Literature DB >> 26450340

Single-Cell Analysis in Cancer Genomics.

Assieh Saadatpour1, Shujing Lai2, Guoji Guo3, Guo-Cheng Yuan4.   

Abstract

Genetic changes and environmental differences result in cellular heterogeneity among cancer cells within the same tumor, thereby complicating treatment outcomes. Recent advances in single-cell technologies have opened new avenues to characterize the intra-tumor cellular heterogeneity, identify rare cell types, measure mutation rates, and, ultimately, guide diagnosis and treatment. In this paper we review the recent single-cell technological and computational advances at the genomic, transcriptomic, and proteomic levels, and discuss their applications in cancer research.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 26450340      PMCID: PMC5282606          DOI: 10.1016/j.tig.2015.07.003

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  97 in total

1.  Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.

Authors:  Sean C Bendall; Kara L Davis; El-Ad David Amir; Michelle D Tadmor; Erin F Simonds; Tiffany J Chen; Daniel K Shenfeld; Garry P Nolan; Dana Pe'er
Journal:  Cell       Date:  2014-04-24       Impact factor: 41.582

2.  Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape.

Authors:  Eugenio Marco; Robert L Karp; Guoji Guo; Paul Robson; Adam H Hart; Lorenzo Trippa; Guo-Cheng Yuan
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-15       Impact factor: 11.205

Review 3.  Computational and analytical challenges in single-cell transcriptomics.

Authors:  Oliver Stegle; Sarah A Teichmann; John C Marioni
Journal:  Nat Rev Genet       Date:  2015-01-28       Impact factor: 53.242

4.  Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients.

Authors:  Xiaohui Ni; Minglei Zhuo; Zhe Su; Jianchun Duan; Yan Gao; Zhijie Wang; Chenghang Zong; Hua Bai; Alec R Chapman; Jun Zhao; Liya Xu; Tongtong An; Qi Ma; Yuyan Wang; Meina Wu; Yu Sun; Shuhang Wang; Zhenxiang Li; Xiaodan Yang; Jun Yong; Xiao-Dong Su; Youyong Lu; Fan Bai; X Sunney Xie; Jie Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-09       Impact factor: 11.205

5.  Multiplexed ion beam imaging of human breast tumors.

Authors:  Michael Angelo; Sean C Bendall; Rachel Finck; Matthew B Hale; Chuck Hitzman; Alexander D Borowsky; Richard M Levenson; John B Lowe; Scot D Liu; Shuchun Zhao; Yasodha Natkunam; Garry P Nolan
Journal:  Nat Med       Date:  2014-03-02       Impact factor: 53.440

6.  Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue.

Authors:  Michael J Gerdes; Christopher J Sevinsky; Anup Sood; Sudeshna Adak; Musodiq O Bello; Alexander Bordwell; Ali Can; Alex Corwin; Sean Dinn; Robert J Filkins; Denise Hollman; Vidya Kamath; Sireesha Kaanumalle; Kevin Kenny; Melinda Larsen; Michael Lazare; Qing Li; Christina Lowes; Colin C McCulloch; Elizabeth McDonough; Michael C Montalto; Zhengyu Pang; Jens Rittscher; Alberto Santamaria-Pang; Brion D Sarachan; Maximilian L Seel; Antti Seppo; Kashan Shaikh; Yunxia Sui; Jingyu Zhang; Fiona Ginty
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-01       Impact factor: 11.205

7.  Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations.

Authors:  Anders Ståhlberg; Daniel Andersson; Johan Aurelius; Maryam Faiz; Marcela Pekna; Mikael Kubista; Milos Pekny
Journal:  Nucleic Acids Res       Date:  2010-11-25       Impact factor: 16.971

8.  Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.

Authors:  Jens G Lohr; Viktor A Adalsteinsson; Kristian Cibulskis; Atish D Choudhury; Mara Rosenberg; Peter Cruz-Gordillo; Joshua M Francis; Cheng-Zhong Zhang; Alex K Shalek; Rahul Satija; John J Trombetta; Diana Lu; Naren Tallapragada; Narmin Tahirova; Sora Kim; Brendan Blumenstiel; Carrie Sougnez; Alarice Lowe; Bang Wong; Daniel Auclair; Eliezer M Van Allen; Mari Nakabayashi; Rosina T Lis; Gwo-Shu M Lee; Tiantian Li; Matthew S Chabot; Amy Ly; Mary-Ellen Taplin; Thomas E Clancy; Massimo Loda; Aviv Regev; Matthew Meyerson; William C Hahn; Philip W Kantoff; Todd R Golub; Gad Getz; Jesse S Boehm; J Christopher Love
Journal:  Nat Biotechnol       Date:  2014-04-20       Impact factor: 54.908

9.  An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis.

Authors:  Kazuki Kurimoto; Yukihiro Yabuta; Yasuhide Ohinata; Yukiko Ono; Kenichiro D Uno; Rikuhiro G Yamada; Hiroki R Ueda; Mitinori Saitou
Journal:  Nucleic Acids Res       Date:  2006-03-17       Impact factor: 16.971

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

Authors:  Nicholas E Navin
Journal:  Genome Biol       Date:  2014-08-30       Impact factor: 13.583

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  52 in total

1.  Single Cell Omics Approach: A Paradigm Shift in Diagnosis and Therapy of Cancer.

Authors:  Shailendra Dwivedi; Purvi Purohit; Praveen Sharma
Journal:  Indian J Clin Biochem       Date:  2019-01-10

2.  A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data.

Authors:  Martin Barron; Siyuan Zhang; Jun Li
Journal:  Nucleic Acids Res       Date:  2018-02-16       Impact factor: 16.971

Review 3.  Precision targeted therapy of ovarian cancer.

Authors:  Justin Sapiezynski; Oleh Taratula; Lorna Rodriguez-Rodriguez; Tamara Minko
Journal:  J Control Release       Date:  2016-10-14       Impact factor: 9.776

4.  Epigenetic therapy in a new era of medicine: creating and integrating molecular profiles of patients.

Authors:  Ebrahim Afshinnekoo; Christopher E Mason
Journal:  Ann Transl Med       Date:  2016-11

Review 5.  High-dimension single-cell analysis applied to cancer.

Authors:  Lili Wang; Kenneth J Livak; Catherine J Wu
Journal:  Mol Aspects Med       Date:  2017-08-30

Review 6.  Mechanisms and clinical implications of tumor heterogeneity and convergence on recurrent phenotypes.

Authors:  Jasmine A McQuerry; Jeffrey T Chang; David D L Bowtell; Adam Cohen; Andrea H Bild
Journal:  J Mol Med (Berl)       Date:  2017-09-04       Impact factor: 4.599

Review 7.  Recent Advances in the Analysis of Single Cells.

Authors:  Lucas Armbrecht; Petra S Dittrich
Journal:  Anal Chem       Date:  2016-12-07       Impact factor: 6.986

Review 8.  RNA-Seq methods for transcriptome analysis.

Authors:  Radmila Hrdlickova; Masoud Toloue; Bin Tian
Journal:  Wiley Interdiscip Rev RNA       Date:  2016-05-19       Impact factor: 9.957

9.  Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics.

Authors:  Feng Guo; Sixing Li; Mehmet Umut Caglar; Zhangming Mao; Wu Liu; Andrew Woodman; Jamie J Arnold; Claus O Wilke; Tony Jun Huang; Craig E Cameron
Journal:  Cell Rep       Date:  2017-11-07       Impact factor: 9.423

10.  Robust lineage reconstruction from high-dimensional single-cell data.

Authors:  Gregory Giecold; Eugenio Marco; Sara P Garcia; Lorenzo Trippa; Guo-Cheng Yuan
Journal:  Nucleic Acids Res       Date:  2016-05-20       Impact factor: 16.971

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