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.

Basic information

Original name

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

Authors

SUTTON, L.A., V. LJUNGSTROM, A. ENJUANES, D. CORTESE, A. SKAFTASON, E. TAUSCH, Kateřina STAŇO KOZUBÍK (203 Czech Republic, belonging to the institution), F. NADEU, M. ARMAND, Jitka MALČÍKOVÁ (203 Czech Republic, belonging to the institution), T. PANDZIC, J. FORSTER, Z. DAVIS, D. OSCIER, D. ROSSI, P. GHIA, J.C. STREFFORD, Šárka POSPÍŠILOVÁ (203 Czech Republic, guarantor, belonging to the institution), S. STILGENBAUER, F. DAVI, E. CAMPO, K. STAMATOPOULOS and R. ROSENQUIST

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

30205 Hematology

Country of publisher

Italy

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 11.047

RIV identification code

RIV/00216224:14740/21:00119057

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000624937600007

Keywords in English

CLINICAL IMPACTRECURRENT MUTATIONSCLONAL EVOLUTIONLABORATORY STANDARDSTP53NOTCH1SF3B1CLLBIRC3PROGRESSION

Abstract

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.

Links

GA19-15737S, research and development project

Name: Alternativní mechanismy deregulace p53 dráhy u chronické lymfocytární leukémie

Investor: Czech Science Foundation, Alternative mechanisms of deregulation of the p53 pathway in chronic lymphocytic leukemia

NV19-03-00091, research and development project

Name: 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: Ministry of Health of the CR

90091, large research infrastructures

Name: 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 and 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, vol. 106, No 3, p. 682-691. ISSN 0390-6078. Available from: 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 and 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, vol.~106, No~3, p.~682-691. ISSN~0390-6078. Available from: https://dx.doi.org/10.3324/haematol.2019.234716.

Detailed Information on Publication Record