Myeloid Leukemia

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Index 299 CBFB–MYH11 fusion, breakpoints, 163 frequency in acute myeloid leukemia, 163 prognosis, 163, 164 reverse transcription-polymerase chain reaction, diagnosis with qualitative analysis, amplification reactions, 167, 173 control gene, 168, 173 isoforms, 164, 166 sensitivity, 166, 167 validation, 168, 169, 173 materials, 164, 173 primers and probes, 164, 165 real-time quantitative polymerase chain reaction, control gene, 170, 171, 173 diagnostics, 169–171, 173, 174 EAC protocol, 50, 51 interpretation, 171–173 minimal residual disease monitoring, 171–174 primers, 49 validation, 171–173 CD antigens, Dotscan microarray immunophenotyping of acute myeloid leukemia, antibody microarray construction, 245, 246 data recording and analysis, 246, 249, 250 diagnostics, 244 leukocyte binding, 246, 249 materials, 245 overview, 242, 243 overview, 241, 242 Cell synchronization, overview, 14 two-day culture, 18, 23 Chimerism testing, applications, graft rejection prediction, 276, 277 relapse detection, 277 DNA isolation, nails, 282, 283, 287, 288 peripheral blood or bone marrow, 282, 287 sorted cells, 283, 288 flow cytometry sorting, 281, 282, 287 fluorescence in situ hybridization and sex chromosome analysis in sex-matched transplants, cell application to slides, 285 fluorescence microscopy, 287, 293 hybridization, 287, 288, 293 pretreatment, 287 washing and counterstaining, 287, 293 genetic markers, 277 materials, 277–281, 287 overview, 275, 276 sensitivity, 276 small terminal repeat polymerase chain reaction and capillary electrophoresis with electrochemical detection, 283–285, 288–292 Chromosome deletion, 15, 154, 189, 194–195 del(4)(q12q12), see FIP1L1– PDGFRA fusion of derivative chromosome 9 (der[9]), 107–111 Chronic myeloid leukemia (CML), see also BCR–ABL fusion, progression, 93, 94 treatment, 69, 70 CML, see Chronic myeloid leukemia Cytogenetics,
300 Index and AML, 213, 236, 238, 242, 244 coupled with fluorescence in situ hybridization, 13–25 and der(9) deletions, 107–111 history, 107 D DEPC, see Diethylpyrocarbonate Diethylpyrocarbonate (DEPC), ribonuclease decontamination, 5, 11 DNA extraction, FLT3 mutation analysis, 190, 191 DNA isolation, approaches, 7, 8 chimerism testing, nails, 282, 283, 287, 288 peripheral blood or bone marrow, 282, 287 sorted cells, 283, 288 high salt extraction of highmolecular weight genomic DNA, 9 spin column isolation of genomic DNA, 8, 9 DNA microarray, acute myeloid leukemia gene expression profiling, biotin-labeled cRNA, cleanup, 220, 221 fragmentation, 221, 222, 237 synthesis, 220 cDNA, cleanup, 218–220, 237 synthesis, 217, 218 data analysis, hierarchical clustering, 230–232 leave-one-out cross-validation, 229 NetAffx database for functional gene annotation, 235, 236 normalization, 227, 228, 238 principal component analysis, 232 resampling analysis, 230 significance analysis of microarrays, 228 software, 236 statistical significance, 228, 229 support vector machine-based classification, 234 ten-fold cross-validation, 230 work flow, 226, 227 hybridization, 222, 223 materials, 213, 214 microarray sets, 223, 224 mononucleated cell isolation with Ficoll gradient centrifugation, 214, 215 overview, 213 prospects for disease classification, 238, 239 quality control, 225, 226, 237, 238 RNA isolation, 215, 217, 237 scanning and image analysis, 224, 225 time requirements, 236 washing and staining, 224, 237 Dotscan microarray, acute myeloid leukemia immunophenotyping, antibody microarray construction, 245, 246 data recording and analysis, 246, 249, 250 diagnostics, 244 leukocyte binding, 246, 249 materials, 245 overview, 242, 243 E Essential thrombocythemia (ET), acute myeloid leukemia transformation, 254 clinical features, 253, 254 diagnosis, 265 JAK2 V617F mutation detection, allele-specific polymerase chain reaction, amplification reactions, 258– 261
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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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247 Classification of AML by Monocl
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Page 311: 298 Index management, 128 AML, see
Page 315 and 316: 302 Index chimerism analysis in sex
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Page 319: 306 Index Stem cell transplantation
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Myeloid Leukemia

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