TY  - JOUR
AU  - Abbosh, C
AU  - Birkbak, NJ
AU  - Wilson, GA
AU  - Jamal-Hanjani, M
AU  - Constantin, T
AU  - Salari, R
AU  - Le Quesne, J
AU  - Moore, DA
AU  - Veeriah, S
AU  - Rosenthal, R
AU  - Marafioti, T
AU  - Kirkizlar, E
AU  - Watkins, TBK
AU  - McGranahan, N
AU  - Ward, S
AU  - Martinson, L
AU  - Riley, J
AU  - Fraioli, F
AU  - Al, Bakir M
AU  - Gronroos, E
AU  - Zambrana, F
AU  - Endozo, R
AU  - Bi, WL
AU  - Fennessy, FM
AU  - Sponer, N
AU  - Johnson, D
AU  - Laycock, J
AU  - Shafi, S
AU  - Czyzewska-Khan, J
AU  - Rowan, A
AU  - Chambers, T
AU  - Matthews, N
AU  - Turajlic, S
AU  - Hiley, C
AU  - Lee, SM
AU  - Forster, MD
AU  - Ahmad, T
AU  - Falzon, M
AU  - Borg, E
AU  - Lawrence, D
AU  - Hayward, M
AU  - Kolvekar, S
AU  - Panagiotopoulos, N
AU  - Janes, SM
AU  - Thakrar, R
AU  - Ahmed, A
AU  - Blackhall, F
AU  - Summers, Y
AU  - Hafez, D
AU  - Naik, A
AU  - Ganguly, A
AU  - Kareht, S
AU  - Shah, R
AU  - Joseph, L
AU  - Marie, Quinn A
AU  - Crosbie, PA
AU  - Naidu, B
AU  - Middleton, G
AU  - Langman, G
AU  - Trotter, S
AU  - Nicolson, M
AU  - Remmen, H
AU  - Kerr, K
AU  - Chetty, M
AU  - Gomersall, L
AU  - Fennell, DA
AU  - Nakas, A
AU  - Rathinam, S
AU  - Anand, G
AU  - Khan, S
AU  - Russell, P
AU  - Ezhil, V
AU  - Ismail, B
AU  - Irvin-Sellers, M
AU  - Prakash, V
AU  - Lester, JF
AU  - Kornaszewska, M
AU  - Attanoos, R
AU  - Adams, H
AU  - Davies, H
AU  - Oukrif, D
AU  - Akarca, AU
AU  - Hartley, JA
AU  - Lowe, HL
AU  - Lock, S
AU  - Iles, N
AU  - Bell, H
AU  - Ngai, Y
AU  - Elgar, G
AU  - Szállási, Zoltán
AU  - Schwarz, RF
AU  - Herrero, J
AU  - Stewart, A
AU  - Quezada, SA
AU  - Peggs, KS
AU  - Van, Loo P
AU  - Dive, C
AU  - Lin, CJ
AU  - Rabinowitz, M
AU  - Aerts, HJWL
AU  - Hackshaw, A
AU  - Shaw, JA
AU  - Zimmermann, BG
AU  - Swanton, C
TI  - Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution
JF  - NATURE
J2  - NATURE
VL  - 545
PY  - 2017
IS  - 7655
SP  - 446
EP  - 451
PG  - 6
SN  - 0028-0836
DO  - 10.1038/nature22364
UR  - https://m2.mtmt.hu/api/publication/3232913
ID  - 3232913
N1  - These authors contributed equally to this work.
Christopher Abbosh, Nicolai J. Birkbak, Gareth A. Wilson, 
Mariam Jamal-Hanjani, Tudor Constantin, Raheleh Salari & John 
Le Quesne

 D.A.M. and S.V. contributed equally to this work
as joint second authors.
CN TRACERx consortium
CN PEACE consortium
AB  - 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.
LA  - English
DB  - MTMT
ER  - 

TY  - JOUR
AU  - Minarik, G
AU  - Repiska, G
AU  - Hyblova, M
AU  - Nagyova, E
AU  - Soltys, K
AU  - Budis, J
AU  - Duris, F
AU  - Sysak, R
AU  - Gerykova, Bujalkova M
AU  - Vlkova-Izrael, B
AU  - Biró, Orsolya
AU  - Nagy, Bálint
AU  - Szemes, T
TI  - 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
JF  - PLOS ONE
J2  - PLOS ONE
VL  - 10
PY  - 2015
IS  - 12
PG  - 12
SN  - 1932-6203
DO  - 10.1371/journal.pone.0144811
UR  - https://m2.mtmt.hu/api/publication/2992681
ID  - 2992681
AB  - 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.
LA  - English
DB  - MTMT
ER  -