Myeloid Leukemia

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Index 305 BCR–ABL fusion detection in chronic myeloid leukemia, see BCR–ABL fusion cDNA synthesis, 9–11, 76, 77, 120, 122, 123, 181 FIP1L1–PDGFRA fusion detection, see FIP1L1–PDGFRA fusion principles, 27, 28 PRV1 overexpression, see Essential thrombocythemia; Polycythemia vera real-time quantitative polymerase chain reaction for acute myeloid leukemia, see also AML1–ETO fusion; CBFB– MYH11 fusion; PML–RARA fusion, acute myeloid leukemia fusion gene detection, EAC protocol, 50, 51 primers, 49 double-stranded DNA detection, Amplifluor hairpin primers, 33 DNAzyme, 35, 36 light-up probe, 33 SybrGreen I, 31, 32 instrumentation, 43–46 interpretation in absolute quantification, 58–61 minimal residual disease detection, 28, 60–62 normalization, 53, 54 preparation of run, 48, 50 primer and probe design, 46–48 principles, 30 prospects, 63 quality control, 51–53, 62, 63 quantification, absolute, 54, 55 relative, 55, 56 reporting, 56–58 specific fragment detection, hybridization probes, 39 locked nucleic acid, 38, 39 minor groove binder, 37, 38 Molecular Beacon, 39 Scorpion probe, 40, 41, 43 TaqMan assay, 37 RNA isolation, see RNA isolation WT1 overexpression, see WT1 RNA extraction, AML1–ETO fusion transcripts, 150, 151, 160 anticoagulants, 4, 10 approaches, 5 BCR–ABL fusion detection, cDNA synthesis, 76, 77 extraction, 75, 76 materials, 72, 73 commercial kits, 5, 6, 11 DNA microarray analysis of acute myeloid leukemia, 215, 217, 237 gel electrophoresis analysis, 7 guanidium thiocyanate lysis and cesium chloride ultracentrifugation, 6, 7, 11 PML–RARA fusion detection, 134, 135, 144 PRV1 transcripts, 267, 268 ribonuclease avoidance, 5, 10, 11 WT1 transcripts, 203, 209 RT-PCR, see Reverse transcriptionpolymerase chain reaction S SAM, see Significance analysis of microarrays Scorpion probe, fragment detection in real-time quantitative polymerase chain reaction, 40, 41, 43 Significance analysis of microarrays (SAM), principles, 228
306 Index Stem cell transplantation chimerism analysis, see Chimerism testing Support vector machine (SVM), DNA microarray analysis, 234 SVM, see Support vector machine T TaqMan assay, fragment detection in real-time quantitative polymerase chain reaction, 37, 70 Ten-fold cross-validation, DNA microarray analysis, 230 W WT1, functions, 200 leukemia expression, 200–202 overexpression analysis with realtime quantitative polymerase chain reaction, amplification reactions, 204, 205, 209 materials, 202, 203, 208 plasmid standard curve generation, 205, 206 plate preparation, 207–210 rationale, 202 reverse transcription, 203, 204 RNA extraction, 203, 209 tissue distribution, 200
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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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Detecting JAK2 V617F Mutation in MP
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Page 315 and 316: 302 Index chimerism analysis in sex
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Myeloid Leukemia

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