RT Journal Article
SR Electronic
T1 Computational Pan-Genomics: Status, Promises and Challenges
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 043430
DO 10.1101/043430
A1 The Computational Pan-Genomics Consortium
A1 Tobias Marschall
A1 Manja Marz
A1 Thomas Abeel
A1 Louis Dijkstra
A1 Bas E. Dutilh
A1 Ali Ghaffaari
A1 Paul Kersey
A1 Wigard P. Kloosterman
A1 Veli Mäkinen
A1 Adam M. Novak
A1 Benedict Paten
A1 David Porubsky
A1 Eric Rivals
A1 Can Alkan
A1 Jasmijn Baaijens
A1 Paul I. W. De Bakker
A1 Valentina Boeva
A1 Raoul J. P. Bonnal
A1 Francesca Chiaromonte
A1 Rayan Chikhi
A1 Francesca D. Ciccarelli
A1 Robin Cijvat
A1 Erwin Datema
A1 Cornelia M. Van Duijn
A1 Evan E. Eichler
A1 Corinna Ernst
A1 Eleazar Eskin
A1 Erik Garrison
A1 Mohammed El-Kebir
A1 Gunnar W. Klau
A1 Jan O. Korbel
A1 Eric-Wubbo Lameijer
A1 Benjamin Langmead
A1 Marcel Martin
A1 Paul Medvedev
A1 John C. Mu
A1 Pieter Neerincx
A1 Klaasjan Ouwens
A1 Pierre Peterlongo
A1 Nadia Pisanti
A1 Sven Rahmann
A1 Ben Raphael
A1 Knut Reinert
A1 Dick de Ridder
A1 Jeroen de Ridder
A1 Matthias Schlesner
A1 Ole Schulz-Trieglaff
A1 Ashley D. Sanders
A1 Siavash Sheikhizadeh
A1 Carl Shneider
A1 Sandra Smit
A1 Daniel Valenzuela
A1 Jiayin Wang
A1 Lodewyk Wessels
A1 Ying Zhang
A1 Victor Guryev
A1 Fabio Vandin
A1 Kai Ye
A1 Alexander Schönhuth
YR 2016
UL http://biorxiv.org/content/early/2016/08/25/043430.abstract
AB Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic datasets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this paper, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies, and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.