Member Publications

Mellert, H; Foreman, T; Jackson, L; Maar, D; Thurston, S; Koch, K; Weaver, A; Cooper, S; Dupuis, N; Sathyanarayana, UG; Greer, J; Hahn, W; Shelton, D; Stonemetz, P; Pestano, GA; Development and Clinical Utility of a Blood-Based Test Service for the Rapid Identification of Actionable Mutations in Non-Small Cell Lung Carcinoma J Mol Diagn, Vol 19 Issue 3 5/1/17:44-416 doi.org/10.1016/j.jmoldx.2016.11.004 Accepted 28 November 2016, Epub 19 April 2017
Polsky, D; Tadepalli, JS; Chang, G; Fleming, NH; Shao, Y; Pavlick, AC; Osman, I; Furtado, M; Spittle, C; Stonemetz, P; Shelton, D; Karlin-Neumann, G Droplet digital PCR monitoring of BRAF and NRAS plasma DNA as biomarkers of treatment response in stage IV melanoma Journal of Clinical Oncology DOI: 10.1200/jco.2014.32.15_suppl.9019cology Vol 32 32, no. 15_suppl (May 20, 2014) 9019-9019
Karlin-Neumann, G; Applications for ddPCR in Oncology, New Findings Show Liquid Biopsy Can Guide Treatments Wiley Analytical Science 8 October 20
Chang, GA; Tadepalli, JS; Shao, Y; Zhang, Y; Weiss, S; Robinson, E; Spittle, C; Furtado, M; Shelton, DN; Karlin-Neumann, G; Pavlick, A; Osman, I; Polsky, D; Sensitivity of plasma BRAFmutant and NRASmutant cell-free DNA assays to detect metastatic melanoma in patients with low RECIST scores and non-RECIST disease progression Molecular Oncology:1/1/16 Epub: 25 September 2015 p. 157-65 Vol 1 No. 1 Pub Med 264477
Beaver, JA; Jelovac, D; Balukrishna, S; Cochran, RL; Croessmann, S; Zabransky, DJ; Wong, HY; Valda Toro, P; Cidado, J; Blair, BG; Chu, D; Burns, T; Higgins, MJ; Stearns, V; Jacobs, L; Habibi, M; Lange, J; Hurley, PJ; Lauring, J; VanDenBerg, DA; Kessler, J; Jeter, S; Samuels, ML; Maar, D; Cope, L; Cimino-Mathews, A; Argani, P; Wolff, AC; Park, BH; Detection of cancer DNA in plasma of patients with early-stage breast cancer 5/15/14 Volume 2 Issue 1 PubMed 2454125
Chang, GA;Wiggins, JM;Corless, BC;Syeda, MM;Tadepalli, JS;Blake, S;Fleming, N;Darvishian, F;Pavlick, A;Berman, R;Shapiro, R;Shao, Y;Karlin-Neumann, G;Spittle, C;Osman, I;Polsky, D; TERT, BRAF, and NRAS mutational heterogeneity between paired primary and metastatic melanoma tumors Journal of Investigative Dermatology 2/19/20 PubMed 32087194
Heredia, NJ;Belgrader, P;Wang, S;Koehler, R;Regan, J;Cosman, AM;Saxonov, S;Hindson, B;Tanner, SC;Brown, AS;Karlin-Neumann, G;Droplet Digital™ PCR quantitation of HER2 expression in FFPE breast cancer samples, Methods, 1/1/13, S20-3 Vol 59 Issue 1 PMID 23036330
Corless, B;Chang, G;Cooper, S;Syeda, M;Shao, Y;Osman, I;Karlin-Neumann, G;Polsky, D; Development of novel mutation-specific droplet digital PCR assays detecting TERT promoter mutations in tumor and plasma samples October 1, 2018

exRNAQC Consortium, Anckaert J, Avila Cobos F, Decock A, Deleu J, De Wever O, De Wilde J, Dhondt B, D’huyvetter T, Everaert C, Fierro C, Helsmoortel HH, Hendrix A, Hulstaert E, Kuersten S, Mestdagh P, Morlion A, Nijs N, Nuytens J, Philippron A, Piofczyk T, Schoofs K, Schroth GP, Vanden Eynde E, Vandesompele E, Van Maerken T, Van Paemel R, Verniers K, Yigit N: Performance of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study. bioRxiv 2021.05.11.442610; doi: https://doi.org/10.1101/2021.05.11.442610.

Drandi D, Decruyenaere P, Ferrante M, Offner F, Vandesompele J, Ferrero S. Nucleic Acid Biomarkers in Waldenström Macroglobulinemia and IgM-MGUS: Current Insights and Clinical Relevance. Diagnostics (Basel). 2022 Apr 12;12(4):969. doi: 10.3390/diagnostics12040969. PMID: 35454017; PMCID: PMC9028641.

Schoofs K, Philippron A, Avila Cobos F, Koster J, Lefever S, Anckaert J, De Looze D, Vandesompele J, Pattyn P, De Preter K. Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions. Sci Data. 2022 Mar 14;9(1):86. doi: 10.1038/s41597-022-01176-x. PMID: 35288573; PMCID: PMC8921197.

Hulstaert E, Levanon K, Morlion A, Van Aelst S, Christidis AA, Zamar R, Anckaert J, Verniers K, Bahar-Shany K, Sapoznik S, Vandesompele J, Mestdagh P. RNA biomarkers from proximal liquid biopsy for diagnosis of ovarian cancer. Neoplasia. 2022 Feb;24(2):155-164. doi: 10.1016/j.neo.2021.12.008. Epub 2022 Jan 5. PMID: 34998206; PMCID: PMC8740458.

Decruyenaere P, Offner F, Vandesompele J. Circulating RNA biomarkers in diffuse large B-cell lymphoma: a systematic review. Exp Hematol Oncol. 2021 Feb 16;10(1):13. doi: 10.1186/s40164-021-00208-3. PMID: 33593440; PMCID: PMC7885416.

Hulstaert E, Morlion A, Avila Cobos F, Verniers K, Nuytens J, Vanden Eynde E, Yigit N, Anckaert J, Geerts A, Hindryckx P, Jacques P, Brusselle G, Bracke KR, Maes T, Malfait T, Derveaux T, Ninclaus V, Van Cauwenbergh C, Roelens K, Roets E, Hemelsoet D, Tilleman K, Brochez L, Kuersten S, Simon LM, Karg S, Kautzky- Willers A, Leutner M, Nöhammer C, Slaby O, Prins RW, Koster J, Lefever S, Schroth GP, Vandesompele J, Mestdagh P. Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas. Cell Rep. 2020 Dec 29;33(13):108552. doi: 10.1016/j.celrep.2020.108552. PMID: 33378673.

Hulstaert E, Morlion A, Levanon K, Vandesompele J, Mestdagh P. Candidate RNA biomarkers in biofluids for early diagnosis of ovarian cancer: A systematic review. Gynecol Oncol. 2021 Feb;160(2):633-642. doi: 10.1016/j.ygyno.2020.11.018. Epub 2020 Nov 27. PMID: 33257015.

Van Paemel R, De Koker A, Caggiano C, Morlion A, Mestdagh P, De Wilde B, Vandesompele J, De Preter K. Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome. Epigenetics. 2021 Jun-Jul;16(7):797-807. doi: 10.1080/15592294.2020.1827714. Epub 2020 Oct 19. PMID: 33074045; PMCID: PMC8216177.

Van Paemel R, De Koker A, Vandeputte C, van Zogchel L, Lammens T, Laureys G, Vandesompele J, Schleiermacher G, Chicard M, Van Roy N, Vicha A, Tytgat GAM, Callewaert N, De Preter K, De Wilde B. Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study. Epigenetics. 2021 Jan- Feb;16(2):196-208. doi: 10.1080/15592294.2020.1790950. Epub 2020 Jul 14. PMID: 32662719; PMCID: PMC7889189.

Helsmoortel H, Everaert C, Lumen N, Ost P, Vandesompele J. Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope? Noncoding RNA Res. 2018 May 23;3(2):64-74. doi: 10.1016/j.ncrna.2018.05.001. Erratum in: Noncoding RNA Res. 2020 Nov 07;5(4):220-221. PMID: 30159441; PMCID: PMC6096408.

Everaert C, Helsmoortel H, Decock A, Hulstaert E, Van Paemel R, Verniers K, Nuytens J, Anckaert J, Nijs N, Tulkens J, Dhondt B, Hendrix A, Mestdagh P, Vandesompele J. Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles. Sci Rep. 2019 Nov 26;9(1):17574. doi: 10.1038/s41598-019-53892-x. PMID: 31772251; PMCID: PMC6879519.

Dhondt B, De Bleser E, Claeys T, Buelens S, Lumen N, Vandesompele J, Beckers A, Fonteyne V, Van der Eecken K, De Bruycker A, Paul J, Gramme P, Ost P. Discovery and validation of a serum microRNA signature to characterize oligo- and polymetastatic prostate cancer: not ready for prime time. World J Urol. 2019 Dec;37(12):2557-2564. doi: 10.1007/s00345-018-2609-8. Epub 2018 Dec 21. PMID: 30578441.

Zeka F, Decock A, Van Goethem A, Vanderheyden K, Demuynck F, Lammens T, Helsmoortel HH, Vermeulen J, Noguera R, Berbegall AP, Combaret V, Schleiermacher G, Laureys G, Schramm A, Schulte JH, Rahmann S, Bienertová-Vašků J, Mazánek P, Jeison M, Ash S, Hogarty MD, Moreno-Smith M, Barbieri E, Shohet J, Berthold F, Van Maerken T, Speleman F, Fischer M, De Preter K, Mestdagh P, Vandesompele J. Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients. JCI Insight. 2018 Dec 6;3(23):e97021. doi: 10.1172/jci.insight.97021. PMID: 30518699; PMCID: PMC6328024.

Buelens S, Claeys T, Dhondt B, Poelaert F, Vynck M, Yigit N, Thas O, Ost P, Vandesompele J, Lumen N, Kumps C. Prognostic and Therapeutic Implications of Circulating Androgen Receptor Gene Copy Number in Prostate Cancer Patients Using Droplet Digital Polymerase Chain Reaction. Clin Genitourin Cancer. 2018 Jun;16(3):197-205.e5. doi: 10.1016/j.clgc.2017.12.008. Epub 2017 Dec 29. PMID: 29366632.

Alexander RP, Kitchen RR, Tosar JP, Roth M, Mestdagh P, Max KEA, Rozowsky J, Kaczor- Urbanowicz KE, Chang J, Balaj L, Losic B, Van Nostrand EL, LaPlante E, Mateescu B, White BS, Yu R, Milosavljevic A, Stolovitzky G, Spengler RM. Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop. Front Genet. 2022 Jan 3;12:778416. doi: 10.3389/fgene.2021.778416. PMID: 35047007; PMCID: PMC8762274.

Morlion A, Everaert C, Nuytens J, Hulstaert E, Vandesompele J, Mestdagh P. Custom long non-coding RNA capture enhances detection sensitivity in different human sample types. RNA Biol. 2021 Oct 15;18(sup1):215-222. doi: 10.1080/15476286.2021.1971438. Epub 2021 Sep 1. PMID: 34470578; PMCID: PMC8682977.

Vergauwen G, Tulkens J, Pinheiro C, Avila Cobos F, Dedeyne S, De Scheerder MA, Vandekerckhove L, Impens F, Miinalainen I, Braems G, Gevaert K, Mestdagh P, Vandesompele J, Denys H, De Wever O, Hendrix A. Robust sequential biophysical fractionation of blood plasma to study variations in the biomolecular landscape of systemically circulating extracellular vesicles across clinical conditions. J Extracell Vesicles. 2021 Aug;10(10):e12122. doi: 10.1002/jev2.12122. Epub 2021 Aug 14. PMID: 34429857; PMCID: PMC8363909.

Van Paemel R, Vandeputte C, Raman L, Van Thorre J, Willems L, Van Dorpe J, Van Der Linden M, De Wilde J, De Koker A, Menten B, Devalck C, Vicha A, Grega M, Schleiermacher G, Iddir Y, Chicard M, van Zogchel L, Stutterheim J, Lak NSM, Tytgat GAM, Laureys G, Speleman F, De Wilde B, Lammens T, De Preter K, Van Roy N. The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples. Eur J Cancer. 2022 Jan;160:12-23. doi: 10.1016/j.ejca.2021.09.022. Epub 2021 Nov 16. PMID: 34794856

Philippron A, Depypere L, Oeyen S, De Laere B, Vandeputte C, Nafteux P, De Preter K, Pattyn P. Evaluation of a marker independent isolation method for circulating tumor cells in esophageal adenocarcinoma. PLoS One. 2021 May 7;16(5):e0251052. doi: 10.1371/journal.pone.0251052. eCollection 2021. PMID: 33961658

Van Paemel R, Vlug R, De Preter K, Van Roy N, Speleman F, Willems L, Lammens T, Laureys G, Schleiermacher G, Tytgat GAM, Astrahantseff K, Deubzer H, De Wilde B. The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: a review. Eur J Pediatr. 2020 Feb;179(2):191-202. doi: 10.1007/s00431-019-03545-y. Epub 2020 Jan 3. PMID: 31897843

Van Roy N, Van Der Linden M, Menten B, Dheedene A, Vandeputte C, Van Dorpe J, Laureys G, Renard M, Sante T, Lammens T, De Wilde B, Speleman F, De Preter K. Shallow Whole Genome Sequencing on Circulating Cell-Free DNA Allows Reliable Noninvasive Copy-Number Profiling in Neuroblastoma Patients. Clin Cancer Res. 2017 Oct 15;23(20):6305-6314. doi: 10.1158/1078-0432.CCR-17-0675. Epub 2017 Jul 14. PMID: 28710315 description