Sample Set Annotation Tool: Molecular Classification of AIDS-Related Lymphomas

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Gene expression profiling (GEP) of ARL patient samples was done to determine whether gene expression signatures derived from HIV- lymphomas retained their ability to molecularly classify HIV+ lymphomas. The GEP-based predictors robustly classified ARL tumors, distinguishing molecular Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), as well as activated B-cell-like (ABC) and germinal center B-cell-like (GCB) molecular subtypes of DLBCL.

Gene expression profiles were used to identify coordinately regulated gene sets and pathways that differ between HIV+ and HIV- lymphomas of corresponding molecular subtype.

Hypothesis

Experimental Design

Frozen tumor biopsies were obtained from 20 HIV-positive patients with an AIDS-defining lymphoma. Cases were ascertained at the University of Nebraska Medical Center and through the NCI AIDS and Cancer Specimen Resource tumor bank. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on 17 ARL cases. Details of all 20 HIV-positive patients can be found in the supplementary file below.

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

17 Samples Loaded: 17

Species

Human (Homo sapiens)

Sample Source

Jejunum , Colon , Lung , Neck , Lymph node biopsy

Disease

HIV, Lymphoma

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Gender	!Sample_title	pathology diagnosis	age at diagnosis	ebv status
GSM429903	Male	1373 (HIV+)	DLBCL	37	negative
GSM429904	Male	1374 (HIV+)	DLBCL	33	negative
GSM429905	Male	1375 (HIV+)	DLBCL (PC)	46	positive
GSM429906	Male	1376 (HIV+)	High Grade, UC		negative
GSM429907	Male	1377 (HIV+)	DLBCL		negative

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Sample ID	Gender	!Sample Title	Pathology diagnosis	Age at diagnosis	Ebv status	Specimen	Tumor biopsy origin	Molecular diagnosis
GSM429903	Male	1373 (HIV+)	DLBCL	37	negative	frozen ARL tumor biopsy	LN	BL
GSM429904	Male	1374 (HIV+)	DLBCL	33	negative	frozen ARL tumor biopsy	Lung	GCB DLBCL
GSM429905	Male	1375 (HIV+)	DLBCL (PC)	46	positive	frozen ARL tumor biopsy	Colon	DLBCL_NC
GSM429906	Male	1376 (HIV+)	High Grade, UC		negative	frozen ARL tumor biopsy	Sm Bowel	DLBCL_NC
GSM429907	Male	1377 (HIV+)	DLBCL		negative	frozen ARL tumor biopsy	LN	BL
GSM429908	Male	1378 (HIV+)	DLBCL (PC)	33	positive	frozen ARL tumor biopsy	Jejunum	ABC DLBCL
GSM429909	Male	1379 (HIV+)	DLBCL	57	positive	frozen ARL tumor biopsy	Hilar/Lung	DLBCL_NC
GSM429910	Male	1380 (HIV+)	High Grade, UC	32	positive	frozen ARL tumor biopsy	LN	BL
GSM429911	Male	1383 (HIV+)	DLBCL	35	positive	frozen ARL tumor biopsy	Colon	GCB DLBCL
GSM429912	Male	1387 (HIV+)	DLBCL		positive	frozen ARL tumor biopsy	Hilar	DLBCL_NC
GSM429913	Male	1388 (HIV+)	High Grade, UC	31	negative	frozen ARL tumor biopsy	Pleural Fluid	ABC DLBCL
GSM429914	Male	1390 (HIV+)	DLBCL (PC)	24	positive	frozen ARL tumor biopsy	LN	ABC DLBCL
GSM429915	Male	1391 (HIV+)	DLBCL	38	negative	frozen ARL tumor biopsy	Mediastinal/Atrial	BL
GSM429916	Male	1392 (HIV+)	High Grade, UC	34	negative	frozen ARL tumor biopsy	Neck	GCB DLBCL
GSM429917	Male	1397 (HIV+)	DLBCL (PC)	43	positive	frozen ARL tumor biopsy	LN	ABC DLBCL
GSM429918	Male	S02 (HIV+)	DLBCL (PC)		positive	frozen ARL tumor biopsy	LN	ABC DLBCL
GSM429919	Male	S03 (HIV+)	DLBCL (PC)		positive	frozen ARL tumor biopsy	Spinal/Epidural	ABC DLBCL

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SIDRA