Detail
Článek
Článek online
FT
Medvik - BMČ
  • Je něco špatně v tomto záznamu ?

Targeted next-generation sequencing in chronic lymphocytic leukemia: a high-throughput yet tailored approach will facilitate implementation in a clinical setting

LA. Sutton, V. Ljungström, L. Mansouri, E. Young, D. Cortese, V. Navrkalova, J. Malcikova, AF. Muggen, M. Trbusek, P. Panagiotidis, F. Davi, C. Belessi, AW. Langerak, P. Ghia, S. Pospisilova, K. Stamatopoulos, R. Rosenquist,

. 2015 ; 100 (3) : 370-6. [pub] 20141205

Jazyk angličtina Země Itálie

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc16000476

Next-generation sequencing has revealed novel recurrent mutations in chronic lymphocytic leukemia, particularly in patients with aggressive disease. Here, we explored targeted re-sequencing as a novel strategy to assess the mutation status of genes with prognostic potential. To this end, we utilized HaloPlex targeted enrichment technology and designed a panel including nine genes: ATM, BIRC3, MYD88, NOTCH1, SF3B1 and TP53, which have been linked to the prognosis of chronic lymphocytic leukemia, and KLHL6, POT1 and XPO1, which are less characterized but were found to be recurrently mutated in various sequencing studies. A total of 188 chronic lymphocytic leukemia patients with poor prognostic features (unmutated IGHV, n=137; IGHV3-21 subset #2, n=51) were sequenced on the HiSeq 2000 and data were analyzed using well-established bioinformatics tools. Using a conservative cutoff of 10% for the mutant allele, we found that 114/180 (63%) patients carried at least one mutation, with mutations in ATM, BIRC3, NOTCH1, SF3B1 and TP53 accounting for 149/177 (84%) of all mutations. We selected 155 mutations for Sanger validation (variant allele frequency, 10-99%) and 93% (144/155) of mutations were confirmed; notably, all 11 discordant variants had a variant allele frequency between 11-27%, hence at the detection limit of conventional Sanger sequencing. Technical precision was assessed by repeating the entire HaloPlex procedure for 63 patients; concordance was found for 77/82 (94%) mutations. In summary, this study demonstrates that targeted next-generation sequencing is an accurate and reproducible technique potentially suitable for routine screening, eventually as a stand-alone test without the need for confirmation by Sanger sequencing.

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc16000476
003      
CZ-PrNML
005      
20160125123059.0
007      
ta
008      
160108s2015 it f 000 0|eng||
009      
AR
024    7_
$a 10.3324/haematol.2014.109777 $2 doi
035    __
$a (PubMed)25480502
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a it
100    1_
$a Sutton, Lesley-Ann $u Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.
245    10
$a Targeted next-generation sequencing in chronic lymphocytic leukemia: a high-throughput yet tailored approach will facilitate implementation in a clinical setting / $c LA. Sutton, V. Ljungström, L. Mansouri, E. Young, D. Cortese, V. Navrkalova, J. Malcikova, AF. Muggen, M. Trbusek, P. Panagiotidis, F. Davi, C. Belessi, AW. Langerak, P. Ghia, S. Pospisilova, K. Stamatopoulos, R. Rosenquist,
520    9_
$a Next-generation sequencing has revealed novel recurrent mutations in chronic lymphocytic leukemia, particularly in patients with aggressive disease. Here, we explored targeted re-sequencing as a novel strategy to assess the mutation status of genes with prognostic potential. To this end, we utilized HaloPlex targeted enrichment technology and designed a panel including nine genes: ATM, BIRC3, MYD88, NOTCH1, SF3B1 and TP53, which have been linked to the prognosis of chronic lymphocytic leukemia, and KLHL6, POT1 and XPO1, which are less characterized but were found to be recurrently mutated in various sequencing studies. A total of 188 chronic lymphocytic leukemia patients with poor prognostic features (unmutated IGHV, n=137; IGHV3-21 subset #2, n=51) were sequenced on the HiSeq 2000 and data were analyzed using well-established bioinformatics tools. Using a conservative cutoff of 10% for the mutant allele, we found that 114/180 (63%) patients carried at least one mutation, with mutations in ATM, BIRC3, NOTCH1, SF3B1 and TP53 accounting for 149/177 (84%) of all mutations. We selected 155 mutations for Sanger validation (variant allele frequency, 10-99%) and 93% (144/155) of mutations were confirmed; notably, all 11 discordant variants had a variant allele frequency between 11-27%, hence at the detection limit of conventional Sanger sequencing. Technical precision was assessed by repeating the entire HaloPlex procedure for 63 patients; concordance was found for 77/82 (94%) mutations. In summary, this study demonstrates that targeted next-generation sequencing is an accurate and reproducible technique potentially suitable for routine screening, eventually as a stand-alone test without the need for confirmation by Sanger sequencing.
650    _2
$a alely $7 D000483
650    _2
$a exprese genu $7 D015870
650    _2
$a frekvence genu $7 D005787
650    12
$a vysoce účinné nukleotidové sekvenování $7 D059014
650    _2
$a lidé $7 D006801
650    _2
$a chronická lymfatická leukemie $x diagnóza $x genetika $x metabolismus $x patologie $7 D015451
650    12
$a mutace $7 D009154
650    _2
$a myeloidní diferenciační faktor 88 $x genetika $x metabolismus $7 D053594
650    _2
$a nádorové proteiny $x genetika $x metabolismus $7 D009363
650    _2
$a fosfoproteiny $x genetika $x metabolismus $7 D010750
650    _2
$a prognóza $7 D011379
650    _2
$a receptor Notch1 $x genetika $x metabolismus $7 D051881
650    _2
$a malý jaderný ribonukleoprotein U2 $x genetika $x metabolismus $7 D017413
650    _2
$a nádorový supresorový protein p53 $x genetika $x metabolismus $7 D016159
655    _2
$a časopisecké články $7 D016428
655    _2
$a práce podpořená grantem $7 D013485
700    1_
$a Ljungström, Viktor $u Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.
700    1_
$a Mansouri, Larry $u Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.
700    1_
$a Young, Emma $u Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.
700    1_
$a Cortese, Diego $u Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.
700    1_
$a Navrkalova, Veronika $u Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
700    1_
$a Malcikova, Jitka $u Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
700    1_
$a Muggen, Alice F $u Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands.
700    1_
$a Trbusek, Martin $u Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
700    1_
$a Panagiotidis, Panagiotis $u First Department of Propaedeutic Medicine, School of Medicine, University of Athens, Greece.
700    1_
$a Davi, Frederic $u Laboratory of Hematology and Universite Pierre et Marie Curie, Hopital Pitie-Salpetriere, Paris, France.
700    1_
$a Belessi, Chrysoula $u Hematology Department, Nikea General Hospital, Pireaus, Greece.
700    1_
$a Langerak, Anton W $u Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands.
700    1_
$a Ghia, Paolo $u Università Vita-Salute San Raffaele, Milan, Italy Division of Molecular Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy.
700    1_
$a Pospisilova, Sarka $u Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
700    1_
$a Stamatopoulos, Kostas $u Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden Institute of Applied Biosciences, CERTH, Thessaloniki, Greece Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece.
700    1_
$a Rosenquist, Richard $u Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden richard.rosenquist@igp.uu.se.
773    0_
$w MED00001963 $t Haematologica $x 1592-8721 $g Roč. 100, č. 3 (2015), s. 370-6
856    41
$u https://pubmed.ncbi.nlm.nih.gov/25480502 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20160108 $b ABA008
991    __
$a 20160125123222 $b ABA008
999    __
$a ok $b bmc $g 1102757 $s 924682
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2015 $b 100 $c 3 $d 370-6 $e 20141205 $i 1592-8721 $m Haematologica $n Haematologica $x MED00001963
LZP    __
$a Pubmed-20160108

Najít záznam

Citační ukazatele

Pouze přihlášení uživatelé

Možnosti archivace