RID Data Submission

Users are welcome to submit integration site information and patient demographics in the following Excel templates (examples are shown in these templates):

1. Integration site data (download the template here)
patient/sample_idtissue/cell typechromosomepositionprovirus_strandLTRcount
C906PBMCchr16366159+5LTR1
A907PBMCchr27866678-3LTR1
B909CD4chr31000506+both1

  • Provirus strand is defined as “+” if the provirus integrated in the same orientation as the chromosome being integrated and “-“ if the provirus integrated in the opposite orientation.
2. Patient demographic if available (download the template here)
patient_idtissueage(yr)genderrace/eithnicitytrasmission_moderetrovirus_diagnosis_date(MM/DD/YYYY)plasma_viral_RNA_level_at_diagnosisCD4_nadirdisease_classificationtherapytherapy_initiation_date(MM/DD/YYYY)therapy_duration(yr)sampling_dateclinical_status_and_comorbid_illness_at_samplinginfection_duration_prior_to_sampling(yr)disease_classification_duration_prior_to_sampling(yr)therapy_duration_prior_to_sampling(yr)proviral_DNA_copies_at_samplingviral_RNA_copies_at_diagnosisviral_RNA_copies_at_samplingabsolute_lymphocite_count(10^9/L)CD4_at_diagnosisCD4_at_samplingCD4_before_therapynumber_clones_detectedoligconality_index(Gini_index)sample_comment
C906PBMC59FBlackMSN8/8/00TDF+FTC+RTG8/9/00178/8/1750 copies/1 million PBMC5.4 log10/copies ml plasma2.1 log10 copies/ml plasma22 cells/µl
A907PBMC6MBlackmother to child8/8/12TDF+FTC+NVP8/9/1258/9/1751 copies/1 million PBMC3.9 log10/copies ml plasma< 1.7 log10 copies/ml plasma243 cells/µl
B909CD459FWhitedrug use8/8/05TDF+FTC+ATZ/r8/10/05128/10/1752 copies/1 million PBMC5.6 log10/copies ml plasma2.9 log10 copies/ml plasma24 cells/µl
ATL8PBMC69FWhite1/1/07ATL8/11/08diagnosis83 copies/100 PBMC43.92.43%
ATL9PBMC55MCaribbean2/1/05ATL8/12/08complete remission83 copies/100 PBMC43.92.43%
ATL10PBMC70MBlack6/7/99ATL8/13/08relapse83 copies/100 PBMC43.92.43%

The integration site data and patient demographics should be sent via email to Wei Shao at rid@mail.nih.gov with the Excel file(s) attached.

© RID. Supported by Advanced Biomedical Computing Center at Leidos/FNLCR.