Targeted capture enrichment assay for non-invasive prenatal testing of large and small size sub-chromosomal deletions and duplications

Abstract 4550: Dried blood sot sampling as a minimally invasive and accessible method for investigating circulating tumor DNA in diverse cancer settings
Amit Roshan, Fazlur R. Talukdar, Angela An, Emma-Jane Ditter, Ze Zhou, Paulius D. Mennea, Linfang Wu, Maria C. Neofytou, Anita Balakrishnan, Claire M. Connell, Gabriel Funingana, Giovanni Codacci-Pisanelli, Girma Mulisa, Tamrat Abebe, Constanza Linossi, Hui Zhao, Wendy N. Cooper, Huiqi Yang, Rajesh Jena, James D. Brenton, Pippa Corrie, Rebecca C. Fitzgerald, Simon Pacey, Richard Baird and Nitzan Rosenfeld 2025. Abstract 4550: Dried blood sot sampling as a minimally invasive and accessible method for investigating circulating tumor DNA in diverse cancer settings. Cancer Research. 85 (8_Suppl_1), p. Abstract nr 4550. https://doi.org/10.1158/1538-7445.am2025-4550

A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.
Wang, H., Mennea, P.D., Chan, Y.K.E., Cheng, Z., Neofytou, M.C., Surani, A.A., Vijayaraghavan, A., Ditter, E.J., Bowers, R., Eldridge, M.D., Shcherbo, D.S., Smith, C.G., Markowetz, F., Cooper, W.N., Kaplan, T., Rosenfeld, N. and Zhao, H. 2025. A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data. Genome Biology. 26 141. https://doi.org/10.1186/s13059-025-03607-5

Breast Cancer Detection and Treatment Monitoring Using a Noninvasive Prenatal Testing Platform: Utility in Pregnant and Nonpregnant Populations.
Lenaerts, L., Che, H., Brison, N., Neofytou, M., Jatsenko, T., Lefrère, H., Maggen, C., Villela, D., Verheecke, M., Dehaspe, L., Croitor, A., Hatse, S., Wildiers, H., Neven, P. and Amant, F. 2020. Breast Cancer Detection and Treatment Monitoring Using a Noninvasive Prenatal Testing Platform: Utility in Pregnant and Nonpregnant Populations. Clinical Chemistry. 66 (11), pp. 1414-1423. https://doi.org/10.1093/clinchem/hvaa196

Predicting fetoplacental mosaicism during cfDNA-based NIPT.
Neofytou, M. 2020. Predicting fetoplacental mosaicism during cfDNA-based NIPT. Current Opinion in Obstetrics and Gynecology. 32 (2), pp. 152-158. https://doi.org/10.1097/gco.0000000000000610

Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA
Huiwen Che, Darine Villela, Eftychia Dimitriadou, Cindy Melotte, Nathalie Brison, Maria Neofytou, Kris Van Den Bogaert, Olga Tsuiko, Koen Devriendt, Eric Legius, Masoud Zamani Esteki, Thierry Voet and Joris Robert Vermeesch 2020. Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA. Genetics in Medicine. 22 (5), pp. P962-973. https://doi.org/10.1038/s41436-019-0748-y

Genomewide copy number alteration screening of circulating plasma DNA: potential for the detection of incipient tumors
L. Lenaerts, P. Vandenberghe, N. Brison, H. Che, M. Neofytou, M. Verheecke, L. Leemans, C. Maggen, B. Dewaele, L. Dehaspe, S. Vanderschueren, D. Dierickx, V. Vandecaveye, F. Amant and J. R. Vermeesch 2019. Genomewide copy number alteration screening of circulating plasma DNA: potential for the detection of incipient tumors. Annals of Oncology. 30 (1), pp. p85-95. https://doi.org/10.1093/annonc/mdy476

Maternal Constitutional and Acquired Copy Number Variations
Maria Neofytou and Joris Robert Vermeesch 2018. Maternal Constitutional and Acquired Copy Number Variations. in: Noninvasive Prenatal Testing (NIPT): Applied Genomics in Prenatal Screening and Diagnosis Academic Press. pp. 179-188

Unbiased genomewide screening of circulating plasma DNA for cancer detection
L. Lenaerts, N. Brison, M. Neofytou, H. Che, L. Dehaspe, M. Verheecke, C. Maggen, B. Dewaele, S. Vanderschueren, V. Vandecaveye, P. Vandenberghe, J. Vermeesch and F. Amant 2018. Unbiased genomewide screening of circulating plasma DNA for cancer detection. Annals of Oncology. 29 (Supplement 8), p. viii479. https://doi.org/10.1093/annonc/mdy294

Maternal liver transplant: Another cause of discordant fetal sex determination using cell-free DNA.
Maria Neofytou, Nathalie Brison, Kris Van den Bogaert, Luc Dehaspe, Koen Devriendt, Anja Geerts and Joris R. Vermeesch 2018. Maternal liver transplant: Another cause of discordant fetal sex determination using cell-free DNA. Prenatal Diagnosis. 38 (2), pp. 148-150. https://doi.org/10.1002/pd.5194

MeDIP combined with in-solution targeted enrichment followed by NGS: Inter-individual methylation variability of fetal-specific biomarkers and their implementation in a proof of concept study for NIPT
Anna Keravnou, Marios Ioannides, Charalambos Loizides, Kyriakos Tsangaras, Achilleas Achilleos, Petros Mina, Elena Kypri, Michael D. Hadjidaniel, Maria Neofytou, Skevi Kyriacou, Carolina Sismani, George Koumbaris and Philippos C. Patsalis 2018. MeDIP combined with in-solution targeted enrichment followed by NGS: Inter-individual methylation variability of fetal-specific biomarkers and their implementation in a proof of concept study for NIPT. PLoS ONE. 13 (6) e0199010. https://doi.org/10.1371/journal.pone.0199010

Predicting fetoplacental chromosomal mosaicism during non-invasive prenatal testing
Nathalie Brison, Maria Neofytou, Luc Dehaspe, Baran Bayindir, Kris Van Den Bogaert, Griet Van Buggenhout, Leila Dardour, Hilde Peeters, Hilde Van Esch, Annick Vogels, Thomy de Ravel, Eric Legius, Koen Devriendt and Joris R. Vermeesch 2018. Predicting fetoplacental chromosomal mosaicism during non-invasive prenatal testing. Prenatal Diagnosis. 38 (4), pp. 258-266. https://doi.org/10.1002/pd.5223

Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions
Anna Keravnou, Marios Ioannides, Kyriakos Tsangaras, Charalambos Loizides, Michael D. Hadjidaniel, Elisavet a. Papageorgiou, Skevi Kyriakou, Pavlos Antoniou, Petros Mina, Achilleas Achilleos, Maria Neofytou, Elena Kypri, Carolina Sismani, George koumbaris and Philippos C. Patsalis 2016. Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions. Genetics Research. 98 e15. https://doi.org/10.1017/S0016672316000136

Cell-free DNA analysis of targeted genomic regions in maternal plasma for non-invasive prenatal testing of trisomy 21, trisomy 18, trisomy 13, and fetal sex
George Koumbaris, Elena Kypri, Kyriakos Tsangaras, Achilleas Achilleos, Petros Mina, Maria Neofytou, Voula Velissariou, Georgia Christopoulou, Ioannis Kallikas, Alicia González-Liñán, Egle Benusiene, Anna Latos-Bielenska, Pietryga Marek, Alfredo Santana, Nikoletta Nagy, Márta Széll, Piotr Laudanski, Elisavet A. Papageorgiou, Marios Ioannides and Philippos C. Patsalis 2016. Cell-free DNA analysis of targeted genomic regions in maternal plasma for non-invasive prenatal testing of trisomy 21, trisomy 18, trisomy 13, and fetal sex. Clinical Chemistry. 62 (6), pp. 848-855. https://doi.org/10.1373/clinchem.2015.252502