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Lecture on cancer genomics by Esa Pitkänen

We are happy to announce a public lecture on cancer genomics by Esa Pitkänen from the University of Helsinki. This lecture should be of interest to a broad range of researchers of cancer, as well as researchers with a general interest in the rapid development of human whole-genome seuencing and precision medicine.

Esa is a computational biologist with extensive hands-on experience of large-scale biological data analyses.

Note! We will also have a visit by Sigve Nakken, bioinformatician from the Hovig group at Oslo Universtity Hospital ( at the same day Nov 27th. Sigve is part of the analysis team of the Norwegian cancer concortium (, and has extensive experience of cancer exome sequencing and analysis.

In addition to the seminar, we will spend the afternoon on discussions around strategies and technical details regarding

* sampling, clonality, purity and QC
* somatic variant calling (SNV, indels, CNV, structural variation)
* functional annotation of variants
* pros and cons of exome vs WGS
* reference genomes (the Norwegian concortium is planning to soon move to hg38)
* future contacts and knowledge sharing

If you want to participate in these discussions, please sign up at your prefered time(s) at the doodle, thanks! The more the merrier!


Speaker: Esa Pitkänen, Genome-Scale Biology Program & Finnish Center of Excellence in Cancer Genetics Research, the University of Helsinki
Date: Nov 27, 2015
Time: 11.15-12.00 am
Place: B10:2, Entrance A11, BMC, Husargatan 3, Uppsala (see attached map)
Host: Björn Nystedt,


Discovery of recurrent somatic events in whole-genome sequencing data of colorectal cancers and uterine leiomyomas
Cancer is a disease of the genome, driven by somatic mutations. We discuss the analysis of whole-genome sequencing (WGS) data from tumor and matching normal samples aiming at the identification of recurrent somatic events driving tumor progression. Approaches utilized in the Aaltonen lab WGS analysis workflow will be covered, including identification of somatic single-nucleotide variants, indels, structural and copy number variants, and transposable elements, as well as estimation of tumor heterogeneity. We will conclude by introducing two recent discoveries involving these approaches. First, we discuss the occurrence of recurring mutations at the transcription factor CTCF binding sites in gastrointestinal tumors, particularly colorectal cancers (Katainen et al. Nat Genet 2015). Second, we describe the catastrophic shattering and subsequent reassembly of genomes, or chromothripsis, in uterine leiomyomas (Mehine et al. NEJM 2013).