Comparative analysis of targeted next-generation sequencing
panels for the detection of gene mutations in chronic
lymphocytic leukemia: an ERIC multi-center study

J 2021

Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study

SUTTON, L.A., V. LJUNGSTROM, A. ENJUANES, D. CORTESE, A. SKAFTASON et. al.

Základní údaje

Originální název

Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study

Autoři

SUTTON, L.A., V. LJUNGSTROM, A. ENJUANES, D. CORTESE, A. SKAFTASON, E. TAUSCH, Kateřina STAŇO KOZUBÍK (203 Česká republika, domácí), F. NADEU, M. ARMAND, Jitka MALČÍKOVÁ (203 Česká republika, domácí), T. PANDZIC, J. FORSTER, Z. DAVIS, D. OSCIER, D. ROSSI, P. GHIA, J.C. STREFFORD, Šárka POSPÍŠILOVÁ (203 Česká republika, garant, domácí), S. STILGENBAUER, F. DAVI, E. CAMPO, K. STAMATOPOULOS a R. ROSENQUIST

Vydání

haematologica, PAVIA, FERRATA STORTI FOUNDATION, 2021, 0390-6078

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30205 Hematology

Stát vydavatele

Itálie

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 11.047

Kód RIV

RIV/00216224:14740/21:00119057

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.3324/haematol.2019.234716

UT WoS

000624937600007

Klíčová slova anglicky

CLINICAL IMPACTRECURRENT MUTATIONSCLONAL EVOLUTIONLABORATORY STANDARDSTP53NOTCH1SF3B1CLLBIRC3PROGRESSION

Štítky

CF GEN, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 15. 10. 2024 14:28, Ing. Martina Blahová

Anotace

V originále

Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads >= 100x ranged from 94.299.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) 5%). We sought to investigate low-frequency mutations further by using a high-sensitivity assay containing unique molecular identifiers, which confirmed the presence of several minor subclonal mutations. Thus, while amplicon-based approaches can be adopted for somatic mutation detection with VAF 5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.

Návaznosti

GA19-15737S, projekt VaV

Název: Alternativní mechanismy deregulace p53 dráhy u chronické lymfocytární leukémie

Investor: Grantová agentura ČR, Alternativní mechanismy deregulace p53 dráhy u chronické lymfocytární leukémie

NV19-03-00091, projekt VaV

Název: Komplexní prognostický a prediktivní panel pro pacienty s chronickou lymfocytární leukémií: nástroj sekvenování nové generace vhodný pro klinickou praxi i studium genetického pozadí průběhu choroby

Investor: Ministerstvo zdravotnictví ČR, Comprehensive prognostic and predictive panel for chronic lymphocytic leukemia: a next-generation sequencing tool suitable for clinical practice and study of genetic architecture behind the disease progress

90091, velká výzkumná infrastruktura

Název: NCMG

Citovat

SUTTON, L.A., V. LJUNGSTROM, A. ENJUANES, D. CORTESE, A. SKAFTASON, E. TAUSCH, Kateřina STAŇO KOZUBÍK, F. NADEU, M. ARMAND, Jitka MALČÍKOVÁ, T. PANDZIC, J. FORSTER, Z. DAVIS, D. OSCIER, D. ROSSI, P. GHIA, J.C. STREFFORD, Šárka POSPÍŠILOVÁ, S. STILGENBAUER, F. DAVI, E. CAMPO, K. STAMATOPOULOS a R. ROSENQUIST. Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study. haematologica. PAVIA: FERRATA STORTI FOUNDATION, 2021, roč. 106, č. 3, s. 682-691. ISSN 0390-6078. Dostupné z: https://dx.doi.org/10.3324/haematol.2019.234716.

@article{1781888,
   author = {Sutton, L.A. and Ljungstrom, V. and Enjuanes, A. and Cortese, D. and Skaftason, A. and Tausch, E. and Staňo Kozubík, Kateřina and Nadeu, F. and Armand, M. and Malčíková, Jitka and Pandzic, T. and Forster, J. and Davis, Z. and Oscier, D. and Rossi, D. and Ghia, P. and Strefford, J.C. and Pospíšilová, Šárka and Stilgenbauer, S. and Davi, F. and Campo, E. and Stamatopoulos, K. and Rosenquist, R.},
   article_location = {PAVIA},
   article_number = {3},
   doi = {http://dx.doi.org/10.3324/haematol.2019.234716},
   keywords = {CLINICAL IMPACTRECURRENT MUTATIONSCLONAL EVOLUTIONLABORATORY STANDARDSTP53NOTCH1SF3B1CLLBIRC3PROGRESSION},
   language = {eng},
   issn = {0390-6078},
   journal = {haematologica},
   title = {Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study},
   url = {https://haematologica.org/article/view/9711},
   volume = {106},
   year = {2021}
}

TY  - JOUR
ID  - 1781888
AU  - Sutton, L.A. - Ljungstrom, V. - Enjuanes, A. - Cortese, D. - Skaftason, A. - Tausch, E. - Staňo Kozubík, Kateřina - Nadeu, F. - Armand, M. - Malčíková, Jitka - Pandzic, T. - Forster, J. - Davis, Z. - Oscier, D. - Rossi, D. - Ghia, P. - Strefford, J.C. - Pospíšilová, Šárka - Stilgenbauer, S. - Davi, F. - Campo, E. - Stamatopoulos, K. - Rosenquist, R.
PY  - 2021
TI  - Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study
JF  - haematologica
VL  - 106
IS  - 3
SP  - 682-691
EP  - 682-691
PB  - FERRATA STORTI FOUNDATION
SN  - 03906078
KW  - CLINICAL IMPACTRECURRENT MUTATIONSCLONAL EVOLUTIONLABORATORY STANDARDSTP53NOTCH1SF3B1CLLBIRC3PROGRESSION
UR  - https://haematologica.org/article/view/9711
N2  - Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads >= 100x ranged from 94.299.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) 5%). We sought to investigate low-frequency mutations further by using a high-sensitivity assay containing unique molecular identifiers, which confirmed the presence of several minor subclonal mutations. Thus, while amplicon-based approaches can be adopted for somatic mutation detection with VAF 5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.
ER  -

SUTTON, L.A., V. LJUNGSTROM, A. ENJUANES, D. CORTESE, A. SKAFTASON, E. TAUSCH, Kateřina STAŇO KOZUBÍK, F. NADEU, M. ARMAND, Jitka MALČÍKOVÁ, T. PANDZIC, J. FORSTER, Z. DAVIS, D. OSCIER, D. ROSSI, P. GHIA, J.C. STREFFORD, Šárka POSPÍŠILOVÁ, S. STILGENBAUER, F. DAVI, E. CAMPO, K. STAMATOPOULOS a R. ROSENQUIST. Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study. \textit{haematologica}. PAVIA: FERRATA STORTI FOUNDATION, 2021, roč.~106, č.~3, s.~682-691. ISSN~0390-6078. Dostupné z: https://dx.doi.org/10.3324/haematol.2019.234716.

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