Myeloid Leukemia

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Index 297 Index A software, 236 ABL, see BCR–ABL fusion statistical significance, 228, Acute myeloid leukemia (AML), 229 CD antigen immunophenotyping, support vector machine-based Dotscan microarray analysis, classification, 234 antibody microarray ten-fold cross-validation, 230 construction, 245, 246 work flow, 226, 227 data recording and analysis, hybridization, 222, 223 246, 249, 250 materials, 213, 214 diagnostics, 244 microarray sets, 223, 224 leukocyte binding, 246, 249 mononucleated cell isolation with materials, 245 Ficoll gradient centrifugation, overview, 242, 243 214, 215 flow cytometry, 242, 243 overview, 213 classification schemes, 242–244 prospects for disease DNA microarray gene expression classification, 238, 239 profiling, quality control, 225, 226, 237, biotin-labeled cRNA, 238 cleanup, 220, 221 RNA isolation, 215, 217, 237 fragmentation, 221, 222, 237 scanning and image analysis, 224, synthesis, 220 225 cDNA, time requirements, 236 cleanup, 218–220, 237 washing and staining, 224, 237 synthesis, 217, 218 FLT3 mutations, see FLT3 mutations data analysis, gene fusion analysis, see AML1–ETO hierarchical clustering, 230– fusion; CBFB–MYH11 fusion; 232 PML–RARA fusion leave-one-out cross-validation, real-time quantitative polymerase 229 chain reaction, see Reverse NetAffx database for transcription-polymerase chain functional gene annotation, reaction 235, 236 WT1 overexpression, see WT1 normalization, 227, 228, 238 Acute promyelocytic leukemia (APL), principal component analysis, see also PML–RARA fusion, 232 course, 128 resampling analysis, 230 treatment, 128 significance analysis of All-trans retinoic acid, acute microarrays, 228 promyelocytic leukemia 297
298 Index management, 128 AML, see Acute myeloid leukemia AML1–ETO fusion, frequency in acute myeloid leukemia, 149 prognosis, 149 reverse transcription-polymerase chain reaction, control gene, 152, 160 data analysis, 157, 158, 160 materials, 150 minimal residual disease monitoring, competitive polymerase chain reaction, 154 control gene, 154 overview, 152–154 real-time quantitative polymerase chain reaction, 154–156, 160 qualitative analysis, 151, 152, 160 quality control, 158, 159 real-time quantitative polymerase chain reaction, EAC protocol, 50, 51 primers, 49 reverse transcription, 151, 160 RNA extraction, 150, 151, 160 Antibody microarray, see Dotscan microarray APL, see Acute promyelocytic leukemia Arsenic trioxide, acute promyelocytic leukemia management, 128 B Banding, see G-banding BCR–ABL fusion, breakpoints, 72 fluorescence in situ hybridization, interpretation and reporting, 111– 113 materials, 111, 112 minimal residual disease detection, 108, 111 probes, 108–110 prognostic value, 108, 109 gene products, 107, 108 mutation and imatinib mesylate resistance, detection of mutations, materials, 96, 97 semi-nested polymerase chain reaction, 95–102 sequencing reaction and analysis, 99, 100, 102–104 overview, 94, 95 Philadelphia chromosome, 69, 72, 85, 93, 96, 101, 107 qualitative reverse transcriptionpolymerase chain reaction, atypical transcripts, 82, 83 p210 transcripts, 83, 84, 90 real-time quantitative polymerase chain reaction, amplification reactions, 80–82, 85 control gene, 80, 85 interpretation, 82, 85, 87, 89 materials, 72–75 plasmid standards, cloning, 78, 79 dilutions, 79, 84, 85 polymerase chain reaction, 78 primers and probes, 80, 85 principles, 70 quality control samples, 79, 80 RNA extraction, 75, 76 treatment response monitoring, 70 Bone marrow, culture and harvest, materials, 16, 21 overnight culture, 18, 22, 23 synchronization, see Cell synchronization transplantation chimerism analysis, see Chimerism testing
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M E T H O D S I N M O L E C U L A R
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M E T H O D S I N M O L E C U L A R
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© 2006 Humana Press Inc. 999 River
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vi Preface comprehensive review of
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viii Contents 11 Detection of the F
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x Contributors D. GARY GILLILAND
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RNA and DNA From Leukocytes 1 1 Iso
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RNA and DNA From Leukocytes 3 mine
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RNA and DNA From Leukocytes 5 late
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RNA and DNA From Leukocytes 7 9. Us
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RNA and DNA From Leukocytes 9 16. C
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RNA and DNA From Leukocytes 11 3. I
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Cytogenetic and FISH Techniques 13
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Real-Time RT-PCR Strategies 27 3 Ov
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Real-Time RT-PCR Strategies 29
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Real-Time RT-PCR Strategies 31 cifi
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Real-Time RT-PCR Strategies 33 2.1.
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Real-Time RT-PCR Strategies 35 Fig.
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Real-Time RT-PCR Strategies 37 2.1.
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Real-Time RT-PCR Strategies 39 the
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Real-Time RT-PCR Strategies 43 duri
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MyiQ single color 400 nm 585 nm 96
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Real-Time RT-PCR Strategies 47 side
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Table 2 Real-Time Quantitative Poly
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Real-Time RT-PCR Strategies 51 AML-
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Real-Time RT-PCR Strategies 53 the
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Real-Time RT-PCR Strategies 55 plas
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Real-Time RT-PCR Strategies 57 betw
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Real-Time RT-PCR Strategies 59 Ct C
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Real-Time RT-PCR Strategies 63 asse
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Real-Time RT-PCR Strategies 65 21.
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Real-Time RT-PCR Strategies 67 50.
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Quantitative PCR for Monitoring CML
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Detection of BCR-ABL Mutations 93 5
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Detection of BCR-ABL Mutations 95 F
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Detection of BCR-ABL Mutations 97 2
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Detection of BCR-ABL Mutations 99 o
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Detection of BCR-ABL Mutations 101
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Deletion of Derivative Chromosome 9
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Diagnosis of PML-RARA-Positive APL
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Duplexed QZyme RT-PCR for APL Analy
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Diagnosis of AML1-MTG8 (ETO)-Positi
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Diagnosis of CBFB-MYH11-Positive AM
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165 Table 1 Primers for CBFB-MYH11
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FIP1L1-PDGFRA in Hypereosinophilic
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FLT3 Mutations in AML 189 12 FLT3 M
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FLT3 Mutations in AML 191 3.1.1. DN
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FLT3 Mutations in AML 193 Table 2 R
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FLT3 Mutations in AML 195 Fig. 2. D
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FLT3 Mutations in AML 197 10. Kiyoi
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WT1 Expression in AML and MDS 199 1
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WT1 Expression in AML and MDS 201 T
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WT1 Expression in AML and MDS 205 T
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WT1 Expression in AML and MDS 207 F
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Classification of AML by DNA-Oligon
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233 Classification of AML by DNA-Ol
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Classification of AML by Monoclonal
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Classification of AML by Monoclonal
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Page 315 and 316: 302 Index chimerism analysis in sex
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Myeloid Leukemia

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