Difference between revisions of "Task Force Biobank Procedures"
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*Performing an experiment on stabilizers for RNA during shipment | *Performing an experiment on stabilizers for RNA during shipment | ||
*As part of [https://www.synthesys.info/ SYNTHESYS+] Work Package 3, performing a landscape analysis of existing biobank standard operating procedures | *As part of [https://www.synthesys.info/ SYNTHESYS+] Work Package 3, performing a landscape analysis of existing biobank standard operating procedures | ||
| + | *Serving on the [https://www.earthbiogenome.org/ EBP] [https://www.earthbiogenome.org/subcommittee-sample-collection-processing Scientific Subcommittee: Sample Collection and Processing]. | ||
=Accomplishments= | =Accomplishments= | ||
| Line 17: | Line 18: | ||
=Related Resources= | =Related Resources= | ||
| − | *[https://library.ggbn.org/share/s/D0bTJmODQLC5T0FCDsKkiw Mulcahy DG, Macdonald KS III, Brady SG, Meyer C, Barker KB, Coddington J. 2016. Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA. PeerJ 4:e2528] [https://peerj.com/articles/2528/ https://doi.org/10.7717/peerj.2528] | + | |
| − | *[https://library.ggbn.org/share/s/4suHINq8SY6_0YjgG9HflA Zimkus, Breda & Hassapakis, Craig & Houck, Marlys. (2018). Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation. Amphibian and Reptile Conservation. 12. 1-27] | + | * [https://doi.org/10.1089/bio.2016.0078 Bourque, D.A., Naaum, A.M., Distel, D.L. and Hanner, R.H. (2017) Whole Genome Amplification Provides Suitable Control DNA for Use in DNA Barcoding Applications. Biopreservation and Biobanking, 15, 277-279.] |
| + | * [https://www.isber.org/page/BPR Campbell, L.D., Astrin, J.J., De Souza, Y., Giri, J.G., A., P.A., Rawley-Payne, M., Rush, A., Sieffert, N. (eds.) (2018) ISBER Best Practices: Recommendations for Repositories - Guidance for the Collection, Handling, Storage, and Distribution of Biological and Environmental Specimens. ISBER.] | ||
| + | * [https://library.ggbn.org/share/s/D0bTJmODQLC5T0FCDsKkiw Mulcahy DG, Macdonald KS III, Brady SG, Meyer C, Barker KB, Coddington J. 2016. Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA. PeerJ 4:e2528] [https://peerj.com/articles/2528/ https://doi.org/10.7717/peerj.2528] | ||
| + | * [https://library.ggbn.org/share/s/4Gu5BXoZSSe1eTlTcz1sqw Sharpe, A., Barrios, S., Gayer, S., Allan-Perkins, E., Stein, D., Appiah-Madson, H.J., Falco, R. and Distel, D.L. (2020) DESS deconstructed: Is EDTA solely responsible for protection of high molecular weight DNA in this common tissue preservative? PLOS ONE, 15, e0237356.] | ||
| + | * [https://library.ggbn.org/share/s/4suHINq8SY6_0YjgG9HflA Zimkus, Breda & Hassapakis, Craig & Houck, Marlys. (2018). Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation. Amphibian and Reptile Conservation. 12. 1-27] | ||
| + | * [https://doi.org/10.14351/0831-0005-28.1.77 Zimkus, B.M. and Ford, L.S. (2014) Best practices for genetic resources associated with natural history collections: Recommendations for practical implementation. Collection Forum, 28, 77-112.] | ||
| + | * [https://enveurope.springeropen.com/articles/10.1186/s12302-022-00618-y Zizka, V.M.A., Koschorreck, J. , Khan, J. and Astrin, J.J. (2022) Long-term archival of environmental samples empowers biodiversity monitoring and ecological research] | ||
=Getting Involved= | =Getting Involved= | ||
| − | Email us at | + | Email us at [mailto:info@ggbn.org info@ggbn.org] to: |
*Join the Task Force | *Join the Task Force | ||
*Volunteer to lead an experiment | *Volunteer to lead an experiment | ||
| Line 27: | Line 34: | ||
=Current Members= | =Current Members= | ||
*Jonas Astrin, Zoological Research Museum A. Koenig (2016-present), Chair | *Jonas Astrin, Zoological Research Museum A. Koenig (2016-present), Chair | ||
| + | *Ken Hayes, Bernice Pauahi Bishop Museum (2021-present), Co-Chair | ||
*Katie Barker, Smithsonian National Museum of Natural History (2016-present) | *Katie Barker, Smithsonian National Museum of Natural History (2016-present) | ||
*Mike Bruford, Cardiff University (2017-present) | *Mike Bruford, Cardiff University (2017-present) | ||
*Marta Castelhano, Cornell University (2016-present) | *Marta Castelhano, Cornell University (2016-present) | ||
*Jon Coddington, Smithsonian National Museum of Natural History (2016-present) | *Jon Coddington, Smithsonian National Museum of Natural History (2016-present) | ||
| + | *Kelli DeLeon, Bernice Pauahi Bishop Museum (2021-present) | ||
*Dan Distel, Ocean Genome Legacy (2016-present) | *Dan Distel, Ocean Genome Legacy (2016-present) | ||
*Gabi Droege, Botanic Garden and Botanical Museum Berlin-Dahlem (2016-present) | *Gabi Droege, Botanic Garden and Botanical Museum Berlin-Dahlem (2016-present) | ||
| + | *Chris Huddleston, Smithsonian National Museum of Natural History (2021-present) | ||
*Andrew Iloh, Biodiversity and Climate Research, Biotechnology Research Center (2016-present) | *Andrew Iloh, Biodiversity and Climate Research, Biotechnology Research Center (2016-present) | ||
| − | |||
*Kim Labuschagne, National Zoological Gardens (2016-present) | *Kim Labuschagne, National Zoological Gardens (2016-present) | ||
*Jackie Mackenzie-Dodds, Natural History Museum London (2016-present) | *Jackie Mackenzie-Dodds, Natural History Museum London (2016-present) | ||
*Li Qiyuan, Beijing Genomics Institute (2016-present) | *Li Qiyuan, Beijing Genomics Institute (2016-present) | ||
| − | |||
*Julie Strand, Randers Regnskov Tropical Zoo (2016-present) | *Julie Strand, Randers Regnskov Tropical Zoo (2016-present) | ||
| + | *Jianbo Sun, China National Genebank (2021-present) | ||
*Michal Vinkler, Charles University in Prague (2016-present) | *Michal Vinkler, Charles University in Prague (2016-present) | ||
*Breda Zimkus, Museum of Comparative Zoology Harvard University (2016-present) | *Breda Zimkus, Museum of Comparative Zoology Harvard University (2016-present) | ||
Latest revision as of 11:28, 22 August 2022
Contents
Program of Work
Improve biobank standard operating procedures and sample preservation by:
- Conducting and publishing results on targeted sample preservation studies
- Identifying and filling gaps in best practices related to the management of genomic samples
Current Activities
- Performing a long-term experiment on fixed animal tissue preservation; testing common preservatives across wider range of taxa
- Currently testing Qiagen RNAlater, RNAlater surrogate, Qiagen AllProtect, ethanol, propylene glycol, DESS (DMSO/NaCl), and tissue lysis buffer
- Performing an experiment on stabilizers for RNA during shipment
- As part of SYNTHESYS+ Work Package 3, performing a landscape analysis of existing biobank standard operating procedures
- Serving on the EBP Scientific Subcommittee: Sample Collection and Processing.
Accomplishments
- Contributed to the ISBER, 2018, ISBER Best Practices - Recommendations for Biorepositories
- Reviewed the collection, processing, storage and transportation of animal and plant genetic resources for inclusion in ISO biobanking standard (ISO/AWI 20387).
Related Resources
- Bourque, D.A., Naaum, A.M., Distel, D.L. and Hanner, R.H. (2017) Whole Genome Amplification Provides Suitable Control DNA for Use in DNA Barcoding Applications. Biopreservation and Biobanking, 15, 277-279.
- Campbell, L.D., Astrin, J.J., De Souza, Y., Giri, J.G., A., P.A., Rawley-Payne, M., Rush, A., Sieffert, N. (eds.) (2018) ISBER Best Practices: Recommendations for Repositories - Guidance for the Collection, Handling, Storage, and Distribution of Biological and Environmental Specimens. ISBER.
- Mulcahy DG, Macdonald KS III, Brady SG, Meyer C, Barker KB, Coddington J. 2016. Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA. PeerJ 4:e2528 https://doi.org/10.7717/peerj.2528
- Sharpe, A., Barrios, S., Gayer, S., Allan-Perkins, E., Stein, D., Appiah-Madson, H.J., Falco, R. and Distel, D.L. (2020) DESS deconstructed: Is EDTA solely responsible for protection of high molecular weight DNA in this common tissue preservative? PLOS ONE, 15, e0237356.
- Zimkus, Breda & Hassapakis, Craig & Houck, Marlys. (2018). Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation. Amphibian and Reptile Conservation. 12. 1-27
- Zimkus, B.M. and Ford, L.S. (2014) Best practices for genetic resources associated with natural history collections: Recommendations for practical implementation. Collection Forum, 28, 77-112.
- Zizka, V.M.A., Koschorreck, J. , Khan, J. and Astrin, J.J. (2022) Long-term archival of environmental samples empowers biodiversity monitoring and ecological research
Getting Involved
Email us at info@ggbn.org to:
- Join the Task Force
- Volunteer to lead an experiment
Current Members
- Jonas Astrin, Zoological Research Museum A. Koenig (2016-present), Chair
- Ken Hayes, Bernice Pauahi Bishop Museum (2021-present), Co-Chair
- Katie Barker, Smithsonian National Museum of Natural History (2016-present)
- Mike Bruford, Cardiff University (2017-present)
- Marta Castelhano, Cornell University (2016-present)
- Jon Coddington, Smithsonian National Museum of Natural History (2016-present)
- Kelli DeLeon, Bernice Pauahi Bishop Museum (2021-present)
- Dan Distel, Ocean Genome Legacy (2016-present)
- Gabi Droege, Botanic Garden and Botanical Museum Berlin-Dahlem (2016-present)
- Chris Huddleston, Smithsonian National Museum of Natural History (2021-present)
- Andrew Iloh, Biodiversity and Climate Research, Biotechnology Research Center (2016-present)
- Kim Labuschagne, National Zoological Gardens (2016-present)
- Jackie Mackenzie-Dodds, Natural History Museum London (2016-present)
- Li Qiyuan, Beijing Genomics Institute (2016-present)
- Julie Strand, Randers Regnskov Tropical Zoo (2016-present)
- Jianbo Sun, China National Genebank (2021-present)
- Michal Vinkler, Charles University in Prague (2016-present)
- Breda Zimkus, Museum of Comparative Zoology Harvard University (2016-present)
