Index. Index 377. ASH, see Allele-specific hybridization

Transcription

1 Index 377 Index A Allele-specific hybridization (ASH), genotyping principles, 14, 15 Amplification refractory mutation system-polymerase chain reaction (ARMS-PCR), cystic fibrosis diagnosis, amplification, 231, 232 electrophoresis, 232, 233 Elucigene assay, evaluation, 233, 234 materials, 228, 229 hemoglobinopathy diagnosis, amplification reactions, hemoglobin variants, 210 materials, 210, 211 β-thalassemia, 209 principles, 11, 12 ARMS-PCR, see Amplification refractory mutation systempolymerase ASH, see Allele-specific hybridization B Base excision sequence scanning (BESS), principles, 26, 27 Becker muscular dystrophy, see Muscular dystrophy BESS, see Base excision sequence scanning C Carbodimide modification, mutation detection applications, 25 CCM, see Chemical cleavage of mismatch CF, see Cystic fibrosis CFLP, see Cleavage fragment-length polymorphism Chemical cleavage of mismatch (CCM), principles, 25 Chromosome aneuploidy, see Quantitative fluorescencepolymerase Cleavage fragment-length polymorphism (CFLP), principles, 27 Comparative sequence analysis (CSA), analysis and interpretation in GeneScan, analysis parameters, 119, 120, 123 matrix installation, 119 mutation indicators, navigation, 120, 121 size standard creation, external size standards, 117, 118 internal size standards, 118, 119, 123 trace viewing, 120, 122, 123 commercial systems, 116,

2 378 Index gel opening and extraction in GeneScan, 117, 123 principles, 28, 115, 116 sequencing reactions and electrophoresis, 116, 117, 122, 123 Conformation-sensitive gel electrophoresis (CSGE), principles, 23 Costs, diagnostic mutation detection considerations, 22 CSA, see Comparative sequence analysis CSGE, see Conformation-sensitive gel electrophoresis Cystic fibrosis (CF), amplification refractory mutation system-pcr, amplification, 231, 232 electrophoresis, 232, 233 Elucigene assay, evaluation, 233, 234 materials, 228, 229 error rate in diagnosis, 222 gene mutations, 221 heteroduplex assay, amplification, 230, 231, 242 evaluation, 230, 231 heteroduplex analysis, 230 materials, 228 overview, 222, 223 INNO-LiPA CFTR assay, amplification, 234, 235, 242 color development, 236, 237, 242, 243 denaturation and hybridization, 235, 236, 242, 243 evaluation, 237, 243 materials, 229 overview, 222, 224 stringent wash, 236, 242, 243 oligonucleotide ligation assay, DNA preparation, 239 electrophoresis, 240 evaluation, materials, 229 overview, 222, 225, 226 polymerase, 239 probing, 239 related diseases, 222, 223 sensitivity comparison of assays, D Deming circle, phases, 359, 360 Denaturing gradient gel electrophoresis (DGGE), dystrophin-associated muscular dystrophy gene mutations, advantages, 314, 315 gel electrophoresis and visualization, 333, 336 gel preparation, , 336, 337 materials, 326 polymerase, 331, 335 primers, familial adenomatous polyposis, gel electrophoresis, 258, 264 materials, 250, 252, 253 polymerase, 257, 264 principles, 23, 24 β-thalassemia diagnosis, 207, 209 Denaturing high-performance liquid chromatography (DHPLC), amplification product size and purity determination, 51 gradient selection for mutation detection, 51 heteroduplex formation, 50, 51, 64

3 Index 379 limitations, 21 materials, 48, 49, neurofibromatosis type 1 testing, buffers, 295, 296 materials, 293 overview, 289, 290 polymerase and primers, sample table construction, 302 temperature and gradient conditions, 300, 301 polymerase, 49, 50, 60 principles, 24, 45, 46, 48 separation gradient determination, 51 separation temperature, 51 Transgenomic WAVE DNA Fragment Analysis System and software operation, 45, 46, 48, 51 54, 56 59, 64, 65 DGGE, see Denaturing gradient gel electrophoresis DHPLC, see Denaturing highperformance liquid chromatography DNA methylation analysis, differential cleavage by chemicals, 18, 19 differential cleavage by methylation-sensitive restriction enzymes, 18, 19 differential reactivity with sodium bisulfite, 19 DNA microarrays, genotyping principles, 15, 16 sequencing, 30, 31 DNA mutation, definition, 9 detection, see specific techniques frequency considerations in detection, 9 polymorphisms, 9 sensitivity of detection in clinical diagnosis, 20 DNA mutation scanning, principles, 19, 20 techniques, see specific techniques DNA sequencing, accuracy, 27, 28 automated fluorescent sequencing, BigDye terminator cycle sequencing kits, 91, 92, 111, 116 capillary electrophoresis, 87, 99, 100 chemistries of sequencing, 82, 83 commercial sequencers, 82 cycle sequencing, 84, 86 data analysis, 84, 87, 95 DYEnamic ET cycle sequencing kits, 92, 93, 111 gel electrophoresis, 86, 87, 96, 98, 99 internal quality control, materials, Meta-polymerase chain reaction, 85 primers, 83, 84, 87 principles, 81, 82 Sequencer software analysis of sequence, 105, 107, 113 Staden package software analysis of sequence, contig assembly, 101, 103 mutation detection, 104, 112 sequence file transfer, 100, 101

4 380 Index template preparation, 83, 85, 86, 88 90, 111 troubleshooting, unincorporated dye terminator removal, 84, 86, 93 96, 111 comparative sequence analysis, see Comparative sequence analysis dideoxy nucleotides, 27 familial adenomatous polyposis, cycle sequencing, 262, 265 materials, 250, 253, 255, 263 polymerase, 260, 261, 264, 265 mass spectrometry, 28 minisequencing, 12 multiple endocrine neoplasia testing, fluorescent dye sequencing, materials, 274, 275 overview, 270 primers, specificity in mutation detection, 28 Duchenne muscular dystrophy, see Muscular dystrophy Dystrophin, see Muscular dystrophy E ECM, see Enzyme cleavage of mismatch Enzyme cleavage of mismatch (ECM), principles, 25, 26 Ethics, genetic testing, committees, 371, 372 informed consent, 371 F Familial adenomatous polyposis (FAP), clinical features, 245 denaturing gradient gel electrophoresis analysis, gel electrophoresis, 258, 264 materials, 250, 252, 253 polymerase, 257, 264 DNA sequencing, cycle sequencing, 262, 265 materials, 250, 253, 255, 263 polymerase, 260, 261, 264, 265 gene mutations, 245, 246 linkage analysis, intragenic markers, 262, 265 linked markers, 263 materials, 253, 256 overview, 249 polymerase, 262, 263, 265 restriction fragment length polymorphism, 262, 263 mutation analysis in affected individuals, presymptomatic testing, 248, 249 protein truncation test, gel electrophoresis, 255, 257, 263, 264 materials, 250, 251 polymerase, 255, 263 single-strand conformational polymorphism analysis, gel electrophoresis, 259, 264 materials, 250, 254 polymerase, 258, 259, 264 silver staining of gel, 259, 260, 264 FAP, see Familial adenomatous polyposis

5 Index 381 FISH, see Fluorescence in situ hybridization Fluorescence in situ hybridization (FISH), neurofibromatosis type 1, detection and visualization of probe signal, 295 hybridization, 294, 295 materials, 290, 292 nick translation, 293 overview, 289 probe denaturation, 294 probe preparation, 294 slide denaturation, 294 washes, 295 Fragile X disease, loci, 157 microsatellite analysis, interpretation, 173, 175 materials, 162, 164 polymerase, 169, 170, 181 primers, 169, 178, 179 principles, 159, 160, 176, 177 polymerase of trinucleotide repeats, amplification reaction, 167, 168, 181 gel electrophoresis of products, 168, 169, 181 interpretation, 172, 173 materials, , 178 principles, 159, 176, 177 premutations versus full mutations, 157, 158, 175 repeat size range, 157, 175 Southern blot analysis, blot stripping and storage, 167, 180 blotting, 166, 180 G hybridization, 166, 167, 180 interpretation, materials, 160, 161, 178 principles, 159, 175, 176 probe labeling, 166, 178, 180 restriction digestion and gel electrophoresis, 164, 165, washing and autoradiography, 167, 180 Gap-PCR, see Gap-polymerase Gap-polymerase (Gap-PCR), hemoglobininopathy diagnosis, amplification reactions, 211, 212 materials, 210, 211 β-thalassemia, 204, 205, , 215 GeneChip, see DNA microarrays Gene dosage, multiplex amplifiable probe hybridization, see Multiplex amplifiable probe hybridization techniques for study, overview, Genetic testing, counseling importance, definition, 369, 370 ethics, see Ethics, genetic testing laboratory validation, 373, 374 purposes, 372 quality management, see Quality management, clinical diagnostic molecular testing regulation, see Regulation, genetic testing

6 382 Index H HD, see Huntington s disease Hemoglobinopathies, see Hemoglobin variants; Hereditary persistence of fetal hemoglobin; Thalassemias Hemoglobin variants, diagnosis, allele-specific oligonucleotide hybridization, 210 amplification refractory mutation system-pcr, 210 sickle-cell disease, 210 types, 210 Hereditary persistence of fetal hemoglobin (HPFH), diagnosis, 209, 210 Heteroduplex analysis, cystic fibrosis diagnosis, amplification, 230, 231, 242 evaluation, 230, 231 heteroduplex analysis, 230 materials, 228 overview, 222, 223 denaturing high-performance liquid chromatography, see Denaturing highperformance liquid chromatography principles, 23 HPFH, see Hereditary persistence of fetal hemoglobin Huntington s disease (HD), polymerase -based diagnosis, amplification reaction, 189, 199 challenges, 184, 185, 198 interpretation, , 201 materials, , 199 polyacrylamide gel electrophoresis of products and hybridization, 185, 186, , primers, 184, 185 Southern blot analysis of genomic DNA, agarose gel electrophoresis, 192, 193 blotting, 194 hybridization and autoradiography, 194, 195, 200, 201 interpretation, 197 materials, probe radiolabeling, 194, 200 restriction enzyme digestion, 192, 199, 200 sample preparation, 193, 194, 200 trinucleotide repeats, 183 I INNO-LiPA CFTR assay, amplification, 234, 235, 242 color development, 236, 237, 242, 243 denaturation and hybridization, 235, 236, 242, 243 evaluation, 237, 243 materials, 229 overview, 222, 224 stringent wash, 236, 242, 243 Invader, genotyping principles, 14 L Ligase, genotyping principles, 13, 14 LightCycler system, principles, 13 Linkage analysis, familial adenomatous polyposis, intragenic markers, 262, 265

7 Index 383 linked markers, 263 materials, 253, 256 overview, 249 polymerase, 262, 263, 265 restriction fragment length polymorphism, 262, 263 MEN1 families without MEN1 gene mutation, analysis, 279 materials, 275 overview, 270 spinal muscular atrophy, 347, 350, 353, 355 M MAPH, see Multiplex amplifiable probe hybridization MEN, see Multiple endocrine neoplasia Microsatellite analysis, fragile X disease diagnosis, see Fragile X disease linkage analysis, 11 Multiple endocrine neoplasia (MEN), DNA sequencing, fluorescent dye sequencing, materials, 274, 275 overview, 270 primers, familial medullary thyroid carcinoma, 268 linkage for MEN1 families without MEN1 gene mutation, analysis, 279 materials, 275 overview, 270 RET mutation detection with restriction digests, materials, 274 overview, polymerase, 275, 276, 279 restriction digestion and gel electrophoresis, 275, 277 types, 267, 268 Multiplex amplifiable probe hybridization (MAPH), data analysis, , 138 filter preparation, 129, 130, 138 fluorescence detection, 133, 134, 139 hybridization, 131, 138 materials, 128, 129, 138 polymerase, 131, 138, 139 posthybridization washes, 131, 138 prehybridization, 130, 138 principles, radioisotope detection, 132, 133, 139 Multiplex polymerase chain reaction, dystrophin-associated muscular dystrophy gene mutations, amplification, 327, 328 batch preparation, 327, 329, 335 carrier detection with quantitative PCR, , 329, 330, 336, 337 gel electrophoresis of products, 328, 329, 330, 336, 337 materials, 323, 326 prenatal diagnosis, 319 primers, 313, 314, 317, 318 optimization, 7

8 384 Index Muscular dystrophy, dystrophin-associated muscular dystrophy gene mutations, 311 dystrophin gene mutation detection, approaches, denaturing gradient gel electrophoresis, advantages, 314, 315 gel electrophoresis and visualization, 333, 336 gel preparation, , 336, 337 materials, 326 polymerase, 331, 335 primers, intragenic and flanking markers for Duchenne muscular dystrophy gene haplotyping and analysis, 324, 325, multiplex polymerase chain reaction, amplification, 327, 328 batch preparation, 327, 329, 335 carrier detection with quantitative PCR, , 329, 330, 336, 337 gel electrophoresis of products, 328, 329, 330, 336, 337 materials, 323, 326 prenatal diagnosis, 319 primers, 313, 314, 317, 318 MutS, mismatched DNA binding and mutation detection, 27 N Neurofibromatosis type 1, clinical features, 285 denaturing high-performance liquid chromatography, buffers, 295, 296 materials, 293 overview, 289, 290 polymerase and primers, sample table construction, 302 temperature and gradient conditions, 300, 301 fluorescence in situ hybridization, detection and visualization of probe signal, 295 hybridization, 294, 295 materials, 290, 292 nick translation, 293 overview, 289 probe denaturation, 294 probe preparation, 294 slide denaturation, 294 washes, 295 NF1 gene function and mutations, prenatal testing, 288 NF1, see Neurofibromatosis type 1 O OLA, see Oligonucleotide ligation assay Oligonucleotide ligation assay (OLA), cystic fibrosis diagnosis, DNA preparation, 239 electrophoresis, 240 evaluation, materials, 229 overview, 222, 225, 226 polymerase, 239 probing, 239

9 Index 385 P PCR, see Polymerase Polymerase (PCR), ARMS-PCR, see Amplification refractory mutation systempolymerase cystic fibrosis diagnosis, see Cystic fibrosis denaturing high-performance liquid chromatography, see Denaturing highperformance liquid chromatography familial adenomatous polyposis diagnosis, see Familial adenomatous polyposis fragile X disease diagnosis, see Fragile X disease gap-pcr, see Gap-polymerase gene dosage studies, Huntington s disease diagnosis, see Huntington s disease LightCycler system, 13 Meta-polymerase, 85 microsatellite analysis for linkage analysis, 11 minisequencing, 12 multiplex amplifiable probe hybridization, 131, 138, 139 multiplex PCR, see Multiplex polymerase optimization, see Polymerase optimization post-amplification manipulation, 22 protein truncation test, see Protein truncation test pyrosequencing, 14 quantitative fluorescence-pcr, see Quantitative fluorescence-polymerase spinal muscular atrophy analysis, see Spinal muscular atrophy TaqMan system, 12, 13 Polymerase optimization, annealing temperature, 5 buffers, 1, 2 cycle number, 5 denaturing temperature, 4 difficult templates, 6, 7 dntps, 2 elongation temperature and time, 5 enhancers, 6 final extension cycle, 5 hot start PCR, 5, 6 importance, 1 magnesium chloride, 2 melting temperature, 3, 4 multiplex PCR, 7 polymerases, 2, 3 primers, concentration, 2 design, 3, 4 GC content, 3 length, 3 reaction mix, 4 templates, 3 thermal cyclers, 5 Protein functional assays, mutation detection, 29 Protein truncation test (PTT), advantages, 68, 76 denaturing gel electrophoresis of proteins, 74, 75, 77, 78 familial adenomatous polyposis, gel electrophoresis, 255, 257, 263, 264 materials, 250, 251 polymerase, 255, 263 genomic DNA versus RNA as starting material, 67

10 386 Index limitations, 68, 76, 77 materials, 70 72, 77 polymerase, 73, 74, 78 principles, 29, 67 RNA reverse transcription, 67, 72, 73, 76 stages, 68 70, 77 tail incorporation during polymerase, 67, 68, 76 transcription/translation of amplification products, 74, 77 PTT, see Protein truncation test Q QF-PCR, see Quantitative fluorescence-polymerase Quality management, clinical diagnostic molecular testing, definition, 360 Deming circle, 359, 360 importance, 359 organization of laboratory, 360, 361 quality controls, daily practice, first-line controls, 362, 363 second-line controls, 362, 363 third-line controls, repeatability of tests, 362 reproducibility of tests, 362 standards, 361, 362 system for quality management, benefits, 364, 365 document control, 366 internal audits, 366, 467 Quantitative fluorescencepolymerase (QF-PCR), chromosome aneuploidy detection in fetus, amniotic fluid sample preparation, 149, 152 amplification product clean-up, 150, 151, 153 capillary electrophoresis, 151, 154 chorionic villus and tissue sample preparation, 149, 152 DNA preparation, 149, 150, 152, 153 Genotyper analysis, 151, 154 interpretation, 151, 152, 154, 155 materials, 147, 148 overview, 141 polymerase, 150, 153 primers, 146 principles, 141, 142 contamination avoidance, 149, 152 maternal cell contamination of fetal samples, 142, 144 mosaicism in prenatal samples, 144, 147 R Regulation, genetic testing, ethics, 371, 372 international documents, 370 laboratory validation, 373, 374 national documents, 370, 371 research transition to clinical testing, 374, 375 training and workload of staff, 373 Restriction fragment length polymorphism (RFLP), genotyping, 10 RET, see Multiple endocrine neoplasia RFLP, see Restriction fragment length polymorphism Ribonuclease mismatch cleavage, principles, 26

11 Index 387 S Sickle cell disease, see Hemoglobin variants Single-nucleotide polymorphisms (SNPs), fluorescence detection, 21 linkage analysis, 11 Single-strand conformational polymorphism (SSCP), dideoxyfingerprinting, 22, 23 familial adenomatous polyposis, gel electrophoresis, 259, 264 materials, 250, 254 polymerase, 258, 259, 264 silver staining of gel, 259, 260, 264 principles, 22, 23 SMA, see Spinal muscular atrophy SMN gene, see Spinal muscular atrophy SNPs, see Single-nucleotide polymorphisms Southern blot, fragile X disease diagnosis, see Fragile X disease Huntington s disease diagnosis, see Huntington s disease b-thalassemia diagnosis, 206, 207 Spinal muscular atrophy (SMA), carrier testing, de novo deletion detection, 346, 347 direct testing, 345, 346, 348, 349, , 355 linkage analysis, 347, 350, 353, 355 direct SMN1 deletion detection, materials, 348 overview, 344, 345 polymerase, 350, 353, 354 prenatal testing, 347, 348 SMN gene mutations, 343, 340 types and clinical features, 343, 344 SSCP, see Single-strand conformational polymorphism T Thalassemias, β-thalassemia diagnosis, amplification refractory mutation system-pcr, 209 denaturing gradient gel electrophoresis, 207, 209 gap-pcr, , 215 gene mutations, restriction enzyme digestion, 214, 215 Southern blot, 206, 207 β-thalassemia diagnosis, Transgenomic WAVE DNA Fragment Analysis System, see Denaturing highperformance liquid chromatography