Neptune: an environment for the delivery of genomic medicine.
Journal
Genetics in medicine : official journal of the American College of Medical Genetics
ISSN: 1530-0366
Titre abrégé: Genet Med
Pays: United States
ID NLM: 9815831
Informations de publication
Date de publication:
10 2021
10 2021
Historique:
received:
10
11
2020
accepted:
13
05
2021
pubmed:
15
7
2021
medline:
26
10
2021
entrez:
14
7
2021
Statut:
ppublish
Résumé
Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .
Identifiants
pubmed: 34257418
doi: 10.1038/s41436-021-01230-w
pii: S1098-3600(21)05140-6
pmc: PMC8487966
mid: NIHMS1734646
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1838-1846Subventions
Organisme : NHGRI NIH HHS
ID : U01 HG008676
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008672
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008684
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008679
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008666
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008680
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008673
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008685
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG006379
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008664
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008701
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001863
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG008657
Pays : United States
Investigateurs
Debra Abrams
(D)
Samuel E Adunyah
(SE)
Ladia Albertson-Junkans
(L)
Berta Almoguera
(B)
Darren C Ames
(DC)
Paul Appelbaum
(P)
Samuel Aronson
(S)
Sharon Aufox
(S)
Lawrence J Babb
(LJ)
Adithya Balasubramanian
(A)
Hana Bangash
(H)
Melissa Basford
(M)
Lisa Bastarache
(L)
Samantha Baxter
(S)
Meckenzie Behr
(M)
Barbara Benoit
(B)
Elizabeth Bhoj
(E)
Suzette J Bielinski
(SJ)
Harris T Bland
(HT)
Carrie Blout
(C)
Kenneth Borthwick
(K)
Erwin P Bottinger
(EP)
Mark Bowser
(M)
Harrison Brand
(H)
Murray Brilliant
(M)
Wendy Brodeur
(W)
Pedro Caraballo
(P)
David Carrell
(D)
Andrew Carroll
(A)
Lisa Castillo
(L)
Victor Castro
(V)
Gauthami Chandanavelli
(G)
Theodore Chiang
(T)
Rex L Chisholm
(RL)
Kurt D Christensen
(KD)
Wendy Chung
(W)
Christopher G Chute
(CG)
Brittany City
(B)
Beth L Cobb
(BL)
John J Connolly
(JJ)
Paul Crane
(P)
Katherine Crew
(K)
David R Crosslin
(DR)
Jyoti Dayal
(J)
Mariza De Andrade
(M)
Jessica De la Cruz
(J)
Josh C Denny
(JC)
Shawn Denson
(S)
Tim DeSmet
(T)
Ozan Dikilitas
(O)
Michael J Dinsmore
(MJ)
Sheila Dodge
(S)
Phil Dunlea
(P)
Todd L Edwards
(TL)
Christine M Eng
(CM)
David Fasel
(D)
Alex Fedotov
(A)
Qiping Feng
(Q)
Mark Fleharty
(M)
Andrea Foster
(A)
Robert Freimuth
(R)
Christopher Friedrich
(C)
Stephanie M Fullerton
(SM)
Birgit Funke
(B)
Stacey Gabriel
(S)
Vivian Gainer
(V)
Ali Gharavi
(A)
Richard A Gibbs
(RA)
Andrew M Glazer
(AM)
Joseph T Glessner
(JT)
Jessica Goehringer
(J)
Adam S Gordon
(AS)
Chet Graham
(C)
Robert C Green
(RC)
Justin H Gundelach
(JH)
Heather S Hain
(HS)
Hakon Hakonarson
(H)
Maegan V Harden
(MV)
John Harley
(J)
Margaret Harr
(M)
Andrea Hartzler
(A)
M Geoffrey Hayes
(MG)
Scott Hebbring
(S)
Nora Henrikson
(N)
Andrew Hershey
(A)
Christin Hoell
(C)
Ingrid Holm
(I)
Kayla M Howell
(KM)
George Hripcsak
(G)
Jianhong Hu
(J)
Elizabeth Duffy Hynes
(ED)
Gail P Jarvik
(GP)
Joy C Jayaseelan
(JC)
Yunyun Jiang
(Y)
Yoonjung Yoonie Joo
(YY)
Sheethal Jose
(S)
Navya Shilpa Josyula
(NS)
Anne E Justice
(AE)
Divya Kalra
(D)
Elizabeth W Karlson
(EW)
Brendan J Keating
(BJ)
Melissa A Kelly
(MA)
Eimear E Kenny
(EE)
Dustin Key
(D)
Krzysztof Kiryluk
(K)
Terrie Kitchner
(T)
Barbara Klanderman
(B)
Eric Klee
(E)
David C Kochan
(DC)
Viktoriya Korchina
(V)
Leah Kottyan
(L)
Emily Kudalkar
(E)
Alanna Kulchak Rahm
(AK)
Iftikhar J Kullo
(IJ)
Philip Lammers
(P)
Eric B Larson
(EB)
Matthew S Lebo
(MS)
Magalie Leduc
(M)
Ming Ta Michael Lee
(MTM)
Niall J Lennon
(NJ)
Kathleen A Leppig
(KA)
Nancy D Leslie
(ND)
Rongling Li
(R)
Wayne H Liang
(WH)
Chiao-Feng Lin
(CF)
Jodell E Linder
(JE)
Noralane M Lindor
(NM)
Todd Lingren
(T)
James G Linneman
(JG)
Cong Liu
(C)
Wen Liu
(W)
Xiuping Liu
(X)
John Lynch
(J)
Hayley Lyon
(H)
Alyssa Macbeth
(A)
Harshad Mahadeshwar
(H)
Lisa Mahanta
(L)
Bradley Malin
(B)
Teri Manolio
(T)
Maddalena Marasa
(M)
Keith Marsolo
(K)
Michelle L McGowan
(ML)
Elizabeth McNally
(E)
Jim Meldrim
(J)
Frank Mentch
(F)
Hila Milo Rasouly
(HM)
Jonathan Mosley
(J)
Shubhabrata Mukherjee
(S)
Thomas E Mullen
(TE)
Jesse Muniz
(J)
David R Murdock
(DR)
Shawn Murphy
(S)
Mullai Murugan
(M)
Donna Muzny
(D)
Melanie F Myers
(MF)
Bahram Namjou
(B)
Yizhao Ni
(Y)
Robert C Onofrio
(RC)
Aniwaa Owusu Obeng
(AO)
Thomas N Person
(TN)
Josh F Peterson
(JF)
Lynn Petukhova
(L)
Cassandra J Pisieczko
(CJ)
Siddharth Pratap
(S)
Cynthia A Prows
(CA)
Megan J Puckelwartz
(MJ)
Ritika Raj
(R)
James D Ralston
(JD)
Arvind Ramaprasan
(A)
Andrea Ramirez
(A)
Luke Rasmussen
(L)
Laura Rasmussen-Torvik
(L)
Soumya Raychaudhuri
(S)
Heidi L Rehm
(HL)
Marylyn D Ritchie
(MD)
Catherine Rives
(C)
Beenish Riza
(B)
Dan M Roden
(DM)
Elisabeth A Rosenthal
(EA)
Avni Santani
(A)
Schaid Dan
(S)
Steven Scherer
(S)
Stuart Scott
(S)
Aaron Scrol
(A)
Soumitra Sengupta
(S)
Ning Shang
(N)
Himanshu Sharma
(H)
Richard R Sharp
(RR)
Rajbir Singh
(R)
Patrick M A Sleiman
(PMA)
Kara Slowik
(K)
Joshua C Smith
(JC)
Maureen E Smith
(ME)
Duane T Smoot
(DT)
Jordan W Smoller
(JW)
Sunghwan Sohn
(S)
Ian B Stanaway
(IB)
Justin Starren
(J)
Mary Stroud
(M)
Jessica Su
(J)
Casey Overby Taylor
(CO)
Kasia Tolwinski
(K)
Sara L Van Driest
(SL)
Sean M Vargas
(SM)
Matthew Varugheese
(M)
David Veenstra
(D)
Eric Venner
(E)
Miguel Verbitsky
(M)
Gina Vicente
(G)
Michael Wagner
(M)
Kimberly Walker
(K)
Theresa Walunas
(T)
Liwen Wang
(L)
Qiaoyan Wang
(Q)
Wei-Qi Wei
(WQ)
Scott T Weiss
(ST)
Quinn S Wells
(QS)
Chunhua Weng
(C)
Peter S White
(PS)
Georgia L Wiesner
(GL)
Ken L Wiley
(KL)
Janet L Williams
(JL)
Marc S Williams
(MS)
Michael W Wilson
(MW)
Leora Witkowski
(L)
Laura Allison Woods
(LA)
Betty Woolf
(B)
Julia Wynn
(J)
Yaping Yang
(Y)
Ge Zhang
(G)
Lan Zhang
(L)
Hana Zouk
(H)
Informations de copyright
© 2021. The Author(s), under exclusive licence to the American College of Medical Genetics and Genomics.
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