Laboratory of Genomics

Dr. habil. Luiza Handschuh

Head of Laboratory

luizahan@ibch.poznan.pl
int. 1249, 1106

Research Projects

Keywords

genomics,
transcriptomics,
next generation sequencing (NGS),
mutation identification,
acute myeloid leukemia,
archaeogenomics,
bioinformatics

Offer

The Laboratory of Genomics possesses an advanced research infrastructure, primarily used for high-throughput second and third generation sequencing. Two Illumina sequencers, NextSeq 550 and NovaSeq 6000, allow sequencing of short reads (150-250 bp), and the only one in Poland so far, Sequel IIe sequencer (Pac-Bio) allows generating long HiFi readings (length up to 25,000 bp, precision> 99.9 %). Both platforms can be used to sequence complete genomes, exomes and transcriptomes. The Laboratory offers support in experiment design, DNA and RNA isolation, material qualitative assessment, library preparation, sequencing, analysis of results, and cost estimation for the grant proposals. In order to verify the NGS results, we provide real-time PCR equipment, including droplet digital PCR (ddPCR) system.

Equipment

NextSeq 550 sequencer (Illumina)
NovaSeq 6000 high-throughput sequencer (Illumina)
Third generation sequencer Sequel IIe (Pacific Biosciences) for long DNA reads with the use of SMRT (single-molecule real-time) technology ·
QX200 Droplet Digital PCR (ddPCR™) quantitative PCR System (BioRad)
Rotor-Gene Q real-time PCR cycler (Qiagen)
2100 Bioanalyzer (Agilent)
Bioruptor NextGen sonicator (Diagenode)
Nanodrop 2000 spectrophotometer (Thermo Scientific)
Qubit 4 Fluorimeter (Invitrogen)
T100 thermal cyclers (Bio-Rad)

Research projects

The Laboratory of Genomics supports numerous projects conducted at the IBCH and other institutions with which cooperates. The most important projects currently carried out in the Laboratory are:

POIR. 04.02.00-30-A004/16-02 - European Center for Bioinformatics and Genomics – a project under which the Genomic Map of Poland (GMP) " is being developed.
POIR 04.02.00-00-D017/20 - ECBiG - European Center for Bioinformatics and Genomics – MOSAIC.

Selected publications

Stolarek I, Zenczak M, Handschuh L, Juras A, Marcinkowska-Swojak M, Spinek A, Dębski A, Matla M, Kóčka-Krenz H, Piontek J; Polish Archaeogenomics Consortium Team; Figlerowicz M. Genetic history of East-Central Europe in the first millennium CE. Genome Biology, 2023, 24:173.
Szóstak N, Handschuh L, Samelak-Czajka A, Tomela K, Schmidt M, Pruss Ł, Milanowska-Zabel K, Kozlowski P, Philips A. Host Factors Associated with Gut Mycobiome Structure. mSystems. 2023, 8:e0098622.
Lewandowski K, Kanduła Z, Gniot M, Paczkowska E, Nawrocka PM, Wojtaszewska M, Janowski M, Mariak M, Handschuh L, Kozlowski P. Essential thrombocythaemia progression to the fibrotic phase is associated with a decrease in JAK2 and PDL1 levels. Annals of Hematology, 2022, 101:2665-2677.
Galka-Marciniak P, Kanduła Z, Tire A, Wegorek W, Gwozdz-Bak K, Handschuh L, Giefing M, Lewandowski K, Kozlowski P. Mutations in the miR-142 gene are not common in myeloproliferative neoplasms. Scientific Reports, 2022, 12:10924.
Szóstak N, Szymanek A, Havránek J, Tomela K, Rakoczy M, Samelak-Czajka A, Schmidt M, Figlerowicz M, Majta J, Milanowska-Zabel K, Handschuh L, Philips A. The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling. Sci Rep. 2022, 12:8470.
Handschuh L, Wojciechowski P, Kazmierczak M, Lewandowski K. Transcript-Level Dysregulation of BCL2 Family Genes in Acute Myeloblastic Leukemia. Cancers. 2021, 13:3175
Philips A, Stolarek I, Handschuh L, Nowis K, Juras A, Trzciński D, Nowaczewska W, Wrzesińska A, Potempa J, Figlerowicz M. Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia. BMC Genomics. 2020, 21:402
Philips A, Nowis K, Stelmaszczuk M, Jackowiak P, Podkowiński J, Handschuh L, Figlerowicz M. Expression Landscape of circRNAs in Arabidopsis thaliana Seedlings and Adult Tissues. Frontiers in Plant Science. 2020, 11:576581
Philips A, Nowis K, Stelmaszczuk M, Podkowiński J, Handschuh L, Jackowiak P, Figlerowicz M. Arabidopsis thaliana cbp80, c2h2, and flk Knockout Mutants Accumulate Increased Amounts of Circular RNAs. Cells. 2020, 9:1937
Szenajch J, Szabelska-Beręsewicz A, Świercz A, Zyprych-Walczak J, Siatkowski I, Góralski M, Synowiec A, Handschuh L. Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. International Journal of Molecular Sciences. 2020, 21:9218
Handschuh L, Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies. Journal of Oncology, 2019, 7239206.
Stolarek I, Handschuh L, Juras A, Nowaczewska W, Kóčka-Krenz H, Michalowski A, Piontek J, Kozlowski P, Figlerowicz M. Goth migration induced changes in the matrilineal genetic structure of the central-east European population. Scientific Reports. 2019, 9:6737
Stolarek I, Juras A, Handschuh L, Marcinkowska-Swojak M, Philips A, Zenczak M, Dębski A, Kóčka-Krenz H, Piontek J, Kozlowski P, Figlerowicz M. A mosaic genetic structure of the human population living in the South Baltic region during the Iron Age. Scientific Reports. 2018, 8:2455
Rakoczy M, Femiak I, Alejska M, Figlerowicz M, Podkowinski J. Sorghum CCoAOMT and CCoAOMT-like gene evolution, structure, expression and the role of conserved amino acids in protein activity. Molecular Genetics and Genomics. 2018, 293:1077-1089
Handschuh L, Wojciechowski P, Kazmierczak M, Marcinkowska-Swojak M, Luczak M, Lewandowski K, Komarnicki M, Blazewicz J, Figlerowicz M, Kozlowski P. NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome. Journal of Translational Medicine, 2018, 16:232.

IBCH logo