Applications in Molecular Diagnostics
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| What is 'p' in chromosome nomenclature? | short arm
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| What is 'q' in chromosome nomenclature? | long arm
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| What is # following 'p' or 'q' in chromosome nomenclature? | regions, bands and subbands seen when staining the chromosome with a staining dye
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| The evaluation of clonality in a suspected case of non-Hodgkin's lymphoma first employs immunopathogical methods and then _________ _________ methods if immunopathological methods are inconclusive | molecular genetics
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| The Southern blot is sensitive and specific for determining B-cell and T-cell clonality (T/F) | True
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| Fresh or frozen specimens (rather than fixed) are preferrable for Southern analysis (T/F) | True
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| Optimal specimens for Southern blot B- and T-cell clonality include... | cell suspensions or frozen sectins prepared from tissues such as lymph node, spleen or cell suspensions prepared from peripheral blood speciments, bone marrow aspirates, body fluids, and fine-needle aspirates.
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| Process of Southern blot analysis of B- and T-cell clonality. | Nucleic acid extraction, restriction fragment analysis, electrophoresis/transfer, probe with TCRBC (T-cell) or J[subscript]K or -6(B-cell) probe.
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| The J[subscript]K probe recognizes what? | the kappa light chain joining segment
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| The J[subscript]6 probe recognizes what? | the immunoglobulin heavy chain joining (J) segments
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| The finding of at least _ novel bands is indicative of a clonal T-cell gene rearrangement (syndrome could be T-cell lymphoproliferative disorder) | 2
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| Approx # of micrograms of DNA required for T- and B-cell clonality Southerns | 30 micrograms
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| Advantages of PCR over Southerns for T- and B-cell clonality assessments | PCR has less cost, labor time, less DNA required, fixed DNA OK, can detect a small population of clonal cells
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| Advantages of Southerns over PCR for T- and B-cell clonality assessments | Less false negatives. PCR can not detect partial rearrangments, chromsomal translocations and somatic hypermutations involving antigen receptor gene loci. Primers may not bind as 100% consensus V and J segments apparently non-existent. Also
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| Polyclonal B-cell rearrangements result in a single band on a gel post PCR with a V[subscript]H and J[subscript]H primers. (T/F) | False
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| Non-Hodgkin's Lymphomas are especially suited for analysis by _____ b/c of a # of recurrent, non-random chromosomal aberrations, grouped as 1) molecular translocations, 2) numberical chromosomal aberrations and 3) gene deletions. | FISH
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| centromeric probes in FISH can be used to detect ________ chromosomal aberrations | numerical
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| FISH offers what primary advantage over cytogenetics in diagnosis leukemia/lymphoma | Cells do not need to be proliferated for FISH. Low mitotic rate of indolent or low-grade NHL is not a problem for FISH.
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| The most frequently mutated gene in human cancers (a tumor suppressor gene) | p53
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| NHL: Burkitt lymphoma is clinically agressive (T/F) | True
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| NHL: Most common translocation in Burkitt lymphoma is a t(8;14)(q24;q32) which results in the translocation of _-___ to the B-cell heavy-chain gene locus | C-MYC
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| NHL: Follicular lymphoma is characteristically associated with a t(14;18) (q32q21) which results in the translocation of the ___-_ to the b-cell heavy-chain gene locus on chromosome 14q32 | BCL-2
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| NHL: Mantle cell lymphoma is usually t(11;14)(q13;q32) involving BCL-1 which stands for __ and the immunoglobulin heavy-chain gene locus on chromosome 14q32. | B-cell leukemia/lymphoma 1
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| NHL: 3 different settings of Burkitt's Lymphoma | 1. endemic - in Africa and assoc'd with EBV. 2. sporadic - throughout world 3. immunodeficiency-related form - primarily in HIV-infected pts
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| NHL: Cyclin D1, associated with Burkitt's Lymphoma, does what? | It is in the BCL1 locus and its exon uninterrupted with translocated to 14q32. It serves drive the progression from G1 to S and drives cells to proliferate when it comes under control of the immunoglobulin regulatory sequences.
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| NHL: Diffuse large B-cell lymphoma is one of the more common/uncommon lymphomas in Western countries | common
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| NHL: Diffuse large B-cell lymphoma involves ___-_ proto-oncogene | BCL-6, a zinc finger transcription factor than normally is expressed in germinal center B-cells.
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| proto-oncogene | a gene normally involved in the regulation of a variety of processes including the cell growth, proliferation, differentiation and apoptosis.
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| In reciprocal translocations in NHL, a proto-oncogene is translocated with either the ______ | immunoglobulin or T-cell-receptor gene loci.
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| Hodgkin's lymphoma accounts for __ % of lymphomas in the US | 14%
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| Hodgkin's lympoma is established based on the morphologic identificatin of neoplastic _______________ and ________________in the appropriate benign inflammatory cell b/g. | Reed-Sternberg cells (RS cells) and Reed-Sternberg variants (RS variants)
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| Why is Hodgkin's lymphoma diagnosed using molecular methods | The RS cells and RS variants comprise only a small (1-2%) %-age of the cells in a tissue sample. PCR does not help b/c monoclonality is not a condition for Hodgkin's lymphoma.
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| minimal residual disease | refers to the presence of persistent small numbers of lymphoma or leukemia cells that are below the level of detection of standard clinical and laboratory evaluations. MRD often causes relapse and death.
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| Monoclonal neoplasms that arise as a result of acquired mutations in hematopoietic progenitor cells | leukemia
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| 4 broad groups of leukemias in order of incidence rate | acute myeoloid leukemia (AML, 10,000/y in US) chronic lymphocytic leukemia (CML, 8,000/y in US) chronic myelogenous leukemia (CML, 4500) acute lymphoblastic leukemia (ALL, 3100)
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| chromosomal translocation responsible for CML | bcr-abl
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| classical oncogenes have a dominant or recessive effect? | dominant
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| classical tumor suppressor genes have a dominant or recessive effect? | recessive
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| ras gene superfamily encodes for _____ (GTP binding motif important for intracellular signalling) | 50 structurally related G proteins
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| K-ras and h-ras are cellular oncogenes evolutionarily related to the ______________, respectively | Kirsten and Harvey murine sarcoma viruses
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| Mutations of ras genese are most commonly _____ ________ that result in gene activation | point mutations
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| many types of _________ leukemia can have ras gene mutations | myeloid
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| ras mutations are most common in chronic _________ leukemia | myelomonocytic
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| some types of lymphoid leukemias can have ras gene mutations as well--like _____ | acute lymphoblastic leukemia
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| ALL stands for | acute lymphoblastic leukemia
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| Oncogenes that cause leukemias by mutations | ras, p53
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| Tumor suppressor gene that causes leukemia by mutation | Rb
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| 40 - 50% of chronic myelomonocytic leukemia have ___ mutations | ras
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| 30 - 40% of AMLs have __ mutations | ras
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| 10 - 20% of aggressive myelodysplastic syndrome have __ mutations | ras
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| 10 - 20% of acute lymphocytic leukemias (ALLs) have __ mutations | ras
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| 6% of AML cases have __ point mutations | p53
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| PTD (of genes) stands for | partial tandem duplication
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| a partial tandem duplication of the part of the flt3 gene are one of the more common molecular abnormalities recognized in ___ | Acute myeloid leukemia (AML)
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| APL stands for | acute promyelocytic leukemia
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| APL: commonly caused by a fusion of which two genes? | promyelocytic leukemia (pml) and retinoic acid receptor alpha (rar alpha)
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| chromosomal translocations in AML usually affect only one allele and are dominant (True/False) | True
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| EGFR stands for | epidermal growth factor receptor
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| The epidermal growth factor signaling pathway is commonly up-regulated in ________ cancer | colorectal
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| cetuximab and panitumumab are monoclonal antibodies to ______ ______ ______ _______ | epidermal growth factor receptor
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| KRAS and BRAF act downstream of _______ ______ _______ _______ in colorectal cancer | epidermal growth factor receptor
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| Colorectal cancer: Mutations in KRAS and BRAF are predictive of a lack of response of colorectal cancer to _________ and _________ | cetuximab and panitumumab
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| What does inv(16)(p13q22) refer to? | An inversion of chromsome 16 at the short arm band 13 and long arm band 22. Commonest abnormality assoc'd with AML w/ abnormal bone marrow eosinophils.
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| What does t(16,16)(p13q22) refer to? | translocation between 2 chromosome 16's. A more rare abnormality assoc'd with AML w/ abnormal bone marrow eosinophils.
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| CML is caused by what translocation? | t(9;22) or the Philadelphia (Ph) chromosome
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| What genes are fused to cause CML? | bcr and the murine leukemia viral oncogene homolog 1 (abl)
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| abl is a tumor suppressor gene (True/False) | False
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| abl is a tumor suppressor gene (True/False) | False
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| imatinib mesylate (a drug used vs CML) | an ATP analog that binds the tyrosine kinase domain of abl.
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| CML: common mechanism for resistence to imatinib mesylate | point mutations in the tyrosine kinase domain of abl.
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| monocyte develops into a ____________ | macrophage
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| ALL | acute lymphoblastic leukemia
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| ALL cells can be subdivided into __-_-___ and __-_-___ | pre-B-cells and pre-T-cells
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| CLL stands for | chronic lymphocytic leukemia
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| CLL is the most common type of ________ in adults | leukemia
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| Two kinds of molecular alterations in cancer | chromosomal abnormalities and nuleotide sequence abnormalities
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| effect of molecular alterations cancer | changes in gene expression
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| somatic mutation in cancer | refers to an acquired (non-germline) mutation
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| tumor cells are highly prone to mutation (True/False) | True
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| The accumulation of genetic abnormalities reflects the progression of tumorigenesis (True/False) | True
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| Activation of proto-oncogene function can be achieved by mutations (_-___) or by translocation (_-___) | H-ras, c-myc
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| microsatellite instability can be detected on a gel in one of two ways | ladderlike banding apttern or a one-repeat unit expansion or contraction
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