Note: Page numbers of article titles are in boldface type.
A
Abbott Molecular Assay, for melanocytic neoplasms, 883–884
Abelson murine leukemia virus oncogene homolog 1, 828
ABO blood group, 809–810
AccuProbe assays, 788–789
Acute leukemia with mixed lineage leukemia translocation, 825–826
Acute lymphoblastic leukemia, 825–826
Acute myeloid leukemia, 824–827, 831
Acute promyelocytic leukemia, 824
Adenoid cystic carcinoma, of breast, 902
Adenoma-carcinoma sequence, in colorectal carcinoma, 836–838
Affirm VPIII microbial identification test, 791–792
Alloimmune thrombocytopenia, platelet antigens in, 814
All-trans retinoic acid, for hematopoietic malignancies, 831
AML 1 protein, in leukemia, 825
Ampullary adenocarcinoma, 862
Amsterdam criteria, for colorectal carcinoma, 839
Anaplastic lymphoma kinase translocation assay, for lymphomas, 823–824
Androgen receptors, in breast carcinoma, 896, 900–901
Angiopoietins, in hepatic adenomas, 877
AntagomiRs, 778
Antibodies, in transfusion medicine, 805–816
Antigens, in transfusion medicine, 805–816
APC gene pathway
in colorectal cancer, 837–839, 852
in small intestinal adenocarcinoma, 863
Apocrine carcinoma, of breast carcinoma, 896, 900
Appendix, adenocarcinoma of, 861–866
ARID1 gene
in ovarian cancer, 912
in uterine carcinoma, 920
Array comparative genomic hybridization, for melanocytic neoplasms, 885
ATRA, for leukemia, 831
B
B cells, clonal populations of, 818–820
Basal-like subtype, of breast carcinoma, 895–896
B-cell leukemia/lymphoma-2 (BCL-2) translocation assay, for lymphomas, 820–821
BCL-2 gene, in breast carcinoma, 899
BCL-2 like protein 11, 822
BCL-2 translocation assay, for lymphomas, 820–821
BCL-6 translocation assay, for lymphomas, 821
BCR-ABL gene, in leukemia, 828
Beta-catenin
in cholangiocarcinoma, 877
in gall bladder adenoma, 878
in pancreatic neoplasms, 876
in uterine carcinoma, 917–918
Biliary tract, neoplasms of, 878
Biomarkers, microRNA, 773–786
BIOMED-2 protocol, for clonal T-cell populations, 820
Blastomyces dermatitidis, 788
BLOODChip system, for transfusion medicine, 808
BRAF gene
in colorectal carcinoma, 845–846, 850, 852, 855
in melanocytic neoplasms, 883, 886–888
in ovarian cancer, 912
in small intestinal adenocarcinoma, 864
Brain and acute leukemia, cytoplasmic, 828
Branched DNA assays, 767–769, 790
Breakpoint cluster region protein, in leukemia, 828
Breast carcinoma, 891–909
basal-like subtype of, 895–896
classification of, 891–892
claudin low subtype of, 895–896
ductal carcinoma in situ type of, 902–903
ERBB2-enriched subtype of, 894–895
histologic subtypes of, 893, 895–902
adenoid cystic carcinoma, 902
apocrine carcinoma, 900
invasive lobular carcinoma, 897–898
invasive micropapillary carcinoma, 900
invasive papillary carcinoma, 899–900
medullary carcinoma, 901–902
metaplastic carcinoma, 901
mucinous carcinoma, 899
neuroendocrine carcinoma, 899
secretory carcinoma, 902
tubular carcinoma/cribriform carcinoma, 898–899
incidence of, 891
interferon-related group of, 896
luminal A subtype of, 892–893
luminal B subtype of, 894
molecular apocrine subtype of, 896
progression pathways for, 903
Brenner tumors, 913
Burkitt lymphoma, 820, 822
C
Cadherins
in breast carcinoma, 895–896
in gastric carcinoma, 870
in hepatic adenomas, 877
in uterine carcinoma, 917–918
Cancer, microRNA expression profiling for, 773–786
Candida, 791–792
Carcinoembryonic antigen, in breast carcinoma, 902
Carcinosarcoma, uterine, 919–920
CBFB gene, in leukemia, 825
CCAAT enhancer binding protein alpha, in leukemia, 827
CCND1 gene, in breast carcinoma, 899–900
CDKN gene, in ovarian cancer, 913
Celiac disease, small intestinal adenocarcinoma in, 862
Cell-free nucleic acid amplification tests, 814
Cellular myelocytomatosis translocation assay, for lymphomas, 821–822
Chlamydia trachomatis, 792–793
Cholangiocarcinoma, 877–878
Chromogenic in situ hybridization, 770
Chromosomal aberrations, in hematopoietic malignancies, 831–832
Chromosomal instability, in gastric carcinoma, 868
Chronic myelogenous leukemia, 828, 831–832
Chronic myelomonocytic leukemia, 831–832
Clathrin chain polypeptide-like gene, in aplastic lymphoma, 823
Claudin low subtype, of breast carcinoma, 895–896
Clear cell carcinoma
ovarian, 912–913
uterine, 920–921
C-MYC gene, in lymphomas, 821–822, 831
Coccidioides immitis, 788
Colorectal carcinoma, 835–836
APC gene pathway in, 837, 839
classification of, 835–836, 843, 845–846
clinical features of, 836
epidemiology of, 836
hereditary nonpolyposis colon cancer (Lynch syndrome), 839–844
molecular genetics of, 836–837
pathology of, 846–848
pathophysiology of, 836–837
protective factors against, 837
risk factors for, 836
sporadic microsatellite instability, 846
testing for
algorithm for, 852–854
BRAF mutation, 855
germline, 852
KRAS mutation, 851, 855
lymph nodes, 854
mismatch repair, 847–848
MSI, 849–851
new methods for, 854
pitfalls in, 848–849
predictive markers for, 854–855
quality assurance in, 848
reporting results of, 851
staging, 854
treatment of, 855–856
Vogelstein model of, 837, 839
Colton blood group system, 811
Comparative genomic hybridization, for breast carcinoma, 894
Conventional cytogenetics (CCs), for lymphomas and leukemias, 822–825
Core-binding factor, in leukemia, 825
CpG island methylator (CIMP) phenotype, of colorectal carcinoma, 843–846, 851, 854
Cribriform carcinoma, of breast, 898–900
Cromer blood group system, 812
CTLA-4 antibody, for melanocytic neoplasms, 886
CTNNB1 gene
in ovarian cancer, 913
in uterine carcinoma, 917–918
Cyclin D1, in pancreatic neoplasms, 876
Cyclin-D 1 (BCL-2) gene translocation assay, for lymphomas, 821
Cytogenetics, for lymphomas and leukemias, 822–825
Cytokeratins, in breast carcinoma, 895, 902
D
Dabrafenib, for melanocytic neoplasms, 887
Dacarbazine, for melanocytic neoplasms, 886
DEK-NUP214 chimeric protein, in leukemia, 826
Denaturing gradient gel electrophoresis, 762–763
Diego blood group system, 811
Digital PCR, 795
DNA assays, branched, 767–769
DNA sequencing, 757–760
Dombrock blood group system, 811
Ductal adenocarcinoma, of pancreas, 876
Ductal carcinoma in situ, 902–903
Duffy blood group system, 811
E
Economic issues, in molecular pathology, 751
Ecotropic viral integration site-1 gene, 826
EMA gene, in breast carcinoma, 900, 902
Endometrioid carcinoma, ovarian
high-grade, 914
low-grade, 913
Endothelins, epigenetic inactivation of, in colorectal cancer, 856
Enterococcus, 791
Enterococcus faecalis, 791
Epidermal growth factor
in breast carcinoma, 895, 902
in uterine carcinoma, 920
Epigenetic inactivation, of endothelins, in colorectal carcinoma, 856
Epithelial cell adhesion molecule, in colorectal carcinoma, 841
Epithelial membrane antigen, in breast carcinoma, 900
Epithelial-mesenchymal transition, in breast carcinoma, 903
ERBB2 gene, in breast carcinoma, 896, 898
ERBB2-enriched subtype, of breast carcinoma, 894–895
Escherichia coli, 791
Esophageal neoplasms, 867–873
ESR-1, gene, in breast carcinoma, 899
Estrogen receptor(s), in breast carcinoma, 903
Estrogen receptor gene (ESR-1), in breast carcinoma, 892, 894, 899
ETSV6-NTRK3 gene fusion, in breast carcinoma, 902
EV11 gene, in leukemia, 826
Evaluation of Genomic Applications in Practice and Prevention, testing recommendations of, 853
F
Fine needle aspiration samples, microRNA technology using, 780–781
FLT3 gene, in leukemia, 827
Fluorescent in situ hybridization (FISH), 770
for gastric carcinoma, 869
for leukemias, 824–829
for lymphomas, 821–823
for melanocytic neoplasms, 883–885
Fluorescent resonance energy transfer (FRET)
for microbiology, 794
for platelet antigen genotyping, 812
Fms-related tyrosine kinase 3 gene, in leukemia, 827
Follicular lymphoma, 820–821
Formalin-fixed tissues, microRNA technology using, 779–781
G
Gall bladder, neoplasms of, 878
Gardnerella vaginalis, 791–792
Gastric neoplasms, 867–873
GCDFP, in breast carcinoma, 900
Gel electrophoresis, denaturing gradient, 762–763
Gemcitabine, for pancreatic neoplasms, 876
Genotyping, of red cells, 809–812
Gen-Probe tests, for microbiology, 788–789
Germline mutations
in colorectal carcinoma, 848, 852
in immunoglobulins, 818
in small intestinal adenocarcinoma, 864
GUCY2C test, in colorectal carcinoma, 854
Gynecologic cancers, 911–925
ovarian, 911–915
uterine, 915–921
H
Hairy cell leukemia, 823–824
HEA BeadChip system, for transfusion medicine, 808
Helicobacter pylori infections, gastric carcinoma in, 868
Hematopoietic neoplasms, molecular tests for, 817–833
clonal T- and B-cell populations, 818–820
leukemias, 824–829
lymphomas, 820–824
myelodysplastic syndromes, 829–831
myeloproliferative neoplasms, 829–830
Hepatitis C virus, 796
Hepatocellular carcinoma, 877
Hepatomegaly nuclear factor 1, in hepatic adenomas, 877
HER-2 gene
in breast carcinoma, 894–895
in gastric carcinoma, 869–870
in uterine carcinoma, 919–920
Hereditary nonpolyposis colon cancer (Lynch syndrome), 839–844, 852
uterine cancer and, 916
Herpes simplex virus, 794–795
High-resolution melting analysis, 763
Histoplasma capsulatum, 788
Hologic-Gen-Probe microbiology tests, 794
Human immunodeficiency virus, 794–796
Human leukocyte antigens, in platelets, 812–814
Human papillomavirus, hybrid capture for, 766–767
Human platelet antigens nomenclature system, 812–813
Hybrid capture technique, 766–767, 789–790
Hybridization-protection assays, for microbiology, 788–789
I
Imatinib, for melanocytic neoplasms, 887–888
Immunoglobulin(s), clonal populations of, 818–820
Immunohistochemistry
for breast carcinoma, 894–895
for colorectal carcinoma, 849
for gastric carcinoma, 869
for small intestinal adenocarcinoma, 863
Influenza virus, 796
In situ hybridization, 770, 790–791. See also Fluorescent in situ hybridization (FISH).
Interferon(s)
in breast carcinoma, 896
in melanocytic neoplasms, 886
Interleukin(s), for melanocytic neoplasms, 886
International Society of Blood Transfusion, notation system of, 809
Invasive lobular carcinoma, 897–898
Invasive micropapillary carcinoma, of breast, 900
Invasive papillary carcinoma, of breast, 899–900
Ipilimumab, for melanocytic neoplasms, 886–888
IRF genes, in breast carcinoma, 901
Isocitrate dehydrogenase, in leukemias, 828
J
JAK2 gene, in myeloproliferative syndrome, 829–830
Juvenile (secretory) carcinoma, of breast, 902
K
Kell blood group system, 811
Kidd blood group system, 811
Kirsen rat sarcoma viral oncogene. See KRAS gene.
KIT gene
in breast carcinoma, 902
in leukemia, 827
in melanocytic neoplasms, 883, 886–888
inhibitors of, 887–888
Klebsiella pneumoniae, 791
Knops blood group system, 812
KRAS gene
in colorectal carcinoma, 845–846, 851, 855
in ovarian cancer, 912–913
in pancreatic neoplasms, 876
in small intestinal adenocarcinoma, 863–864
L
Late breaker techniques, for microbiology, 799
Leukemias, molecular tests for, 821, 824–829
LifeCodes RBC system, for transfusion medicine, 808
Liver, neoplasms of, 876–878
Luminal A type, of breast carcinoma, 892
Luminal B type, of breast carcinoma, 894
LW blood group system, 811–812
Lymph nodes, investigation of, in colorectal carcinoma, 854
Lynch syndrome, 839–844, 852, 916–917
M
Major breakpoint region
in BCL-2 gene, 820
in BCL-6 gene, 821
Malignant melanoma. See Melanocytic neoplasms.
Malignant mixed müllerian tumor, uterine, 919–920
MALT lymphomas, 822–823
Mantle cell lymphoma, 821
Mass spectroscopy, for microbiology, 798–799
Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF), for microbiology, 798–799
Medullary carcinoma, of breast, 901–902
Megakaryoblastic leukemia, 826
Melanocytic neoplasms, 881–890
differential diagnosis of, 882
genetics of, 883
testing of, 883–886
treatment of, 886–888
types of, 882
Melanoma. See Melanocytic neoplasms.
MEN1 gene, in pancreatic neoplasms, 876
Metaplastic carcinoma, of breast, 901
Microbiology, diagnostic, 787–803
highly multiplexed PCR panels for, 796–797
late breaker techniques for, 799
mass spectroscopy in, 798–799
next-generation sequencing for, 797–798
nucleic acid amplification tests for, 792–796
probe techniques for, 788–792
Micropapillary carcinoma, invasive, 900
MicroRNA expression profiling, 773–786
applications of, 776–777
clinical perspective of, 775–776
diagnostic implications of, 782
for colorectal cancer, 855–856
in clinical specimens, 777–778
in formalin-fixed tissues, 779–781
isolation step in, 781
overview of, 773–774
prognostic implications of, 782
purification in, 778–779
Microsatellite instability
in colorectal carcinoma, 843–845, 847–851
in gastric carcinoma, 869
in small intestinal adenocarcinoma, 863–864
in uterine carcinoma, 916
Mismatch repair gene (MMR) defects
in colorectal carcinoma, 839, 841–842, 847–849, 853
in small intestinal adenocarcinoma, 863–864
Mixed lineage leukemia, 825–826
MKL1 gene, in leukemia, 826
MLH genes
in colorectal carcinoma, 839–840, 848, 850–852
in small intestinal adenocarcinoma, 864
in uterine carcinomas, 916
MLL gene, in leukemias, 825–826, 828
MMR (mismatch repair gene) defects
in colorectal carcinoma, 839, 841–842, 847–849, 853
in small intestinal adenocarcinoma, 863–864
MNS blood group system, 810–811
Molecular apocrine subtype, of breast carcinoma, 896
Molecular beacon technology, for microbiology, 794
Molecular pathology and diagnosis
impact of, 749–751
in biliary tract neoplasms, 878
in breast carcinoma, 891–909
in colorectal carcinomas, 835–859
in cutaneous melanocytic neoplasms, 881–890
in esophageal neoplasms, 867–873
in gallbladder neoplasms, 878
in gastric neoplasms, 867–873
in gynecologic cancers, 911–925
in hematopoietic neoplasms, 817–833
in liver neoplasms, 876–878
in pancreatic neoplasms, 875–876
in small intestinal and appendiceal neoplasms, 861–866
in transfusion medicine, 805–816
microbiology, 787–803
microRNAs in, 773–786
techniques for, 753–772
Molecular tree technique, for microbiology, 790
MSH genes
in colorectal carcinoma, 839, 841, 848–849, 851–852
in uterine carcinoma, 916, 920
MSI. See Microsatellite instability.
Mucinous carcinoma, of breast, 899
Mucosal-associated lymphoid tissue translocation assay, for lymphomas, 822–823
MultiCode RTx system, for microbiology, 794–795
Multiplex polymerase chain reaction, 755
for colorectal carcinoma, 854–855
for transfusion medicine, 808
MYC gene, in breast carcinoma, 900
Mycobacterium, nontuberculous, 788
Mycobacterium tuberculosis, 788–789
Myelodysplastic syndromes, 829–831
Myeloproliferative neoplasms, 829–830
MYH11 gene, in leukemia, 825
Myoepithelial cells, in breast carcinoma, 903
N
NAATs (nucleifc acid smplification tests), 792–796, 814
National Comprehensive Cancer Network guidelines, for colorectal carcinoma, 849, 852–853
Neisseria gonorrhea, 788, 792–793
NeoGenomics probes, for melanocytic neoplasms, 883–884
Neuroendocrine carcinoma, of breast, 899
Nevi. See Melanocytic neoplasms.
Next-generation sequencing, for microbiology, 797–798
Northern hybridization, 763–764
NPM1 gene, in leukemia, 826–827
Nucleic acid amplification tests
cell-free, for transfusion medicine, 814
for microbiology, 792–796
Nucleophosmin gene, in aplastic lymphoma, 823
O
Octreotide, for pancreatic neoplasms, 876
Oncotype Dx colon cancer assay, 854–855
One-step nucleic acid amplification, for colorectal carcinoma, 854
Ovarian cancer, 911–915
carcinogenesis in, dualistic model of, 914–915
incidence of, 911
type I
clear cell carcinoma, 912–913
low-grade endometrioid carcinoma, 913
low-grade serous carcinoma, 912
mucinous carcinoma, 913
type II
high-grade endometrioid carcinoma, 914
serous carcinoma, 913–914
P
p53 gene
in breast carcinoma, 894–895, 899
in gall bladder adenocarcinoma, 878
in gall bladder adenoma, 878
in ovarian cancer, 914
in pancreatic neoplasms, 876
in small intestinal adenocarcinoma, 863
in uterine carcinoma, 919–920
Pancreas, neoplasms of, 875–876
Paracoccidioides brasiliensis, 788
PAX8 gene, in ovarian cancer, 914
PBX1 gene, in leukemia, 828
PCR. See Polymerase chain reaction.
Peptide nucleic acid fluorescence in situ hybridization, for microbiology, 790–791
Personalized medicine, microRNA expression profiling for, 773–786
Phenotyping, of red cells, 809–812
Philadelphia chromosome, 828–829
PIK3CA gene
in breast carcinoma, 894, 900
in ovarian cancer, 912–914
in uterine carcinoma, 917, 920
Plasma, microRNA purification in, 778–779
Plasma cell myelomas, 822
Platelet antigens and antibodies, in transfusion medicine, 805–816
PLEKHA7 gene, in breast carcinoma, 898
PMS2 gene
in colorectal carcinoma, 839–840, 848–849
in small intestinal adenocarcinoma, 864
in uterine carcinomas, 916
Polymerase chain reaction, 753–754
for colorectal carcinoma, 849–850, 854–855
for immunoglobulin rearrangement, 819
for leukemias, 826–829
for lymphomas, 820–824
for microbiology, 795–797
for platelet antigen genotyping, 812
for T-cell receptor rearrangement, 819–820
for transfusion medicine, 808–814
highly multiplexed, 796–797
in microRNA purification, 779, 781
multiplex, 755
real-time, 754–755, 781
reverse transcriptase, 754
Pre–B-cell leukemia transcription factor 1, 828
Probe techniques, for microbiology, 788–792
Progesterone receptors, in breast carcinoma, 903
Promyelocytic leukemia gene, 824
Pseudomonas aeruginosa, 791
PTEN gene
in breast carcinoma, 901
in ovarian cancer, 913–914
in uterine carcinoma, 916–917
Pyrosequencing, 759, 761–762
Q
Quality assurance, in testing
for colorectal cancer, 750–751
for small intestinal adenocarcinoma, 864–865
QUASAR study, for colon cancer, 854–855
R
RAS genes, in melanocytic neoplasms, 883
RAS-RAF-MEK-ERK pathway, in uterine carcinoma, 917
RASSF1A gene, in uterine carcinoma, 917
RBM15 gene, in leukemia, 826
Real-time polymerase chain reaction, 754–755, 781
Red blood cells antigens and antibodies, in transfusion medicine, 805–816
Respiratory syncytial virus, 796
Respiratory viruses, panels for, 796–797
Restriction fragment length polymorphism analysis, 764, 808
Retinoic acid receptor-alpha (RARA) gene, 824
Reverse line-blot hybridization, 764–766
Reverse transcriptase, in microRNA purification, 779
Reverse transcriptase polymerase chain reaction, 754
Rh blood group, 810
Ribophorin 1 gene, in leukemia, 826
RNA-binding motif protein 15, in leukemia, 826
RPN1 gene, in leukemia, 826
RUN1 gene, in leukemia, 828
Run-related transcription factor 1 gene, in leukemia, 824–825
S
Sanger sequencing, for transfusion medicine, 808
Secretory carcinoma, of breast, 902
Serous carcinoma
ovarian
high-grade, 912–914
low-grade, 912
uterine, 919
Serrated polyp pathway, in colorectal carcinoma, 840, 845–846
Sexually transmitted diseases, NAATs for, 792–794
Silver in situ hybridization, for gastric carcinoma, 869–870
Single nucleotide polymorphisms
in platelets, 813
in red cells, 809–812
Smad4 gene
in pancreatic neoplasms, 876
in small intestinal adenocarcinoma, 863
Small intestine, adenocarcinoma of, 861–866
Southern blot hybridization, 763–764
for immunoglobulin rearrangement, 819
for lymphomas, 822
for T-cell receptor rearrangement, 819
Spindle cells, in breast carcinoma, 901
Spitzoid lesions. See Melanocytic neoplasms.
Squamous cells, in breast carcinoma, 901
Staphylococcus, 791
STAT1 gene, in breast carcinoma, 901
Stool DNA, in colorectal carcinoma, 854
Strand displacement amplification, 755–756, 792
T
T cells, clonal populations of, 818–820
TaqMan test, for microbiology, 794
T-cell factor 3, in leukemia, 828
TCF3 gene, in leukemia, 828
Teratomas, ovarian, 913
TMSB10 gene, in breast carcinoma, 898
TOP2A gene, in breast carcinoma, 901
Transcription-mediated amplification, 756–757, 792–793
Transfusion medicine, molecular testing in, 805–816
advantages of, 806–807
cell-free nucleic acid, 814
limitations of, 807
notation for, 809
platelet antigen expression in, 812–814
red cell antigen expression in, 809–812
techniques for, 807–808
terminology of, 809
Trastuzumab
for gastric carcinoma, 869–870
for uterine carcinoma, 920
Trichomonas vaginalis, 791–792
TRK fused gene, in aplastic lymphoma, 823
Tropomysins, in aplastic lymphoma, 823
Tubular carcinoma, of breast, 898–900
Tumor necrosis factor, in breast carcinoma, 901
U
Uterine carcinomas, 915–921
treatment of, 918
type I, 915–918
type II, 918–921
V
Vascular endothelial growth factor
in gastric carcinoma, 869
in small intestinal adenocarcinoma, 863
Vemurafenib, for melanocytic neoplasms, 886–887
Vogelstein model, for colorectal carcinoma, 837–839
VPIII microbial identification test, 791–792
W
Wilms’ tumor gene, in leukemia, 827
Wnt/b-catenin pathway
in breast carcinoma, 899
in ovarian cancer, 913
WT1 gene, in leukemia, 827
X
xTAG technology, 755
Z
Zelboraf, for melanocytic neoplasms, 886–887
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