Manual of Histological Techniques Santosh Kumar Mondal
INDEX
ABCDEFGHIJKLMNOPQRSTUVWXYZ
Page numbers followed by ‘b’ box; ‘f’ figure; ‘fc’ flowchart; and ‘t’ indicate table respectively.
A
Abbott molecule Inc. 169
Abdominal fat aspiration 93
Accentuators and accelerators 31
Acetic acid 3, 82, 83
Acetic acid-zinc-formalin 176
Acetone 6, 49
Acetylcholinesterase 104
histochemical method 104
reagent 104
tissue preparation 104
Acid decalcifier 85
neutralization of 82
Acid fast bacilli 138
Acid hydrolysis 56, 57
Acid mucins 45
Acid phosphatase 102
Acidic mucin 39
Acid-zinc-formalin 176
Acinar cell carcinoma 194
Acquired ciliary abnormalities 136
Acquired glomerular basement membrane 135
Acrylic plastics, application of 131
Acrylic resin 130
sectioning cutting of 132
staining of 132
Actin 193
Adapters 216
Adenocarcinoma 194
Adenosine triphosphatase 102, 103
histochemical method 103
Adenovirus 166
Adhesive, histologic sections 111
Adrenal cortical tumors 194
Adsorption 30
Agar 8
Agar method 125
Agyrophil
staining 105
substances 105
Air inlet 7f
Alcian blue 40, 41, 45, 179
PAS technique 45
stains acid mucins 44f
Alcohol 3, 47
Alcohol, containing fixative 111
Alcohol fixative 125
advantages 3
disadvantages of 3t
hemosiderin 79
Aldehydes 1
Alizarin Red S method for calcium 78
Alkaline Congo red technique 94
Alkaline phosphatase 102, 193, 154
Alkaline salt solution 94
Alpha amylase 193
Alpha-fetoprotein 193
Alport's syndrome 136
Alum hematoxylin 32
staining, principle of 32
with eosin 34
Aluminium ammonium sulfate 32
Aluminium hydroxide 45
Aluminium potash sulfate 32
Alveolar macrophages 62
Amido black technique 70
Amino acid 38
histochemical methods 54
Aminopropyltriethoxysilane 15, 113
Ammoniacal silver solution 90
Amorphous element 62
compositions 62
functions 63
staining 63
Amplification Refractory Mutation System 161
Amplitude 147
and wavelength 147f
Amputated specimens 81
Amylase 42
Amyloid 93, 94
fibrils 135
staining for 93
Amyloidosis 135
Anaplastic lymphoma kinase 193
Anderson's disease 53
Androgen receptor 194
Angiosarcoma 25, 116
Annotation 210
Anomalies, congenital 156
Anorexia nervosa 180
Antibody 107
binding 107, 122
problem, primary 122
Antigen 107
Antigen-antibody complex, detection of 56
Antigen, factor VIII related 195
Antigen masking 122
Antigen retrieval methods 111, 203t
Antigenic epitopes 113
Anti-immunoglobulin 154
Antinuclear antibody 141
Apathy's medium 17
Apoptosis 200
Appendix 43f
Aqueous acetic acid 75, 83
Aqueous mounting media 17
Aqueous nitric acid 83
Aqueous potassium ferrocyanide 74
Argentaffin 77
Argentaffin staining 105
Arginase-1 193
Array 210
block 210
comparative genomic hybridization 163, 219
Artefactual pigments 70
Asbestos 73
Aspergillus oryzae 42
Aspergillus species 162
Atrophy 137
Autoclave method 113
Automated paraffin embedding 8f
Automated tissue processing 9, 9f
Automatic hones 13
Automatic knife sharpeners 14
Automatic staining 37
Automatic tissue processing 10f
for cell blocks 128
Automatic tissue, stainer machine 37f
Automation in immunohistochemistry 120
Automation technique 9
Autonomic nervous system 88
Autopsy specimen 2
Avidin-Biotin method 110, 110f
advantages 110
disadvantages 110
three-step technique 110
Axon 88
Axonal degeneration 137
Azo dye method 101
B
B 72.3 193
Bacteria, detection of 161
Bacterial artificial chromosome 205
Baker's acid hematin method 52
Barcode, use of 231
Basal cell carcinoma 195
Basal lamina 137
Basophilia 57
Benzidine-nitroprusside method 70
Benzoyl peroxide 131
BerEP4 193
Best carmine method 46
Beta catenin 193
Beta-actin gene, 200 BP fragment of 179
Bielschowsky's method 90, 91
Bile duct adenoma 20f
Bile pigments 72, 76
Binocular
light microscope 148
microscope, parts of 148f
Bioinformatics 214f
Biopsy
adequacy of 181
of gingiva 93
of kidney 93
of rectum 93
small
for urgent work 9
rapid processing for 9
short processing 9
Biotin 110
Biphasic connective tumors 195t
Biphasic tumor 25
Birefringence 49, 93
Bloated cell morphology 24
Blocking out molds 15
types of 15
Blood cells 154
Body, abnormal conditions of 40t
Bone 86
Bone and decalcification 80
Bone cells 80
Bone, constituents of 80
Bone cutting 81
Bone, decalcification solutions 81, 82t
Bone, histology 81
Bone marrow 174
aspirates 174, 176, 178t
biopsy specimens 176t
necrosis clinical conditions associated 180b
reticulin, grading of 179t
specimens, storage of 184
storage iron, grading of 178, 178t
trephine biopsy 174
indication for 178b
indications of 174
turn around time for 80, 184t
Bone specimen
fixatives for 81
replacement surgery 81
size of 81
Bone techniques 81
Bone tumors, diagnosis of 81
Bone, types of 80
Borax ferricyanide 52
Borax solution 78
Bouin's, components of 83
Bouin's fluid 4, 57
advantages 4t
disadvantages of 4
Bowman's space 106f
Brasil's alcoholic picro-formol fixative 5
Breast carcinoma 116, 118t, 119f, 163, 194
Breast imaging reporting data system 189
Breast lesions
nonpalpable 188
palpable 188
Breast tissue 23t
Brunner's gland of duodenum 39
Buffer solutions, preparation of 114, 234
Buffered formic acid 84
Buffered neutral formalin 176
Buffers 234
citrate buffer 234
phosphate buffer 234
phosphate citrate buffer 235
tris-HCL buffer 235
Burkitt's lymphoma 117f, 163
immunophenotype 201f
tumor cells of 117f
Burstone's for alkaline phosphatase 101
C
CA 19–9 193
CA-125 193
Cadherins, types of 193
Calcified thyroid nodules 191
Calcium 73
Calcium chloride 86
Calcium, deposits 78
Calcium oxalate test 85
Calcium stains 73
Caldesmon 195
Calponin 195
Calretinin 195
Cancellous bone 80
Candida albicans 182
Capsular invasion 24
Carazzi's hematoxylin 32–34
Carbohydrates 38
classification of 38
types of 39, 40f, 41t
Carbol fuchsin 96, 98
Carbon 73
Carbon dioxide method 85
Carbon monoxide 144
Carbowax 8
advantages 8
disadvantages of 8t
Carboxyl group 39
Carboxylate 39
nonsulfated uronic acid mucin 39
sialomucin 39
Carcinoembryonic antigen 195
Carcinoma 116
Carmine 31
stock solution 46
working solution 46
Carnoy's fixative 3, 83
Cassettes 15f
Caudal type homeobox 194
Caveolin-1 195
CD10 195
CD117 (c-KIT) 195
CD31 195
CD34 195
CD99 (MIC2) 195
CDX2 195
Celestine blue solution 65
Cell block 123, 124, 126
methods for 124
preparation of 123
use of 123, 124, 125f
Cell body 88
Cell membrane 202
Cell membrane-cytoplasm 115
Cellienttm automated method 125
Celloidin 8, 66
Cells, type of 61
Cellular
compartment 115
component 61
Cellulose 40
Central nervous system 88
Centrifugation and fixation 124
Centromeric probes 155
Cerebrosides 38, 47, 48
Cervical cancers 200
Channel 210
Chatter 22f, 26
Chelating agents 82, 84, 87
Chemical test 85
Chip 208
Chitin 40
Chloroacetate esterase 179
Chloroform 3, 7
Cholangiocarcinoma 194
Cholesterol 48
Chromaffin granules 77
Chromic acids 48
Chromic oxide 74
removal of 74
Chromidial substances 89
Chromogen substrates, different 114
Chromogenic in situ hybridization 155, 171fc
Chromogranin 195, 202
Chromogranin A 204
Chromosomal
abnormalities in tumors 170f
analysis, methods of 214f
aneusomies 170
disorders 170
translocation 173f
Chromosome 18 pair 172
Chromosome microdissection 220
Chromosome painting 218
Chymotrypsin method 112
Cirrhosis of liver 146f
Cirrhotic nodules of liver 67f
Citrate buffer 122
Citrus fruit oils 7
CK20, use for different carcinoma 117
CK7, use for different carcinoma 117
CK7-/CK20+ carcinoma 202fc
Clear cell carcinoma 194
Clearing 6
Clots 123
Coccus cacti 31
Cocktail probe 166
Coherent rays 147
Cold acetone 111
Cole's hematoxylin 32
Collagen
common types of 63t
fibers 63
in trephine biopsy 179t
type of 63
College of American Pathologist 231, 232t
Colloid carcinoma 42
Colloidal metal label 108
Colon, adenocarcinoma 41f
Color fixation fluid (aegerter) 144
Colorectal carcinoma 194
Columbic attractions 29
Compact bone 80
Comparative genomic hybridization 208f
Comparative genomic hybridization array 211
disadvantage 211
use of 211
Congo red 93, 94
solution 95
stain 94f, 179
Conjugate foci 147
Connective tissue 64
mucin 39
staining 61
Copper 73
and copper associated protein 78
stains 73
Core biopsy
definition 185
gauge of needle 186
number of biopsy core 186
pathology of breast lesions 187t
post procedure complications 186
Core needle biopsy 185
benefits 189t
drawbacks of 189t
special types of 188
Cori's disease 53
Corrective action and preventive action 231
Cortical bone 80
Covalent bonding 29
Cresyl fast violet stain 89
Cresyl violet
differentiator 90
solution 90
Critical values 231
Cross-linking agents 4
Cryoglobulins 136
Cryostat 18, 19
Cryostat mounting media 20
Cryostat object disk 22
Cryostat sections
advantage of 18
procedure 20, 21
staining of 23
Cryptococcus neoformans 182
Crystal violet
solution 95
staining 24
Crystals 136
Cutting hard tissues 15
Cutting sections 14
Cyclohexene dioxide 130
Cyclooxygenase 2 195
Cystic cavities 143
Cystine crystals in cystinosis 136
Cytochrome oxidase 103
Cytogenetic G-banded karyotype 172f
Cytokeratins 195
antigen 118f
positive for 118f
Cytologic atypia 20f
Cytological preparations 111
Cytomegalovirus 166, 182
Cytopathology 123
Cytoplasm 202
Cytoplasmic
characteristics 129
structures 96
D
Daily quality check in staining 229
Dako envision 114
Dako's liquid permanent red 116
Decalcification 57, 82, 83
process, factors of 86
technique of 82
test for 85
Decalcifying agent
advantages 87
choice of 82
classification of 82
disadvantages of 87
volume of 86
Dehydrate slides 171
Dehydrating fluid 6
Dendrites 88
Dendrons 88
Deoxyribose 56
Deparaffinize 98
histologic sections 43
Dermal papilla, tips of 141f
Dermatitis herpetiformis 141f
Dermatomyositis 137
Desmin 195
Desmoplastic small round cell tumor 119
Diabetic nephropathy 136
Diaminobenzidine tetrahydrochloride 103
Diamond knives 13
Diastase 42, 44
Diazonium salt 102
Diazotization-coupling method for tyrosine 55
Dibutyl phthalate 131
Diethyl dioxide 6
Diffuse large B-cell lymphoma 118f
Dioxane 6
Diploid cell 153
Diploid nucleus 172f
Diseases of obscure nature 134, 137
Disposable blades 12
Distilled water 4
Disulfides 55
dMMR genes, loss of function 202fc
DNA 56, 205, 222
acridine orange stain 60
analysis 152
linkage analysis 153
phylogenic analysis of 163
restriction fragment length polymorphisms 153
slot and dot-blots 152
southern blot 152
cloning 162
counterstain 169
extracted from sample 154f
fragments of 154
methylation 151
microarray 163f, 163, 205
paternity testing, used for 162
polymerase 157
probes, types of 155
resequencing 212
restriction enzyme cleavage of 154f
segment of 151, 162
sequencing 151, 162, 213
type of 215
techniques specific 57
Drying 26
Dubin-Johnson pigments 70, 72
Ductal carcinoma 188f
Dust cell 62
Dye and tissues 28
Dyes, classification of 31
Dynein 137
E
Eager's method for degenerating axons 91
E-cadherin 193
Ehrlich's alum hematoxylin 32
Elastic fibers 63, 64, 66
Elastic tissues 69
Elastin and elastic fiber-microfibrillar protein 63
Electrolytic ionization 82
Electron microscope, analytical 134, 136f
Electron microscopy 129, 134
fixation of tissues 5
limitations of 137
types of 134
Electrophoretic method 82, 87
of decalcification 84
Embedding 7
and paraffin sections 128
medium 42
Endogenous peroxidase 113
activity 122f
Endogenous pigments 70
Endometrial carcinoma 42
Endometrium 194
in proliferative stage 160f
Endoneural macrophages 137
Endothelial cell 115
damage to 136
Enzyme-antienzyme complex 108
Enzyme deficiency 53
Enzyme digestion 112
method for nucleic acids 59
Enzyme disorders, congenital 72
Enzyme extraction of
DNA 59
RNA 60
Enzyme histochemistry 100, 105, 131
applications of 102
methods 56
principles of 100
techniques 102
Enzyme label 108
Enzyme-labile 39
Enzyme resistant 39
Enzyme, types of 101
Enzymes 100, 138
use of 42
Eosin
stain 32
uses of 37
Epidermal basement membrane zone 140
Epithelial cell 136
marker for detecting 115
Epithelial membrane antigen 195
Epithelial mucin 39
Epitopes 107
Epoxide group anhydrides 130
Epoxy plastics, disadvantages of 130
Epoxy resins 130
Epstein-Barr nuclear antigen 2 182
Epstein-Barr virus 162, 166, 179, 182
ERG loci 172f
Esters 48
Estrogen receptor 190f
Ethanol 5
Ethanol rinse method 125
Ethyl alcohol 6
Ethylenediaminetetraacetic acid 82–84, 176
ETOH 23
Eumycetoma 36f, 106f
Evans and Krajjan fluid 84
Ewing's sarcoma 42, 116, 119, 170, 196
Exhaust outlet 7
Exogenous pigments 70
F
Fabry's disease 53, 136
Fanconi syndrome 180
Farrant's medium 17
Fast technology analysis 189
Fat cells 62
Fat soluble dyes, demonstration with 48
Fatty acids 47, 48
Fatty tissue 23f
problematic 26
Ferric iron 73, 74
Ferrous and ferric iron 75
Ferrous iron 75
Feulgen nucleal reaction for DNA 57
Fibrin 64
Fibrinoid materials 64
Fibroblasts 61
functions 61
Fibrous element 63
Fibrous proteins 54
Fifty percent ethanol rinse method 124
Filter hybridization 152
Final reaction product 101
Fine needle aspiration 189
Fine needle aspiration cytology 185, 192
benefits 189t, 191t
drawbacks of 189t
limitations of 191t
Fixation
principles of 143
secondary 5
Fixative 3
choice of 42
classification of 1
concentration of 5
for different cellular component 5t
for mucins 40
formaldehyde containing 2
physical agents 4
routine formalin 2
time in minutes 57
Fixed paraffin embedded 111
Fixed tissue 19
FLI-1 195
Floating out sections 14
Fluorescence 138
metachromasia 60
resonance energy transfer 216
Fluorescent in situ hybridization 164, 167, 171fc, 176, 189
analysis 173f
basic steps of 167
diagnostic tests 170t
labeling in 167
principle of 168f
probes 167
procedures 168
single day protocol 171
symbol or abbreviation 168t
Fluorescent label 108
Fluorescent methods 56
Fluorescent microscope 139
Fluorescent stains 93
Fluorescent technique 101
Fluorochromes 108
commonly used 138
Fluoroscein isothiocyanate 138
Focal segmental glomerulosclerosis 136
Foil clamping system 133
Follicular neoplasm 191
Forbe's disease 53
Forensic applications 162
Formaldehyde 2, 2t
Formalin 48, 111, 121
Formalin fixative 125
Formalin fixed
hemosiderin 79
paraffin embedded 167, 229
Formalin nitric acid 83
Formalin pigment, removal of 3, 74
Formalin-fixed paraffin-embedded 151
Formalin-nitric acid 82, 87
Formic acid 48, 82–84
Formol-acetic acid alcohol 23
Fouchet technique
for bile pigments 76
modified 72
Fouchet's solution 76
Free nucleotides 157
Freeze drying 26
use of 27
Freezing artifacts 24
technical problems 24
Frequency 147
Fresh cryostat sections 103
Frozen section 20f, 85, 110, 119
accuracy of 24
advantage of 18
and smear 120
basic principle of 18
consultation 18
contraindications of 25
disadvantages of 23
errors during interpretations 25
indications of 24
instrument 20f
problems and solutions 25
procedure-steps by steps 22
technique 21f
Frozen tissue
and paraffin-embedded tissue, differences 19t
sections, procedure for 139
Fuelgen reaction 57
Fungal hyphae 36f
Fungal mycetoma 36f, 106f
Fungal pathogens, differential diagnosis of 182
Fungal rRNA genes 162
Fungi, detection of 162
Fusion of green 167
G
Galectin 196
Gallocyanin-chrome alum technique 58, 59
Gangliolipidosis 53
Ganglion cells 104
Gangliosidosis 53
Gastrointestinal
carcinoma 42
stromal tumor 116
GATA3 196
GATA4 196
Gaucher's disease 53
Gelatin 8
embedding 146
in floating out bath 15
Gemelin technique for bile pigments 76
Gene
amplifications 170
detection of 156
chip’ 205
expression 162
microarray 208
profile 163
in nucleus 168f
Genes
coding sequences of 163
noncoding regions of 163
Genetic
diseases 63, 134, 136
fingerprinting 162
mapping, useful for 162
mutations 238
testing 161
Genome-wide analyses 218
Genomic probe, requirement for 165t
Germ cell tumor 116, 194
Giemsa
stain for parasites 98
stock solution of 98
Gill's hematoxylin 32
Gimenez method for Helicobacter pylori 97
Glacial acetic acid 3, 4, 37
Glass knives 12
Glees and Marsland's modification technique 90
Glial fibrillary acidic protein 196
Glomerular
basement membrane 141
capillaries 106f
Glomerulonephritis 141
Glucose-6-phosphatase 53
Glutaraldehyde 2, 2f
Glycerine jelly 17
Glycerol 15, 130
Glycoconjugates 38
Glycogen 42
extraction by enzymes 44
storage disease 53f, 136
Glycol methacrylate
embedding 132
processing 132
Glycolipids 38
Glypican-3 196
Gmelin technique 72
Golgi apparatus 38
Gomori's
aldehyde Fuchsin method 66
metal precipitate technique 101
silver impregnation method 66
silver solution, preparation of 66
Gooding and Stewart's decalcification fluid 177
Gordon and Sweet's silver impregnation method 67
Gouge 26
Gram's iodine, modified 95
Gram-negative organism 96, 106f
Gram-Twort stain 95
Granulomas in bone marrow, causes of 180t
Granulomatous disease 174
Granulosa cell tumor 116
Grocott's
silver methenamine stain 105f
methenamine silver stain 179, 182
Gum sucrose 20
H
H&E staining method 133
Hamazaki-Wesenberg bodies 70, 72
Hand sharpening 13
Hanta virus 136
Hapten-labeled antibody 108
Hard tissues, treatment of 85
Harris's alum hematoxylin 33
Harris's hematoxylin 31, 32
Heat 4, 64
Heat mediated antigen 111
Heat mediated antigen retrieval 112
first theory 112
second theory 112
third theory 112
Heat shock protein 161, 196
Heat-mediated antigen retrieval fluids 114
Heidenhain hematoxylin 32, 35
Helicobacter pylori 161
Helly's fluid 4, 176
Hematoxylin 31, 32
and eosin stain 64, 93, 117f, 176
and essin (H & E) section 72
nuclear stain 36
Heme component 70
Hemoglobin 70
Hemosiderin 70
Hemozoin pigment 74
Hepatitis C virus 162
Hepatocellular carcinoma 71, 200
Hepatocyte paraffin 1 196
Her2/neu (ERBB2) 196
Hereditary diffuse gastric mutation 194
Hereditary disease 236
Hereditary nephritis 136
Herpes simplex virus 166
Hers’ disease 53
Hirschsprung's disease 102
suspected 104
Histiocytes 61
Histochemical reactions 100
types of 101
Histochemical stains 100
common 105t
Histochemistry 100
Histoclear 7
Histological techniques 1
Histopathology
interlaboratory quality assessment 229
laboratory, quality control in 229fc
quality control 227, 228t
Histophysical methods 54
HMB-45 196
hMLH1 and hMSH2 199
Hodgkin lymphoma 116
case of 126
Hofbauer cells 62
Hollow
organs 146
viscera 143
Honing 13f
plate glass 13
procedure of 13
Horseradish peroxidase 116, 154
Hu 199
Hukill and Putt's method 70, 75
Human chorionic gonadotropin 199
Human genome project 205
Human herpes virus 8 182, 196
Human immunodeficiency virus 136, 162, 166, 182
Human papilloma virus 162, 166
Hyalinizing trabecular adenoma 191
Hyaluronic acid 44
Hybrid antibody 108
Hybridization 164, 171
mix solution 171
probes 162
system 169
Hydrochloric acid 74, 82, 83
Hydrogen bonding 29
Hydrogen ion concentration 5
Hydrogen peroxide 122f
Hydrolases 101
Hydrophobic bonding 28
Hypercellular marrow 183f
Hypo’ solution 91
Hypocellular bone marrow
clinical conditions associated with 180b
common causes 180b
I
Illumina sequencing 212f
advantages of 216
method 216
use 216
Illumination system 149
Immune complexes 135
Immunoenzyme 115
Immunofluorescence 115
direct and indirect 140f
granular 141f
pattern in different
glomerulonephritis 141t
skin diseases 140t
staining method, indirect 139
technique 138
diagnostic use of 140
direct 138, 139
technical aspects 138
Immunoglobulin in frozen sections 108
Immunohistochemical
markers 193
in hematolymphoid disorders 197t
organ specific 194t
pattern of staining 202t
specific tumors 196t
tumor type specific 194t
methods 56
different 108t
quality control measures for 202
stains in hematology 177t
techniques 107
Immunohistochemistry 107, 131, 176, 177, 182
concept of 56
diagnostic use of 193
different techniques 107
false-negative 116, 204
false-positive 116, 203
Her-2-neu/Cerb-2 118t
in surgical pathology 193
interpretation of 203
markers to diagnose specific tumor 116t
on frozen section 118
panels 178
protocol 121f
protocol in multiple staining 115f
staining protocol 114
technical aspects of 110
used for 83
Immunology and histology 107
Impregnation 7, 7f
In situ hybridization 83, 164, 179, 182
applications of 166
methods of
detection system 166
glass slides 165
laboratory 165
post-hybridization wash 166
probe labels 165
probes 165
protease digestion 165
tissue fixation 165
troubleshooting 166
mRNA 167
protocol 166
technique 164
Infectious disease 134, 136
applications 161
Inflammatory myopathy 137
Inhibin 199
Intercellular substance 62, 80
types of 80
Interphase
cytogenetics 155
scoring criteria 170
Intestinal parasite 162
Intramolecular rearrangement 102
Iodine staining 93
Ion exchange resins 84
Ionizing radiation 180
Iron 73
exchange resins 87
hematoxylin 32, 34, 64
stains 73
Isopropyl alcohol 5
J
Jamshidi needle 175, 175f
Joint Committee 232
Jone's methenamine silver 106f
Jone's technique 68
K
Kaiserling I solution 143
Kaposi's sarcoma 116
Kappa light chain diseases 135
Kardasewitch's method 3
Keratan sulfate 40
Keratin retain 99
Kidney biopsy 106f
Kidney disease 141
Kidney tissue, shattering in 21f
Kiton-Red-Almond green technique 70
Knife
angle in microtomy 12f
materials 12
sharpening 13, 14
Korean Society of Thyroid Radiology 190
Krabbe's disease 53, 137
L
Labeled antibody methods 108
Labeled, direct method 108, 108f
advantage 109
disadvantages 109
use 108
Labeled, indirect method 109, 109f
Laboratory Information System 231
Lactate dehydrogenase 103
Lamellar bone 80
Langerhans cell histiocytosis 116
Laser-assisted micro dissection 220
different types 220
Laser capture microdissection 220, 222f
Latent membrane protein 1 182
Lead, stains 73
Lecithins 48
Leishmania donovani 182
Leishmaniasis 162
Lendrum's technique 85, 95
Lepra bacilli in dermis 97f
Lepromatous leprosy 97f
Leuckhart's embedding iron 15
with paraffin 16f
without paraffin 16f
Leukocyte common antigen 117f
Ligase chain reaction 160, 225, 225f
advantages of 226
different steps in 224
Light microscope
component of 148
principle of 148f
Light source 149
daylight 149
electric light 149
sunlight 149
Light, wavelengths of 147
Limitations 24
Lipids 47
based polar and nonpolar groups 48
based solubility of 49fc
classification of 47, 48
compound lipid 47
derived lipid 47
simple lipid 47
demonstration of 48
fixation of 48
hydrophilic 47
identification of 48
Lovern's definition 47
neutral 48
solubility of 48
staining, control sections 49
Lipofuscins 72, 77
Liposarcoma 42
Liquefied nitrogen 19
Lithium carbonate solution 90
Littoral cell 62
Liver kidney microsomal antibody 141
Lobular
carcinoma 188f
neoplasia 191
Locus-specific probes 155
Long Ziehl-Neelsen method for lipofuscin 77
Loyez's hematoxylin 32
LR White
embedding 132
processing 132
Lung
biopsies 189
lesions 189
Luxol fast blue solution 90
Luxol fast blue-cresyl violet 89
Lyases 101
Lymph node 62, 71
Lymphoblastic
luekemia 119
lymphoma, acute 177
Lymphocyte 115
Lymphocytic leukemia, chronic 177
Lymphoid follicles 36f
Lymphoid tissue 62
Lymphoma 119
Lysosomes 72
M
Macrophages 61
functions 61
Madura foot 36f, 106f
Magnification System 149
Malarial pigment, removal of 74
Malignancies, different 42
Malignant cells 41f
Malignant round cell tumors 119t
Mallory and Parker's hematoxylin method 73, 78
Mallory's phosphotungstic acid hematoxylin 36
Mallory's PTAH 69
Manual processing 8
Mart-1 (Melan-A) 199
Martius scarlet blue 179
Masson trichrome stain 64
Masson-Fontana method 76, 105
Mast cell 62
functions 62
Mayer's Egg albumen-glycerol 15
Mayer's hematoxylin 31–33
May-Grunwald-Giemsa 176
Mc Ardle's disease 53
MDM2 amplification, detection of 156
Measles virus 166
Melanin pigments 72
Melanoma 194
Melanosis coli 70, 72
Meninges 88
Mercurial fixatives 176
Mercuric chloride 4, 176
Mercuric chloride fixative
advantages 4t
disadvantages of 4t
Mercuric fixatives 4, 111
Mercury
manometer 7
pigment, removal of 74
Merkel cell polyomavirus 202
Mesangial cell 62
Mesenchymal tumors 116
Mesothelioma 116, 194
Metabolic bone diseases, diagnosis of 81
Metabolic diseases 134, 136
Metachromasia 28, 40
with certain dyes 94
Metachromatic stain 28, 42, 93, 95
Metaphase nuclei 173f
Metaphase scoring criteria 170
Methanol 6
Methyl methacrylate 131
embedding 131
procedure 86
monomer 131
processing 131
Methyl violet 94
Methylation 212
Methylene blue 24
Methyl-green-pyronin method 58
MIB1 (Ki-67) 199
Micro fluidic sanger sequencing 215
Microarray 205
and NGS, comparison of 208t
clinical applications of 211
different
sequencing methods 207t
steps in 206f
glossary of 210
interpretation of 207f, 210
limitations of 212
principle 208
pros and cons of 210f
steps in 209
technique 208
types of 205
cellular microarray 206
DNA microarray 205
peptide microarrays 206
protein microarrays 205
transfection microarrays 206
Microdeletion syndrome 170
Microdissection 156, 156f, 220
technique, laser capture 156f
Microglia 62
Microorganisms, detection of 182
Microsatellite markers 218
Microscope 148
cleaning of lenses 150
maintenance 149
routine care 149
Microtome
knife, setting 11f
knives 11, 11f
monitoring 229
setting of 14
types of 10
base sledge microtome 10, 11
freezing microtome 10
rocking microtome 11
rotary microtome 10, 10f, 11f
sliding microtome 10, 11f
ultrathin microtome 10
vibrotome 10
Microtomy 6, 10
Microwave 4
antigen retrieval method 112
fixation 126
heating method 112
technique 82, 84
Mineralized bone 81
Minimal change disease 136, 170
Mitochondrial antibody 141
Mitochondrial myopathy 137
Mixed tumor 25
MOC-31 199
Molecular
beacon 159
diagnostic
changes 236
techniques 151
techniques, specimen requirements 151
genetic changes in different tumors 237
techniques, different 64t
Monoclonal gammopathy 177
Monomer-polymer embedding medium 86
Monorefringent 49
Mordants 31
Motorized microtome 129
Mounting
fluid, preservation in 144
in glass jars 146
in perspex jars 145
media
functions of 17
types of 17t
Mouse anti-human antibody 109
MUC 199
Mucicarmine stain 40, 46f
Mucin expression 42t
Mucinous carcinoma 41f, 194
Mucins 38, 40, 43
characteristics 39
Mucoepidermoid carcinoma 42
Mucopolysaccharidoses 53, 136
Mucoproteins and glycoproteins 38
Mucosal glands of appendix 36f
Multicolor FISH 218
Multiple ligation-dependent probe amplification 218, 219
Multiplex polymerase chain reaction
advantages of 222
process overview 224f
Murine double minute type 2 199
Museum fluid 146
Museum jars, preparation of 145
Museum technique 142
fixative for 143
Mutations in different cancers 161
Mycobacteria 161
Mycobacterium leprae 97
Mycobacterium tuberculosis 160f
Myelin 89
Myelodysplastic syndrome 170, 177, 180
Myeloid leukemia, acute 177
Myeloid leukemia, chronic 155
Myeloma, multiple 116
Myeloperoxidase 119
Myo D1 199
Myofilaments like actin 54
Myogenin 200
Myopathy with tubular aggregates 137
N
N-acetyl-o-acetyl sialomucin 44
NANOG 200
Naphthoic acid hydrazide reaction 58
Napsin A 200
Nathan alcohol formalin substitute 127
National Accreditation Board for hospitals 231
National Accreditation Board 231
National External Quality Assessment service 231
Natural dyes 31
N-cadherin 194
Needle biopsy 192
Needle tract seeding of tumor 187
Nemaline rod myopathy 137
Neoplasms 134, 136
Nerve fibers 104
Nerves and ganglia, detection of 104
Nervous system 88
Nested polymerase chain reaction 223
advantages of 223
different steps of 224f
Neural ceroid lipofuscinosis 136
Neuroendocrine tumor 116, 194
Neurofibrillary plaques 92
Neurofibrillary tangles 91
Neurogenic tumors 42
Neutral buffered formalin 81, 96, 176
Neutral lipids 47
Neutral mucin 39
Next-generation sequencing 216, 219
bioinformatics 216
data analysis 214f
different steps 213f
first generations 216
limitations of 217
pros and cons of 210t
second generation 216
third generation 216
uses of 217
Nicotinamide-adenine dinucleotide 103
Niemann-Pick disease 53
Nile blue sulfate method 52
Ninhydrin-Schiff method 55
Nissl substance 89
Nitric acid 82, 83, 87
Nocardia 97
Nodular lymphocyte predominant 116
Nonconformities 230
non-Hodgkin lymphoma 116
Nontumor pathology 212
Normal saline needle rinse method 125
Northern blotting, steps in 155f
Notch 200
Notch signaling controls cell proliferation 200
Notch, subtypes 200
NOTCH 3 200
NOTCH 4 200
NOTCH1 200
Nuclear 202
stain 64
Nuclei 45, 68
in frozen sections 5
Nucleic acid 56
sources of 151
staining 54, 56
Nucleoproteins, groups of 54
Nucleus 88, 136
Nucleus-cell membrane 115
O
OCT 3/4 200
Oil red O stain technique 51
Oleic acid 48
Oligodendroglia 88
Oligo probe, requirement for genomic 165t
Oligonucleotide
ligation 213
probes 165
Oligoprobes 165, 166
Operating temperature 19
Optimum cutting temperature 20, 139, 220
Optimum temperature 19
Organ transplantation 161
Orth's fluid 4
Osmium tetroxide 48
reduction of 48
Osmolality 5
Osteoblastic activity 180
Osteocalcin 200
Osteoclasts 62, 80
Osteogenic sarcoma 42
Osteonectin 200
Ovarian carcinoma 42
Ovarian cyst 146
Ovarian stroma 24
Overnight schedule 9
Oxidizing agent 2, 3
Oxidoreductase 101
P
Page's solochrome cyanine technique 90
Pancreas, ductal 194
Paneth cells in gastrointestinal tract 99
Papillary
lesions of breast 191
thyroid carcinoma 200
Paraffin 81
section cutting 14
wax 7, 8, 129
sectioning 16t
sections for IHC 113
Paraffin-embedded specimens 110
Paragon 130
Paraplast 8
Parotid mass 21f
Parvovirus B19 182
Pathological specimens, preservation of 142
PAX 200
PAX 2 194, 200
PAX 5 200
PAX 8 200
Penicillium marneffei 182
Pepsin method 112
Peracetic acid 52
Perenyi's fluid 82, 83, 85
Performic acid-alcian blue method 55
Performic acid-Schiff method 52
Perikaryon 88
Periodic acid solution 43
Periodic acid-Schiff 38, 41, 64, 71, 179, 182
positive materials 43f
positive substances 43
reaction 42
stain with diastase pretreatment 40
technique 43, 68, 72
Peripheral nerve biopsy 134, 137
Peripheral nervous system 88
Perls’ Prussian blue reaction 70, 74
composition of 74
fixative 74
positive control section 75
principle of technique 74
sections 74
staining method 75
Perls’ Prussian blue stain 73
Perls’ stain 131, 178
Peroxidase-antiperoxidase 108, 109
complex method 109
method 116
Peroxide technique 70
Perspex plastic jars 145
pH in histochemical methods 103
pH of staining solution 64
Phloxine solution 98
Phloxine-tartrazine technique 98
Phosphatides 38
Phosphatidylcholine 48
Phosphatidylethanolamine 48
Phospholipids 38, 47, 51
and cerebrosides 52
Phosphorylase 104
histochemical method 104
reagent 104
Phosphotungstic acid hematoxylin 54, 64, 68
Picric acid 82, 83
containing fixatives 111
fixatives 4
method 3
paraformaldehyde 111
Pigment and minerals 70
Pigment cells 62
functions 62
Pigment in histologic sections 71t
Plaques 91
Plasma cell 99, 115
functions 62
myeloma 183f
Plasma proteins 138
Plasma-thrombin method 125
Plastering technique 26
Plastics 130
basic techniques for embedding 133
embedded tissue 111
infiltration of 130
media, classification of 130
sectioning 132, 133
Pleural fluid 136
Pneumocystis carinii 162, 182
Pneumocystis jiroveci 162, 182
Podoplanin (D2-40) 200
Polarized light, examination 49
Poly glycol methacrylate 131
Polyacrylamide gels 152, 154
Polychromasia 30
Polychromatic stains 130
Polychrome methylene blue 24
Polyester plastics 131
Poly-l-lysine 15
coated slides 178
Polymer chain indirect method 109f
two steps 109
Polymer technique 114
Polymerase chain reaction 156, 179
advantages 158t
allele-specific 179
applications of 161, 222fc
competitive 179
different steps in 157f, 158f
disadvantages of reverse transcriptase 158t
limiting dilution 179
long and accurate 179
machine, parts 157f
modifications of 179
multiple template 222
multiplex 159, 179
nested 159, 179
procedure 157
quantitative 158, 179
real time 158, 179
seminested 160
technique
advantages 161
disadvantages 161
reverse transcriptase 179t
variants of 157
Polymorphism 163, 218
repeat-length 210t
single nucleotide 210
Polymyositis 137
Polysaccharides 38
Pompe's diseas 53
Porphyrin pigments 72
Potassium dichromate 4
Preimplantation genetic diagnosis 161
Pressure cooker method 112
Primitive neuroectodermal tumor 119, 170
Proficiency testing 231
Progesterone receptor immunomarker 190f
Progressive multifocal leukoencephalopathy 166
Prostate
cancer 116
specific antigen 200
tumor cell 172f
Prostatic acid phosphatase 201
Prostatic adenocarcinoma 200
Protease method 112
Protein 54
analysis 153
component globin 70
denaturating agents 1, 3
Proteinaceous deposits 135
Proteoglycans 39
Proteolytic enzyme methods 111
Protozoal, differential diagnosis of 182t
Protozoans, detection of 162
Prussian blue 72
Pseudomelanosis 72
Pseudospecific signal 204
Pulvertaft-Kaiserling III solution 144
Pyrosequencing 211f, 215
advantages of 215
limitations of 216
uses 215
Q
Quality assessment, external 231
Quality assurance 227
components of 228f
Quality control 227
analytical aspects of 230
post-analytic aspect of 231
pre-analytical aspects of 227
Quality manual 227
Quantitative polymerase chain reaction 158, 159f
advantages 159
disadvantages 159
Quenching 26
Quick score 118
R
Rabbit anti-human antibody 109
Radio label 108
Radioisotopes 108
Rapid amplification, DNA ends 179
Rapid H&E staining method 23
Rapid onsite evaluation 192
Rapid processing 9
for small biopsies 9
for urgent work 9
Rapid staining, using 34
Rapid-freezing 26
Ray
fast 94
slow 94
Reagents 169
graded alcohol 169
preparation of 169
Real image, formation of 147f
Red blood cell 71, 96, 99
Reed-Sternberg cells 126, 200
Regaud's (Moller's) fluid 4
Renal
biopsies 112
cell carcinoma 42
diseases 134, 135
Research applications 162
Resin embedding media 129
Resinous mounting media 17
Resins 8
preparation of 86
Respiratory viruses 162
Reticular
cell 62
fibers 63
Reticulin 66
fibers 63, 67, 67f, 68
stain 67f, 131
Rhabdomyosarcoma 42, 116
marker of 193
Rhodamine stock solution 78
Rhodamine technique, modified 78
Ribonucleic acid 56
RNA, analysis 153
northern blotting 153
RNA messenger 151
RNA staining 58
Romhanyi's solution 144
Rotary microtome 12f
Routine formalin fixation 176
Russell bodies 99
Rutenberg and Seligman technique 101
S
S-100 protein 201
SALL4 201
Sampling errors 24
Sandhoff disease 53
Sanger sequencing 211f, 213
steps of 209f
Sarcoma 116
SATB2 201
Scanning electron microscope 134, 135f
Schiff's reagent 43, 100
Schistosome pigment 74
Schmeltzer's method 70, 73
Schmorl's reaction 72
for melanin 77
Schultz's carbon monoxide technique 144
Schwann cells 137
Scores for
intensity 118
proportion 118
Scorpion 159
Segmental demyelination 137
Seminoma 42
Serial analysis of gene expression 205
Serine 38
Serous carcinoma 194
Sex-determining region YHMG box 201
SOX 2 201
SOX 9 201
SOX10 201
Sex-mismatched organ transport 170
Shandon cytoblock method 125
Shattering 26
Silica 73
Silver 73
impregnation technique 66
ISH 155
solution 67
Single molecule real time 213
Single nucleotide pleomorphism 159f, 163, 211
Skeletal muscle 134
Skeletal muscle biopsy 102, 137
Slides and drying, placing of 14
Small biopsies 9
Small intestine 194
Smooth muscle antibody 141
Smooth muscle cell 115
Sodium acetate, and formalin 176
Sodium chloride 2
Sodium dithionite 145
Sodium hydroxide 144
Solid organs 143
slice of 143
Solid tissue 151
biopsies 151
Solubility 30
Solution, preparation of 233, 234
Soma 88
Southern blot 153f, 219
Southern blot technique 182t
different steps of 152f
Southgate's mucicarmine method 45
Specimen
and biopies 81
bile-containing 143
fixation of 143
mounted 146f
of uterus cervix 146f
preparation of 142
presentation of 145
type 151
Spectral karyotyping 218
Spindle cell proliferation 126f
Spongy bone 80
Spot or feature 210
Squamous cell carcinoma 194, 200
Staining 130
basis of 30f
different types of 31f
direct 31
method/techniques 35, 36, 43, 45, 50t
choice of 40
multiple 108
multiple 114
pattern 41
procedure, using 34
progressive 32
regressive 32
selective 30
solution, composition of 34, 35, 45
theory of 30
chemical theories 30
physical theories 30
tissues, basic concept 28
Stains 42, 93, 105t
and dyes 30
preparation of 45
Standard operating procedure 227
Stellite-tipped knives 13
Stereotactic core needle biopsy 188
Stewart's fluid 84
Stock
catalyzed monomer 86
stain solution 94
Stomach, adenocarcinoma 194
Strept Avidin-Biotin method 108
Streptavidin 110
Streptavidin-biotin technique 109, 110, 114
Streptomyces avidinii 110
Stropping 13
Subarray 210
Subendothelial granular deposits 135
Succinate dehydrogenase 103
Sudan black B stain 51
Sudan IV dye 49
Sulfated mucin 39
Sulfated sialomucin 39
Sulfatidoses 53
Sulfomucin 39
Sulfonate 39
Sulfonic groups 39
Sulfuric acid 45
Surface decalcification 85
Surgical specimens, processing of 86
Synaptophysin 201
Synthetic resin embedding 86
T
Tape method 133
Taqman 159
Tartrazine 98
Tay-Sachs disease 53
Telomerase repeat amplification protocol 160
Temperature, use of 130
Tetramethyl rhodamine isothiocyanate 138
Thermotoga maritima (TMA) 157, 208
Thermus aquaticus 157
Thermus thermophilus 157
Thioflavin T method 95
Threonine 38
Thrombin and plasma, using 123
Thrombomodulin 201
Thrombotic microangiopathies 136
Thymic carcinoma 194
Thyroglobulin 201
Thyroid carcinoma 116
Thyroid lesion 190, 191
Thyroid transcription factor-1 201
positivity 200f
Tigroid 89
Tinctorial
method 70
staining 131
Tirmann-Schmelzer's turnbull blue technique 75
Tissue
blocks, trimming of 14
coagulum 125
clot method 124
constituents 45
cutting, microtome 14f
elements 97, 105t
staining of 28
fixation and fixatives 1
macrophages 61
microarrays 209
penetration 5
processing 6
steps in 6
quality 151, 152
retain dyes 29
sample influence molecular 151
types 19, 151, 161, 168
dividing cells 168
nondividing cells 168
very hard 129
Tissue-Tek System 16
Toluene (toluol) 7
Toluidine blue 130, 179
Tool edge 12
Total magnification 149
Total quality management 227
Toxoplasma gondii 182
Toxoplasmosis 162
Trabecular bone 80
Traditional method 108
Transferases 101
Transmission electron microscope 134, 135f
Transplant pathology 170
Tray of cups 16
Trephine biopsy 175, 175f, 178, 183
bone marrow fibrosis 183f
decalcification of 177
procedure 174
care of 176
different steps of 175f
report format 184b
specimen, processing of 177
step by step procedure 181f
Trephine core biopsy 183f
Trichloroacetic acid 5
Trichrome stain 178
factors of 64
Trisomy 21 detected 172
TRMPRSS2 172
Tru-cut biopsy 185
18-gauge needle 185
and surgical excision 187t
from breast mass 186f
from lung mass 190f
from mass 187f
in diagnosis of breast lesions 187t
needle 186f
of breast 190f
infiltrating 188f
lesions 191
of lung mass procedure 190
of prostate 187f
organ-specific lesions 188
procedure of 185
Trypsin method 112
Tubuloreticular structures 136
Tumors 116
cases of 81
cell displacement 191
classification 163
heterogeneity of 25
specific markers 195t
types of 116t, 196t
Tungsten
carbide tipped knives 12
hematoxylin 32, 35
Turnaround time 82, 231
Turnbull's blue reaction 73
Twort's stain 95
Tyrosinase (melanoma) 102
U
Unique accession number 228
barcoding 228
linear barcode 228
Unlabeled antibody methods 108
Unlabeled enzyme-antienzyme complex method 109
Uric acid 73
and urates, stains 73
Urinary bladder 194
cancer 116
Uroplakin 201
USG-guided CNB 190
V
Vacuum
embedding 7f
impregnation 7, 128
apparatus 7
procedure 7
Vacuum-assisted core biopsy 188
Van der Waal's force 29
van Gieson 131
solution 65
technique 65
Variable number of tandem repeats 153
Varicella-zoster-infected cell 136
Vascular endothelial growth factor 202
Vascular invasion 24
Verhoeff's hematoxylin 32, 35
Verhoeff's van Gieson method 65
Vibratome 11
Vimentin 119, 202
Vinyl cyclohexane dioxide 130
Viral capsid 136
Viral infections, detection of 166
Virtual image 147
formation of 148
Viruses, detection of 162
Volume
changes 5
to volume preparation 233
Von Ebner's fluid 83
Von Gierke's disease 53
Von Kossa's technique for calcium 78
W
Wade-Fite method, modified 96, 97f
Warthin-Starry technique 105
Water vacuum pump 7f
Wavelength 138
Wavy lines 22f, 26
Waxes 6
Weak acids 83
Wedge-shaped knife 12
Weigert's iron hematoxylin 34, 64
Weight to volume preparation 233
Western blots for protein analysis 155f
Whatman 43, 144
Whole
exome sequencing 217
genome sequencing 217
Wilms’ tumor 116
Working solution 94
Woven bone 80
WT1 202
X
Xenopus laevis 165
Xylene 7, 90
artifacts 24
peanut oil 96
Xylol 28
Y
Yellow signal 155, 167, 170
Z
Zamboni's solution 111
Zebra bodies 136
Zellweger syndrome 136
Zenker's 57
fixative 82, 83, 98, 111, 126, 176
fluid 4, 64, 74, 126
formalin 81–83
solution 165
Zenker-formol 52, 57, 76
Ziehl-Neelsen method 72, 96
fixative 96
reagent 96
sections 96
staining method 96
Ziehl-Neelsen stain 179
Zinc-free chloride 24
Zwemer's chrome-glycerol jelly 23
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