Quantitative characterization of tumor cell-free DNA shortening.

BMC Genomics
Juntang GuoJin Huang


Previous studies found that cell-free DNA (cfDNA) generated from tumors was shorter than that from healthy cells, and selecting short cfDNA could enrich for tumor cfDNA and improve its usage in early cancer diagnosis and treatment monitoring; however, the underlying mechanism of shortened tumor cfDNA was still unknown, which potentially limits its further clinical application. Using targeted sequencing of cfDNA in a large cohort of solid tumor patient, sequencing reads harboring tumor-specific somatic mutations were isolated to examine the exact size distribution of tumor cfDNA. For the majority of studied cases, 166 bp remained as the peak size of tumor cfDNA, with tumor cfDNA showing an increased proportion of short fragments (100-150 bp). Less than 1% of cfDNA samples were found to be peaked at 134/144 bp and independent of tumor cfDNA purity. Using whole-genome sequencing of cfDNA, we discovered a positive correlation between cfDNA shortening and the magnitude of chromatin inaccessibility, as measured by transcription, DNase I hypersensitivity, and histone modifications. Tumor cfDNA shortening occurred simultaneously at both 5' and 3' ends of the DNA wrapped around nucleosomes. Tumor cfDNA shortening exhibited two distincti...Continue Reading


Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Oct 12, 2004·Biostatistics·Adam B OlshenMichael Wigler
Sep 12, 2006·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Naoyuki UmetaniDave S B Hoon
Jan 20, 2007·Bioinformatics·E S Venkatraman, Adam B Olshen
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
May 25, 2010·Nucleic Acids Research·Alain R ThierryFranck Molina
Jun 19, 2010·Clinical Chemistry·H Christina FanStephen R Quake
Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Dec 15, 2010·Science Translational Medicine·Y M Dennis LoRossa W K Chiu
Sep 13, 2011·PloS One·Florent MouliereAlain R Thierry
May 1, 2012·Nature Biotechnology·Scott L CarterGad Getz
Jun 23, 2012·Nature Reviews. Molecular Cell Biology·Karolin LugerDavid J Tremethick
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Nov 29, 2014·Current Protocols in Bioinformatics·Geraldine A Van der AuweraMark A DePristo
Jan 24, 2015·Science·Mathias UhlénFredrik Pontén
Feb 28, 2015·Genome Biology·Marina LizioUNKNOWN FANTOM consortium
Mar 4, 2015·Proceedings of the National Academy of Sciences of the United States of America·Florent Mouliere, Nitzan Rosenfeld
Sep 24, 2015·Proceedings of the National Academy of Sciences of the United States of America·Kun SunYuk Ming Dennis Lo
Jun 28, 2016·Nature Reviews. Genetics·C David Allis, Thomas Jenuwein
Jul 20, 2016·PLoS Genetics·Hunter R UnderhillJay Shendure
Oct 7, 2016·Science·Cristina Morales TorresPaola Scaffidi
Dec 3, 2016·Nucleic Acids Research·Simon A ForbesPeter J Campbell
Feb 25, 2017·Nature Reviews. Cancer·Jonathan C M WanNitzan Rosenfeld
May 16, 2018·Proceedings of the National Academy of Sciences of the United States of America·W K Jacky LamY M Dennis Lo
Oct 31, 2018·Proceedings of the National Academy of Sciences of the United States of America·Peiyong JiangRossa W K Chiu
Nov 9, 2018·Science Translational Medicine·Florent MouliereNitzan Rosenfeld
May 31, 2019·Nature·Stephen CristianoVictor E Velculescu

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