Computational pan-genomics: status, promises and challenges.
Tobias Marschall,Manja Marz,Manja Marz,Thomas Abeel,Louis Dijkstra,Bas E. Dutilh,Ali Ghaffaari,Ali Ghaffaari,Paul Kersey,Wigard P. Kloosterman,Veli Mäkinen,Adam M. Novak,Benedict Paten,David Porubsky,Eric Rivals,Can Alkan,Jasmijn A. Baaijens,Paul I.W. de Bakker,Valentina Boeva,Raoul J. P. Bonnal,Francesca Chiaromonte,Rayan Chikhi,Francesca D. Ciccarelli,Robin Cijvat,Erwin Datema,Cornelia M. van Duijn,Evan E. Eichler,Evan E. Eichler,Corinna Ernst,Eleazar Eskin,Erik Garrison,Mohammed El-Kebir,Gunnar W. Klau,Jan O. Korbel,Eric-Wubbo Lameijer,Benjamin Langmead,Marcel Martin,Paul Medvedev,John C. Mu,Pieter B. Neerincx,Klaasjan G. Ouwens,Pierre Peterlongo,Nadia Pisanti,Sven Rahmann,Ben Raphael,Knut Reinert,Dick de Ridder,Jeroen de Ridder,Matthias Schlesner,Ole Schulz-Trieglaff,Ashley D. Sanders,Siavash Sheikhizadeh,Carl Shneider,Sandra Smit,Daniel Valenzuela,Jiayin Wang,Lodewyk F. A. Wessels,Y. Zhang,Victor Guryev,Fabio Vandin,Kai Ye,Alexander Schönhuth +61 more
TLDR
Already available approaches to construct and use pan-genomes are examined, the potential benefits of future technologies and methodologies are discussed, and open challenges from the vantage point of the above-mentioned biological disciplines are reviewed.Abstract:
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 data sets. 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 article, 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.read more
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Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Peter Ebert,Peter A. Audano,Qihui Zhu,Bernardo Rodriguez-Martin,David Porubsky,Marc Jan Bonder,Marc Jan Bonder,Arvis Sulovari,Jana Ebler,Weichen Zhou,Rebecca Serra Mari,Feyza Yilmaz,Xuefang Zhao,Xuefang Zhao,PingHsun Hsieh,Joyce V. Lee,Sushant Kumar,Jiadong Lin,Tobias Rausch,Yu Chen,Jingwen Ren,Martin Santamarina,Wolfram Höps,Hufsah Ashraf,Nelson T. Chuang,Xiaofei Yang,Katherine M. Munson,Alexandra P. Lewis,Susan Fairley,Luke J. Tallon,Wayne E. Clarke,Anna O. Basile,Marta Byrska-Bishop,André Corvelo,Uday S. Evani,Tsung Yu Lu,Mark Chaisson,Junjie Chen,Chong Li,Harrison Brand,Harrison Brand,Aaron M. Wenger,Maryam Ghareghani,Maryam Ghareghani,Maryam Ghareghani,William T. Harvey,Benjamin Raeder,Patrick Hasenfeld,Allison A. Regier,Haley J. Abel,Ira M. Hall,Paul Flicek,Oliver Stegle,Oliver Stegle,Mark Gerstein,Jose M. C. Tubio,Zepeng Mu,Yang I. Li,Xinghua Shi,Alex Hastie,Kai Ye,Kai Ye,Zechen Chong,Ashley D. Sanders,Michael C. Zody,Michael E. Talkowski,Michael E. Talkowski,Ryan E. Mills,Scott E. Devine,Charles Lee,Charles Lee,Jan O. Korbel,Tobias Marschall,Evan E. Eichler +73 more
TL;DR: In this article, the authors present 64 assembled haplotypes from 32 diverse human genomes, which integrate all forms of genetic variation, even across complex loci, and identify 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing.
Journal ArticleDOI
Genome graphs and the evolution of genome inference
TL;DR: This work surveys various projects underway to build and apply graph-based structures-which it is referred to as genome graphs-and discusses the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce.
Journal ArticleDOI
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies.
TL;DR: SyRI is presented, a pairwise whole-genome comparison tool for chromosome-level assemblies that starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearrange regions.
Journal ArticleDOI
The design and construction of reference pangenome graphs with minigraph
Heng Li,Xiaowen Feng,Chong Chu +2 more
TL;DR: A graph-based data model and associated formats are proposed to represent multiple genomes while preserving the coordinate of the linear reference genome and it is demonstrated that this model can efficiently construct a pangenome graph and compactly encode tens of thousands of structural variants missing from the current reference genome.
Journal ArticleDOI
Graphtyper enables population-scale genotyping using pangenome graphs
Hannes P. Eggertsson,Hannes P. Eggertsson,Hakon Jonsson,Snaedis Kristmundsdottir,Snaedis Kristmundsdottir,Eirikur Hjartarson,Birte Kehr,Gisli Masson,Florian Zink,Kristjan E. Hjorleifsson,Aslaug Jonasdottir,Adalbjorg Jonasdottir,Ingileif Jonsdottir,Ingileif Jonsdottir,Daniel F. Gudbjartsson,Daniel F. Gudbjartsson,Páll Melsted,Páll Melsted,Kari Stefansson,Kari Stefansson,Bjarni V. Halldorsson,Bjarni V. Halldorsson +21 more
TL;DR: Graphtyper as discussed by the authors realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths.
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
A global reference for human genetic variation.
Adam Auton,Gonçalo R. Abecasis,David Altshuler,Richard Durbin,David R. Bentley,Aravinda Chakravarti,Andrew G. Clark,Peter Donnelly,Evan E. Eichler,Paul Flicek,Stacey Gabriel,Richard A. Gibbs,Eric D. Green,Matthew E. Hurles,Bartha Maria Knoppers,Jan O. Korbel,Eric S. Lander,Charles Lee,Hans Lehrach,Elaine R. Mardis,Gabor T. Marth,Gil McVean,Deborah A. Nickerson,Jeanette Schmidt,Stephen T. Sherry,Jun Wang,Richard K. Wilson,Eric Boerwinkle,Harsha Doddapaneni,Yi Han,Viktoriya Korchina,Christie Kovar,Sandra L. Lee,Donna M. Muzny,Jeffrey G. Reid,Yiming Zhu,Yuqi Chang,Qiang Feng,Qiang Feng,Xiaodong Fang,Xiaodong Fang,Xiaosen Guo,Xiaosen Guo,Min Jian,Min Jian,Hui Jiang,Hui Jiang,Xin Jin,Tianming Lan,Guoqing Li,Jingxiang Li,Yingrui Li,Shengmao Liu,Xiao Liu,Xiao Liu,Yao Lu,Xuedi Ma,Meifang Tang,Bo Wang,Guangbiao Wang,Honglong Wu,Renhua Wu,Xun Xu,Ye Yin,Dandan Zhang,Wenwei Zhang,Jiao Zhao,Meiru Zhao,Xiaole Zheng,Namrata Gupta,Neda Gharani,Lorraine Toji,Norman P. Gerry,Alissa M. 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Grant,Carla Gallo,Giovanni Poletti,Danish Saleheen,Asif Rasheed,Lisa D. Brooks,Adam Felsenfeld,Jean E. McEwen,Yekaterina Vaydylevich,Audrey Duncanson,Michael Dunn,Jeffery A. Schloss +517 more
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Journal ArticleDOI
The sequence of the human genome.
J. Craig Venter,Mark Raymond Adams,Eugene W. Myers,Peter W. Li,Richard J. Mural,Granger G. Sutton,Hamilton O. Smith,Mark Yandell,Cheryl A. Evans,Robert A. Holt,Jeannine D. Gocayne,Peter Amanatides,Richard M. Ballew,Daniel H. Huson,Jennifer R. Wortman,Qing Zhang,Chinnappa D. Kodira,Xiangqun H. Zheng,Lin Chen,Marian P. Skupski,Gangadharan Subramanian,Paul Thomas,Jinghui Zhang,George L. Gabor Miklos,Catherine R. Nelson,Samuel Broder,Andrew G. Clark,J. H. Nadeau,Victor A. McKusick,Norton D. Zinder,Arnold J. Levine,Richard J. Roberts,M. I. Simon,Carolyn W. Slayman,Michael W. Hunkapiller,Randall Bolanos,Arthur L. Delcher,Ian M. Dew,Daniel Fasulo,Michael Flanigan,Liliana Florea,Aaron L. Halpern,Sridhar Hannenhalli,Saul A. Kravitz,Samuel Levy,Clark M. Mobarry,Knut Reinert,Karin A. Remington,Jane Abu-Threideh,Ellen M. Beasley,Kendra Biddick,Vivien Bonazzi,Rhonda Brandon,Michele Cargill,Ishwar Chandramouliswaran,Rosane Charlab,Kabir Chaturvedi,Zuoming Deng,Valentina Di Francesco,Patrick Dunn,Karen Eilbeck,Carlos Evangelista,Andrei Gabrielian,Weiniu Gan,Wangmao Ge,Fangcheng Gong,Zhiping Gu,Ping Guan,Thomas J. Heiman,Maureen E. Higgins,Rui-Ru Ji,Zhaoxi Ke,Karen A. Ketchum,Zhongwu Lai,Yiding Lei,Zhenya Li,Jiayin Li,Yong Liang,Xiaoying Lin,Fu Lu,Gennady V. Merkulov,Natalia Milshina,Helen M. Moore,Ashwinikumar K Naik,Vaibhav A. Narayan,Beena Neelam,Deborah Nusskern,Douglas B. Rusch,Steven L. Salzberg,Wei Shao,Bixiong Chris Shue,Jingtao Sun,Zhen Yuan Wang,Aihui Wang,Xin Wang,Jian Wang,Ming-Hui Wei,Ron Wides,Chunlin Xiao,Chunhua Yan,Alison Yao,Jane Ye,Ming Zhan,Weiqing Zhang,Hongyu Zhang,Qi Zhao,Liansheng Zheng,Fei Zhong,Wenyan Zhong,Shiaoping C. Zhu,Shaying Zhao,Dennis A. Gilbert,Suzanna Baumhueter,Gene Spier,Christine Carter,Anibal Cravchik,Trevor Woodage,Feroze Ali,Huijin An,Aderonke Awe,Danita Baldwin,Holly Baden,Mary Barnstead,Ian Barrow,Karen Beeson,Dana A. Busam,Amy Carver,Ming Lai Cheng,Liz Curry,Steve Danaher,Lionel Davenport,Raymond Desilets,Susanne Dietz,Kristina Dodson,Lisa Doup,Steven Ferriera,Neha Garg,Andres Gluecksmann,Brit J. Hart,Jason Haynes,Charles Haynes,Cheryl Heiner,Suzanne Hladun,Damon Hostin,Jarrett Houck,Timothy Howland,Chinyere Ibegwam,Jeffery Johnson,Francis Kalush,Lesley Kline,Shashi Koduru,Amy Love,Felecia Mann,David May,Steven McCawley,Tina C. McIntosh,Ivy McMullen,Mee Moy,Linda Moy,Brian Murphy,Keith Nelson,Cynthia Pfannkoch,Eric Pratts,Vinita Puri,Hina Qureshi,Matthew Reardon,Robert Rodriguez,Yu-Hui Rogers,Deanna Romblad,Bob Ruhfel,Richard T. Scott,Cynthia Sitter,Michelle Smallwood,Erin Stewart,Renee Strong,Ellen Suh,Reginald Thomas,Ni Ni Tint,Sukyee Tse,Claire Vech,Gary Wang,Jeremy Wetter,Sherita Williams,Monica Williams,Sandra Windsor,Emily Winn-Deen,Keriellen Wolfe,Jayshree Zaveri,Karena Zaveri,Josep F. Abril,Roderic Guigó,Michael J. Campbell,Kimmen Sjölander,Brian Karlak,Anish Kejariwal,Huaiyu Mi,Betty Lazareva,Thomas Hatton,Apurva Narechania,Karen Diemer,Anushya Muruganujan,Nan Guo,Shinji Sato,Vineet Bafna,Sorin Istrail,Ross Lippert,Russell Schwartz,Brian P. Walenz,Shibu Yooseph,David Allen,Anand Basu,James Baxendale,Louis Blick,Marcelo Caminha,John Carnes-Stine,Parris Caulk,Yen-Hui Chiang,My Coyne,Carl Dahlke,Anne Deslattes Mays,Maria Dombroski,Michael Donnelly,Dale Ely,Shiva Esparham,Carl Fosler,Harold Gire,Stephen Glanowski,Kenneth Glasser,Anna Glodek,Mark Gorokhov,Ken Graham,Barry Gropman,Michael Harris,Jeremy Heil,Scott Henderson,Jeffrey Hoover,Donald Jennings,Catherine Jordan,James Jordan,John Kasha,Leonid Kagan,Cheryl L. Kraft,Alexander Levitsky,Mark Lewis,Xiangjun Liu,John Lopez,Daniel Ma,William H. Majoros,Joe McDaniel,Sean C. Murphy,Matthew Newman,Trung Hieu Nguyen,Ngoc Nguyen,Marc Nodell,Sue Pan,Jim Peck,Marshall Peterson,William Rowe,Robert Sanders,John Scott,Michael Simpson,Thomas J. Smith,Arlan Sprague,Timothy B. Stockwell,Russell Turner,Eli Venter,Mei Wang,Meiyuan Wen,David Wu,Mitchell Wu,Ashley Xia,Ali Zandieh,Xiaohong Zhu +272 more
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Journal ArticleDOI
The Human Genome Browser at UCSC
W. James Kent,Charles W. Sugnet,Terrence S. Furey,Krishna M. Roskin,Tom H. Pringle,Alan M. Zahler,and David Haussler +6 more
TL;DR: A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu.
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