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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #365060

Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

Title: A strategy for building and using a human reference pangenome

Author
item LLAMAS, BASTIEN - University Of Adelaide
item NARZISI, GIUSEPPE - New York Genome Center
item SCHNEIDER, VALERIE - National Institutes Of Health (NIH)
item AUDANO, PETER - University Of Washington Medical School
item BIEDERSTEDT, EVAN - Memorial Sloan Kettering
item BLAUVELT, LON - University Of California Santa Cruz
item Bradbury, Peter
item CHANG, XIN - University Of California Santa Cruz
item CHIN, CHEN-SHAN - Dnanexus
item FUNGTAMMASAN, ARKARACHAI - Dnanexus
item CLARKE, WAYNE - New York Genome Center
item CLEARY, ALAN - National Center For Genome Resources
item EBLER, JANA - Max Planck Institute For Informatics
item EIZENGA, JORDAN - University Of California Santa Cruz
item SIBBESEN, JONAS - University Of California Santa Cruz
item MARKELLO, CHARLES - University Of California Santa Cruz
item GARRISON, ERIK - University Of California Santa Cruz
item Lazo, Gerard
item LIN, MICHAEL - Dnanexus
item MAHMOUD, MEDHAT - Baylor College Of Medicine
item MARSCHALL, TOBIAS - Saarland University
item MINKIN, LLIA - Pennsylvania State University
item MONLONG, JEAN - University Of California Santa Cruz
item MUSUNURI, RAJEEVA - New York Genome Center
item SAGAYARADJ, SAGAYAMARY - Uc Davis Medical Center
item NOVAK, ADAM - University Of California Santa Cruz
item RAUTIAINEN, MIKKO - Max Planck Institute For Informatics
item REGIER, ALLISON - Washington University
item SEDLAZECK, FRITZ - Baylor College Of Medicine
item SIREN, JOUNI - University Of California Santa Cruz
item SOUILMI, YASSINE - University Of Adelaide
item SOUILMI, YASSINE - National Institute Of Standards And Technology
item WRIGHTSMAN, TRAVIS - Cornell University - New York
item YOKOYAMA, TOSHIYUKI - University Of Tokyo
item ZENG, QIANDONG - Labcorp
item ZOOK, JUSTIN - National Institute Of Standards And Technology
item PATEN, BENEDICT - University Of California Santa Cruz
item BUSBY, BEN - National Institutes Of Health (NIH)

Submitted to: F1000Research
Publication Type: Other
Publication Acceptance Date: 10/14/2019
Publication Date: 10/14/2019
Citation: Llamas, B., Narzisi, G., Schneider, V., Audano, P.A., Biederstedt, E., Blauvelt, L., Bradbury, P., Chang, X., Chin, C., Fungtammasan, A., Clarke, W.E., Cleary, A., Ebler, J., Eizenga, J.M., Sibbesen, J.A., Markello, C.J., Garrison, E., Lazo, G.R., Lin, M.F., Mahmoud, M., Marschall, T., Minkin, L., Monlong, J., Musunuri, R.L., Sagayaradj, S., Novak, A.M., Rautiainen, M., Regier, A., Sedlazeck, F.J., Siren, J., Souilmi, Y., Souilmi, Y., Wrightsman, T., Yokoyama, T., Zeng, Q., Zook, J.M., Paten, B., Busby, B. 2019. A strategy for building and using a human reference pangenome. F1000Research. 8:1751. https://doi.org/10.12688/f1000research.19630.1.
DOI: https://doi.org/10.12688/f1000research.19630.1

Interpretive Summary: In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics hackathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to write software tools. Although, a high-quality human reference genome exists that represents a single individual, DNA of all humans contain a lot of sequence variation and whole DNA segments not present in the reference genome. A representation of the genomic variation present in all individuals of a species is called a pangenome. Some software tools already exist to create and use a graphical representation of a pangenome. The pangenomics hackathon assembled experts in the field who developed new software and organized test data sets with the goal of creating a reference human pangenome. Some participants investigated the application of these methods to other species such as corn and wheat.

Technical 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 hackathon. 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