Precision Diagnosis of Acute Infectious Diseases; Neuroinflammatory Cohort
NCT ID: NCT02910037
Last Updated: 2021-05-27
Study Results
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View full resultsBasic Information
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COMPLETED
NA
214 participants
INTERVENTIONAL
2016-06-01
2017-07-31
Brief Summary
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Detailed Description
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Conditions
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Study Design
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NA
SINGLE_GROUP
DIAGNOSTIC
NONE
Study Groups
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patients enrolled for mNGS testing
Patients with meningitis and/or encephalitis will be enrolled in this study in order to analyze the clinical utility of mNGS for pathogen detection. There is no control group for this study (Investigators will identify historical controls by retrospective chart review and clinical reimbursement documents).
mNGS for pathogen detection
This assay is a laboratory-validated metagenomic test for comprehensive detection of viruses, bacteria, fungi, and parasites in clinical samples.
Interventions
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mNGS for pathogen detection
This assay is a laboratory-validated metagenomic test for comprehensive detection of viruses, bacteria, fungi, and parasites in clinical samples.
Other Intervention Names
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Eligibility Criteria
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Exclusion Criteria
* Prisoners
* University of California employees / students or close associates of any of the key personnel on the study
* Outpatients and/or patients with chronic illness
Inclusion:
Demographic Criteria
1. Age: any (no age limit)
2. Language: any (with the use of interpreting services for obtaining consent)
For the following, the infectious syndromes include meningitis, encephalitis, fever, sepsis, and pneumonia:
Clinical Criteria
1. Hospital admission or transfer with diagnosis of an presumed infectious syndrome or clinical presentation consisting with an infectious syndrome, as defined below:
* Meningitis: fever \>38°C and abnormal imaging or CSF pleocytosis (CSF white blood cell count (WBC) \> 5 /mm\^3) +/- stiff neck, +/- headache, +/- seizure
* Encephalitis: pleocytosis and at least one of the following: altered mental status, seizures, new onset of focal neurologic findings, abnormal EEG, acute brain abnormalities on neuroimaging
2. No known diagnosis of non-infectious etiology responsible for symptoms
3. Time of enrollment: within 7 days of onset of symptoms, either initial presentation or acute exacerbation of presumed infectious syndrome.
Specimen Criteria
1. cerebrospinal fluid available within 7 days of symptom onset AND within 3 days of hospital admission or transfer unless evidence for acute exacerbation as defined by abrupt decline in clinical status, worsening pleocytosis or other laboratory parameters
2. Minimum of 600 microliters (uL) of clinical sample, stored at 4 degrees Celsius (C) no more than 5 days (ideally frozen in -70 degrees Celsius within 24 hours of collection)
3. No more than 3 freeze-thaw cycles
1 Minute
110 Years
ALL
No
Sponsors
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California Initiative to Advance Precision Medicine
OTHER
Sandler Foundation
UNKNOWN
Bowes Foundation
UNKNOWN
Charles and Helen Schwab Foundation
UNKNOWN
University of California, Davis
OTHER
University of California, Los Angeles
OTHER
Children's Hospital Los Angeles
OTHER
Children's Hospital Colorado
OTHER
St. Jude Children's Research Hospital
OTHER
Children's National Research Institute
OTHER
University of California, Berkeley
OTHER
DNAnexus, Inc.
UNKNOWN
Syapse, Inc.
UNKNOWN
University of California, San Francisco
OTHER
Responsible Party
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Principal Investigators
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Charles Y Chiu, MD, PhD
Role: PRINCIPAL_INVESTIGATOR
University of California, San Francisco
Hannah Sample, BS
Role: STUDY_DIRECTOR
University of California, San Francisco
Locations
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University of California, Davis Medical Center
Davis, California, United States
Children's Hospital Los Angeles
Los Angeles, California, United States
University of California, Los Angeles Medical Center
Los Angeles, California, United States
University of California, San Francisco Medical Center
San Francisco, California, United States
Children's Hospital Colordao
Denver, Colorado, United States
Children's National Medical Center
Washington D.C., District of Columbia, United States
St. Jude Children's Research Hospital
Nashville, Tennessee, United States
Countries
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References
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Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014 Jun 19;370(25):2408-17. doi: 10.1056/NEJMoa1401268. Epub 2014 Jun 4.
Greninger AL, Messacar K, Dunnebacke T, Naccache SN, Federman S, Bouquet J, Mirsky D, Nomura Y, Yagi S, Glaser C, Vollmer M, Press CA, Kleinschmidt-DeMasters BK, Dominguez SR, Chiu CY. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med. 2015 Dec 1;7:113. doi: 10.1186/s13073-015-0235-2.
Naccache SN, Peggs KS, Mattes FM, Phadke R, Garson JA, Grant P, Samayoa E, Federman S, Miller S, Lunn MP, Gant V, Chiu CY. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin Infect Dis. 2015 Mar 15;60(6):919-23. doi: 10.1093/cid/ciu912. Epub 2015 Jan 7.
Greninger AL, Naccache SN, Messacar K, Clayton A, Yu G, Somasekar S, Federman S, Stryke D, Anderson C, Yagi S, Messenger S, Wadford D, Xia D, Watt JP, Van Haren K, Dominguez SR, Glaser C, Aldrovandi G, Chiu CY. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study. Lancet Infect Dis. 2015 Jun;15(6):671-82. doi: 10.1016/S1473-3099(15)70093-9. Epub 2015 Mar 31.
Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martinez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J Jr, Miller S, Chiu CY. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014 Jul;24(7):1180-92. doi: 10.1101/gr.171934.113. Epub 2014 Jun 4.
Wilson MR, Shanbhag NM, Reid MJ, Singhal NS, Gelfand JM, Sample HA, Benkli B, O'Donovan BD, Ali IK, Keating MK, Dunnebacke TH, Wood MD, Bollen A, DeRisi JL. Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep Sequencing. Ann Neurol. 2015 Nov;78(5):722-30. doi: 10.1002/ana.24499. Epub 2015 Aug 24.
Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dallas R, Maron G, Hayden R, Messacar K, Dominguez SR, Miller S, Chiu CY. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. N Engl J Med. 2019 Jun 13;380(24):2327-2340. doi: 10.1056/NEJMoa1803396.
Chiu CY, Coffey LL, Murkey J, Symmes K, Sample HA, Wilson MR, Naccache SN, Arevalo S, Somasekar S, Federman S, Stryke D, Vespa P, Schiller G, Messenger S, Humphries R, Miller S, Klausner JD. Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016. Emerg Infect Dis. 2017 Oct;23(10):1964-1968. doi: 10.3201/eid2310.161986.
Murkey JA, Chew KW, Carlson M, Shannon CL, Sirohi D, Sample HA, Wilson MR, Vespa P, Humphries RM, Miller S, Klausner JD, Chiu CY. Hepatitis E Virus-Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing. Open Forum Infect Dis. 2017 Jun 13;4(3):ofx121. doi: 10.1093/ofid/ofx121. eCollection 2017 Summer.
Provided Documents
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Document Type: Study Protocol and Statistical Analysis Plan
Related Links
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brief description of PDAID study and referral link
summary of the PDAID project, sponsored by the California Initiative to Advance Precision Medicine
video describing metagenomic next-generation sequencing and its use for diagnosis of infections
The UCSF Center for Next-Gen Precision Diagnostics
Other Identifiers
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P0509948
Identifier Type: -
Identifier Source: org_study_id
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