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  • Sutton, LAKarolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden. (author)

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

  • Article/chapterEnglish2021

Publisher, publication year, extent ...

  • 2020-04-09
  • Ferrata Storti Foundation (Haematologica),2021

Numbers

  • LIBRIS-ID:oai:prod.swepub.kib.ki.se:146100648
  • http://kipublications.ki.se/Default.aspx?queryparsed=id:146100648URI
  • https://doi.org/10.3324/haematol.2019.234716DOI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-441150URI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • 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 94.2-99.8%. 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 VAF >0.5%. Reproducibility was assessed by looking at the inter-laboratory variation in detecting mutations and 107/115 (93% concordance) of mutations were detected by all 6 centers, while the remaining 8/115 (7%) variants were undetected by a single center and 6/8 of these variants concerned minor subclonal mutations (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 VAFs >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.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Ljungström, Viktor,1986-Uppsala universitet,Science for Life Laboratory, SciLifeLab,Experimentell och klinisk onkologi,Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.(Swepub:uu)viklj600 (author)
  • Enjuanes, AInst Invest Biomed August Pi i Sunyer IDIBAPS, Barcelona, Spain.;Ctr Invest Biomed Red Canc CIBERONC, Barcelona, Spain.;Univ Barcelona, Hosp Clin Barcelona, Barcelona, Spain. (author)
  • Cortese, DKarolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden. (author)
  • Skaftason, AKarolinska Institutet,Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden. (author)
  • Tausch, EUlm Univ, Dept Internal Med 3, Ulm, Germany. (author)
  • Kozubik, KSMasaryk Univ, Ctr Mol Med, CEITEC Cent European Inst Technol, Brno, Czech Republic.,Ulm Univ, Dept Internal Med 3, Ulm, Germany.,Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Ctr Res & Technol, Inst Appl Biosci, Thessaloniki, Greece. (author)
  • Nadeu, FInst Invest Biomed August Pi i Sunyer IDIBAPS, Barcelona, Spain.;Ctr Invest Biomed Red Canc CIBERONC, Barcelona, Spain.;Univ Barcelona, Hosp Clin Barcelona, Barcelona, Spain. (author)
  • Armand, MSorbonne Univ, Hop Pitie Salpetriere, AP HP, Dept Hematol, Paris, France. (author)
  • Malcikova, JMasaryk Univ, Ctr Mol Med, CEITEC Cent European Inst Technol, Brno, Czech Republic. (author)
  • Pandzic, T (author)
  • Forster, JUniv Southampton, Fac Med, Canc Sci, Southampton, Hants, England. (author)
  • Davis, ZRoyal Bournemouth Hosp, Dept Hematol, Bournemouth, Dorset, England. (author)
  • Oscier, DRoyal Bournemouth Hosp, Dept Hematol, Bournemouth, Dorset, England. (author)
  • Rossi, DOncol Inst Southern Switzerland, Hematol Dept, Bellinzona, Switzerland.;Inst Oncol Res, Bellinzona, Switzerland. (author)
  • Ghia, PUniv Vita Salute San Raffaele, Div Expt Oncol, Milan, Italy.;IRCCS, San Raffaele Sci Inst, Milan, Italy. (author)
  • Strefford, JCUniv Southampton, Fac Med, Canc Sci, Southampton, Hants, England. (author)
  • Pospisilova, SMasaryk Univ, Ctr Mol Med, CEITEC Cent European Inst Technol, Brno, Czech Republic. (author)
  • Stilgenbauer, S (author)
  • Davi, FSorbonne Univ, Hop Pitie Salpetriere, AP HP, Dept Hematol, Paris, France. (author)
  • Campo, EInst Invest Biomed August Pi i Sunyer IDIBAPS, Barcelona, Spain.;Ctr Invest Biomed Red Canc CIBERONC, Barcelona, Spain.;Univ Barcelona, Hosp Clin Barcelona, Barcelona, Spain. (author)
  • Stamatopoulos, KKarolinska Institutet (author)
  • Rosenquist, RKarolinska Institutet,Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Univ Hosp, Karolinska Univ Lab, Clin Genet, Stockholm, Sweden. (author)
  • Djureinovic, TatjanaUppsala universitet,Experimentell och klinisk onkologi,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik(Swepub:uu)tatdj291 (author)
  • Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.Science for Life Laboratory, SciLifeLab (creator_code:org_t)

Related titles

  • In:Haematologica: Ferrata Storti Foundation (Haematologica)106:3, s. 682-6911592-87210390-6078

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