Classification and Personalized Prognostic Assessment on the Basis of Clinical and Genomic Features in Myelodysplastic Syndromes.

Purpose: Recurrently mutated genes and chromosomal abnormalities have been identified in myelodysplastic syndromes (MDS). We aim to integrate these genomic features into disease classification and prognostication.
Methods: We retrospectively enrolled 2,043 patients. Using Bayesian networks and Dirichlet processes, we combined mutations in 47 genes with cytogenetic abnormalities to identify genetic associations and subgroups. Random-effects Cox proportional hazards multistate modeling was used for developing prognostic models. An independent validation on 318 cases was performed.
Results: We identify eight MDS groups (clusters) according to specific genomic features. In five groups, dominant genomic features include splicing gene mutations ( SF3B1 , SRSF2 , and U2AF1 ) that occur early in disease history, determine specific phenotypes, and drive disease evolution. These groups display different prognosis (groups with SF3B1 mutations being associated with better survival). Specific co-mutation patterns account for clinical heterogeneity within SF3B1 - and SRSF2 -related MDS. MDS with complex karyotype and/or TP53 gene abnormalities and MDS with acute leukemia-like mutations show poorest prognosis. MDS with 5q deletion are clustered into two distinct groups according to the number of mutated genes and/or presence of TP53 mutations. By integrating 63 clinical and genomic variables, we define a novel prognostic model that generates personally tailored predictions of survival. The predicted and observed outcomes correlate well in internal cross-validation and in an independent external cohort. This model substantially improves predictive accuracy of currently available prognostic tools. We have created a Web portal that allows outcome predictions to be generated for user-defined constellations of genomic and clinical features.
Conclusion: Genomic landscape in MDS reveals distinct subgroups associated with specific clinical features and discrete patterns of evolution, providing a proof of concept for next-generation disease classification and prognosis.
Competing Interests: Manja MeggendorferEmployment: MLL Munich Leukemia Laboratory Marianna RossiConsulting or Advisory Role: Pfizer, Celgene, IQvia, Janssen Emanuele AngelucciHonoraria: Celgene, Vertex Pharmaceuticals Incorporated (MA) and CRISPR Therapeutics AG (CH)Consulting or Advisory Role: Novartis, Bluebird BioTravel, Accommodations, Expenses: Janssen-Cilag Massimo BernardiHonoraria: CelgeneConsulting or Advisory Role: PfizerTravel, Accommodations, Expenses: Medac, Amgen, Sanofi, Jazz Pharmaceuticals, BioTest, Abbvie, Takeda Lorenza BorinLeadership: CelgeneSpeakers' Bureau: GenzymeTravel, Accommodations, Expenses: Genzyme Benedetto BrunoHonoraria: Jazz Pharmaceuticals, Novartis, AmgenResearch Funding: Amgen Valeria SantiniHonoraria: Celgene/Bristol-Myers Squibb, Novartis, Janssen-CilagConsulting or Advisory Role: Celgene/Bristol-Myers Squibb, Novartis, Menarini, Takeda, PfizerResearch Funding: CelgeneTravel, Accommodations, Expenses: Janssen-Cilag, Celgene Andrea BacigalupoHonoraria: Pfizer, Therakos, Novartis, Sanofi, Jazz Pharmaceuticals, Riemser, Merck Sharp & Dohme, Janssen-Cilag, Gilead Sciences, Kiadis Pharma, Astellas PharmaConsulting or Advisory Role: Novartis, Kiadis Pharma, Gilead Sciences, Astellas PharmaSpeakers' Bureau: Pfizer, Therakos, Novartis, Sanofi, Riemser, Merck Sharp & Dohme, Adienne, Jazz PharmaceuticalsTravel, Accommodations, Expenses: Sanofi, Therakos, Jazz Pharmaceuticals Maria Teresa VosoHonoraria: Celgene/Jazz, AbbvieConsulting or Advisory Role: Celgene/JazzSpeakers' Bureau: CelgeneResearch Funding: Celgene Esther OlivaHonoraria: Celgene, Novartis, Amgen, Alexion PharmaceuticalsConsulting or Advisory Role: Amgen, Celgene, NovartisSpeakers' Bureau: Celgene, NovartisPatents, Royalties, Other Intellectual Property: Royalties for QOL-E instrument Francesco PassamontiSpeakers' Bureau: Novartis, AOP Orphan Pharmaceuticals Niccolò BolliConsulting or Advisory Role: JanssenSpeakers' Bureau: Celgene, Amgen Alessandro RambaldiHonoraria: Amgen, OmerosConsulting or Advisory Role: Amgen, Omeros, Novartis, Astellas Pharma, Jazz PharmaceuticalsTravel, Accommodations, Expenses: Celgene Wolfgang KernEmployment: MLL Munich Leukemia LaboratoryLeadership: MLL Munich Leukemia LaboratoryStock and Other Ownership Interests: MLL Munich Leukemia Laboratory Shahram KordastiHonoraria: Beckman Coulter, GWT-TUD, Alexion PharmaceuticalsConsulting or Advisory Role: Syneos HealthResearch Funding: Celgene, Novartis Guillermo SanzHonoraria: CelgeneConsulting or Advisory Role: Abbvie, Celgene, Helsinn Healthcare, Janssen, Roche, Amgen, Boehringer Ingelheim, Novartis, TakedaSpeakers' Bureau: TakedaResearch Funding: CelgeneTravel, Accommodations, Expenses: Celgene, Takeda, Gilead Sciences, Roche Pharma AG Armando SantoroConsulting or Advisory Role: Bristol-Myers Squibb, Servier, Gilead Sciences, Pfizer, Eisai, Bayer AG, MSD, Sanofi, ArQuleSpeakers' Bureau: Takeda, Roche, Abbvie, Amgen, Celgene, AstraZeneca, ArQule, Lilly, Sandoz, Novartis, Bristol-Myers Squibb, Servier, Gilead Sciences, Pfizer, Eisai, Bayer AG, MSD Uwe PlatzbeckerHonoraria: Celgene/JazzConsulting or Advisory Role: Celgene/JazzResearch Funding: Amgen, Janssen, Novartis, BerGenBio, CelgenePatents, Royalties, Other Intellectual Property: part of a patent for a TFR-2 antibody (Rauner et al. Nature Metabolics 2019)Travel, Accommodations, Expenses: Celgene Pierre FenauxHonoraria: CelgeneResearch Funding: Celgene Torsten HaferlachEmployment: MLL Munich Leukemia LaboratoryLeadership: MLL Munich Leukemia LaboratoryConsulting or Advisory Role: IlluminaNo other potential conflicts of interest were reported.