TABLE 1.
Population-level statistics regarding the TORCH panela
| Official name | HMP orgID | HMP orgName | ClinicalFreq (%) | RPKM value |
PopFreq | |
|---|---|---|---|---|---|---|
| Reference | Maximum | |||||
| Toxoplasma gondii | NA | NA | 2.2b | 0 | 0.000116 | 0.00409856 |
| Rubella virus | VIRL|gi|9790308|ref|NC_001545.1| | Rubella virus, complete genome | 1.6b | NA | NA | NA |
| Cytomegalovirus | VIRL|gi|155573622|ref|NC_006273.2| | Human herpesvirus 5, complete genome | 1.6b | 0 | 0.199486 | 0.00526411 |
| Herpes simplex virus | VIRL|gi|9629378|ref|NC_001806.1| | Human herpesvirus 1, complete genome | 1.6b | 0 | 0.00606 | 0.00050635 |
| VIRL|gi|9629267|ref|NC_001798.1| | Human herpesvirus 2, complete genome | 1.1b | 0 | 0.005336 | 5.73225E−05 | |
| Human parvovirus B19 | VIRL|gi|9632996|ref|NC_000883.1| | Human parvovirus B19, complete genome | 8.1b | 0 | 1.904969 | 3.8215E−05 |
| Treponema pallidum | BACT_1204 | Treponema pallidum subsp. pallidum SS14 | 4.36c | 0 | 0 | 0 |
| Hepatitis B virus | VIRL|gi|21326584|ref|NC_003977.1| | Hepatitis B virus, complete genome | 35.614c | 0 | 12.60268 | 0.00794872 |
The TORCH organisms include Toxoplasma gondii, others (Treponema pallidum [causing syphilis], hepatitis B virus [HBV], and human parvovirus B19), rubella virus, cytomegalovirus (CMV), and herpes simplex virus (HSV). T. gondii is not part of the Human Microbiome Project (HMP), and thus, no orgName or orgID is provided. Rubella virus was not detected because, as an RNA virus, it does not fit in the NIPT library protocol. Clinical frequency (ClinicalFreq) is predefined elsewhere, mostly as the rate of positive serological screening tests among the individual study populations, while population frequency (PopFreq) is the frequency of nonzero samples of a particular organism directly derived from the indicator matrix of the study population. NA, not available.
Data are taken from reference 16.
Data are taken from reference 17.