Myeloid Leukemia

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Index 303 AML1–ETO fusion monitoring with reverse transcriptionpolymerase chain reaction, competitive polymerase chain reaction, 154 control gene, 154 overview, 152–154 real-time quantitative polymerase chain reaction, 154–156, 160 CBFB–MYH11 fusion monitoring with real-time quantitative polymerase chain reaction, 171–174 fluorescence in situ hybridization detection of BCR–ABL fusion, 108, 111 PML–RARA fusion detection with reverse transcriptionpolymerase chain reaction, 118, 128, 129 real-time quantitative polymerase chain reaction for acute myeloid leukemia detection, 28, 60–62 Minor groove binder, fragment detection in real-time quantitative polymerase chain reaction, 37, 38 Molecular Beacon, fragment detection in real-time quantitative polymerase chain reaction, 39 MRD, see Minimal residual disease Myelodysplastic syndrome (MDS), WT1 overexpression, see WT1 Myeloproliferative disorders, see Essential thrombocythemia; Idiopathic myelofibrosis; Polycythemia vera MYH11, see CBFB–MYH11 fusion N–P NetAffx, functional gene annotation, 235, 236 PCA, see Principal component analysis PCR, see Polymerase chain reaction PDGFRA, see FIP1L1–PDGFRA fusion Percentage of malignant cells, enrichment and diagnostic considerations, 2, 4 Peripheral blood, harvesting, 19 Philadelphia chromosome, see BCR–ABL fusion PML–RARA fusion, breakpoints, 115, 128 isoforms and prognostic value, 115, 118 real-time quantitative polymerase chain reaction, EAC protocol, 50, 51 primers, 49 Qzyme system, calibration curves, 133, 134, 143, 144 duplex single-tube amplification reactions, 135–137, 143–145 interpretation, 137–139, 145 isoform detection, 129, 130, 142, 143 limit of detection, 139, 140, 145 limit of quantification, 140, 141, 145 materials, 130–132, 143 overview, 129, 130, 132, 143 reproducibility, 141, 142, 146 RNA extraction and quantification, 134, 135, 144 reverse transcription-polymerase chain reaction, Biomed-1 protocol, 116, 117 cDNA synthesis, 120, 122, 123 first-round and nested polymerase chain reaction, 121, 123 gel electrophoresis, 121, 213, 124 materials, 118–120
304 Index minimal residual disease detection, 118, 128, 129 overview, 116, 117 primers, 117 RNA isolation, 120–122 transcript abundance, 118, 121 Polycythemia vera (PV), acute myeloid leukemia transformation, 254 clinical features, 253, 254 diagnosis, 265 JAK2 V617F mutation detection, allele-specific polymerase chain reaction, amplification reactions, 258– 261 materials, 257, 258, 260 principles, 254, 255 BsaXI restriction analysis, digestion, 260–262 gel electrophoresis, 260, 262 materials, 258 overview, 255, 257 polymerase chain reaction, 259, 260 PRV1 overexpression analysis with reverse transcriptionpolymerase chain reaction, amplification reactions, 269–271 cDNA verification, 269, 270 DNase treatment, 268 gel electrophoresis and analysis, 270, 271 materials, 266, 267 overview, 265, 266 peripheral blood granulocyte purification, 267, 270 reverse transcription, 269 RNA extraction, 267, 268 Polymerase chain reaction (PCR), see also specific techniques aliquoting of samples, 3 chimerism analysis, see Chimerism testing contamination prevention, 1, 2 DNA isolation, see DNA isolation FIP1L1–PDGFRA fusion analysis, amplification reactions, 182–184, 186, 187 materials, 179 overview, 177 sequencing, 185, 187 white blood cell isolation and nucleic acid extraction, 179– 181, 186 FLT3 mutations, amplification reactions, 191, 192, 195, 196 primers, 191 JAK2 V617F mutation detection in myeloproliferative disorders with allele-specific polymerase chain reaction, amplification reactions, 258–261 materials, 257, 258, 260 principles, 254, 255 sensitivity, 1 Principal component analysis (PCA), DNA microarray analysis, 232 PRV1, see Essential thrombocythemia; Polycythemia vera PV, see Polycythemia vera Q, R Qzyme® system, see PML–RARA fusion RARA, see also PML–RARA fusion, fusion partners, 116 Real-time polymerase chain reaction, see BCR–ABL fusion; Reverse transcription-polymerase chain reaction Reverse transcription-polymerase chain reaction (RT-PCR),
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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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Myeloid Leukemia

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