Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Clonal genotype and population structure inference from single-cell tumor sequencing.

Literature DB >> 27183439

Clonal genotype and population structure inference from single-cell tumor sequencing.

Andrew Roth^1,2, Andrew McPherson^1,3, Emma Laks¹, Justina Biele¹, Damian Yap^1,4, Adrian Wan¹, Maia A Smith¹, Cydney B Nielsen^1,4, Jessica N McAlpine⁵, Samuel Aparicio^1,4, Alexandre Bouchard-Côté⁶, Sohrab P Shah^1,4,7.

Abstract

Single-cell DNA sequencing has great potential to reveal the clonal genotypes and population structure of human cancers. However, single-cell data suffer from missing values and biased allelic counts as well as false genotype measurements owing to the sequencing of multiple cells. We describe the Single Cell Genotyper (https://bitbucket.org/aroth85/scg), an open-source software based on a statistical model coupled with a mean-field variational inference method, which can be used to address these problems and robustly infer clonal genotypes.

Entities: Disease Species

Mesh：

Year: 2016 PMID： 27183439 DOI： 10.1038/nmeth.3867

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

17 in total

Review 1. Single-cell sequencing-based technologies will revolutionize whole-organism science.

Authors: Ehud Shapiro; Tamir Biezuner; Sten Linnarsson
Journal: Nat Rev Genet Date: 2013-07-30 Impact factor: 53.242

2. Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics.

Authors: Charles Gawad; Winston Koh; Stephen R Quake
Journal: Proc Natl Acad Sci U S A Date: 2014-11-25 Impact factor: 11.205

3. Delineating cancer evolution with single-cell sequencing.

Authors: Nicholas E Navin
Journal: Sci Transl Med Date: 2015-07-15 Impact factor: 17.956

4. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.

Authors: Peter Eirew; Adi Steif; Jaswinder Khattra; Gavin Ha; Damian Yap; Hossein Farahani; Karen Gelmon; Stephen Chia; Colin Mar; Adrian Wan; Emma Laks; Justina Biele; Karey Shumansky; Jamie Rosner; Andrew McPherson; Cydney Nielsen; Andrew J L Roth; Calvin Lefebvre; Ali Bashashati; Camila de Souza; Celia Siu; Radhouane Aniba; Jazmine Brimhall; Arusha Oloumi; Tomo Osako; Alejandra Bruna; Jose L Sandoval; Teresa Algara; Wendy Greenwood; Kaston Leung; Hongwei Cheng; Hui Xue; Yuzhuo Wang; Dong Lin; Andrew J Mungall; Richard Moore; Yongjun Zhao; Julie Lorette; Long Nguyen; David Huntsman; Connie J Eaves; Carl Hansen; Marco A Marra; Carlos Caldas; Sohrab P Shah; Samuel Aparicio
Journal: Nature Date: 2014-11-26 Impact factor: 49.962

5. 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

6. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

Authors: Andrew McPherson; Andrew Roth; Emma Laks; Tehmina Masud; Ali Bashashati; Allen W Zhang; Gavin Ha; Justina Biele; Damian Yap; Adrian Wan; Leah M Prentice; Jaswinder Khattra; Maia A Smith; Cydney B Nielsen; Sarah C Mullaly; Steve Kalloger; Anthony Karnezis; Karey Shumansky; Celia Siu; Jamie Rosner; Hector Li Chan; Julie Ho; Nataliya Melnyk; Janine Senz; Winnie Yang; Richard Moore; Andrew J Mungall; Marco A Marra; Alexandre Bouchard-Côté; C Blake Gilks; David G Huntsman; Jessica N McAlpine; Samuel Aparicio; Sohrab P Shah
Journal: Nat Genet Date: 2016-05-16 Impact factor: 38.330

7. Inferring clonal evolution of tumors from single nucleotide somatic mutations.

Authors: Wei Jiao; Shankar Vembu; Amit G Deshwar; Lincoln Stein; Quaid Morris
Journal: BMC Bioinformatics Date: 2014-02-01 Impact factor: 3.169

Review 8. Current challenges in the bioinformatics of single cell genomics.

Authors: Luwen Ning; Geng Liu; Guibo Li; Yong Hou; Yin Tong; Jiankui He
Journal: Front Oncol Date: 2014-01-27 Impact factor: 6.244

9. Inferring clonal composition from multiple sections of a breast cancer.

Authors: Habil Zare; Junfeng Wang; Alex Hu; Kris Weber; Josh Smith; Debbie Nickerson; ChaoZhong Song; Daniela Witten; C Anthony Blau; William Stafford Noble
Journal: PLoS Comput Biol Date: 2014-07-10 Impact factor: 4.475

10. Clonal evolution in breast cancer revealed by single nucleus genome sequencing.

Authors: Yong Wang; Jill Waters; Marco L Leung; Anna Unruh; Whijae Roh; Xiuqing Shi; Ken Chen; Paul Scheet; Selina Vattathil; Han Liang; Asha Multani; Hong Zhang; Rui Zhao; Franziska Michor; Funda Meric-Bernstam; Nicholas E Navin
Journal: Nature Date: 2014-07-30 Impact factor: 49.962

45 in total

Review 1. Machine learning approaches to drug response prediction: challenges and recent progress.

Authors: George Adam; Ladislav Rampášek; Zhaleh Safikhani; Petr Smirnov; Benjamin Haibe-Kains; Anna Goldenberg
Journal: NPJ Precis Oncol Date: 2020-06-15

2. Computational enhancement of single-cell sequences for inferring tumor evolution.

Authors: Sayaka Miura; Louise A Huuki; Tiffany Buturla; Tracy Vu; Karen Gomez; Sudhir Kumar
Journal: Bioinformatics Date: 2018-09-01 Impact factor: 6.937

3. Genotyping tumor clones from single-cell data.

Authors: Nicholas E Navin; Ken Chen
Journal: Nat Methods Date: 2016-06-29 Impact factor: 28.547

4. Mutational landscape of primary, metastatic, and recurrent ovarian cancer reveals c-MYC gains as potential target for BET inhibitors.

Authors: Charles Li; Elena Bonazzoli; Stefania Bellone; Jungmin Choi; Weilai Dong; Gulden Menderes; Gary Altwerger; Chanhee Han; Aranzazu Manzano; Anna Bianchi; Francesca Pettinella; Paola Manara; Salvatore Lopez; Ghanshyam Yadav; Francesco Riccio; Luca Zammataro; Burak Zeybek; Yang Yang-Hartwich; Natalia Buza; Pei Hui; Serena Wong; Antonella Ravaggi; Eliana Bignotti; Chiara Romani; Paola Todeschini; Laura Zanotti; Valentina Zizioli; Franco Odicino; Sergio Pecorelli; Laura Ardighieri; Dan-Arin Silasi; Babak Litkouhi; Elena Ratner; Masoud Azodi; Gloria S Huang; Peter E Schwartz; Richard P Lifton; Joseph Schlessinger; Alessandro D Santin
Journal: Proc Natl Acad Sci U S A Date: 2018-12-24 Impact factor: 11.205

5. Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.

Authors: Davis J McCarthy; Raghd Rostom; Yuanhua Huang; Daniel J Kunz; Petr Danecek; Marc Jan Bonder; Tzachi Hagai; Ruqian Lyu; Wenyi Wang; Daniel J Gaffney; Benjamin D Simons; Oliver Stegle; Sarah A Teichmann
Journal: Nat Methods Date: 2020-03-16 Impact factor: 28.547