MOLECULAR METHODS

11.Which statement best describes a DNA polymorphism?

1. Which double-stranded DNA molecule has the highest melting
A. A point mutation arising in a gene
temperature?
B. Any change in DNA that is associated with abnormal function
A. An oligonucleotide with a repeating sequence of A-A-A at the 5 ́ end
C. A change in the base sequence of DNA that is translated into an abnormal
B. A molecule of 5,000 base pairs with a high number of A-T base pairs
protein
C. An oligonucleotide with a large number of repeating C-G-C codons
D. A variation in DNA that occurs with a frequency of at least 1%
D. A DNA polymer of 100,000 base pairs
Which of the following is the most common type of polymorphism?
2. Which base pair sequence is most likely to serve as a binding site for a
A. Single nucleotide polymorphism (SNP)
restriction endonuclease?
B. Variable number tandem repeat (VNTR)
A. A-T-T-C-A
C. Short tandem repeat (STR)
T-A-A-G-T
D. Short repetitive interspersed element (SINES)
B. C-T-A-C-T-G
G-A-T-G-A-C
13. Which of the following mechanisms facilitates DNA separation by
C. C-A-C
capillary electrophoresis?
G-T-G
A. Molecular sieving
D. D. A-A-G-C-T-T
B. Partitioning
T-T-C-G-A-A
C. Adsorption
D. Deflection
3. Cloning a human gene into a bacterium in order to make a large
molecular probe requires which vector?
14. The polymerase chain reaction (PCR) involves three processes. Select the
A. Plasmid
order in which these occur.
B. Bacterial microsome
A. Extension→Annealing→Denaturation
C. 30S bacterial ribosome
B. Annealing→Denaturation→Extension
D. Single-stranded DNA
C. Denaturation→Annealing→Extension
D. Denaturation→Extension→Annealing
4. What process can be used to make a DNA probe produce a fluorescent
or chemiluminescent signal?
15. In the PCR cycle, how is denaturation accomplished?
A. Enzymatic attachment of acridinium esters to terminal ends of the probe
A. Heat
B. B. Substitution of biotinylated or fluorescent nucleotides into the probe
B. Alkali treatment
C. Splicing the gene for β-galactosidase into the probe
C. Addition of sulfonylurea
D. Heat denaturation of the probe followed by acid treatment
D. Formamide
5. What term describes the products produced when DNA is digested by
16. What is the composition of the primer used in PCR?
restriction endonucleases?
A. A cocktail of enzymes and nucleotide triphosphates that bind to the target
A. Mosaicisms
B. An oligonucleotide complementary to bases at the 3 ́ end of the target
B. Chimeras
C. A small piece of dsDNA that attaches to the template
C. Amplicons
D. A probe made of mRNA that binds downstream from the target
D. Restriction fragment length polymorphisms
17. The master mix solution used for PCR contains which of the following
7. What reagent is most commonly used to stain DNA separated by
reagents?
electrophoresis?
A. Deoxyribonucleotide triphosphates
A. Silver nitrate
B. Deoxyribonucleotide monophosphates
B. Nicotinamide adenine dinucleotide
C. Deoxyribonucleosides
C. Cationic dye
D. Ribonucleotide monophosphates
D. Ethidium bromide
18. What is the unique characteristic of the DNApolymerase, Taq DNA
8. Which technique is used to detect DNA containing a specific base sequence
polymerase, used in PCR?
by applying a labeled probe to DNA bands immobilized onto nitrocellulose
A. It can be enzyme labeled
paper following electrophoresis?
B. It is more efficient than eukaryotic polymerases
A. Southern blot
C. It is heat stable
B. Northern blot
D. It works with DNA of any species
C. Dot blot
D. Western blot

9. Which of the following types of mutation causes the premature termination

of protein synthesis?
19. In PCR methods, how can several targets be copied simultaneously and
A. Missense
detected?
B. Nonsense
A. By following the increase in absorbance at 260 nm during melting
C. Insertion
B. By labeling multiple primers with specific fluors
D. Frame shift
C. By substitution of hybridization probes for primers
D. By analysis of adenosine tail signatures
10. In humans, which component of a gene is translated into a protein?
A. Intron
20. Which formula predicts the number of PCR products that can be
B. Exon
produced?
C. Promoter
A. 2n where n is the number of cycles
D. TATA box
B. N4 where N is the number of cycles
C. p2 + 2pq + q2 = 1 where p and q are the number of primers
D. N2/2 where N is the number of cycles
21. How can PCR be applied to the detection of human immunodeficiency
and other RNA viruses?
A. The virus must be inserted into human DNA by viral integrase prior to
PCR
B. Substitute deoxyuridine triphosphate in place of deoxythymidine
triphosphate in the master mix
C. Add a heat-stable reverse transcriptase enzyme to the master mix
D. Substitute ribonucleotide triphosphates for deoxyribonucleotide
triphosphates in the master mix
22. Which statement best describes the method of branched DNA signal
amplification?
A. The DNA template is amplified directly using patented enzymes
B. Multiple primers are used to create branches of the template DNA,
permitting multiple extension sites
C. The target DNA is denatured and hybridized to RNA, and the hybrid
molecules are amplified by both DNA and RNA polymerases
D. The target DNA is bound by multiple probes, and those are amplified
instead of the target DNA
23. A PCR reaction is performed, and the negative control demonstrates the
presence of a detectable number of PCR products (amplicons) by capillary
electrophoresis. What is the most likely cause?
A. False-positive post-PCR hybridization reaction due to low stringency
B. Dimerization of PCR primers
C. Contamination of control sample with a trace amount of template DNA
D. Background signal from gel fluorescence or inadequate removal of
unbound probe
24. How can a false-negative PCR test caused by the presence of an inhibitor
of the reaction in a patient’s sample be detected?
A. Using a positive control
B. Using an internal control
C. Performing each test in duplicate
D. Performing serial dilutions of the sample
25. All of the following are requirements for reducing contamination in DNA
amplification methods except:
A. Use of aerosol barrier pipette tips when transferring samples or reaction
products
B. Preparation of reagents in a dead air box or biological cabinet
C. A separate area for performing preamplification, postamplification, and
detection steps
D. Pretreatment of samples with high-intensity ultraviolet light
26. Which method has been used successfully to reduce contamination in the
preamplification stage of PCR?
A. Substitution of deoxyuridine triphosphate for deoxythymidine triphosphate
in the master mix
B. Use of low-molecular-size primers
C. Use of a denaturation temperature above 95°C
27. How are PCR methods adapted to yieldquantitative data?
A. By comparing PCR product to an internal standard
B. By applying a conversion factor to the PCR signal that converts it to copies
per milliliter
C. By determining the mass of PCR product using ultraviolet
spectrophotometry
D. By making serial dilutions of the sample
28. A PCR analysis of a vaginal sample for Chlamydia trachomatis gives a
negative result (optical density of biotinylated reaction product below the
cutoff point). The internal control result is also below the cutoff. Positive and
negative controls produced acceptable results. What action should be taken?
A. The test should be reported as negative
B. The sample should be diluted and the test repeated
C. The result should not be reported and the sample should be repeated
D. A preliminary result of negative should be reported but should be
confirmed by further testing using a different method of analysis
29In real-time PCR analysis, the absolute concentration of PCR product is
determined by plotting which two values?
A. Fluorescent intensity versus melting temperature
B. The threshold cycle versus concentration
C. The well factor versus threshold cycle
D. The melting temperature versus concentration
30. In real-time PCR, quantitation can be done without standards of known
copy number. Relative quantitation (estimated concentration) is possible
because:
A. Each cycle generates a twofold increase in product
B. Each cycle threshold represents a 10-fold increase in product
C. The fluorescence of two samples can be compared directly
D. Concentration is proportional to fluorescence at the endpoint of the PCR
reaction
31. Which real-time PCR parameter can be used to detect the presence of a
contaminant?
A. Threshold cycle
B. Baseline
C. Melting temperature
D. Relative fluorescent intensity
32. In real-time PCR, what value is needed in order to determine the
threshold?
A. Background signal
B. Melting temperature
C. Maximum fluorescence
D. Threshold cycle
33. In real-time PCR, which of the following methods is not based on using a
probe?
A. TaqMan
B. Molecular beacon
C. Scorpion
D. SYBR green
34. Which statement accurately describes the process of fluorescent in situ
hybridization (FISH)?
A. Hybridization is performed on DNA extracted from cells
B. Hybridization is performed directly on intact chromosomes
C. Hybridization probes are attached to histones associated with the
chromosomes
D. Hybridization occurs by attachment to the probe only at the centromere
35. Which type of specimen would be unsuitable for FISH analysis?
A. Paraffin-embedded tissue
B. Cells with chromosomes in metaphase
C. Cells with chromosomes in interphase
D. A cell suspension containing maternal and fetal blood
36. FISH can distinguish each of the following chromosomal abnormalities
except:
A. Aneuploidy
B. Translocation
C. Deletion
D. Trinucleotide repeats
37. In microarray and macroarray analysis, which molecules are labeled?
A. The immobilized DNA molecules
B. The sample DNA 6. How can cell proliferation be explained by the BCR/ABL gene
C. Both target and sample molecules rearrangement that occurs in the 9:22 translocation that causes the Ph1
D. The substrate matrix chromosome of CML?
A. It causes underexpression of p53
38. How can all of the mRNA within a sample be amplified to prepare B. A hybrid protein is made that up-regulates the cell cycle
microarray probes? C. Translocation induces a point mutation in the ABL oncogene
A. A specific primer for each mRNA must be synthesized D. ABL activates p23
B. A primer is made to the polyA tail of mRNA
C. Nonspecific attachment of T7 polymerase occurs when the cells are treated 7. Which statement accurately describes the clinical utility of translocation
with detergent testing in leukemia?
D. Random primer sets are used under low stringency conditions A. Relapse is predicted by any new translocation occurring after treatment
B. Specific translocations associated with a type of leukemia will occur in all
39. What is the difference between a microarray and a macroarray DNA cases
assay? C. Translocation products for each leukemia subtype are always the same
A. The number of targets is larger on a macroarray D. Translocation is a sensitive way to identify surviving leukemic cells
B. The molecular size of each target is larger on a macroarray following treatment
C. The amount of each target is larger on a macroarray
D. The substrate used for a macroarray is different from a microarray 8. Which is the most sensitive method of minimal residual disease testing in
chronic myelogenous leukemia?
40. Protein microarray analysis requires the use of which of the following A. Karyotyping analysis
techniques to generate protein profile data? B. FISH
A. Electrophoresis C. Flow cytometry
B. Mass spectroscopy D. RT-PCR
C. Thin-layer chromatography
D. Gas chromatography 9. How can cell proliferation be explained by the BCL 2 translocation t(14;18)
that occurs in up to 90% of persons with follicular B-cell lymphoma?
MOLECULAR DIAGNOSTICS A. p53 is underexpressed
B. A hybrid protein is made that up-regulates the cell cycle
C. Transcription of the BCL 2 oncogene is increased by the translocation
1. Which method is most useful for confirmation that a culture isolate is
D. The BCL 2 gene joins with the p21 gene,
Group B streptococcus?
making it inactive
A. Southern blotting
10. Which mechanism is responsible for retinoblastoma?
B. Polymerase chain reaction
A. Mutation of a tumor suppressor gene
C. Direct hybridization
B. Mutation of a tyrosine kinase gene
D. Probe capture assay
C. Activation of an oncogene
D. Deletion of a gene encoding a GTPase activator
2. In situ hybridization (ISH) tests for human papilloma virus (HPV) using
cervical smears differ from immunochemical staining of tissue in which
11. Which oncogene is involved in the etiology of Burkitt’s lymphoma?
regard?
A. ABL
A. ISH has lower analytical sensitivity
B. Myc
B. ISH has lower analytical specificity
C. Ras
C. ISH differentiates subtypes more easily
D. HER/neu
D. ISH differentiates cervical neoplasia from
genital warts
12. The majority of cases of Duchenne’s muscular dystrophy are caused by
which type of genetic damage?
3. Which method is most sensitive for detection of viral meningitis?
A. Point mutation
A. Viral culture
B. Insertion
B. CSF WBC count
C. Deletion
C. Specific antibody testing of CSF for viral antigens
D. Trinucleotide repeats
D. Real-time RT-PCR
13. How are cases of Duchenne’s muscular dystrophy not detected by PCR
4. What gene must be amplified in PCR to differentiate methicillin-resistant
usually confirmed?
Staphylococcus aureus from methicillin-resistant coagulase-negative
A. DNA sequencing
Staphylococcus?
B. Linkage analysis
A. orfX
C. Macroarray analysis
B. mecA
D. Dystrophin protein staining
C. VanA
D. iles-2
14. Inheritance of BRCA1 or BRCA2 mutations increases the risk of breast
and ovarian cancer by which mechanism?
5. Which statement best describes real-time PCR testing for Mycobacterium
A. Oncogene production
tuberculosis?
B. Transcription signaling by the mutant protein
A. The test is positive only in cases of smear-positive and culture-positive
C. Deficient tumor suppressor function
infections
D. Chimeric protein production
B. The test has a sensitivity of > 99% on all specimen types when compared to
culture
15. Polymorphisms of the cytochrome p450 genes are important in identifying
C. The test can detect 85%–90% of smear-negative, culture-positive infections
which condition?
D. The test sensitivity is near 100% but specificity is approximately 80%
A. Poor drug metabolism
B. Risk for primary biliary cirrhosis
C. Progression of hepatitis C to hepatic cirrhosis
D. Parentage in cases where HLA results are inconclusive
16. Approximately how may mutations have been identified in the gene
coding for the cystic fibrosis trans membrane conductor regulator protein
(CFTR)?
A. 10
B. 100
C. 1,000
D. 10,000
Which statement about CF is accurate?
A. A sweat chloride test is abnormal in all forms of CF
B. Immunoreactive trypsin is deficient in all persons with CF
C. Some CF mutations can cause male infertility with no other symptoms
D. The CF genotype always predicts the severity of the disease
D. Mitochondrial DNA sequencing
25. In order to prove exclusion in DNA paternity testing, why must two genes
be identified that must come from the biological father and did not?
A. A single exclusion can result from laboratory error
B. A single exclusion can result from germ line mutation within one locus
being tested
C. The biological father may be a blood relative to the alleged father
D. The biological mother may be different than the purported mother
26. Hereditary hemochromatosis is the result of which type of mutation?
A. Nonsense mutation
B. Microdeletion
C. Translocation
D. Single nucleotide substitution

Which of the following alleles has the highest frequency in the general
population?
A. ΔF508 (cystic fibrosis) 27. p21 is a GTP binding protein produced by which
B. Factor V-Leiden (hereditary thrombophilia) oncogene?
C. Prothrombin G20210A (hereditary thrombophilia) A. RET
D. Methylene tetrahydrofolate reductase mutation C677T homocysteinemia B. Ras
C. HER-2/neu
D. N-Myc
19. HLA typing can be done by which molecular method?
A. PCR analysis using 96 well microtrays with allele or groups specific 28. Which of the following thalassemias can be detected by PCR followed by
primers in each blotting with a single specific oligonucleotide probe?
B. Restriction fragment length polymorphism testing A. α-Thalassemia
C. Direct hybridization with WBCs on a peripheral blood film B. Hemoglobin S/β-thalassemia
D. Fluorescent in situ hybridization reactions with peripheral blood C. β-Thalassemia
lymphocytes D. Hemoglobin S/β-thalassemia

20. Which statement best describes the relationshipbetween HLA DNA typing 29. Which method is used to determine if the hemoglobin C gene is present in
and serological haplotypes? fetal cells?
A. One or two bands are seen for each locus correlating to reactivity with a A. Chromosome painting
specific antigen or group of antigens B. FISH
B. HLA alleles cannot be related to HLA antigens because antisera specificity C. Restriction enzyme analysis
is unrelated to genetic polymorphism D. PCR followed by blotting with a specific oligonucleotide probe
C. A single antibody specificity always corresponds to a single allele
D. Not all HLA genes produce antigens recognized by antibodies 30. In flow cytometry, the term “gating” refers to:
A. Selection of a subpopulation of cells to count
21. Highest-resolution HLA typing is needed for which of the following B. Determining the fluorescent emission spectrum of cells of interest
transplants? C. Interference caused by binding of more than a single antibody
A. Heart D. Selecting the appropriate counting aperture
B. Liver
C. Kidney 31. Which of the following parameters are used to gate cells processed by the
D. Bone marrow flow cytometer?
A. Font surface fluorescence versus incident laser intensity
22. Which method of DNA analysis is used most oftento detect the B. Forward light scatter versus side scatter
hemoglobin S gene? C. The ratio of light emitted at two different wavelengths
A. FISH D. Impedance amplitude versus background conductance
B. PCR followed by RFLP
C. Cytogenetic analysis of chromosome 11 32. In general, which statement best characterizes the relationship between
D. Labeled probe painting of chromosome 11 white blood cells and light scattering in flow cytometry?
A. Forward scatter is related to cell size and side scatter to granularity
23. Which of the following genetic diseases is caused by an expanded B. Forward scatter is related to nuclear density and side scatter to size
trinucleotide repeat? C. Forward scatter is inversely related to size and side scatter is directly
A. Prader–Willi syndrome related to size
B. Angelman’s syndrome D. Forward scatter is related to shape and side scatter to size
C. Fragile X syndrome
D. Williams’ syndrome 33. Fluorescent dyes most commonly conjugated to antibodies used in flow
cytometry are:
24. Which is the most common method used for parentage testing in the A. Fluorescein isothiocyanate and Texas red
United States? B. Calcofluor white and Texas red
A. Short tandem repeat analysis C. Phycoerythrin and fluorescein isothiocyanate
B. Nuclear DNA sequencing D. Acridine orange and rhodamine
C. HLA DNA typing
34. A cell population is positive for surface markers CD45, CD3, CD4, and
Tdt. Which type of leukocytes are these?
A. Lymphocytes
B. Granulocytes
C. Monocytes
D. Early myeloid precursors

35. A FISH test is performed on a slide of peripheral blood leukocytes. The

test uses a dual fusion probe, consisting of a Spectrum Green labeled probe to
the BCR 22 q11.2 locus, and a Spectrum Orange labeled probe to ABL 9q34.
What disease is this test for?
A. Chronic myelogenous leukemia
B. Multiple myeloma
C. Bladder cancer
D. Thyroid cancer

36. A tissue sample for DNA analysis by PCR was processed for DNA by
simple lysis and proteinase K digestion. The lysate was diluted 1:100 and its
absorbance measured in an ultraviolet spectrophotometer at 260 nm and 280
nm. The absorbance ratio 260:280 was 1.2. What does this indicate?
A. The DNA concentration is too high for PCR
B. The DNA concentration is too low for PCR
C. The sample contains too much protein
D. The sample is optimal for PCR

Which method of analysis is considered the most reliable means of detecting

mutations of BRCA, p53, BRAF, and other genes linked to cancer?
A. FISH
B. Immunohistochemistry
C. Sequencing
D. STR analysis

38. An assay based on the principle of proteomics may be used for which of
the following?
A. Screening for colorectal cancer
B. Screening for lung cancer
C. Identifying malignant ovarian masses
D. Identifying malignant breast tumors

39. What method is used to identify maternal cell contamination in

amniocentesis and chorionic villus samples (CVS)?
A. STR analysis
B. FISH
C. Microarray analysis
D. MicroRNA (MiRNA) analysis

40. What is the clinical significance of K-ras testing?

A. K-Ras mutations make tumor cells more susceptible to chemotherapy
B. K-Ras is a tumor suppressor gene and mutations are associated with
increased lifetime risk of malignancy
C. K-Ras mutations result in treatment resistance to growth factor receptor
inhibitors
D. K-Ras is used to identify the tissue of origin