Neptune
Neptune generates structured clinical genomic reports and integrates them into electronic health records to support interpretation and delivery of SNVs, CNVs, pharmacogenomics, and polygenic risk scores.
Key Features:
- Clinical Report Customization: Generates customizable clinical reports tailored to specific gene panels and variant types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores.
- Variant Reanalysis: Supports variant reanalysis workflows to update variant interpretations and report content over time.
- EHR Integration: Integrates structured genetic data into electronic health record (EHR) systems to deliver genomic results within patient records.
- High-Throughput Capability: Applied in high-throughput clinical sequencing projects and has processed over 15,000 clinical genomic reports.
Scientific Applications:
- Clinical reporting for targeted gene panels: Produces reports for targeted gene panels of varying sizes, including examples of 68- and 153-gene panels, to support clinical genetic testing.
- Pharmacogenomics and polygenic risk reporting: Reports pharmacogenomic results and polygenic risk scores alongside variant findings for integration into clinical workflows.
- High-throughput clinical sequencing projects: Enables large-scale generation and delivery of clinical genomic reports in high-throughput sequencing contexts.
Methodology:
Manages the reporting process from genomic data generation to delivery into EHR systems, handling SNVs, CNVs, pharmacogenomics, and polygenic risk scores while enabling report customization and supporting variant reanalysis workflows.
Topics
Details
- License:
- MIT
- Cost:
- Free of charge
- Tool Type:
- command-line tool
- Operating Systems:
- Mac, Linux, Windows
- Programming Languages:
- Python, Java
- Added:
- 12/1/2021
- Last Updated:
- 11/24/2024
Operations
Publications
Eric V, Yi V, Murdock D, Kalla SE, Wu T, Sabo A, Li S, Meng Q, Tian X, Murugan M, Cohen M, Kovar C, Wei W, Chung WK, Weng C, Wiesner GL, Jarvik GP, Muzny D, Gibbs RA, Abrams D, Adunyah SE, Albertson-Junkans L, Almoguera B, Ames DC, Appelbaum P, Aronson S, Aufox S, Babb LJ, Balasubramanian A, Bangash H, Basford M, Bastarache L, Baxter S, Behr M, Benoit B, Bhoj E, Bielinski SJ, Bland HT, Blout C, Borthwick K, Bottinger EP, Bowser M, Brand H, Brilliant M, Brodeur W, Caraballo P, Carrell D, Carroll A, Castillo L, Castro V, Chandanavelli G, Chiang T, Chisholm RL, Christensen KD, Chung W, Chute CG, City B, Cobb BL, Connolly JJ, Crane P, Crew K, Crosslin DR, Dayal J, De Andrade M, De la Cruz J, Denny JC, Denson S, DeSmet T, Dikilitas O, Dinsmore MJ, Dodge S, Dunlea P, Edwards TL, Eng CM, Fasel D, Fedotov A, Feng Q, Fleharty M, Foster A, Freimuth R, Friedrich C, Fullerton SM, Funke B, Gabriel S, Gainer V, Gharavi A, Gibbs RA, Glazer AM, Glessner JT, Goehringer J, Gordon AS, Graham C, Green RC, Gundelach JH, Hain HS, Hakonarson H, Harden MV, Harley J, Harr M, Hartzler A, Hayes MG, Hebbring S, Henrikson N, Hershey A, Hoell C, Holm I, Howell KM, Hripcsak G, Hu J, Hynes ED, Jarvik GP, Jayaseelan JC, Jiang Y, Joo YY, Jose S, Josyula NS, Justice AE, Kalra D, Karlson EW, Keating BJ, Kelly MA, Kenny EE, Key D, Kiryluk K, Kitchner T, Klanderman B, Klee E, Kochan DC, Korchina V, Kottyan L, Kudalkar E, Rahm AK, Kullo IJ, Lammers P, Larson EB, Lebo MS, Leduc M, Lee MT(, Lennon NJ, Leppig KA, Leslie ND, Li R, Liang WH, Lin C, Linder JE, Lindor NM, Lingren T, Linneman JG, Liu C, Liu W, Liu X, Lynch J, Lyon H, Macbeth A, Mahadeshwar H, Mahanta L, Malin B, Manolio T, Marasa M, Marsolo K, McGowan ML, McNally E, Meldrim J, Mentch F, Rasouly HM, Mosley J, Mukherjee S, Mullen TE, Muniz J, Murdock DR, Murphy S, Murugan M, Muzny D, Myers MF, Namjou B, Ni Y, Onofrio RC, Obeng AO, Person TN, Peterson JF, Petukhova L, Pisieczko CJ, Pratap S, Prows CA, Puckelwartz MJ, Raj R, Ralston JD, Ramaprasan A, Ramirez A, Rasmussen L, Rasmussen-Torvik L, Raychaudhuri S, Rehm HL, Ritchie MD, Rives C, Riza B, Roden DM, Rosenthal EA, Santani A, Dan S, Scherer S, Scott S, Scrol A, Sengupta S, Shang N, Sharma H, Sharp RR, Singh R, Sleiman PM, Slowik K, Smith JC, Smith ME, Smoot DT, Smoller JW, Sohn S, Stanaway IB, Starren J, Stroud M, Su J, Taylor CO, Tolwinski K, Van Driest SL, Vargas SM, Varugheese M, Veenstra D, Venner E, Verbitsky M, Vicente G, Wagner M, Walker K, Walunas T, Wang L, Wang Q, Wei W, Weiss ST, Wells QS, Weng C, White PS, Wiesner GL, Wiley KL, Williams JL, Williams MS, Wilson MW, Witkowski L, Woods LA, Woolf B, Wynn J, Yang Y, Zhang G, Zhang L, Zouk H. Neptune: an environment for the delivery of genomic medicine. Genetics in Medicine. 2021;23(10):1838-1846. doi:10.1038/s41436-021-01230-w. PMID:34257418. PMCID:PMC8487966.