Kari Lavikka

Kari Lavikka
University of Helsinki | HY · Research Programs Unit

Master of Science

About

10
Publications
945
Reads
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47
Citations
Citations since 2017
10 Research Items
47 Citations
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2017201820192020202120222023051015
2017201820192020202120222023051015

Publications

Publications (10)
Article
Full-text available
Homologous recombination DNA-repair deficiency (HRD) is a common driver of genomic instability and confers a therapeutic vulnerability in cancer. The accurate detection of somatic allelic imbalances (AIs) has been limited by methods focused on BRCA1/2 mutations and using mixtures of cancer types. Using pan-cancer data, we revealed distinct patterns...
Preprint
Full-text available
L1 retrotransposons are the only protein-coding active transposable elements in the human genome. Although silenced during normal conditions, they are highly expressed in human epithelial cancers including high-grade serous ovarian cancer (HGSC), where they transcribe to form L1 mRNA and subsequently integrate into the genome by a process called re...
Preprint
Full-text available
Ovarian high-grade serous carcinoma (HGSC) is typically diagnosed at an advanced stage, with multiple genetically heterogeneous clones existing in the tumors long before therapeutic intervention. Herein we characterized HGSC evolutionary states using whole-genome sequencing data from 214 samples of 55 HGSC patients in the prospective, longitudinal,...
Article
Extensive utilization of organoids from high-grade serous ovarian carcinoma (HGSOC), the most common and lethal ovarian cancer, has been hampered by low success rates of long-term culture and scarcity of fresh tumor material. Here we present the development of a novel method for efficient generation, expansion and use of HGSOC organoids from cryopr...
Poster
High-grade serous ovarian cancer (HGSC) is the most common form of epithelial ovarian cancer, typically diagnosed at advanced stage with five-year survival of only 38%. Herein, we used 149 treatment-naïve and 65 after-treatment samples subjected to whole-genome sequencing from 55 HGSC patients to reconstruct evolutionary histories, characterize clo...
Presentation
This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Proffered Abstracts section (PR003) of the Conference Proceedings. Citation Format: Alexandra Lahtinen, Kari Lavikka, Yilin Li, Sanaz Jamalzadeh, Anni Virtanen, Rainer Lehtonen, Olli Carpén, Sakari Hietanen, Kaisa Huhtinen, Antti Häkkinen...
Preprint
Full-text available
The broad research use of organoids from high-grade serous ovarian carcinoma (HGSC) has been hampered by low culture success rates and limited availability of fresh tumor material. Here we describe a method for generation and long-term expansion of HGSC organoids with efficacy markedly improved over previous reports (55% vs. 23-38%). We established...
Presentation
Full-text available
Current genome browsers have rigid visualization capabilities and depend on specific file formats. We present a declarative, grammar-based approach for building interactive genomic visualizations and demonstrate its utility with two case studies involving high-grade serous ovarian cancer data.
Article
Full-text available
PURPOSE Circulating tumor DNA (ctDNA) detection is a minimally invasive technique that offers dynamic molecular snapshots of genomic alterations in cancer. Although ctDNA markers can be used for early detection of cancers or for monitoring treatment efficacy, the value of ctDNA in guiding treatment decisions in solid cancers is controversial. Here,...
Article
Anduril is an analysis and integration framework that facilitates the design, use, parallelization and reproducibility of bioinformatics workflows. Anduril has been upgraded to use Scala for pipeline construction, which simplifies software maintenance, and facilitates design of complex pipelines. Additionally, Anduril's bioinformatics repository ha...

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