TY - JOUR
T1 - Nine out of ten samples were mistakenly switched by The Orang-utan Genome Consortium
AU - Banes, Graham L.
AU - Fountain, Emily D.
AU - Karklus, Alyssa
AU - Fulton, Robert
AU - Antonacci-Fulton, Lucinda
AU - Nelson, Joanne O.
N1 - Funding Information:
This research was performed using the compute resources and assistance of the University of Wisconsin-Madison Center for High Throughput Computing (CHTC) in the Department of Computer Sciences. The CHTC is supported by UW-Madison, the Advanced Computing Initiative, the Wisconsin Alumni Research Foundation, the Wisconsin Institutes for Discovery, and the National Science Foundation, and is an active member of the Open Science Grid, which is supported by the National Science Foundation and the U.S. Department of Energy’s Office of Science. We thank Audubon Zoo, Birmingham Zoo, Cameron Park Zoo, the Center for Great Apes, Cheyenne Mountain Zoo, Cincinnati Zoo & Botanical Garden, Cleveland Metroparks Zoo, Columbus Zoo and Aquarium, Dallas Zoo, El Paso Zoo, Fort Wayne Children’s Zoo, Houston Zoo, Indianapolis Zoo, Kansas City Zoo, Little Rock Zoo, Louisville Zoo, Metro Richmond Zoo, Milwaukee County Zoo, Phoenix Zoo, Sedgwick County Zoo, Topeka Zoo, Toronto Zoo and ZooTampa at Lowry Park for providing samples from known descendants, and the Orangutan Species Survival Plan (SSP) for approval by recommendation to the SSP’s member institutions. We are especially grateful to Dr Cynthia Steiner, who provided metadata from the San Diego Zoo Institute for Conservation Research. This work was funded in part by the Arcus Foundation, the Eppley Foundation for Research, Inc., the Ronna Noel Charitable Trust, and the Institute of Museum and Library Services through National Leadership Grant MG-249168-OMS-21 (all to GLB). AK was supported by the Morris Animal Foundation. Research reported in this publication was also supported in part by the Office of the Director, National Institutes of Health, under award number P51OD011106 to the Wisconsin National Primate Research Center and conducted in part at a facility constructed with support from the Research Facilities Improvement Program under grant numbers RR15459-01 and RR020141-01. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Funding Information:
This research was performed using the compute resources and assistance of the University of Wisconsin-Madison Center for High Throughput Computing (CHTC) in the Department of Computer Sciences. The CHTC is supported by UW-Madison, the Advanced Computing Initiative, the Wisconsin Alumni Research Foundation, the Wisconsin Institutes for Discovery, and the National Science Foundation, and is an active member of the Open Science Grid, which is supported by the National Science Foundation and the U.S. Department of Energy’s Office of Science. We thank Audubon Zoo, Birmingham Zoo, Cameron Park Zoo, the Center for Great Apes, Cheyenne Mountain Zoo, Cincinnati Zoo & Botanical Garden, Cleveland Metroparks Zoo, Columbus Zoo and Aquarium, Dallas Zoo, El Paso Zoo, Fort Wayne Children’s Zoo, Houston Zoo, Indianapolis Zoo, Kansas City Zoo, Little Rock Zoo, Louisville Zoo, Metro Richmond Zoo, Milwaukee County Zoo, Phoenix Zoo, Sedgwick County Zoo, Topeka Zoo, Toronto Zoo and ZooTampa at Lowry Park for providing samples from known descendants, and the Orangutan Species Survival Plan (SSP) for approval by recommendation to the SSP’s member institutions. We are especially grateful to Dr Cynthia Steiner, who provided metadata from the San Diego Zoo Institute for Conservation Research. This work was funded in part by the Arcus Foundation, the Eppley Foundation for Research, Inc., the Ronna Noel Charitable Trust, and the Institute of Museum and Library Services through National Leadership Grant MG-249168-OMS-21 (all to GLB). AK was supported by the Morris Animal Foundation. Research reported in this publication was also supported in part by the Office of the Director, National Institutes of Health, under award number P51OD011106 to the Wisconsin National Primate Research Center and conducted in part at a facility constructed with support from the Research Facilities Improvement Program under grant numbers RR15459-01 and RR020141-01. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - The Sumatran orang-utan (Pongo abelii) reference genome was first published in 2011, in conjunction with ten re-sequenced genomes from unrelated wild-caught individuals. Together, these published data have been utilized in almost all great ape genomic studies, plus in much broader comparative genomic research. Here, we report that the original sequencing Consortium inadvertently switched nine of the ten samples and/or resulting re-sequenced genomes, erroneously attributing eight of these to the wrong source individuals. Among them is a genome from the recently identified Tapanuli (P. tapanuliensis) species: thus, this genome was sequenced and published a full six years prior to the species’ description. Sex was wrongly assigned to five known individuals; the numbers in one sample identifier were swapped; and the identifier for another sample most closely resembles that of a sample from another individual entirely. These errors have been reproduced in countless subsequent manuscripts, with noted implications for studies reliant on data from known individuals.
AB - The Sumatran orang-utan (Pongo abelii) reference genome was first published in 2011, in conjunction with ten re-sequenced genomes from unrelated wild-caught individuals. Together, these published data have been utilized in almost all great ape genomic studies, plus in much broader comparative genomic research. Here, we report that the original sequencing Consortium inadvertently switched nine of the ten samples and/or resulting re-sequenced genomes, erroneously attributing eight of these to the wrong source individuals. Among them is a genome from the recently identified Tapanuli (P. tapanuliensis) species: thus, this genome was sequenced and published a full six years prior to the species’ description. Sex was wrongly assigned to five known individuals; the numbers in one sample identifier were swapped; and the identifier for another sample most closely resembles that of a sample from another individual entirely. These errors have been reproduced in countless subsequent manuscripts, with noted implications for studies reliant on data from known individuals.
UR - http://www.scopus.com/inward/record.url?scp=85135831968&partnerID=8YFLogxK
U2 - 10.1038/s41597-022-01602-0
DO - 10.1038/s41597-022-01602-0
M3 - Article
C2 - 35961988
AN - SCOPUS:85135831968
VL - 9
JO - Scientific Data
JF - Scientific Data
SN - 2052-4463
IS - 1
M1 - 485
ER -