Title

Tissue Sampling Methods and Standards for Vertebrate Genomics

Authors

Pamela B. Y. Wong, University of Toronto - Canada; Royal Ontario Museum - Canada
Edward O. Wiley, University of Kansas - Lawrence
Warren E. Johnson, National Cancer Institute at Frederick
Oliver A. Ryder, San Diego Zoo
Stephen J. O'Brien, National Cancer Institute at FrederickFollow
David Haussler, University of California - Santa Cruz
Klaus-Peter Koepfli, National Cancer Institute at Frederick
Marlys L. Houck, San Diego Zoo
Polina L. Perelman, Institute of Cytology and Genetics - Novosibirsk, Russia
Gabriela Mastromonaco, Toronto Zoo - Canada
Andrew C. Bentley, University of Kansas - Lawrence
Byrappa Venkatesh, Institute of Molecular and Cell Biology - Singapore
Ya-ping Zhang, Chinese Academy of Sciences - Kunming; Yunnan University - China
Robert W. Murphy, University of Toronto - Canada; Royal Ontario Museum - Canada; Chinese Academy of Sciences - Kunming
Genome 10K Project Community of Scientists

Document Type

Article

Publication Date

2012

Publication Title

GigaScience

Keywords

Genome 10K, Sequencing, Vertebrates, Genomics, Tissue sampling, Tissue storage, Cell line, Tissue culture, RNA, DNA

ISSN

2047-217X

Volume

1

Issue/No.

8

First Page

1

Last Page

12

Abstract

The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual);three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 μg of DNA); and one-star (ethanol-preserved tissue for 700 μg of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species’ natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota.

Comments

©Wong et al.; licensee BioMed Central Ltd. 2012

Additional Comments

Natural Sciences and Research Council of Canada Discovery grant #: 3148; Assembling Tree of Life grant #: DEB0732819

NSUWorks Citation

Wong, Pamela B. Y.; Edward O. Wiley; Warren E. Johnson; Oliver A. Ryder; Stephen J. O'Brien; David Haussler; Klaus-Peter Koepfli; Marlys L. Houck; Polina L. Perelman; Gabriela Mastromonaco; Andrew C. Bentley; Byrappa Venkatesh; Ya-ping Zhang; Robert W. Murphy; and Genome 10K Project Community of Scientists. 2012. "Tissue Sampling Methods and Standards for Vertebrate Genomics." GigaScience 1, (8): 1-12. https://nsuworks.nova.edu/cnso_bio_facarticles/756

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015