[SURIND=0 (Indicator of disease-related death; integer, 0=alive or death by other cause, 1=disease related death, na=death cause undetermined)]
[SURTIM=4.67 (Follow-up time in months from Pre-Treatment baseline; integer)]
[PCTCELLS=na/na/na/na/na (Percentage of cells with 0 copy/1 copy/2 copies/3 copies/4+ copies; percentage, na=not available)]
[AMPIND=na (Indicator of FISH 1q21 Amplification; string, na=not available)]
[Subgrp7=HY]
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA).
Label
biotin
Label protocol
As recommended by manufacturer
Hybridization protocol
As recommended by manufacturer
Scan protocol
As recommended by manufacturer
Description
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA) More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining The clinic survival follow-up is through November 07, 2005 Disease-related survival: Deaths were coded as disease-related according to a physician chart review. Three deaths had not been coded as of the time of the analysis and these corresponding to the three missing status indicators in the data set. Non-disease related deaths are competing risks, so distribution estimates should use cumulative incidence of disease-related death as the outcome, rather than survival Censored data analysis: Analyses using the status indicator as a grouping variable directly are not recommended. Tests for censored data can be applied, gene-by-gene, as in the published analysis, or disease-related deaths can be matched to a random sample of longer survivors
Data processing
All data used in these analyses were derived with the Affymetrix Microarray Suite GCOS1.1 software.
CEL files are available upon request via a Materials Transfer Agreement. Please contact Dr. John Shaughnessy for details.
