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April 20

ScarfWeb – No code analysis of single-cell genomics data

​Speaker: Göran Karlsson, Nygen Analytics AB (goran.karlsson@nygen.io)
Göran Karlsson is the co-founder of Nygen Analytics and in parallel heads a research group at Lund University, Sweden focusing on single-cell genomic analysis of healthy and malignant hematopoietic stem cells. His group recently published Scarf - a toolkit for memory efficient analysis of large-scale single-cell genomics data https://www.nature.com/articles/s41467-022-32097-3 . Göran Karlsson is also the founder and previous director of the single-cell genomics core facility at Lund University.

ScarfWeb (https://scarfweb.app) is a web-application powered by Scarf that provides the ease of graphical interface while providing the same flexibility as using a programming-based analysis tool. Thus, ScarfWeb allows for advanced single-cell genomic data analysis for users that lack advanced computational/bioinformatic expertise. Users can run an unrestricted number of analyses on their datasets and the results can be exported in publication quality, editable figures. Features include generation of UMAP/tSNE plots, cluster identification, differential gene expression analysis/gene signature identification, creation of dot plots, volcano plots, cell-mapping, and much more. With ScarfWeb users can also store, share, and publish their data.

Start time: 20/04/2023 09:30
End time: 20/04/2023 11:00
Duration: 1 hour 30 minutes
Location: Biomedicum 1, seminar room 1-2
Type: Seminar
Organization: FIMM
Contact person: jenni.lahtela@helsinki.fi
Further information:
Online meeting link:
April 20

5th FICAN seminar Katri Pylkäs

​Inherited breast cancer susceptibility - Identification of novel factors using Northern Finnish breast cancer cohorts

Abstarct

Our research focuses on breast cancer genetics and inherited predisposition to this common disease. Based on the familial clustering of breast cancer, up to 10% of all cases is estimated to be caused by strong inherited predisposition. However, the known predisposing alleles explain less than half of the hereditary component,leaving the causal factors for majority of breast cancer families unknown. Our research aims for the identification of additional inherited predisposing alleles and understanding their effect on disease onset and behavior. Our studies are based on large breast cancer cohorts collected from Northern Finland together with the clinical collaborators. The predisposing genetic variants are searched by using various genomic approaches, addressing both nucleotide level variation and larger scale genomic events. For the functional characterization of the identified alleles, we use functional genomics, biochemical and disease modelling approaches. For example, we have identified several predisposing founder alleles in Northern Finnish population, including MCPH1 c.904_916del (p.Arg304ValfsTer3), SERPINA3c.918-1G>C and ATM c.7570G>C (p.Ala2524Pro). Of these, MCPH1 and SERPINA3
variants are categorized as moderate-risk alleles, whereas ATM variant is defined as a high-risk allele, and the carriers are counselled and monitored accordingly. In our research projects, we will utilize new genomic methods, the latest being optical genome mapping technology, which has been set-up into our laboratory. These are also offered as a service for other research groups and routine clinical diagnostics.

Relevant references for this talk
Kankuri-Tammilehto M, Tervasmäki A, Kraatari-Tiri M, Rahikkala E, Pylkäs K, Kuismin O. ATM c.7570G>C is a high-risk allele for breast cancer. Int J Cancer. 2023 Feb 1;152(3):429-435. doi: 10.1002/ijc.34305.

Koivuluoma S, Tervasmäki A, Kauppila S, Winqvist R, Kumpula T, Kuismin O, Moilanen J, Pylkäs K. Exome sequencingidentifies a recurrent variant in SERPINA3 associating with hereditary susceptibility to breast cancer. Eur J Cancer. 2021
Jan;143:46-51. doi: 10.1016/j.ejca.2020.10.033.

Mantere T, Winqvist R, Kauppila S, Grip M, Jukkola-Vuorinen A, Tervasmäki A, Rapakko K, Pylkäs K. Targeted Next- Generation Sequencing Identifies a Recurrent Mutation in MCPH1 Associating with Hereditary Breast Cancer Susceptibility. PLoS Genet. 2016 Jan 28;12(1):e1005816. doi: 10.1371/journal.pgen.1005816.

Tervasmäki A, Mantere T, Eshraghi L, Laurila N, Tuppurainen H, Ronkainen VP, Koivuluoma S, Devarajan R, Peltoketo H, Pylkäs K. Tumor suppressor MCPH1 regulates gene expression profiles related to malignant conversion and chromosomal assembly.  Int J Cancer. 2019 Oct 15;145(8):2070-2081. doi: 10.1002/ijc.32234.

Start time: 20/04/2023 15:00
End time: 20/04/2023 16:00
Duration:
Location: remotely
Type: Webinar
Organization: Finnish Cancer Center (FICAN)
Contact person: tuula.kallioinen@hus.fi
Further information:
Online meeting link: http://shorturl.at/DKMXY
April 21

Dissertation: Mia Eriksson

​Mia Eriksson University of Helsinki, Faculty of Medicine, Doctoral Program in Population Health, Folkhälsan Research Center
Melancholia or Not; The Mysterious Differences in Depression : A Study of Pathophysiological Differences Between Depressive Subtypes – Findings from The Helsinki Birth Cohort Study

Opponent: Professor Peter Nilsson, Lund University



Start time: 21/04/2023 12:00
End time: 21/04/2023 14:00
Duration: 2 hours
Location: Athena, Hall 107, Siltavuorenpenger 3 A, Helsinki
Type: Dissertation
Organization: UH, Faculty of Medicine
Contact person: mia.eriksson@helsinki.fi
Further information: https://helda.helsinki.fi/handle/10138/356474
Online meeting link: https://shorturl.at/cmoBZ
April 21

Dissertation: Toni Seppälä

​Toni Seppälä, University of Helsinki, Faculty of Medicine, Doctoral Program in Clinical Research
Pretibial injuries : Clinical presentation, treatment paths, and health economic burden

Opponent: docent Ilkka Kaartinen, Tampere University Hospital

Start time: 21/04/2023 12:00
End time: 21/04/2023 14:00
Duration: 2 hours
Location: HUS Puistosairaala, Niilo Hallman sali, Stenbäckinkatu 11
Type: Dissertation
Organization: UH, Faculty of Medicine
Contact person: toni.p.seppala@gmail.com
Further information: https://helda.helsinki.fi/handle/10138/356394
Online meeting link:
April 21

Dissertation: Katarina Johansson

Katarina Johansson, University of Helsinki, Faculty of Medicine, Doctoral Program in Clinical Research
Intraductal papillary mucinous neoplasm of the pancreas : A study with magnetic resonance imaging
Opponent: docent Irina Rinta-Kiikka, University of Tampere


Start time: 21/04/2023 12:00
End time: 21/04/2023 14:00
Duration: 2 hours
Location: HUS Sltasairaala, Kruunuhakasali, Haartmaninkatu 4
Type: Dissertation
Organization: UH, Faculty of Medicine
Contact person: katarina.johansson@helsinki.fi
Further information: https://helda.helsinki.fi/handle/10138/356294
Online meeting link: