Oncogenetics and Forensic Genetics Group
Head: Jiří Drábek
Olomouc node
HOME INSTITUTION
Faculty of Medicine PU in Olomouc
RESEARCH PROGRAMME(S)
RP 3 - Biomarkers of cancers and cancer diagnostics
RP 4 - Early detection and prevention of tumours
Let us not succumb to naive genetic determinism. Yet: you can't defecate genes!
- Mission: To assist physicians and patients, or investigators and crime victims, by extracting the maximum information from the nucleic acid in the specimen being tested.
- Vision: To develop methods that advance the sensitivity of capturing the nucleic acid of interest as a biomarker or trace.
SOFG has genotyping and bioinformatics goals:
Develop methods for comprehensive genomic profiling of FFPE and cfDNA samples.
Development of methods for verifying the presence of CHIP (Clonal Hematopoiesis of Indeterminate Potential) artifacts in prepared sequencing libraries from cfDNA, with the subsequent possibility of their removal.
SELECTED PUBLICATIONS
- Kotková L, Drábek J. Age-related changes in sperm DNA methylation and their forensic and clinical implications. Epigenomics. 2023;15(21):1157-73. DOI: 10.2217/epi-2023-0307
- Angers A, Drabek J, Fabbri M, Petrillo M, Querci M. Whole Genome Sequencing and forensics genomics. JRC125734 ed. Luxembourg: EUR 30766 EN, Publications Office of the European Union; 2021. 65 p., book
- Xiao W, Ren L, Chen Z, Fang LT, Zhao Y, Lack J, Guan M, Zhu B, Jaeger E, Kerrigan L, Blomquist TM, Hung T, Sultan M, Idler K, Lu C, Scherer A, Kusko R, Moos M, Xiao C, Sherry ST, Abaan OD, Chen W, Chen X, Nordlund J, Liljedahl U, Maestro R, Polano M, Drabek J, Vojta P, Kõks S, Reimann E, Madala BS, Mercer T, Miller C, Jacob H, Truong T, Moshrefi A, Natarajan A, Granat A, Schroth GP, Kalamegham R, Peters E, Petitjean V, Walton A, Shen TW, Talsania K, Vera CJ, Langenbach K, de Mars M, Hipp JA, Willey JC, Wang J, Shetty J, Kriga Y, Raziuddin A, Tran B, Zheng Y, Yu Y, Cam M, Jailwala P, Nguyen C, Meerzaman D, Chen Q, Yan C, Ernest B, Mehra U, Jensen RV, Jones W, Li JL, Papas BN, Pirooznia M, Chen YC, Seifuddin F, Li Z, Liu X, Resch W, Wang J, Wu L, Yavas G, Miles C, Ning B, Tong W, Mason CE, Donaldson E, Lababidi S, Staudt LM, Tezak Z, Hong H, Wang C, Shi L. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nat Biotechnol. 2021 Sep;39(9):1141-1150. DOI: 10.1038/s41587-021-00994-5
- Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth GP, Abaan OD, Talsania K, Lack J, Shen TW, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Tezak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Shi L, Wang C, Xiao W; Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nat Biotechnol. 2021 Sep;39(9):1151-1160. DOI: 10.1038/s41587-021-00993-6
COLLABORATION WITHIN THE NICR
Aleksi Šedo
(Prague node, First Faculty of Medicine CU)
Ondřej Slabý
(Brno node, Faculty of Medicine MU/CEITEC MU)
Petr Džubák
(Olomouc node, Faculty of Medicine PU in Olomouc)
SPECIALIZED EXPERTISE AND TECHNOLOGY
Extraction of nucleic acids
qPCR, ddPCR
Massively parallel sequencing on Illumina platform
NanoString nCounter SPRINT