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Blood, Vol. 113, Issue 6, 1294-1303, February 5, 2009
Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA)
Blood Grubor et al.
113: 1294
Supplemental materials for: Grubor et al
Files in this Data Supplement:
- Table S1. Frequency plot summary (PDF, 494 KB) -
Summary of the frequency plot shown in Figure 5. . Each “region” is defined as area covered by probes that share the same frequency up/down. The positions and size are in base pairs. The total number of patients analyzed is 58. No.of.Probes – the number of probes within a given lesion on the 390K array; Start.Probe/End.Probe – the first and last probe within a given area (in genome order); Frequency.up/down – the frequency of amplification/deletion in a given region respectively; No.patients.up/down – the number of patients out of the total (58) where amplifications/deletions were observed; CNV.Max.Frequency.Up/Down denote the maximum CNV frequency within a given region using our CNV database of 500 “normals.” UCSC.URL – UCSC Genome Browser (GoldenPath) Web site links to allow viewing of regions on said Web site.
- Table S2. Segmented data summary (PDF, 360 KB) -
The segmenter calls for all 419 lesions observed in 58 CLL samples. The positions and size are in base pairs. St.Dev – standard deviation; Start.Position/End.Position – respective breakpoint positions of a given lesion on chromosomes; UCSC.URL – UCSC Genome Browser (GoldenPath) Web site links to allow viewing of lesions on said Web site; Known.Gene.no/RefSeq.gene.no – the number of genes within a lesion from UCSC Genes and RefSeq tracks (GoldenPath).
- Figure S1. The value of performing self-self as well as normal vs. standard lab control experiments (JPG, 236 KB)
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Top: Self-self (CLLs vs. PMNs) experiment for sample CLL283. All changes observed (marked by arrows) are true copy number changes in CLL and not CNVs (i.e. variation between unrelated individuals). There is an apparent gain of the Y-chromosome. Bottom: PMNs vs. standard, normal, internal-laboratory control genome. The raw data are in gray and the segmenter output is in dark blue. The segmenter output from the self-self experiment (above) is superimposed (maroon). CNVs shown by the segmenter (blue) are represent normal variations between these two individuals and not related to CLL. Single probe “events” are Restriction Fragment Length Polymorphisms (RFLPs). The apparent gain of the Y-chromosome in B-cells in fact represents a loss of the Y-chromosome in PMNs.
- Figure S2. Genomic lesions revealed in CLL334 using the high-density 2.1 M prototype array (HD2) (JPG, 50.4 KB)
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CLL334 exhibited no discernible lesions on either the 85K or the 390K array, apart from the IGKC and IGH rearrangements. Hybridizing this sample to the HD2 array reveals multiple lesions, some of which occur within larger regions in our dataset, as this one at 2q37.2. The lesion at 2q37.2 is just 8.3kb in size, far too small to be observed with either the 85K or 390K array.
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