TY - JOUR
T1 - Neptune
T2 - an environment for the delivery of genomic medicine
AU - eMERGE Consortium
AU - Eric, Venner
AU - Yi, Victoria
AU - Murdock, David
AU - Kalla, Sara E.
AU - Wu, Tsung Jung
AU - Sabo, Aniko
AU - Li, Shoudong
AU - Meng, Qingchang
AU - Tian, Xia
AU - Murugan, Mullai
AU - Cohen, Michelle
AU - Kovar, Christie
AU - Wei, Wei Qi
AU - Chung, Wendy K.
AU - Weng, Chunhua
AU - Wiesner, Georgia L.
AU - Jarvik, Gail P.
AU - Muzny, Donna
AU - Gibbs, Richard A.
AU - Abrams, Debra
AU - Adunyah, Samuel E.
AU - Albertson-Junkans, Ladia
AU - Almoguera, Berta
AU - Ames, Darren C.
AU - Appelbaum, Paul
AU - Aronson, Samuel
AU - Aufox, Sharon
AU - Babb, Lawrence J.
AU - Balasubramanian, Adithya
AU - Bangash, Hana
AU - Basford, Melissa
AU - Bastarache, Lisa
AU - Baxter, Samantha
AU - Behr, Meckenzie
AU - Benoit, Barbara
AU - Bhoj, Elizabeth
AU - Bielinski, Suzette J.
AU - Bland, Harris T.
AU - Blout, Carrie
AU - Borthwick, Kenneth
AU - Bottinger, Erwin P.
AU - Bowser, Mark
AU - Brand, Harrison
AU - Brilliant, Murray
AU - Brodeur, Wendy
AU - Caraballo, Pedro
AU - Carrell, David
AU - Chute, Christopher G.
AU - Smoot, Duane T.
AU - Taylor, Casey Overby
N1 - Publisher Copyright:
© 2021, The Author(s), under exclusive licence to the American College of Medical Genetics and Genomics.
PY - 2021/10
Y1 - 2021/10
N2 - Purpose: 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. Methods: We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. Results: 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. Conclusion: 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.
AB - Purpose: 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. Methods: We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. Results: 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. Conclusion: 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.
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U2 - 10.1038/s41436-021-01230-w
DO - 10.1038/s41436-021-01230-w
M3 - Article
C2 - 34257418
AN - SCOPUS:85111974906
SN - 1098-3600
VL - 23
SP - 1838
EP - 1846
JO - Genetics in Medicine
JF - Genetics in Medicine
IS - 10
ER -