Index

a-amylase 22

ABI PRISM*® genetic analyzers 55, 116 ABO blood grouping system 2 absorption-inhibition ABO typing 2 adventitious hits 99 agarose gels 33-4, 35 allele ceiling principle 79-80, 83 drop-out 68, 69, 73 specific hybridization 119 allele frequency databases 78-83 allele ceiling principle 79-80, 83 Balding size bias correction 80, 81, 83 profile ceiling principle 82, 83 selection 83

subpopulations 80-2, 83 allelic ladders 58-61 amelogenin locus 53 3-aminophthalhydrazide 19-20 AMP-FLPs see amplified fragment length polymorphisms AmpF/STR® see Identifiler®; PowerPlex® 16

system; SGM Plus®® amplified fragment length polymorphisms

Balding size bias correction 80, 81, 83 Bayesian approach evaluation process 92-3, 95 kinship testing 109-11 biological samples 17-25 collection 3, 19, 20-1 contamination 19, 20 identification and characterization 19-20 presumptive testing 21-3 reference samples 23 sexual and physical assault 21 sources 17-19 storage 23-4 blood biological samples 3, 17-20, 21, 23-4 DNA quantification 32

grouping 2, 121

polymerase chain reaction 44, 46 bones 31-2, 72-3, 129 buccal swabs 23, 46

Cambridge Reference Sequence (CRS) 129 capillary electrophoresis (CE) 54-5, 57-8, 118 CE see capillary electrophoresis Chelex® 100 resin 27-9, 31, 34, 45 chi square tests 78 chromosomal organization 7-9 CODIS see Combined DNA Index System cold cases 101-2

Combined DNA Index System (CODIS) 52,

102-3 contamination biological samples 19, 20 cold cases 102

polymerase chain reaction 45-8 Crick, F. 7

CRS see Cambridge Reference Sequence

D-loop 126 DAPI 33, 35

ddNTPs see dideoxynucleotide triphosphates defendant's fallacy 94 degraded DNA 71-3, 101-2 deionized formamide 55 deoxynucleotide triphosphates (dNTPs) 8, 42, 116

deoxyribonucleic acid (DNA) extraction 27-32

challenging samples 30-2 Chelex®® 100 resin 27-9, 31, 34, 45 FTA®R paper 29-30 general principles 27-30 hair shafts 31 hard tissues 31-2 phenol-chloroform-based 29, 31 seminal fluid 30

silica based methods 28-9, 31, 36 quantification 32-6 agarose gels 33-4, 35

deoxyribonucleic acid (DNA) (Contd.) fluorescence spectrophotometry 35 hybridization 35

real-time polymerase chain reaction 35-6 ultraviolet spectrophotometry 34 replication 40 structure 7-15

chromosomal organization 7-9 coding and regulatory sequence 9-10 extragenic DNA 10 forensic genetics 11 genetic diversity 11 human genome 9-10, 11 short tandem repeats 13, 14 single nucleotide polymorphisms 13-14 tandem repeats 10, 12-13, 14 transposons 10 deoxyribose 8

4',6-diamidino-2-phenylindole 33, 35 dideoxynucleotide triphosphates (ddNTPs)

116-17 dinucleotide repeats 66 dithiothreitol (DTT) 30 DNA see deoxyribonucleic acid DNA IQtm Isolation System 36 dNTPs see deoxynucleotide triphosphates DTT see dithiothreitol

EDNAP see European DNA Profiling Group epithelial cells 17-19, 22, 33 ethidium bromide 33, 35 European DNA Profiling Group (EDNAP) 103 evaluation process 87-95 Bayesian approach 92-3, 95 defendant's fallacy 94 frequentist approach 88-9, 94-5 hierarchies of propositions 87-93 likelihood ratios 89-92, 95 prosecutor's fallacy 91, 93-5 exact tests 78 extragenic DNA 10

familial searching 100-1 flanking DNA 12 fluorescence labelling 54 spectrophotometry 35 formamide 55

frequentist approach 88-9, 94-5 FTA® paper 23-4, 29-30

GeneMapper ID 56, 59, 67 GeneScan® 56, 58, 67 genetic diversity 11

Genotyper® 59-60 geographical ancestry 120 clustering 132

hair follicles 17-19, 23 shafts 31 haplotype frequencies 130-1, 132 Hardy-Weinberg equilibrium (HWE) 75-83

allele frequency databases 78-83 deviations 76-8

infinitely large populations 76-7 migration effects 77 mutations 77 natural selection 77 random mating 77 statistical tests 77-8 heteroplasmy 127-9 heterozygosity 138 hierarchies of propositions 87-93 Bayesian approach 92-3, 95 frequentist approach 88-9, 94-5 likelihood ratios 89-92, 95 homoplasmy 127-9 homozygosity 78, 138 human genome 9-10, 11 karyotype 9 remains 1, 111-12 lineage markers 129 short tandem repeats 71-3 HWE see Hardy-Weinberg equilibrium hybridization-based methods 35 hypervariable regions 126-7, 129

Identifiler® 105, 120, 52, 61

inbreeding 81-2

infinitely large populations 76-7

inhibition of PCR 44-5

internal-lane size standards 56-8

Interpol Standard Set of Loci (ISSOL) 103

interspersed repeats 10

ISSOL see Interpol Standard Set of Loci

Jefferson, Thomas 131 Jeffreys, Alec 2-3

Kastle-Meyer (KM) 21 kinship testing 1, 105-14

absorption-inhibition ABO typing 2 Bayesian approach 109-11 complex relationships 111

human remains 111-12 likelihood ratios 105, 109-10 lineage markers 131 paternity testing 105-11 Punnett squares 106-7 subpopulations 111 KM see Kastle-Meyer

Landsteiner, Karl 2

Lattes, Leone 2

LCN see low copy number leuco-malachite green (LMG) 21

likelihood ratios evaluation process 89-92, 95 kinship testing 105, 109-10 short tandem repeats 78 statements 91 lineage markers 125-35 applications 127-30, 131-2 copy number 125 hypervariable regions 126-7, 129 inheritance 125 interpretation 129-30, 132 mitochondrial genome 125-30 polymorphisms 126, 130-2 Y chromosome 125, 130-2 LINEs see long interspersed elements LMG see leuco-malachite green local Southern method 57-8 locus drop-out 68, 69 long interspersed elements (LINEs) 10 long terminal repeats (LTRs) 10 low copy number (LCN) PCR contamination 44 degraded DNA 101-2 short tandem repeats 68-70, 73 LTRs see long terminal repeats luminol 19-20

match probability 137

statements 88-9 migration effects 77

mitochondrial genome 111, 117, 125-30

mixed profiles 70-1

molecular autopsy 121

Mullis, Kary 3-4

multi-locus exact tests 78

multiplex development 51-3

muscle tissue 72-3

mutations 77

national DNA databases 97-104 adventitious hits 99 cross-border 103

United Kingdom 97-102 United States 102-3 natural selection 77 non-template-dependence 66-7

off-ladder peaks 58-9, 60 overloaded profiles 68

PACE see Police and Criminal Evidence Act paternity index 106, 110-11 paternity testing 1, 105-11

absorption-inhibition ABO typing 2 lineage markers 131 PCR see polymerase chain reaction peak balance 69, 70 personal objects 112, 129 phenol-chloroform-based DNA extraction 29, 31

phosphodiester bonds 8 PicoGreen® 35 Pitchfork, Colin 1

Police and Criminal Evidence Act (PACE) 98 polymerase chain reaction (PCR) 39-50 components 40-2 contamination 45-8 DNA extraction 30 DNA quantification 32, 35-6 DNA replication 40 historical material 3-4, 39-40 hybridization-based methods 35 inhibition 44-5 laboratory set-up 46-8 lineage markers 126 low copy number 44, 68-70, 73, 101-2 post-PCR 47-8 pre-PCR 46-7 primers 41-2 procedure 42-4 reagents and buffers 42 real-time 35-6 sensitivity 45-6 Taq polymerase 40-1, 42-5 template DNA 40 see also short tandem repeats polymorphic information content 138 population genetics see Hardy-Weinberg equilibrium positive paternity statements 109 post-PCR 47-8 power of discrimination 137 power of exclusion 137-8 PowerPlex®R 16 system kinship testing 105, 109, 120 short tandem repeats 52, 61

PowerPlex® Y system 131 pre-PCR 46-7

presentation of evidence see evaluation process presumptive testing 21-3 primers 41-2, 53

extension 36, 118-19 prior odds 92, 110-11 probe hybridization 3 profile ceiling principle 82, 83 frequencies 79, 88, 90 Profiler Plus® 72, 106 prosecutor's fallacy 91, 93-5 prostate specific antigen (PSA) 22 protein markers 2 proteinase K 30, 31 PSA see prostate specific antigen pull-up 67-8

Punnett squares 75-6, 106-7

Quadraplex (QUAD) 52 Quantiblot® 35

random match probabilities 88-9 random mating 77 re-offenders 97

real-time polymerase chain reaction (RT-PCR) 35-6

reference samples 1-2, 23 regulatory sequence 9-10 repetitive DNA 10 restriction digestion 116 enzymes 2-3 Romanov royal family 128 RT-PCR see real-time polymerase chain reaction saliva 17-19, 22

salting-out procedure 28-9, 31, 36 samples see biological samples sampling bias 80, 81, 83 Sanger sequencing 2, 116-17, 118, 126 seminal fluid biological samples 3, 17-19, 21-2 DNA extraction 30 DNA quantification 32-3 sex chromosomes see X chromosome; Y

chromosome SGM 52, 99 SGM Plus® evaluation process 88-9 national DNA databases 99, 101 short tandem repeats 52, 59, 61, 70 short interspersed elements (SINEs) 10

short tandem repeats (STRs) 4, 51-85 allele frequency databases 78-83 allelic ladders 58-61 corrections 78-83 degraded DNA 71-3 detection of polymorphisms 54-5 DNA structure 13, 14 drop-out 68, 69, 73 evaluation process 92 Hardy-Weinberg equilibrium 75-83 internal-lane size standards 56-8 interpretation 56-61, 65-74 kinship testing 111 lineage markers 130-2 low copy number DNA 68-70, 73 mixed profiles 70-1 multiplex development 51-3 national DNA databases 99 overloaded profiles 68 peak balance 69, 70 population genetics 75-83 primers 53 pull-up 67-8

single nucleotide polymorphisms 120-1 split peaks 65-7 standardization 52 structure 51 stutter peaks 65, 69 template DNA 68 silica based DNA extraction 28-9, 31, 36 silver staining 54

SINEs see short interspersed elements single nucleotide polymorphisms (SNPs) 115-23

allele specific hybridization 119 detection 115-19 DNA structure 13-14 forensic applications 117-20 forensic identification 119-20 geographical ancestry 120 historical material 4 kinship testing 111 lineage markers 126, 130 occurrence and structure 115 primer extension 118-19 Sanger sequencing 116-17, 118, 126 short tandem repeats 120-1 SNaPshot™ 118

SNPs see single nucleotide polymorphisms Southern blotting 2-3, 57-8 split peaks 65-7 statements likelihood ratios 91 match probability 88-9

positive paternity 109 uniqueness 89 storage of biological samples 23-4 STRs see short tandem repeats stutter peaks 65, 69 subpopulations allele frequency databases 80-2, 83 kinship testing 111 SYBR® Green 36

tandem repeats 10, 12-13, 14

see also short tandem repeats; variable number tandem repeats Taq polymerase polymerase chain reaction 36, 40-1, 42-5

short tandem repeats 65-7 single nucleotide polymorphisms 117, 118-19 TaqMan® system 36 template DNA 40, 68 terminal transferase 66-7 tetranucleotide repeats 66 theta values 81-2, 83 transposed conditional 91, 93-5

ultraviolet spectrophotometry 34 uniqueness statements 89 United Kingdom NDNAD 97-102

cold cases 101-2 entry criteria 98-9 familial searching 100-1 legislation 98 operation 99-100 rationale 97 technology 99

variable number tandem repeats (VTNRs) 2-3, 4, 12-13 evaluation process 92 lineage markers 130 national DNA databases 99 polymerase chain reaction 39

verbal scales 91-2

VTNRs see variable number tandem repeats

Yfiler® 131

X chromosome amelogenin locus 53 structure 9

Y chromosome amelogenin locus 53 lineage markers 125, 130-2 structure 9

Plate 3.1 Blood is the most common form of biological material that is recovered from crime scenes. (a) Large volumes of blood can be collected using a swab, if the blood is liquid then a syringe or pipette can be used (picture provided by Allan Scott, University of Central Lancashire) (b) Blood on clothing is normally collected by swabbing, or cutting out the stain (picture provided by Elizabeth Wilson)

Plate 6.4 During electrophoresis an argon laser is shone through the window in the capillary. As the labelled PCR products migrate through the gel towards the anode they are separated based on their size. When the laser hits the fluorescent label on the PCR products, the lable is excited and emits fluorescent light that passes though a filter to remove any background noise, and then on to a charged coupled device camera that detects the wavelength of the light and sends the information to a computer where software records the profile

4800, 4000 3200.

Plate 6.5 The application of a matrix file, using the GeneScan® or GeneMapper™ ID software removes the spectral overlap from the raw data (a) to produce peaks within the profile that are composed of only one colour (b)

1800, 1600 1400 1200, 1000 800 600 400 200 0

80 120 160 200 240 280 320 360 400 440 480

100 150 200 300

139 160 250

340 350 400 450 500

K:i 60 90 120 150 180 210 240 270 300 330 360 390 420 450 480 510 540 570 14001200

1000 800 600 400 200 0

225 275 250

500 600

Plate 6.6 Internal-lane size standards are used to size the PCR products precisely. Two commonly used internal-lane size standards are (a) the GeneScan®-500 (Applied Biosystems) and (b) the ILS600 (Promega)

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