@article{MTMT:3232913,
	title = {Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution},
	url = {https://m2.mtmt.hu/api/publication/3232913},
	author = {Abbosh, C and Birkbak, NJ and Wilson, GA and Jamal-Hanjani, M and Constantin, T and Salari, R and Le Quesne, J and Moore, DA and Veeriah, S and Rosenthal, R and Marafioti, T and Kirkizlar, E and Watkins, TBK and McGranahan, N and Ward, S and Martinson, L and Riley, J and Fraioli, F and Al, Bakir M and Gronroos, E and Zambrana, F and Endozo, R and Bi, WL and Fennessy, FM and Sponer, N and Johnson, D and Laycock, J and Shafi, S and Czyzewska-Khan, J and Rowan, A and Chambers, T and Matthews, N and Turajlic, S and Hiley, C and Lee, SM and Forster, MD and Ahmad, T and Falzon, M and Borg, E and Lawrence, D and Hayward, M and Kolvekar, S and Panagiotopoulos, N and Janes, SM and Thakrar, R and Ahmed, A and Blackhall, F and Summers, Y and Hafez, D and Naik, A and Ganguly, A and Kareht, S and Shah, R and Joseph, L and Marie, Quinn A and Crosbie, PA and Naidu, B and Middleton, G and Langman, G and Trotter, S and Nicolson, M and Remmen, H and Kerr, K and Chetty, M and Gomersall, L and Fennell, DA and Nakas, A and Rathinam, S and Anand, G and Khan, S and Russell, P and Ezhil, V and Ismail, B and Irvin-Sellers, M and Prakash, V and Lester, JF and Kornaszewska, M and Attanoos, R and Adams, H and Davies, H and Oukrif, D and Akarca, AU and Hartley, JA and Lowe, HL and Lock, S and Iles, N and Bell, H and Ngai, Y and Elgar, G and Szállási, Zoltán and Schwarz, RF and Herrero, J and Stewart, A and Quezada, SA and Peggs, KS and Van, Loo P and Dive, C and Lin, CJ and Rabinowitz, M and Aerts, HJWL and Hackshaw, A and Shaw, JA and Zimmermann, BG and Swanton, C},
	doi = {10.1038/nature22364},
	journal-iso = {NATURE},
	journal = {NATURE},
	volume = {545},
	unique-id = {3232913},
	issn = {0028-0836},
	abstract = {The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.},
	year = {2017},
	eissn = {1476-4687},
	pages = {446-451},
	orcid-numbers = {Szállási, Zoltán/0000-0001-5395-7509}
}

@article{MTMT:2992681,
	title = {Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance},
	url = {https://m2.mtmt.hu/api/publication/2992681},
	author = {Minarik, G and Repiska, G and Hyblova, M and Nagyova, E and Soltys, K and Budis, J and Duris, F and Sysak, R and Gerykova, Bujalkova M and Vlkova-Izrael, B and Biró, Orsolya and Nagy, Bálint and Szemes, T},
	doi = {10.1371/journal.pone.0144811},
	journal-iso = {PLOS ONE},
	journal = {PLOS ONE},
	volume = {10},
	unique-id = {2992681},
	issn = {1932-6203},
	abstract = {OBJECTIVES: The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods. METHODS: Samples from 130 pregnant women were analyzed by whole genome sequencing on benchtop NGS systems Ion Torrent PGM and MiSeq. The targeted yield of 3 million raw reads on each platform was used for z score calculation. The impact of in silico and physical size selection on analytical performance of the test was studied. RESULTS: Using a z score value of 3 as the cut-off, 98.11% - 100% (104-106/106) specificity and 100% (24/24) sensitivity and 99.06% - 100% (105-106/106) specificity and 100% (24/24) sensitivity were observed for Ion Torrent PGM and MiSeq, respectively. After in silico based size selection both platforms reached 100% specificity and sensitivity. Following the physical size selection z scores of tested trisomic samples increased significantly-p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively. CONCLUSIONS: Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on high-to-ultrahigh throughput NGS systems. The in silico size selection led to higher specificity of the test. Physical size selection performed on isolated DNA led to significant increase in z scores. The observed results could represent a basis for increasing of cost effectiveness of the test and thus help with its penetration worldwide.},
	year = {2015},
	eissn = {1932-6203},
	orcid-numbers = {Biró, Orsolya/0000-0002-4300-3602; Nagy, Bálint/0000-0002-0295-185X}
}