====== Discovery of Structural Variants ======
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| [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=254258568| 392130]] | Schönhuth/Knop | Summer 2021 | Wed 14:15-15:45 (S) in ZOOM |

==== Contents ====

In addition to small mutations in the genome, like the deletion, insertion or substitution of single bases, larger, so called structural variations, like the deletion, insertion, rearrangement, inversion or duplication of whole segments of the genome sequence, play an important role, e.g., in the development of cancer. High-throughput whole-genome sequencing enables detecting structural variations in several ways.

This is a classical literature seminar, i.e., on the first day, topics are introduced and selected by the students. In following sessions, students give a presentation on their topic and afterwards write an essay (“Hausarbeit”). Aspects of scientific writing and presenting will be covered as well.

Talks and essays can be done in German or English.

==== Time table ====

| **Date** | **Topic** |
| 28.04.2021 | [[teaching:2021summer:dsv:introduction|Introduction / Organization / Schedules]] ({{teaching:2021summer:dsv:introduction-280421.pdf|slides}}) |
| 05.05.2021 | [[teaching:2021summer:dsv:how-to-present|How to present]] ({{teaching:2021summer:dsv:howtopresent.pdf|slides}}, {{teaching:2021summer:healthcaretech:rubric_presentation_graduate_school_of_life_sciences.pdf|Presentation Guidelines}})|
| 12.05.2021 | //no seminar// |
| 19.05.2021 |  |
| 26.05.2021 | |
| 02.06.2021 |  |
| 09.06.2021 | |
| 16.06.2021 | |
| 23.06.2021 |  |
| 30.06.2021 |Jonas Waas (NanoVar) |
| 07.07.2020 | |
| 14.07.2020 | |
| 21.07.2020 | |

==== Literature ====

To download some reviews/papers, you have to be in the university network. A tutorial on how to connect to the university network via a VPN client can be found here: https://www.uni-bielefeld.de/einrichtungen/bits/services/netzzugang/vpn/

**Reviews**
  * //Structural Variant Discovery//: [[https://www.nature.com/articles/nrg2958.pdf|Genome structural variation discovery and genotyping]], by Alkan et al., Nature Reviews Genetics, 2011
  * //De Novo Assembly//: [[https://www.nature.com/articles/nrg3933.pdf|Genetic variation and the de novo assembly of human genomes]], Chaisson et al., Nature Reviews Genetics, 2015
  * //Long-range sequencing//: [[https://www.nature.com/articles/s41576-018-0003-4|Piercing the dark matter: bioinformatics of long-range sequencing and mapping]], Sedlazeck, et al., Nature Reviews Genetics, 2018
  * //Somatic Structural Variant Discovery//: [[https://www.nature.com/articles/s41698-021-00155-6.pdf?origin=ppub>|Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology]], van Belzen et al., Nature Precision Oncology, 2021
  * //Whole Genome Sequencing//: [[https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-019-1720-5.pdf|Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing]], Kosugi et al., Genome Biology, 2019

**Papers**
  * [[https://link.springer.com/content/pdf/10.1186/s13059-020-01993-6.pdf|Varlociraptor]]: Koester et al., Genome Biology, 2020 (somatic variants)
  * [[https://academic.oup.com/bioinformatics/article-pdf/28/18/i333/677913/bts378.pdf|Delly]]: Rausch et al., Bioinformatics, 2012 (structural variants, also somatic)
  * [[https://arxiv.org/pdf/1207.3907|FreeBayes]]: Garrison and Marth, arXiv:1207.3907, 2012 (haplotype-aware small variants)
  * [[https://www.nature.com/articles/s41592-020-01056-5|Hifiasm]]: Cheng et al., Nature Methods, 2021 (de novo assembly of “HiFi” reads)
  * [[https://academic.oup.com/bioinformatics/article-pdf/34/18/3094/25731859/bty191.pdf|MiniMap2]]: Heng Li, Bioinformatics, 2018 (overlap graph construction)
  * [[https://www.nature.com/articles/s42003-018-0023-9.pdf|Lancet]]: Narzisi et al., Communications Biology, 2018 (somatic variants)
  * [[https://genome.cshlp.org/content/27/12/2050.full.pdf|GRIDSS]]: Cameron et al., Genome Research, 2017 (rearrangement type variants)
  * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990442/pdf/nihms952902.pdf|Sniffles]]: Sedlazeck et al., Nature Methods, 2018 (structural variants from long reads)
  * [[https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-01968-7.pdf|NanoVar]]: Tham et al., Genome Biology, 2020 (structural variants from long reads)
  * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/pdf/cmb.2012.0021.pdf|SPADES]]: Bankevich et al., Journal of Computational Biology, 2012 (Genome Assembly, de Bruijn graph based)