• Je něco špatně v tomto záznamu ?

The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples

R. Van Paemel, C. Vandeputte, L. Raman, J. Van Thorre, L. Willems, J. Van Dorpe, M. Van Der Linden, J. De Wilde, A. De Koker, B. Menten, C. Devalck, A. Vicha, M. Grega, G. Schleiermacher, Y. Iddir, M. Chicard, L. van Zogchel, J. Stutterheim, NSM....

. 2022 ; 160 (-) : 12-23. [pub] 20211116

Jazyk angličtina Země Velká Británie

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc22011460

BACKGROUND: Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity. PROCEDURE: The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma. RESULTS: Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification. CONCLUSION: In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc22011460
003      
CZ-PrNML
005      
20220506130515.0
007      
ta
008      
220425s2022 xxk f 000 0|eng||
009      
AR
024    7_
$a 10.1016/j.ejca.2021.09.022 $2 doi
035    __
$a (PubMed)34794856
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxk
100    1_
$a Van Paemel, Ruben $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Research Foundation Flanders, Belgium
245    14
$a The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples / $c R. Van Paemel, C. Vandeputte, L. Raman, J. Van Thorre, L. Willems, J. Van Dorpe, M. Van Der Linden, J. De Wilde, A. De Koker, B. Menten, C. Devalck, A. Vicha, M. Grega, G. Schleiermacher, Y. Iddir, M. Chicard, L. van Zogchel, J. Stutterheim, NSM. Lak, GAM. Tytgat, G. Laureys, F. Speleman, B. De Wilde, T. Lammens, K. De Preter, N. Van Roy
520    9_
$a BACKGROUND: Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity. PROCEDURE: The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma. RESULTS: Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification. CONCLUSION: In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.
650    _2
$a mladiství $7 D000293
650    _2
$a nádorové biomarkery $x genetika $7 D014408
650    _2
$a volné cirkulující nukleové kyseliny $x genetika $7 D000073888
650    _2
$a dítě $7 D002648
650    _2
$a předškolní dítě $7 D002675
650    _2
$a variabilita počtu kopií segmentů DNA $x genetika $7 D056915
650    _2
$a studie proveditelnosti $7 D005240
650    _2
$a ženské pohlaví $7 D005260
650    _2
$a lidé $7 D006801
650    _2
$a tekutá biopsie $x metody $7 D000073890
650    _2
$a mužské pohlaví $7 D008297
650    _2
$a prospektivní studie $7 D011446
650    _2
$a retrospektivní studie $7 D012189
655    _2
$a časopisecké články $7 D016428
655    _2
$a práce podpořená grantem $7 D013485
700    1_
$a Vandeputte, Charlotte $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
700    1_
$a Raman, Lennart $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
700    1_
$a Van Thorre, Jolien $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
700    1_
$a Willems, Leen $u Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
700    1_
$a Van Dorpe, Jo $u Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
700    1_
$a Van Der Linden, Malaïka $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
700    1_
$a De Wilde, Jilke $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
700    1_
$a De Koker, Andries $u Center for Medical Biotechnology, Flemish Institute Biotechnology (VIB), Ghent, Belgium; Research Foundation Flanders, Belgium
700    1_
$a Menten, Björn $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
700    1_
$a Devalck, Christine $u Hôpital Universitaire des Enfants Reine Fabiola, Brussels, Belgium
700    1_
$a Vicha, Ales $u Department of Pediatric Hematology and Oncology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
700    1_
$a Grega, Marek $u Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
700    1_
$a Schleiermacher, Gudrun $u Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
700    1_
$a Iddir, Yasmine $u Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
700    1_
$a Chicard, Mathieu $u Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
700    1_
$a van Zogchel, Lieke $u Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
700    1_
$a Stutterheim, Janine $u Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
700    1_
$a Lak, Nathalie S M $u Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
700    1_
$a Tytgat, G A M $u Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
700    1_
$a Laureys, Geneviève $u Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
700    1_
$a Speleman, Frank $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
700    1_
$a De Wilde, Bram $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
700    1_
$a Lammens, Tim $u Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
700    1_
$a De Preter, Katleen $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
700    1_
$a Van Roy, Nadine $u Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. Electronic address: Nadine.VanRoy@UGent.be
773    0_
$w MED00009626 $t European journal of cancer (Oxford, England : 1990) $x 1879-0852 $g Roč. 160, č. - (2022), s. 12-23
856    41
$u https://pubmed.ncbi.nlm.nih.gov/34794856 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y p $z 0
990    __
$a 20220425 $b ABA008
991    __
$a 20220506130507 $b ABA008
999    __
$a ok $b bmc $g 1789184 $s 1162658
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2022 $b 160 $c - $d 12-23 $e 20211116 $i 1879-0852 $m European journal of cancer $n Eur J Cancer $x MED00009626
LZP    __
$a Pubmed-20220425

Najít záznam

Citační ukazatele

Možnosti archivace