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Open Access Review

Tissue sampling methods and standards for vertebrate genomics

Pamela BY Wong12, Edward O Wiley3, Warren E Johnson4, Oliver A Ryder5, Stephen J O’Brien6, David Haussler7, Klaus-Peter Koepfli4, Marlys L Houck5, Polina Perelman8, Gabriela Mastromonaco9, Andrew C Bentley3, Byrappa Venkatesh10, Ya-ping Zhang1213, Robert W Murphy1122* and G10KCOS11*

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada

2 Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen`s Park, Toronto, Ontario, M5S 2C6, Canada

3 Division of Ichthyology, Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, Kansas, 66045, USA

4 Laboratory of Genomic Diversity, National Cancer Institute, 31 Center Drive, Frederick, Maryland, 21702-1201, USA

5 San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California, 92027, USA

6 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 8 Viborgskaya Street, St. Petersburg, 194044, Russia

7 Center for Biomolecular Science and Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, California, 95064, USA

8 Laboratory of Animal Cytogenetics, Institute of Molecular and Cellular Biology, Lavrentiev 10, Novosibirsk, 630090, Russia

9 Reproductive Physiology, Toronto Zoo, 361A Old Finch Avenue, Scarborough, Ontario, M1B 5K7, Canada

10 Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, 138673, Singapore

11 Genome 10 K Community of Scientists. http://www.genome10k.org/, Santa Cruz, California, USA

12 State Key Laboratory of Genetic Resource and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China

13 Laboratory for Conservation and Utilization of Bioresources, Yunnan University, 2 North Cuihu Road, Kunming, Yunnan, 650091, China

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GigaScience 2012, 1:8  doi:10.1186/2047-217X-1-8

Published: 12 July 2012

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.

Keywords:
Genome 10K; Sequencing; Vertebrates; Genomics; Tissue sampling; Tissue storage; Cell line; Tissue culture; RNA; DNA