Enabling precision medicine via standard communication of HTS provenance, analysis, and resultsCitation formats

  • External authors:
  • Gil Alterovitz
  • Dennis Dean
  • Michael R. Crusoe
  • Amanda Bell
  • Anais Hayes
  • Anita Suresh
  • Anjan Purkayastha
  • Charles Hadley S King
  • Dan Taylor
  • Elaine Johanson
  • Elaine E Thompson
  • Eric Donaldson
  • Hiroki Morizono
  • Hsinyi Tsang
  • Jeet K. Vora
  • Jeremy Goecks
  • Jianchao Yao
  • Jonas S Almeida
  • Jonathon Keeney
  • KanakaDurga Addepalli
  • Konstantinos Krampis
  • Krista M. Smith
  • Lydia Guo
  • Mark Walderhaug
  • Marco Schito
  • Matthew Ezewudo
  • Nuria Guimera
  • Paul Walsh
  • Robel Kahsay
  • Srikanth Gottipati
  • Timothy C. Rodwell
  • Toby Bloom
  • Yuching Lai
  • Vahan Simonyan
  • Raja Mazumder

Standard

Enabling precision medicine via standard communication of HTS provenance, analysis, and results. / Alterovitz, Gil; Dean, Dennis; Goble, Carole; Crusoe, Michael R.; Soiland-Reyes, Stian; Bell, Amanda; Hayes, Anais; Suresh, Anita; Purkayastha, Anjan; King, Charles Hadley S; Taylor, Dan; Johanson, Elaine; Thompson, Elaine E; Donaldson, Eric; Morizono, Hiroki; Tsang, Hsinyi; Vora, Jeet K.; Goecks, Jeremy; Yao, Jianchao; Almeida, Jonas S; Keeney, Jonathon; Addepalli, KanakaDurga; Krampis, Konstantinos; Smith, Krista M.; Guo, Lydia; Walderhaug, Mark; Schito, Marco; Ezewudo, Matthew; Guimera, Nuria; Walsh, Paul; Kahsay, Robel; Gottipati, Srikanth; Rodwell, Timothy C.; Bloom, Toby; Lai, Yuching; Simonyan, Vahan; Mazumder, Raja.

In: PLoS Biology, Vol. 16, No. 12, e3000099, 31.12.2018.

Research output: Contribution to journalArticle

Harvard

Alterovitz, G, Dean, D, Goble, C, Crusoe, MR, Soiland-Reyes, S, Bell, A, Hayes, A, Suresh, A, Purkayastha, A, King, CHS, Taylor, D, Johanson, E, Thompson, EE, Donaldson, E, Morizono, H, Tsang, H, Vora, JK, Goecks, J, Yao, J, Almeida, JS, Keeney, J, Addepalli, K, Krampis, K, Smith, KM, Guo, L, Walderhaug, M, Schito, M, Ezewudo, M, Guimera, N, Walsh, P, Kahsay, R, Gottipati, S, Rodwell, TC, Bloom, T, Lai, Y, Simonyan, V & Mazumder, R 2018, 'Enabling precision medicine via standard communication of HTS provenance, analysis, and results' PLoS Biology, vol. 16, no. 12, e3000099. https://doi.org/10.1371/journal.pbio.3000099

APA

Vancouver

Author

Alterovitz, Gil ; Dean, Dennis ; Goble, Carole ; Crusoe, Michael R. ; Soiland-Reyes, Stian ; Bell, Amanda ; Hayes, Anais ; Suresh, Anita ; Purkayastha, Anjan ; King, Charles Hadley S ; Taylor, Dan ; Johanson, Elaine ; Thompson, Elaine E ; Donaldson, Eric ; Morizono, Hiroki ; Tsang, Hsinyi ; Vora, Jeet K. ; Goecks, Jeremy ; Yao, Jianchao ; Almeida, Jonas S ; Keeney, Jonathon ; Addepalli, KanakaDurga ; Krampis, Konstantinos ; Smith, Krista M. ; Guo, Lydia ; Walderhaug, Mark ; Schito, Marco ; Ezewudo, Matthew ; Guimera, Nuria ; Walsh, Paul ; Kahsay, Robel ; Gottipati, Srikanth ; Rodwell, Timothy C. ; Bloom, Toby ; Lai, Yuching ; Simonyan, Vahan ; Mazumder, Raja. / Enabling precision medicine via standard communication of HTS provenance, analysis, and results. In: PLoS Biology. 2018 ; Vol. 16, No. 12.

Bibtex

@article{587b36c23b3941f4a0ffb6148ffe7e1e,
title = "Enabling precision medicine via standard communication of HTS provenance, analysis, and results",
abstract = "A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development.” With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews.",
keywords = "BioCompute Objects, high-throughput sequencing, HTS, NGS, regulatory review, CWL, FHIR, GAG4H, HL7, research objects",
author = "Gil Alterovitz and Dennis Dean and Carole Goble and Crusoe, {Michael R.} and Stian Soiland-Reyes and Amanda Bell and Anais Hayes and Anita Suresh and Anjan Purkayastha and King, {Charles Hadley S} and Dan Taylor and Elaine Johanson and Thompson, {Elaine E} and Eric Donaldson and Hiroki Morizono and Hsinyi Tsang and Vora, {Jeet K.} and Jeremy Goecks and Jianchao Yao and Almeida, {Jonas S} and Jonathon Keeney and KanakaDurga Addepalli and Konstantinos Krampis and Smith, {Krista M.} and Lydia Guo and Mark Walderhaug and Marco Schito and Matthew Ezewudo and Nuria Guimera and Paul Walsh and Robel Kahsay and Srikanth Gottipati and Rodwell, {Timothy C.} and Toby Bloom and Yuching Lai and Vahan Simonyan and Raja Mazumder",
year = "2018",
month = "12",
day = "31",
doi = "10.1371/journal.pbio.3000099",
language = "English",
volume = "16",
journal = "PL o S Biology",
issn = "1545-7885",
publisher = "Public Library of Science",
number = "12",

}

RIS

TY - JOUR

T1 - Enabling precision medicine via standard communication of HTS provenance, analysis, and results

AU - Alterovitz, Gil

AU - Dean, Dennis

AU - Goble, Carole

AU - Crusoe, Michael R.

AU - Soiland-Reyes, Stian

AU - Bell, Amanda

AU - Hayes, Anais

AU - Suresh, Anita

AU - Purkayastha, Anjan

AU - King, Charles Hadley S

AU - Taylor, Dan

AU - Johanson, Elaine

AU - Thompson, Elaine E

AU - Donaldson, Eric

AU - Morizono, Hiroki

AU - Tsang, Hsinyi

AU - Vora, Jeet K.

AU - Goecks, Jeremy

AU - Yao, Jianchao

AU - Almeida, Jonas S

AU - Keeney, Jonathon

AU - Addepalli, KanakaDurga

AU - Krampis, Konstantinos

AU - Smith, Krista M.

AU - Guo, Lydia

AU - Walderhaug, Mark

AU - Schito, Marco

AU - Ezewudo, Matthew

AU - Guimera, Nuria

AU - Walsh, Paul

AU - Kahsay, Robel

AU - Gottipati, Srikanth

AU - Rodwell, Timothy C.

AU - Bloom, Toby

AU - Lai, Yuching

AU - Simonyan, Vahan

AU - Mazumder, Raja

PY - 2018/12/31

Y1 - 2018/12/31

N2 - A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development.” With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews.

AB - A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development.” With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews.

KW - BioCompute Objects

KW - high-throughput sequencing

KW - HTS

KW - NGS

KW - regulatory review

KW - CWL

KW - FHIR

KW - GAG4H

KW - HL7

KW - research objects

UR - https://osf.io/h59uh/

UR - https://www.biorxiv.org/content/early/2018/11/05/191783

U2 - 10.1371/journal.pbio.3000099

DO - 10.1371/journal.pbio.3000099

M3 - Article

VL - 16

JO - PL o S Biology

JF - PL o S Biology

SN - 1545-7885

IS - 12

M1 - e3000099

ER -