Literature DB >> 33123832

Towards systematic nomenclature for cell-free DNA.

Abel J Bronkhorst1, Vida Ungerer1, Frank Diehl2, Philippe Anker3,4,5, Yuval Dor6, Michael Fleischhacker7, Peter B Gahan8, Lisa Hui9,10,11,12, Stefan Holdenrieder1, Alain R Thierry13,14,15,16.   

Abstract

Cell-free DNA (cfDNA) has become widely recognized as a promising candidate biomarker for minimally invasive characterization of various genomic disorders and other clinical scenarios. However, among the obstacles that currently challenge the general progression of the research field, there remains an unmet need for unambiguous universal cfDNA nomenclature. To address this shortcoming, we classify in this report the different types of cfDNA molecules that occur in the human body based on its origin, genetic traits, and locality. We proceed by assigning existing terms to each of these cfDNA subtypes, while proposing new terms and abbreviations where clarity is lacking and more precise stratification would be beneficial. We then suggest the proper usage of these terms within different contexts and scenarios, focusing mainly on the nomenclature as it relates to the domains of oncology, prenatal testing, and post-transplant surgery surveillance. We hope that these recommendations will serve as useful considerations towards the establishment of universal cfDNA nomenclature in the future. In addition, it is conceivable that many of these recommendations can be transposed to cell-free RNA nomenclature by simply exchanging "DNA" with "RNA" in each acronym/abbreviation. Similarly, when describing DNA and RNA collectively, the suffix can be replaced with "NAs" to indicate nucleic acids.

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Year:  2020        PMID: 33123832      PMCID: PMC7981329          DOI: 10.1007/s00439-020-02227-2

Source DB:  PubMed          Journal:  Hum Genet        ISSN: 0340-6717            Impact factor:   4.132


  84 in total

1.  Detection of β cell death in diabetes using differentially methylated circulating DNA.

Authors:  Eitan M Akirav; Jasmin Lebastchi; Eva M Galvan; Octavian Henegariu; Michael Akirav; Vitaly Ablamunits; Paul M Lizardi; Kevan C Herold
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-09       Impact factor: 11.205

2.  Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing.

Authors:  H Christina Fan; Yair J Blumenfeld; Usha Chitkara; Louanne Hudgins; Stephen R Quake
Journal:  Clin Chem       Date:  2010-06-17       Impact factor: 8.327

Review 3.  Neutrophil-Extracellular Traps, Cell-Free DNA, and Immunothrombosis in Companion Animals: A Review.

Authors:  Robert Goggs; Unity Jeffery; Dana N LeVine; Ronald H L Li
Journal:  Vet Pathol       Date:  2019-07-25       Impact factor: 2.221

Review 4.  Fetal fraction and noninvasive prenatal testing: What clinicians need to know.

Authors:  Lisa Hui; Diana W Bianchi
Journal:  Prenat Diagn       Date:  2019-12-10       Impact factor: 3.050

5.  Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence.

Authors:  Giulio Genovese; Anna K Kähler; Robert E Handsaker; Johan Lindberg; Samuel A Rose; Samuel F Bakhoum; Kimberly Chambert; Eran Mick; Benjamin M Neale; Menachem Fromer; Shaun M Purcell; Oscar Svantesson; Mikael Landén; Martin Höglund; Sören Lehmann; Stacey B Gabriel; Jennifer L Moran; Eric S Lander; Patrick F Sullivan; Pamela Sklar; Henrik Grönberg; Christina M Hultman; Steven A McCarroll
Journal:  N Engl J Med       Date:  2014-11-26       Impact factor: 91.245

6.  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

7.  Agrobacterium tumefaciens ribonucleic acid synthesis in tomato cells and crown gall induction.

Authors:  M Stroun; P Anker; P Gahan; A Rossier; H Greppin
Journal:  J Bacteriol       Date:  1971-05       Impact factor: 3.490

8.  Characterization of the cell-free DNA released by cultured cancer cells.

Authors:  Abel Jacobus Bronkhorst; Johannes F Wentzel; Janine Aucamp; Etresia van Dyk; Lissinda du Plessis; Piet J Pretorius
Journal:  Biochim Biophys Acta       Date:  2015-10-31

9.  Quantifying circulating cell-free DNA in humans.

Authors:  Romain Meddeb; Zahra Al Amir Dache; Simon Thezenas; Amaëlle Otandault; Rita Tanos; Brice Pastor; Cynthia Sanchez; Joelle Azzi; Geoffroy Tousch; Simon Azan; Caroline Mollevi; Antoine Adenis; Safia El Messaoudi; Philippe Blache; Alain R Thierry
Journal:  Sci Rep       Date:  2019-03-26       Impact factor: 4.379

10.  Integrated digital error suppression for improved detection of circulating tumor DNA.

Authors:  Aaron M Newman; Alexander F Lovejoy; Daniel M Klass; David M Kurtz; Jacob J Chabon; Florian Scherer; Henning Stehr; Chih Long Liu; Scott V Bratman; Carmen Say; Li Zhou; Justin N Carter; Robert B West; George W Sledge; Joseph B Shrager; Billy W Loo; Joel W Neal; Heather A Wakelee; Maximilian Diehn; Ash A Alizadeh
Journal:  Nat Biotechnol       Date:  2016-03-28       Impact factor: 54.908

View more
  8 in total

Review 1.  The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies.

Authors:  Ugur Gezer; Abel J Bronkhorst; Stefan Holdenrieder
Journal:  Diagnostics (Basel)       Date:  2022-06-01

2.  Artificial Intelligence and Circulating Cell-Free DNA Methylation Profiling: Mechanism and Detection of Alzheimer's Disease.

Authors:  Ray O Bahado-Singh; Uppala Radhakrishna; Juozas Gordevičius; Buket Aydas; Ali Yilmaz; Faryal Jafar; Khaled Imam; Michael Maddens; Kshetra Challapalli; Raghu P Metpally; Wade H Berrettini; Richard C Crist; Stewart F Graham; Sangeetha Vishweswaraiah
Journal:  Cells       Date:  2022-05-25       Impact factor: 7.666

3.  Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA.

Authors:  Mohammad Amin Kerachian; Marjan Azghandi; Sina Mozaffari-Jovin; Alain R Thierry
Journal:  Clin Epigenetics       Date:  2021-10-18       Impact factor: 6.551

Review 4.  Cell-free DNA analysis in current cancer clinical trials: a review.

Authors:  M Cisneros-Villanueva; L Hidalgo-Pérez; M Rios-Romero; A Cedro-Tanda; C A Ruiz-Villavicencio; K Page; R Hastings; D Fernandez-Garcia; R Allsopp; M A Fonseca-Montaño; S Jimenez-Morales; V Padilla-Palma; J A Shaw; A Hidalgo-Miranda
Journal:  Br J Cancer       Date:  2022-01-13       Impact factor: 7.640

5.  Association of neutrophil extracellular traps with the production of circulating DNA in patients with colorectal cancer.

Authors:  Brice Pastor; Jean-Daniel Abraham; Ekaterina Pisareva; Cynthia Sanchez; Andrei Kudriavstev; Rita Tanos; Alexia Mirandola; Lucia Mihalovičová; Veronique Pezzella; Antoine Adenis; Marc Ychou; Thibault Mazard; Alain R Thierry
Journal:  iScience       Date:  2022-01-30

6.  Circulating Cell-Free DNA Level in Prediction of COVID-19 Severity and Mortality: Correlation of with Haematology and Serum Biochemical Parameters.

Authors:  Sridhar Mishra; Krachi Agarwal; Devanshi B Dubey; Deval B Dubey; Shweta Verma; Nida Shabbir; Rashmi Kushwaha; D Himanshu Reddy; Uma Shankar Singh; Wahid Ali
Journal:  Indian J Clin Biochem       Date:  2022-08-21

7.  Cell-Free DNA Fragmentation Patterns in a Cancer Cell Line.

Authors:  Vida Ungerer; Abel J Bronkhorst; Carsten Uhlig; Stefan Holdenrieder
Journal:  Diagnostics (Basel)       Date:  2022-08-04

8.  Dynamics of Plasma and Urinary Extracellular DNA in Acute Kidney Injury.

Authors:  Alexander Jančuška; Alena Potočárová; Alexandra Gaál Kovalčíková; Ľudmila Podracká; Janka Bábíčková; Peter Celec; Ľubomíra Tóthová
Journal:  Int J Mol Sci       Date:  2022-03-21       Impact factor: 5.923

  8 in total

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