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## Genomics Seminar
**Speaker:** [Prof Pjotr Prins](https://thebird.nl/)
**Date:** 11th February 2022
**Venue:** Vivarium and Virtual
**Time:** 11 am

## Pangenome Genotyping

In this talk, Pjotr Prins will discuss pangenomics and the emerging field of pangenetics.

Twenty years ago, the reference genome was a giant leap forward; today, it shows its shortcomings when comparing individuals from mixed genetic backgrounds because the reference genome is *not* representative.
In humans, for example, 10% of the African DNA sequence does not align to the current reference genome.

We have known from the start for insects and pathogens that a reference genome approach is unsatisfactory. What is exciting today is that new pangenome tools are actively being developed. In conjunction with high-fidelity long read sequencing, we are getting a far clearer picture of the genome for genotyping.

### Pjotr Prins Bio
![](https://thebird.nl/pjotrprins.jpg)
Pjotr is a bioinformatician at large & assistant (coding) professor at the Department of Genetics, Genomics and Informatics at [the University of Tennessee Health Science Center](http://www.uthsc.edu/). Pjotr is also director of Genenetwork.org; an [Oxford University Nuffield Department of Medicine](http://www.ndm.ox.ac.uk/home) honorary visiting research fellow in statistical genetics, a former visiting research fellow of the [Personal genomics and bioinformatics department](https://www.umcutrecht.nl/en/Research/Other-research/Center-for-Molecular-Medicine/Section-Genetics/Cuppen) of the University Medical Center Utrecht and the [Groningen Bioinformatics Center](http://www.rug.nl/gbic). As of 2021 Pjotr is an adjunct associate professor at Pwani University, Kenya, and a member of the [ERIBA](https://eriba.umcg.nl/) Laboratory of Genome Structure and Ageing at UMC Groningen, the Netherlands. Pjotr runs a [virtual group](http://thebird.nl/blog/work/group.html) and is a founder, editor and coder for the BioHackrXiv.org and a former editor for the [Journal of Open Source Software (JOSS)](http://joss.theoj.org/). 

***
We organised the first Pangenomics Bio Hacking 2021 conference!
December 9-10, 2021, Aula Sironi, Milano

https://pgbh2021.pangenome.eu/
***

### Further reading:

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

Jouni Sirén, Jean Monlong, Erik Garrison, et al.
Science 374 (6574), 2021
https://www.science.org/doi/pdf/10.1126/science.abg8871

ODGI: understanding pangenome graphs
Andrea Guarracino, Simon Heumos, Sven Nahnsen, Pjotr Prins, Erik Garrison
BioRXiv 2021
https://www.biorxiv.org/content/10.1101/2021.11.10.467921.full.pdf

Eizenga, J. M. and Novak, A. M. and Sibbesen, J. A. and Heumos, S. and Ghaffaari, A. and Hickey, G. and Chang, X. and Seaman, J. D. and Rounthwaite, R. and Ebler, J. and Rautiainen, M. and Garg, S. and Paten, B. and Marschall, T. and Siren, J. and Garrison, E., Pangenome Graphs, Annual Review of Genomics and Human Genetics, 2020.
https://www.annualreviews.org/doi/pdf/10.1146/annurev-genom-120219-080406

Sherman, R. M. and Salzberg, S. L., Pan-Genomics in the Human Genome Era,
Nature Reviews Genetics volume 21, pages 243–254 (2020)
https://www.nature.com/articles/s41576-020-0210-7
