Laboratory of Genomics

Dr. habil. Luiza Handschuh

Head of Laboratory

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

Keywords

genomics
transcriptomics
oncogenomics
archaeogenomics
bioinformatics
next generation sequencing (NGS)
mutation identification,
leukemias and other hematological malignancies

Offer

The Laboratory of Genomics possesses an advanced research infrastructure for high-throughput second and third generation sequencing. Four Illumina sequencers: NovaSeq X Plus, NovaSeq 6000, NextSeq 550 and MiSeq allow sequencing of short reads (150, 250, 300 bp), and the 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, methylomes, 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.

Additionally, the Laboratory has access to the sequencing data of ~10,000 whole human genomes obtained as part of two large projects carried out at IBCH PAN:

European Center for Bioinformatics and Genomics (POIR. 04.02.00-30-A004/16-02) – a project carried out in 2016-2023 (Genomic Map of Poland (GMP), sequences of ~5,700 genomes of Polish inhabitants)
ECBiG - European Center for Bioinformatics and Genomics – MOSAIC (POIR 04.02.00-00-D017/20) – a project carried out in 2021-2023 (sequences of ~4,300 genomes of cardiology and oncology patients)

Equipment

NovaSeq X Plus high-throughput sequencer (Illumina)
NovaSeq 6000 high-throughput sequencer (Illumina)
NextSeq 550 sequencer (Illumina)
MiSeq sequencer (Illumina)
third generation sequencer Sequel IIe (Pacific Biosciences) for long DNA reads with the use of SMRT (single-molecule real-time) technology
automated pipetting station for DNA/RNA isolation – Biomek i5 (Beckman Coulter)
automated pipetting station for sequencing library preparation – Biomek i5 (Beckman Coulter)
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:

Genome of Europe (GoE) – a project funded by the European Union under Horizon Europe and the DIGITAL-2023-CLOUD-AI-04 program, implemented by a consortium of 49 partners from 27 European countries, leader: Erasmus Medical Center, 2024-2028
Development of a universal fast-response platform based on RNA technology, ensuring the national drug and epidemiological safety – a project funded by the Medical Research Agency as part of a competition for the development of innovative therapeutic solutions with RNA technology, leader: Polpharma, 2021-2027
INTERCEPT – Targeted single-cell technology for cancer diagnostics – towards cell-oriented interceptive medicine (UoF/02-WIB-3/2023-004) – a project funded under the Virtual Research Institute Programme from the Polish Science Fund, 2024-2028
ECBiG – European Centre for Bioinformatics and Genomics – MOSAIC 3D (FENG.02.04-IP.04-0012/24) - project co-financed under the European Funds for Smart Economy 2021-2027 Programme (FENG), Action 2.4 Smart Economy Research Infrastructure, 2025-2028
At the dawn of Central European statehood on the example of the Czechia and Poland. Dynasties - elites - societies (late 9th - 11th century) – NCN OPUS 26 LAP project, 2024-2027
Algorithm for the personalizing ovarian cancer treatment based on a spatial transcriptomic model of tumor tissue with single-cell resolution (FENG.02.02-IP.05-0361/23) - FIRST TEAM FNP project, co-financed by the European Regional Development Fund under the European Funds for Smart Economy 2021–2027 (FENG) program, 2024-2028.

Selected publications

Przybysz S, Łojko-Dankowska A, Rakoczy M, Marcinkowska-Swojak M, Zeńczak M, Gwóźdź-Bąk K, Handschuh L, Lewandowski K. Genetic background of Richter transformation of atypical chronic lymphocytic leukemia to diffuse large B-cell lymphoma - a case study. Journal of Applied Genetics. 2025, doi: 10.1007/s13353-025-00999-9.
Hirschfeld AS, Misiorek JO, Dabrowska M, Muszynski J, Gerhart BJ, Zenczak M, Rakoczy M, Rolle K, Switonski PM, Napierala JS, Handschuh L, Napierala M, Badura-Stronka M. Spinocerebellar ataxia 27B (SCA27B)-a systematic review and a case report of a Polish family. Journal of Applied Genetics, 2025, doi: 10.1007/s13353-025-00967-3.
Srinivasan A, Magner D, Kozłowski P, Philips A, Kajdasz A, Wojciechowski P, Wojciechowska M. Global dysregulation of circular RNAs in frontal cortex and whole blood from DM1 and DM2. Human Genetics, 2025, 144, 417-432. doi: 10.1007/s00439-025-02729-x.
Rakoczy M, Podkowinski J, Figlerowicz M. Overexpression of UGPase and SPP genes in Nicotiana tabacum leaves causes accelerated plant development and increased biomass. BioTechnologia, 2025, 106, 31-48. doi: 10.5114/bta/201460.
[From Sanger to genome sequencing - an overview of DNA sequencing technologies] (article in Polish). Marcinkowska-Swojak M, Rakoczy M, Podkowiński J, Handschuh J, Wojciechowski P, Handschuh L. Postępy Biochemii, 2024, 70, 173-189. doi: 10.18388/pb.2021_534.
B. Mirska, M. Zenczak, K. Nowis, I. Stolarek, J. Podkowiński, M. Rakoczy, M. Marcinkowska-Swojak, N. Koralewska, P. Zmora, E. Lenartowicz-Onyekaa, M. Osuch, K. Łasińska, J. Kuczma-Napierała, M. Jaworska, Ł. Madej, M. Ciechomska, A. Jamsheer, K. Kurowski, M. Figlerowicz, L. Handschuh. The landscape of the COVID-19 pandemic in Poland emerging from epidemiological and genomic data, Scientific Reports, 2024, 14, 14416. doi: 10.1038/s41598-024-65468-5.
Szóstak N, Handschuh L, Samelak-Czajka A, Tomela K, Pietrzak B, Schmidt M, Galus Ł, Mackiewicz J, Mackiewicz A, Kozlowski P, Philips A. Gut Mycobiota Dysbiosis Is Associated with Melanoma and Response to Anti-PD-1 Therapy. Cancer Immunology Research, 2024, 12, 427-439. doi: 10.1158/2326-6066.CIR-23-0592.
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. doi: 10.1186/s13059-023-03013-9.
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. doi: 10.1128/msystems.00986-22.
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. Scientific Reports, 2022, 12:8470. doi: 10.1038/s41598-022-12037-3.
Handschuh L, Wojciechowski P, Kazmierczak M, Lewandowski K. Transcript-Level Dysregulation of BCL2 Family Genes in Acute Myeloblastic Leukemia. Cancers. 2021, 13:3175. doi: 10.3390/cancers13133175.
Handschuh L, Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies. Journal of Oncology, 2019, 7239206. doi: 10.1155/2019/7239206.
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, doi: 10.1038/s41598-019-43183-w.
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, doi: 10.1038/s41598-018-20705-6.
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. doi: 10.1186/s12967-018-1608-2.
Handschuh L, Kaźmierczak M, Milewski MC, Góralski M, Łuczak M, Wojtaszewska M, Uszczyńska-Ratajczak B, Lewandowski K, Komarnicki M, Figlerowicz M. Gene expression profiling of acute myeloid leukemia samples from adult patients with AML-M1 and -M2 through boutique microarrays, real-time PCR and droplet digital PCR. International Journal of Oncology, 2018, 52, 656-678. doi: 10.3892/ijo.2017.4233.

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