Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation.
The prospective banking of osteosarcoma tissue samples to promote research endeavors has been realized through the establishment of a nationally centralized biospecimen repository, the Children's Oncology Group (COG) biospecimen bank located at the Biopathology Center (BPC)/Nationwide Children&...
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| Format: | Article |
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0181204&type=printable |
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| author | Jason Glover Tsz-Kwong Man Donald A Barkauskas David Hall Tanya Tello Mary Beth Sullivan Richard Gorlick Katherine Janeway Holcombe Grier Ching Lau Jeffrey A Toretsky Scott C Borinstein Chand Khanna Timothy M Fan COG Osteosarcoma Biology Group |
| author_facet | Jason Glover Tsz-Kwong Man Donald A Barkauskas David Hall Tanya Tello Mary Beth Sullivan Richard Gorlick Katherine Janeway Holcombe Grier Ching Lau Jeffrey A Toretsky Scott C Borinstein Chand Khanna Timothy M Fan COG Osteosarcoma Biology Group |
| author_sort | Jason Glover |
| collection | DOAJ |
| description | The prospective banking of osteosarcoma tissue samples to promote research endeavors has been realized through the establishment of a nationally centralized biospecimen repository, the Children's Oncology Group (COG) biospecimen bank located at the Biopathology Center (BPC)/Nationwide Children's Hospital in Columbus, Ohio. Although the physical inventory of osteosarcoma biospecimens is substantive (>15,000 sample specimens), the nature of these resources remains exhaustible. Despite judicious allocation of these high-value biospecimens for conducting sarcoma-related research, a deeper understanding of osteosarcoma biology, in particular metastases, remains unrealized. In addition the identification and development of novel diagnostics and effective therapeutics remain elusive. The QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office (CSBAO) has developed the High Dimensional Data (HDD) platform to complement the existing physical inventory and to promote in silico hypothesis testing in sarcoma biology. The HDD is a relational biologic database derived from matched osteosarcoma biospecimens in which diverse experimental readouts have been generated and digitally deposited. As proof-of-concept, we demonstrate that the HDD platform can be utilized to address previously unrealized biologic questions though the systematic juxtaposition of diverse datasets derived from shared biospecimens. The continued population of the HDD platform with high-value, high-throughput and mineable datasets allows a shared and reusable resource for researchers, both experimentalists and bioinformatics investigators, to propose and answer questions in silico that advance our understanding of osteosarcoma biology. |
| format | Article |
| id | doaj-art-ab541fd17df649658863b9bd49e7bec6 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-ab541fd17df649658863b9bd49e7bec62025-01-17T05:32:05ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01127e018120410.1371/journal.pone.0181204Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation.Jason GloverTsz-Kwong ManDonald A BarkauskasDavid HallTanya TelloMary Beth SullivanRichard GorlickKatherine JanewayHolcombe GrierChing LauJeffrey A ToretskyScott C BorinsteinChand KhannaTimothy M FanCOG Osteosarcoma Biology GroupThe prospective banking of osteosarcoma tissue samples to promote research endeavors has been realized through the establishment of a nationally centralized biospecimen repository, the Children's Oncology Group (COG) biospecimen bank located at the Biopathology Center (BPC)/Nationwide Children's Hospital in Columbus, Ohio. Although the physical inventory of osteosarcoma biospecimens is substantive (>15,000 sample specimens), the nature of these resources remains exhaustible. Despite judicious allocation of these high-value biospecimens for conducting sarcoma-related research, a deeper understanding of osteosarcoma biology, in particular metastases, remains unrealized. In addition the identification and development of novel diagnostics and effective therapeutics remain elusive. The QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office (CSBAO) has developed the High Dimensional Data (HDD) platform to complement the existing physical inventory and to promote in silico hypothesis testing in sarcoma biology. The HDD is a relational biologic database derived from matched osteosarcoma biospecimens in which diverse experimental readouts have been generated and digitally deposited. As proof-of-concept, we demonstrate that the HDD platform can be utilized to address previously unrealized biologic questions though the systematic juxtaposition of diverse datasets derived from shared biospecimens. The continued population of the HDD platform with high-value, high-throughput and mineable datasets allows a shared and reusable resource for researchers, both experimentalists and bioinformatics investigators, to propose and answer questions in silico that advance our understanding of osteosarcoma biology.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0181204&type=printable |
| spellingShingle | Jason Glover Tsz-Kwong Man Donald A Barkauskas David Hall Tanya Tello Mary Beth Sullivan Richard Gorlick Katherine Janeway Holcombe Grier Ching Lau Jeffrey A Toretsky Scott C Borinstein Chand Khanna Timothy M Fan COG Osteosarcoma Biology Group Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation. PLoS ONE |
| title | Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation. |
| title_full | Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation. |
| title_fullStr | Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation. |
| title_full_unstemmed | Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation. |
| title_short | Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation. |
| title_sort | osteosarcoma enters a post genomic era with in silico opportunities generation of the high dimensional database for facilitating sarcoma biology research a report from the children s oncology group and the quadw foundation |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0181204&type=printable |
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