Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

• Autoři: GONG B.S.; LI D.; KUSKO R.; NOVORADOVSKAYA N.; ZHANG Y.F.; WANG S.Z.; PABON-PENA C.; ZHANG Z.H.; LAI K.; CAI W.S.; LOCOCO J.S.; LADER E.; RICHMOND T.A.; MITTAL V.K.; LIU L.C.; JOHANN D.J.; WILLEY J.C.; BUSHEL P.R.; YU Y.; XU C.; CHEN G.C.; BURGESS D.; CAWLEY S.; GIORDA K.; HASELEY N.; QIU F.J.; WILKINS K.; ARIB H.; ATTWOOLL C.; BABSON K.; BAO L.L.; BAO W.J.; LUCAS A.B.; BEST H.; BHANDARI A.; BISGIN H.; BLACKBURN J.; BLOMQUIST T.M.; BOARDMAN L.; BURGHER B.; BUTLER D.J.; CHANG C.J.; CHAUBEY A.; CHEN T.; CHIERICI M.; CHIN C.R.; CLOSE D.; CONROY J.; COLEMAN J.C.; CRAIG D.J.; CRAWFORD E.; DEL POZO A.; DEVESON I.W.; DUNCAN D.; ETEROVIC A.K.; FAN X.H.; FOOX J.; FURLANELLO C.; GHOSAL A.; GLENN S.; GUAN M.J.; HAAG C.; HANG X.Y.; HAPPE S.; HENNIGAN B.; HIPP J.; HONG H.X.; HORVATH K.; HU J.H.; HUNG L.Y.; JAROSZ M.; KERKHOF J.; KIPP B.; KREIL D.P.; LAPUNZINA P.; LI P.; LI Q.Z.; LI W.H.; LI Z.G.; LIANG Y.; LIU S.Q.; LIU Z.C.; MA C.; MARELLA N.; MARTIN-ARENAS R.; MEGHERBI D.B.; MENG Q.C.; MIECZKOWSKI P.A.; MORRISON T.; MUZNY D.; NING B.T.; PARSONS B.L.; PAWELETZ C.P.; PIROOZNIA M.; QU W.B.; RAYMOND A.; RINDLER P.; RINGLER R.; SADIKOVIC B.; SCHERER A.; SCHULZE E.; SEBRA R.; SHAKNOVICH R.; SHI Q.; SHI T.L.; SILLA-CASTRO J.C.; SMITH M.; LOPEZ M.S.; SONG P.; STETSON D.; STRAHL M.; STUART A.; SUPPLEE J.; SZANKASI P.; TAN H.W.; TANG L.Y.; TAO Y.H.; THAKKAR S.; THIERRY-MIEG D.; THIERRY-MIEG J.; THODIMA V.J.; THOMAS D.; TICHÝ Boris; TOM Nikola; GARCIA E.V.; VERMA S.; WALKER K.; WANG C.; WANG J.W.; WANG Y.X.; WEN Z.N.; WIRTA V.; WU L.H.; XIAO C.L.; XIAO W.Z.; XU S.B.; YANG M.; YING J.M.; YIP S.H.; ZHANG G.L.; ZHANG S.; ZHAO M.R.; ZHENG Y.T.; ZHOU X.Y.; MASON C.E.; MERCER T.; TONG W.D.; SHI L.M.; JONES W.; XU J.S.
• Rok publikování: 2021
• Druh: Článek v odborném periodiku
• Časopis / Zdroj: GENOME BIOLOGY
• Fakulta / Pracoviště MU: Středoevropský technologický institut
• www: https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-021-02315-0.pdf
• Doi: http://dx.doi.org/10.1186/s13059-021-02315-0
• Klíčová slova: Oncopanel sequencing; Target enrichment; Molecular diagnostics; Reproducibility; Analytical performance; Precision medicine
• Popis: BackgroundTargeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.ResultsAll panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.ConclusionThis comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.

Související projekty

• Involvement of Czech Translational Medicine Infrastructure to the European Advanced Translational Research Infrastructure in Medicine
• CEITEC 2020
• 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
• Involvement of Czech Translational Medicine Infrastructure to the European Advanced Translational Research Infrastructure in Medicine