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Blood, Vol. 113, Issue 8, 1741-1748, February 19, 2009
Hidden abnormalities and novel classification of t(15;17) acute promyelocytic leukemia (APL) based on genomic alterations
Blood Akagi et al.
113: 1741
Supplemental materials for: Akagi et al
Files in this Data Supplement:
- Table S1. Primer sequences for determination of SNP sites for case #39 at 11p and for case #18 at 10q (PDF, 76.7 KB)
- Table S2. Primer sequences for PCR (PDF, 74.2 KB)
- Figure S1. Validation of CNN-LOH in case #18 (JPG, 76.7 KB)
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(A) Determination of SNP sequence in 10q CNN-LOH region. Six independent SNP sites (rs10491032, rs363221, rs2099803, rs2104543, rs7075893, and rs7918018) were sequenced. All 6 SNP sites showed only a single nucleotide; no SNP sites showed heterozygosity consistent with CNN-LOH. (B) Determination of copy-number in the 10q region. Copy-number of 10q24.31 (CNN-LOH region) in case #18 was compared to DNA from normal white blood cells using quantitative genomic real-time PCR. Levels of the copy-number were determined as a ratio between 10q24.31 and the reference genomic DNA, 2p21. Results represent the mean of 3 experiments ± SD.
- Figure S2. Expression of c-Myc mRNA in NB4 and PL-21 APL cell lines (JPG, 152 KB)
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(A) SNP-chip results of NB4 and PL-21 APL cell lines, as well as, bone marrow sample of case #48. NB4 cells had amplification of 8q24.21 region, and this region included the MYC gene. On the other hand, the region had a duplication in the PL-21 cells and had a normal copy-number in case #48. (B) Expression of c-Myc mRNA. Levels of c-Myc mRNA in cells from NB4, PL-21, and case #48 were determined by quantitative real-time PCR. Results represent the mean of 3 experiments ± SD.
- Figure S3. Chromosomal region of CNN-LOH in t(15;17) APL samples (JPG, 198 KB)
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When one allele copy-number (red-line) increases and the other allele copy-number (green-line) decreases, the region has loss of heterozygosity; and if the region has normal-copy-number, the sample has copy-number-neutral loss of heterozygosity (CNN-LOH). (A) Chromosome 10q CNN-LOH was found in three cases including #18 (10q22.2 − q-terminal, 58.2 Mb), #39 (10q21.1 − q-terminal, 75.7 Mb), and #66 (10q22.2 − q-terminal, 59.0 Mb). (B) Chromosome 11p CNN-LOH was noted in three cases including #3 (11p-terminal − p11.12, 47.9 Mb), #20 (11p-terminal − p11.12, 47.4 Mb), and #39 (11p-terminal − p14.1, 28.7 Mb). Chromosomal and physical localization, size, as well as genes in the regions, are described in Table 2.
- Figure S4. Comparison of chromosomal changes between diagnosis complete remission samples (JPG, 75.3 KB)
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Chromosomal status of DNA of matched complete remission samples of cases #2, #3, #18, #19, #38, #39, and #50 were compared to samples obtained at diagnosis. Chromosomal alterations including copy-number changes and CNN-LOH were not present in the complete remission samples. Pink, green, and red boxes indicate CNN-LOH (copy-number-neutral loss of heterozygosity), deletion, and duplication including trisomy, respectively. Abbreviations: D, diagnosis; C, complete remission.
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