Molecular Diagnostics, Cytogenetics, Flow Cytometry Wk 2

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Q banding

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fluorochrome dye – quinacrine mustard

AT areas

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G banding

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Giemsa and Trypsin

AT areas

most common

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C banding

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stains the centromere. acid alkali, Giemsa

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nuclear organizer regions

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nucleoli in interphase cells. silver stain. contain randomly repeated ribosomal ribonucleic acid

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aneuploidy

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abnormal number of chromosomes not a multiple of the haploid number

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polyploidy

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chromosome number higher than 46 and multiple of 23

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hypodiploid

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fewer than 46

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near haploid

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23-34

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hyperdiploid

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more than 46

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high hyperdiploidy

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more than 50

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pseudodiploidy

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46 and structural abnormalities

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no genetic loss from the breakage of the chromosome region with subsequent joining in abnormal configuration

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balanced structural aberration

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loss or gain or genetic chromatin from breakage of the chromosome region with subsequent rejoining in abnormal configuration

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unbalanced structural aberration

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pericentric inversion

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one or two breaks in a single chromosome followed by a 180 degree switch of the segment with no gain or loss of material involving the centromere

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paracentric inversion

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one or two breaks in a single chromosome followed by a 180 degree switch of the segment with no gain or loss of material not involving the centromere

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isochromosome

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abnormal division of centromeres, division is perpendicular the centromere axis

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breakage and rejoining of single chromosome with loss of material outside the break point

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ring formation

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robertsonian translocation

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45 chromosomes

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unbalanced translocation

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results in monosomy and trisomy for a segment of the chromosome- occurs when theres a breakage in two chromosomes and each of the broken pieces reunites with another chromosome

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means partial trisomy for part of a chromosome. can result from an unbalanced insertion or unequal crossing over in meiosis or mitosis

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duplication

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involves the breakage and reunion near the centromere regions of two cocentric chromosomes

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Robertsonian

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most common balanced structural rearangement

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Robertsonian

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suitable specimens for cancer cytogenetics

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bone marrow

unstimulated peripheral blood

bone marrow triphene biopsy

solid tissue from biopsies

needle biopsy

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clonal proliferation of malignant leukocytes that arise initially in the bone marrow before disseminating in the peripheral blood, lymph nodes and other organs

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leukemias

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95% of pts have Philidelphia chromosome t(9;22)(q34; q11:2)

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chronic myelogenous leukemia

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functional abnormality for chronic myelogenous leukemia

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new protein forms with growth promoting capabilities that overrides normal cell regulatory mechanisms

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treatment for CML

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Imatinib mesylate blocks the signaling

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t(4:11)(q21;q23)t(12;21)(q13;q22) and

t(1;19)(q23:p13.3)

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recurrent chromosomal abnormalities in ALL

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in flow cytometry, fluorescent signals are emitted by dyes bound to proteins through

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monoclonal antibodies

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main advanage of flow cytometry

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ability to analyze large volume of cells

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flow cytometry; peripheral blood and bone marrow should be processed in what time frame

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24 to 48 hours

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specimens for flow cytometry

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bone marrow, peripheral blood, and lymphoid tissues. body cavity fluids and solid tissues

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development of _________ led to the use of flow cytometry in clinical in the clinical applications

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monoclonal antibodies

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immunophenotying is a name for

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monoclonal antibodies

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cluster of antibodies differentiating the same antigen

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cluster differentiation

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components of a flow cytometer

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fluidics, light source, detection system, computer

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express CD34, CD117 (c-kit), CD 38, and HLA DR

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pluripotential stem cells

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CD34 CD38 CD33 CD13 HLA DR CD117

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myeloid lineage

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loses CD34 and HLA DR and acquires CD15

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promyelocyte

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CD11b temporary loss of CD13 and decrease of CD33

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myelocyte

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CD16 is acquired and CD13 increases

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band

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defined by increase in CD13 CD33 CD11b

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monocytic lineage

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CD14 and CD15 acquired

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promonoyte and mature monocyte

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does not express pan hematopoietic marker CD45

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erythrocytic lineage

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transferrin receptor CD 71

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increases in pronormoblast and down regulated in reticulocytes

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glycophorin A

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appears in basophilic normoblast

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CD41 and CD61 (glycoprotein IIB/ IIIA complex) appear as first markers of

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megakaryocytic differentiation

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(CD41 and CD61) + CD31 and CD36

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megakaryoblast

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CD42 and CD62P and CD63 glycoproteins are seen in

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megakaryocyte, platelets and thrombocytes

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CD34 TdT and HLA DR

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Lymphoid stem cell

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CD19, cytoplasmic CD22, cytoplasmic CD79

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immature B cell

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B cell precursors acquire

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CD10

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cytoplasmic U transported to surface forms

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B cell receptor

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express kappa and lambda light chains

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mature B cells

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CD34 and TdT

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Immature T cell

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CD2 CD7

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first T cell markers

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CD1a and CD5 and co expression of CD4 and CD8

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T cell markers

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CD2 and CD7, cytoplasmic CD3 and CD56

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natural killer cells

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CD4+

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mature T helper cells

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CD8+

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Suppressor T cells

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hypogranularity of neutrophils

increased immature cells

features of blasts and maturing cells

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chronic myelodysplastic syndromes

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increased immature cells

features of blasts and maturing cells

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chronic myeloproliferative disorders

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decrease in CD4+ helper T cells

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HIV

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decrease or absence of glycosylphosphatidylinositol- anchored proteins on RBCs granulocytes and monocytes levels of CD59 correlate with symptoms

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paroxysmal nocturnal hemoglobinuria

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forward scatter is

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proportional to particle size and volume

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side scatter reflects

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surface complexity and internal structures such as granules and vacuoles

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RNA polymerase recognizes the starter sequence called

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promotor

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introns and exons- which one encodes the gene product

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exons

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messenger RNA, formed when _______ are exised

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introns

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to finish mRNA, 5' cap is added along with

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a tail of many adenine nucleotides

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has specific nucleic acid sequence at the point of interaction with mRNA called anticodon

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transfer RNA

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complements a 3 nucleotide sequence codon of the mRNA

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anticodon

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termination codons

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UAA UAG UGA

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Interphase

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G1 S G2

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G0

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cells which exit the cell cycle during G1 remain alive until apoptosis happens

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whch phase does DNA replication take place during

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S phase

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enzyme which produces replication forks

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helicase

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joins the nucleotides and degrades the RNA primers and fills in the correct complementary deoxyribonucleotides

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DNA polymerase

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provides the 3' hydroxyl group required for DNA polymerase activity

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primer

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hybridization of the primer to the template requires this

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primase

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role of p53

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responsible for signaling damaged DNA

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specimens for DNA isolation

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peripheral blood, bone marrow, tissue biopsy, needle aspirates, cheek swabs

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indefinite storage of DNA at what temperature

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-80

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degrade RNA, body's primary defense against pathogens and are found on epidermal surfaces

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ribonucleases

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provides quantitative information no genes being expressed

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mRNA

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basic steps of RNA isolation

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release of RNA, inhibiting of ribonucleases, protein and DNA removal, RNA precipitation

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enzyme based method for amplifying a target sequence to allow detection from a small volume of material

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PCR

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denaturing, annealing, extension

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PCR

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Controls= negative, positive and No DNA

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PCR

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gel electrophoresis dyes

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ethium bromide, SYBR green fluorescent, or autoradiography

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reverse transcripticase enzyme produces cDNA from mRNA

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reverse transcription PCR

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prothrombin G20210A, MTHFR C677T, and

MTHFR A1298T

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coagulation factor V Leiden mutation

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CYP2C9*2

CYP2C9*3

VKORC1

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Mutations that affect metabolism of

antithrombin drug warfarin

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restriction endonucleases

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restriction enzymes

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restriction fragment length polymorphism

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Factor V Leiden

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southern blot technique is used for

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b cell immunoglobin heavy chain gene. t cell receptor gene

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formation of nested series of fragments. based on dideoxynucleotide terminator sequencing

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DNA sequencing

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measures the changes in nucleic acid amplification as replication progresses using fluorescent dyes. used to identify viruses, bacteria and tumor cells with discernible mutations

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real time PCR

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leukemic cells to levels undetectable first by visual bone marrow smear or peripheral blood and later by cytometry assay

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assesment of minimal residual disease

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indicator of treatment efficacy, clinical remission and prognosis

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assesment of minimal residual disease