A strategy for building and using a human reference pangenome.

Bastien Llamas,Gerard R Lazo,Qiandong Zeng,Xian Chang,Ilia Minkin,Ben Busby,Tobias Marschall,Peter A Audano,Giuseppe Narzisi,Evan Biederstedt,Travis Wrightsman,Adam M Novak,Glenn Hickey,Sagayamary Sagayaradj,Fritz J Sedlazeck,Mikko Rautiainen,Jean Monlong,Benedict Paten,Lon Blauvelt,Alan Cleary,Yassine Souilmi,Chen-Shan Chin,Jana Ebler,Arkarachai Fungtammasan,Wayne E Clarke,Erik Garrison,Shilpa Garg,Medhat Mahmoud,Justin M Zook,Jordan Eizenga ,Justin Wagner ,Michael Lin ,Toshiyuki Yokoyama ,Allison Regier ,Peter J Bradbury ,Jouni Sirén ,Rajeeva Musunuri ,Jonas Andreas Sibbesen ,Valérie Schneider ,Charles Markello

doi:10.12688/f1000research.19630.2

Abstract

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.

Highlights

University of Oxford, Any reports and responses or comments on the article can be found at the end of the article
Results and use cases Fundamentally, the motivation behind exploring graph genomes lies in the novel insights we may gain with their applications (Eizenga et al, 2020)
Graph genomes can be used for inference of extension and phasing from sparse information derived from SNP chips and RNA sequencing (RNA-seq)

Summary

Introduction

University of Oxford, Any reports and responses or comments on the article can be found at the end of the article. Author roles: Llamas B: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Narzisi G: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Schneider V: Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Resources, Validation, Writing – Original Draft Preparation, Writing – Review & Editing; Audano PA: Formal Analysis, Methodology, Software, Validation, Writing – Original Draft Preparation, Writing – Review & Editing; Biederstedt E: Formal Analysis, Methodology, Software, Validation, Writing – Original Draft Preparation, Writing – Review & Editing; Blauvelt L: Software, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Bradbury P: Formal Analysis, Investigation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing; Chang X: Formal Analysis, Methodology, Software, Validation, Writing – Original Draft Preparation, Writing – Review & Editing; Chin CS: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Fungtammasan A: Formal Analysis, Methodology, Software, Validation, Writing – Original Draft Preparation, Writing – Review & Editing; Clarke WE: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Cleary A: Formal Analysis, Investigation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing; Ebler J: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Eizenga J: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Sibbesen JA: Formal Analysis, Investigation, Methodology, Project Administration, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Markello CJ: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Garrison E: Conceptualization, Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Garg S: Data Curation, Software, Writing – Original Draft Preparation; Hickey G: Data Curation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Lazo GR: Formal Analysis, Methodology, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Lin MF: Data Curation, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Mahmoud M: Data Curation, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Marschall T: Conceptualization, Formal Analysis, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Minkin I: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Monlong J: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Musunuri RL: Data Curation, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Sagayaradj S: Data Curation, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Novak AM: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Rautiainen M: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Regier A: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Sedlazeck FJ: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Siren J: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Souilmi Y: Data Curation, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Wagner J: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Wrightsman T: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Yokoyama TT: Data Curation, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Zeng Q: Formal Analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Zook JM: Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Paten B: Conceptualization, Data Curation, Methodology, Resources, Software, Supervision, Writing – Review & Editing; Busby B: Conceptualization, Project Administration, Resources, Writing – Original Draft Preparation, Writing – Review & Editing

Methods

Results

Conclusion