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Introduction
There are many people posting on multiple internet forums with persistent symptoms following an exposure to various body fluids. Available clinical tests have not found an explanation. Those affected are contributing metagenomic sequencing data to facilitate a peer-to-peer investigation to attempt and find possible etiologies. If you would like to participate by contributing data, please request a kit for the appropriate sample type from Aperiomics.
Data
Aperiomics is providing the sequencing services for this investigation. They provide a report of organisms detected with their classifier as well as raw Illumina paired-end sequencing data. The table below captures the data collected to date.
| Date | Contributor | Sample Source | Sequencing Type | Forward Reads | Reverse Reads |
|---|---|---|---|---|---|
| 2017-09-21 | undiagnosed | Whole blood | RNA1,2 | R1 | R2 |
| 2017-09-21 | undiagnosed | Whole blood | DNA2 | R1 | R2 |
| 2017-09-27 | undiagnosed | Whole blood | RNA1,2 | R1 | R2 |
| 2017-10-12 | zzz | Saliva | RNA | R1 | R2 |
| 2017-11-22 | undiagnosed | Plasma | RNA | R1 | R2 |
| 2017-11-22 | undiagnosed | Plasma | DNA | R1 | R2 |
1 sample RNA integrity issues, low RNA input
2 too few non-human reads for Aperiomics classifier minimum confidence level
Reports
Below are reports generated by Aperiomics. Some contributors did not get raw data and only have the report. While convenient for getting a quick look, raw data is needed for this investigation.
| Date | Contributor | Sample Source | Sequencing Type | Report |
|---|---|---|---|---|
| 2017-06-20 | Cheesus | Whole blood, Fecal, Urine, Oral swab | DNA | |
| 2017-10-12 | zzz | Saliva | RNA | JPG |
| 2017-11-22 | undiagnosed | Plasma | RNA & DNA |
Experiment Design
While unbiased shotgun metagenomic sequencing is hypothesis free, the sampling depth must be sufficient to detect organisms at the expected abundance levels. See the Experiment Design page for more information.
Quality Control
Tools for analyzing and trimming reads are documented on the Quality Control page.
Methods
Various methods including metagenomics classifiers, de novo assembly, BLAST, etc. will be used during the course of this investigation. See the Methods page for more information.
Contributing
If you would like to contribute to this wiki you can either create a GitHub account and request edit permissions or clone the repository and make a pull request.