Literature DB >> 27681289

Nucleosome mapping in plasma DNA predicts cancer gene expression.

Muhammed Murtaza1, Carlos Caldas2.   

Abstract

A new study demonstrates that genomic sequencing coverage of plasma DNA fragments around transcription start sites reflects the expression levels of genes in corresponding tumors. This approach may enable noninvasive monitoring of treatment-induced changes in gene expression for patients with cancer.

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Year:  2016        PMID： 27681289     DOI： 10.1038/ng.3686

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


  15 in total

1.  Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus.

Authors:  Y M Dennis Lo; K C Allen Chan; Hao Sun; Eric Z Chen; Peiyong Jiang; Fiona M F Lun; Yama W Zheng; Tak Y Leung; Tze K Lau; Charles R Cantor; Rossa W K Chiu
Journal:  Sci Transl Med       Date:  2010-12-08       Impact factor: 17.956

2.  Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.

Authors:  Tim Forshew; Muhammed Murtaza; Christine Parkinson; Davina Gale; Dana W Y Tsui; Fiona Kaper; Sarah-Jane Dawson; Anna M Piskorz; Mercedes Jimenez-Linan; David Bentley; James Hadfield; Andrew P May; Carlos Caldas; James D Brenton; Nitzan Rosenfeld
Journal:  Sci Transl Med       Date:  2012-05-30       Impact factor: 17.956

3.  [Not Available].

Authors:  P MENDEL; L MANDEL
Journal:  C R Hebd Seances Acad Sci       Date:  1948-06-14

4.  Noninvasive in vivo monitoring of tissue-specific global gene expression in humans.

Authors:  Winston Koh; Wenying Pan; Charles Gawad; H Christina Fan; Geoffrey A Kerchner; Tony Wyss-Coray; Yair J Blumenfeld; Yasser Y El-Sayed; Stephen R Quake
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-05       Impact factor: 11.205

5.  Inferring expressed genes by whole-genome sequencing of plasma DNA.

Authors:  Peter Ulz; Gerhard G Thallinger; Martina Auer; Ricarda Graf; Karl Kashofer; Stephan W Jahn; Luca Abete; Gunda Pristauz; Edgar Petru; Jochen B Geigl; Ellen Heitzer; Michael R Speicher
Journal:  Nat Genet       Date:  2016-08-29       Impact factor: 38.330

6.  Detection of circulating tumor DNA in early- and late-stage human malignancies.

Authors:  Chetan Bettegowda; Mark Sausen; Rebecca J Leary; Isaac Kinde; Yuxuan Wang; Nishant Agrawal; Bjarne R Bartlett; Hao Wang; Brandon Luber; Rhoda M Alani; Emmanuel S Antonarakis; Nilofer S Azad; Alberto Bardelli; Henry Brem; John L Cameron; Clarence C Lee; Leslie A Fecher; Gary L Gallia; Peter Gibbs; Dung Le; Robert L Giuntoli; Michael Goggins; Michael D Hogarty; Matthias Holdhoff; Seung-Mo Hong; Yuchen Jiao; Hartmut H Juhl; Jenny J Kim; Giulia Siravegna; Daniel A Laheru; Calogero Lauricella; Michael Lim; Evan J Lipson; Suely Kazue Nagahashi Marie; George J Netto; Kelly S Oliner; Alessandro Olivi; Louise Olsson; Gregory J Riggins; Andrea Sartore-Bianchi; Kerstin Schmidt; le-Ming Shih; Sueli Mieko Oba-Shinjo; Salvatore Siena; Dan Theodorescu; Jeanne Tie; Timothy T Harkins; Silvio Veronese; Tian-Li Wang; Jon D Weingart; Christopher L Wolfgang; Laura D Wood; Dongmei Xing; Ralph H Hruban; Jian Wu; Peter J Allen; C Max Schmidt; Michael A Choti; Victor E Velculescu; Kenneth W Kinzler; Bert Vogelstein; Nickolas Papadopoulos; Luis A Diaz
Journal:  Sci Transl Med       Date:  2014-02-19       Impact factor: 17.956

7.  Circulating mutant DNA to assess tumor dynamics.

Authors:  Frank Diehl; Kerstin Schmidt; Michael A Choti; Katharine Romans; Steven Goodman; Meng Li; Katherine Thornton; Nishant Agrawal; Lori Sokoll; Steve A Szabo; Kenneth W Kinzler; Bert Vogelstein; Luis A Diaz
Journal:  Nat Med       Date:  2007-07-31       Impact factor: 53.440

8.  Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.

Authors:  Matthew W Snyder; Martin Kircher; Andrew J Hill; Riza M Daza; Jay Shendure
Journal:  Cell       Date:  2016-01-14       Impact factor: 41.582

9.  Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing.

Authors:  Rebecca J Leary; Mark Sausen; Isaac Kinde; Nickolas Papadopoulos; John D Carpten; David Craig; Joyce O'Shaughnessy; Kenneth W Kinzler; Giovanni Parmigiani; Bert Vogelstein; Luis A Diaz; Victor E Velculescu
Journal:  Sci Transl Med       Date:  2012-11-28       Impact factor: 17.956

10.  Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.

Authors:  Muhammed Murtaza; Sarah-Jane Dawson; Katherine Pogrebniak; Oscar M Rueda; Elena Provenzano; John Grant; Suet-Feung Chin; Dana W Y Tsui; Francesco Marass; Davina Gale; H Raza Ali; Pankti Shah; Tania Contente-Cuomo; Hossein Farahani; Karey Shumansky; Zoya Kingsbury; Sean Humphray; David Bentley; Sohrab P Shah; Matthew Wallis; Nitzan Rosenfeld; Carlos Caldas
Journal:  Nat Commun       Date:  2015-11-04       Impact factor: 14.919
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  9 in total

1.  Analysis of recurrently protected genomic regions in cell-free DNA found in urine.

Authors:  Havell Markus; Jun Zhao; Tania Contente-Cuomo; Michelle D Stephens; Elizabeth Raupach; Ahuva Odenheimer-Bergman; Sydney Connor; Bradon R McDonald; Bethine Moore; Elizabeth Hutchins; Marissa McGilvrey; Michelina C de la Maza; Kendall Van Keuren-Jensen; Patrick Pirrotte; Ajay Goel; Carlos Becerra; Daniel D Von Hoff; Scott A Celinski; Pooja Hingorani; Muhammed Murtaza
Journal:  Sci Transl Med       Date:  2021-02-17       Impact factor: 19.319

Review 2.  Emerging concepts in liquid biopsies.

Authors:  Samantha Perakis; Michael R Speicher
Journal:  BMC Med       Date:  2017-04-06       Impact factor: 8.775

3.  Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers.

Authors:  Daniela Bezdan; Kirill Grigorev; Cem Meydan; Fanny A Pelissier Vatter; Michele Cioffi; Varsha Rao; Matthew MacKay; Kiichi Nakahira; Philip Burnham; Ebrahim Afshinnekoo; Craig Westover; Daniel Butler; Chris Mozsary; Timothy Donahoe; Jonathan Foox; Tejaswini Mishra; Serena Lucotti; Brinda K Rana; Ari M Melnick; Haiying Zhang; Irina Matei; David Kelsen; Kenneth Yu; David C Lyden; Lynn Taylor; Susan M Bailey; Michael P Snyder; Francine E Garrett-Bakelman; Stephan Ossowski; Iwijn De Vlaminck; Christopher E Mason
Journal:  iScience       Date:  2020-11-25

4.  Feasibility of circulating tumor DNA analysis in dogs with naturally occurring malignant and benign splenic lesions.

Authors:  Patricia Filippsen Favaro; Samuel D Stewart; Bradon R McDonald; Jacob Cawley; Tania Contente-Cuomo; Shukmei Wong; William P D Hendricks; Jeffrey M Trent; Chand Khanna; Muhammed Murtaza
Journal:  Sci Rep       Date:  2022-04-15       Impact factor: 4.996

5.  Evaluation of plasma nucleosome concentrations in dogs with a variety of common cancers and in healthy dogs.

Authors:  H M Wilson-Robles; T Bygott; T K Kelly; T M Miller; P Miller; M Matsushita; J Terrell; M Bougoussa; T Butera
Journal:  BMC Vet Res       Date:  2022-08-31       Impact factor: 2.792

Review 6.  Liquid biopsies to predict CDK4/6 inhibitor efficacy and resistance in breast cancer.

Authors:  Sasha C Main; David W Cescon; Scott V Bratman
Journal:  Cancer Drug Resist       Date:  2022-06-22

7.  Circulating Cell-Free DNA and Colorectal Cancer: A Systematic Review.

Authors:  Veronika Vymetalkova; Klara Cervena; Linda Bartu; Pavel Vodicka
Journal:  Int J Mol Sci       Date:  2018-10-26       Impact factor: 5.923

Review 8.  Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond.

Authors:  Laura Keller; Yassine Belloum; Harriet Wikman; Klaus Pantel
Journal:  Br J Cancer       Date:  2020-09-24       Impact factor: 7.640

9.  OCRDetector: Accurately Detecting Open Chromatin Regions via Plasma Cell-Free DNA Sequencing Data.

Authors:  Jiayin Wang; Liubin Chen; Xuanping Zhang; Yao Tong; Tian Zheng
Journal:  Int J Mol Sci       Date:  2021-05-28       Impact factor: 5.923
  9 in total

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