P Ji; Nancy R Zhang
Journal: Nucleic Acids Res Date: 2014-12-03 Impact factor: 16.971

6. Tumour evolution inferred by single-cell sequencing.

Authors: Nicholas Navin; Jude Kendall; Jennifer Troge; Peter Andrews; Linda Rodgers; Jeanne McIndoo; Kerry Cook; Asya Stepansky; Dan Levy; Diane Esposito; Lakshmi Muthuswamy; Alex Krasnitz; W Richard McCombie; James Hicks; Michael Wigler
Journal: Nature Date: 2011-03-13 Impact factor: 49.962

7. Global copy number profiling of cancer genomes.

Authors: Xuefeng Wang; Mengjie Chen; Xiaoqing Yu; Natapol Pornputtapong; Hao Chen; Nancy R Zhang; R Scott Powers; Michael Krauthammer
Journal: Bioinformatics Date: 2015-11-16 Impact factor: 6.937

8. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.

Authors: Itay Tirosh; Andrew S Venteicher; Christine Hebert; Leah E Escalante; Anoop P Patel; Keren Yizhak; Jonathan M Fisher; Christopher Rodman; Christopher Mount; Mariella G Filbin; Cyril Neftel; Niyati Desai; Jackson Nyman; Benjamin Izar; Christina C Luo; Joshua M Francis; Aanand A Patel; Maristela L Onozato; Nicolo Riggi; Kenneth J Livak; Dave Gennert; Rahul Satija; Brian V Nahed; William T Curry; Robert L Martuza; Ravindra Mylvaganam; A John Iafrate; Matthew P Frosch; Todd R Golub; Miguel N Rivera; Gad Getz; Orit Rozenblatt-Rosen; Daniel P Cahill; Michelle Monje; Bradley E Bernstein; David N Louis; Aviv Regev; Mario L Suvà
Journal: Nature Date: 2016-11-02 Impact factor: 69.504

DNA copy number profiling using single-cell sequencing.

1. A faster circular binary segmentation algorithm for the analysis of array CGH data.

2. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.

Review 3. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications.

4. Genome-wide copy number analysis of single cells.

5. Allele-specific copy number profiling by next-generation DNA sequencing.

6. Tumour evolution inferred by single-cell sequencing.

7. Global copy number profiling of cancer genomes.

8. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.

9. Assessment of megabase-scale somatic copy number variation using single-cell sequencing.

Review 10. Cancer genomics: one cell at a time.

1. SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing.

2. Copy Number Variation Detection by Single-Cell DNA Sequencing with SCOPE.

3. SCCNV: A Software Tool for Identifying Copy Number Variation From Single-Cell Whole-Genome Sequencing.

4. Single-cell sequencing of the small and AT-skewed genome of malaria parasites.

5. PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity.

6. MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data.

Review 7. Methods for copy number aberration detection from single-cell DNA-sequencing data.

8. Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes.

Review 9. Single-cell multiomics: technologies and data analysis methods.

Review 10. Computational Methods for Single-Cell Imaging and Omics Data Integration.