Sample Set Annotation Tool: Whole Blood Transcriptional Response to Early Acute HIV

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

The objective of this study is to: 1) Characterize the transcriptional signature of early acute HIV infection. 2) Eucidate the evolution of the signature in both anti-retroviral treated and untreated populations over a 24 week time course. 3) Correlate clinical and disease related parameters to heterogenaity in the transcriptional signature to identify pathways explaining clinical heterogeneity 4) Compare the acute signature of HIV infection to other acute viral signatures.

Hypothesis

Experimental Design

58 acute HIV patients were recruited from locations in Africa (n=43) and the United States (n=15). These patients were allocated into training (n=18), test (n=10) and validation sets (n=30). Patient samples were collected at study enrollment (confirmed acute) for all patients and at weeks 1,2,4,12,and 24 for training and test set constituents. 13 of 15 US patients initiated anti-retroviral therapy after after enrollment and before the week 1 visit. The remaining 2 US patients and 43 African patients were not placed on therapy through the 24 week time course. Matched uninfected controls patients were also recruited from each site (n= 55). In total 232 samples were collected.

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

47 Samples Loaded: 47

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

HIV

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Age	Ethnicity	Gender	Illness	!Sample_title
GSM728539	24	African	Male	HIV	702010773E
GSM728540	20	African	Male	HIV	702010600E
GSM728541	27	African	Female	HIV	702010943E
GSM728542	20	African	Female	HIV	703011182E
GSM728543	28	African	Male	HIV	702010721E

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Samples Viewer / Editor

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Sample ID	Age	Ethnicity	Gender	Illness	!Sample Title	Race	Treatment	Viral load	Cd4 count	Dataset	Feibig stage	Calculated viral set point	Week
GSM728539	24	African	Male	HIV	702010773E	African Lomwe	NO	89047	460	Validation Set	4	16,218	E
GSM728540	20	African	Male	HIV	702010600E	African Ngoni	NO	528269	312	Validation Set	4	44,668	E
GSM728541	27	African	Female	HIV	702010943E	African Sena	NO	175561	385	Validation Set	5	not enough visits to calculate	E
GSM728542	20	African	Female	HIV	703011182E	African Chewa	NO	955474	213	Validation Set	5	331,131	E
GSM728543	28	African	Male	HIV	702010721E	African Ngoni	NO	107421	ND	Validation Set	5-6	unstable VL - no set point	E
GSM728544	27	African	Female	HIV	703011545E	African Chewa	NO	21975	404	Validation Set	5	81,283	E
GSM728545	33	African	Male	Healthy	702011045E	African Yao	NA	NA	843	Validation Set	NA	NA	E
GSM728546	45	African	Male	HIV	702010901E	African Lomwe	NO	7347	ND	Validation Set	4	Increasing after 6 months	E
GSM728547	34	African	Male	Healthy	702011037E	African Lambia	NA	NA	867	Validation Set	NA	NA	E
GSM728548	34	African	Female	Healthy	703011322E	African Ngoni	NA	NA	1197	Validation Set	NA	NA	E
GSM728549	24	African	Male	Healthy	702010553E	African Sena	NA	NA	1156	Validation Set	NA	NA	E
GSM728550	22	African	Female	Healthy	702011072E	African Ngoni	NA	NA	1220	Validation Set	NA	NA	E
GSM728551	23	African	Male	Healthy	703010242E	African Ngoni	NA	NA	654	Validation Set	NA	NA	E
GSM728552	29	African	Male	HIV	703011244E	African Chewa	NO	502273	256	Validation Set	4	229,087	E
GSM728553	19	African	Female	HIV	703010256E	African Chewa	NO	254060	352	Validation Set	3	18,621	E
GSM728554	20	African	Male	HIV	703011190E	African Nyanja	NO	696540	523	Validation Set	5	114,815	E
GSM728555	29	African	Male	HIV	702010955E	African Ngoni	NO	750000	147	Validation Set	1-2	not enough visits to calculate	E
GSM728556	33	African	Male	HIV	702011241E	African Lomwe	NO	750000	477	Validation Set	3	not enough visits to calculate	E
GSM728557	26	African	Male	Healthy	702011053E	African Ngoni	NA	NA	633	Validation Set	NA	NA	E
GSM728558	25	African	Female	Healthy	702011086E	African Mang'anja	NA	NA	907	Validation Set	NA	NA	E
GSM728559	28	African	Female	HIV	702010968E	African Ngoni	NO	301630	460	Validation Set	4	not enough visits to calculate	E
GSM728560	30	African	Male	HIV	702010634E	African Sena	NO	86811	478	Validation Set	5-6	24,547	E
GSM728561	28	African	Female	HIV	702010419E	African Khokhola	NO	400	512	Validation Set	4	42,658	E
GSM728562	24	African	Female	HIV	702010838E	African Chewa	NO	66913	ND	Validation Set	5	48,978	E
GSM728563	29	African	Male	Healthy	702011014E	African Lomwe	NA	NA	638	Validation Set	NA	NA	E
GSM728564	32	African	Male	Healthy	702010979E	African Yao	NA	NA	697	Validation Set	NA	NA	E
GSM728565	37	African	Male	HIV	703011432E	African Chewa	NO	345260	285	Validation Set	3	unstable VL - no set point	E
GSM728566	24	African	Male	Healthy	702010992E	African Yao	NA	NA	605	Validation Set	NA	NA	E
GSM728567	28	African	Male	Healthy	703010337E	African Lomwe	NA	NA	466	Validation Set	NA	NA	E
GSM728568	26	African	Male	HIV	702010984E	African Mang'anja	NO	54623	377	Validation Set	5	not enough visits to calculate	E
GSM728569	25	African	Male	HIV	702011184E	African Lomwe	NO	517988	387	Validation Set	4	not enough visits to calculate	E
GSM728570	23	African	Female	Healthy	703011039E	African Chewa	NA	NA	625	Validation Set	NA	NA	E
GSM728571	40	African	Male	HIV	702011143E	African Lomwe	NO	750000	446	Validation Set	1-2	not enough visits to calculate	E
GSM728572	34	African	Male	HIV	703011157E	African Chewa	NO	44255	ND	Validation Set	4	only 1 visit	E
GSM728573	28	African	Male	HIV	702010809E	African Sena	NO	9876	ND	Validation Set	5	6,166	E
GSM728574	31	African	Female	Healthy	702010846E	African Sena	NA	NA	907	Validation Set	NA	NA	E
GSM728575	23	African	Female	Healthy	702011099E	African Ngoni	NA	NA	655	Validation Set	NA	NA	E
GSM728576	31	African	Male	HIV	703010976E	African Chewa	NO	450505	163	Validation Set	3	77625	E
GSM728577	60	African	Female	Healthy	702010545E	African Sena	NA	NA	1097	Validation Set	NA	NA	E
GSM728578	20	African	Female	HIV	702010813E	African Lomwe	NO	80929	836	Validation Set	4	131,826	E
GSM728579	21	African	Female	HIV	703011165E	African Chewa	NO	750000	409	Validation Set	5	323,594	E
GSM728580	25	African	Male	HIV	702010520E	African Sena	NO	526815	190	Validation Set	5	only 1 visit	E
GSM728581	23	African	Female	HIV	703010863E	African Ngoni	NO	103456	547	Validation Set	4	unstable VL - no set point	E
GSM728582	26	African	Male	HIV	702010852E	African Lomwe	NO	750000	343	Validation Set	1-2	575,440	E
GSM728583	24	African	Male	HIV	702010930E	African Ngoni	NO	93167	288	Validation Set	5	only 1 visit	E
GSM728584	24	African	Female	HIV	702010824E	African Lomwe	NO	54208	ND	Validation Set	5	2,884	E
GSM728585	28	African	Female	Healthy	702011101E	African Lomwe	NA	NA	816	Validation Set	NA	NA	E

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