Chapter 2: Methods of molecular analysis

Question 1

_____ describes the study of chromosome structure.

Answer 1

Cytogenetics

Question 2

True or false: Cytogenetics is most applicable for chromosomal analysis of solid tumors.

Answer 2

False - lymphoma and leukemia are most easily sorted into single cells (via blood, bone marrow, lymph node biopsy).

Solid tumor cells are tightly adhered and often destroyed in the denaturization process.
Solid tumor cells often have a low MI, making it difficult to find enough metaphase cells to obtain good quality prep samples.

Question 3

Chromosome number and structure is analyzed via cytogenetics when the cells are in what phase of DNA synthesis?

Answer 3

Metaphase (when chromosomes are condensed and appear as 2 sister chromatids)

Question 4

The ability of single stranded nucleic acids to re-form a complimentary sequence is fundamental to techniques used in molecular analysis. This process is termed ___.

Answer 4

Hybridization

Question 5

Which blotting technique is used to analyze the structure of DNA?

Answer 5

Southern blotting

Question 6

Which blotting technique is used to characterize specific amino acid sequences in proteins?

Answer 6

Western blotting

Question 7

Which blotting technique is used to analyze the structure of RNA?

Answer 7

Northern blotting

Question 8

What cytogenetic technique allows for visualization & detection of target sequences that are of clinical interest?

Answer 8

FISH (fluorescence in situ hybridization)

The method allows for screening of a larger number of cells (>200 or more) for analysis than classical chromosomal cytogenetics.

Question 9

What type of tissue specimen(s) can be used for FISH analysis?

Answer 9

Metaphase cells (dividing): Blood, bone marrow, biopsies of lymph nodes, etc. (same for cytogenetic studies)

Interphase cells (non-dividing): Direct prep (cells and slide prep-smears) as well as paraffin embedded tissue

Question 10

What test can be performed to visualize abnormalities (amplifications, deletions, etc) on whole chromosomes?

Answer 10

FISH (requires specific abnormality to be ‘known’ so that probe can be made to fluoresce)

Question 11

____ is a type of chromosomal microarray analysis (CMA) that compares a patients entire genome against a control to identify differences between the two, thus locating regions of genomic imbalance

Answer 11

Comparative genomic hybridization

Question 12

Which chromosomal microarray analysis (CMA) is best at detecting balance rearrangements (inversions or translocations) - CGH or SNP arrays?

Answer 12

SNP arrays - CGH can only detect large blocks of over-represented (duplication) or under represented (deletions) in chromosomal DNA

Question 13

Which chromosomal microarray analysis (CMA) is best at detecting duplications and deletions - CGH or SNP arrays?

Answer 13

CGH

Duplication = green emission
Deletions = red emission
No change compared to control = yellow emission

Question 14

_____ provides a whole genome analysis by visual inspection of every chromosome (number and structure)

Answer 14

Karyotyping

Note that the resolution of a
karyotype is limited to what you can see under the microscope. This
includes all aneuploidies, structural rearrangements, large deletions,
and large duplications.

Chromosomal imbalances that are smaller than 5-7 million base pairs are usually considered to be beyond
the detection limit of routine cytogenetic analysis. These submicroscopic imbalances (deletions and duplications) are often called CNVs, and their presence does not necessarily confer a disease
phenotype.

Question 15

What are the two chromosomal microarray analysis (CMA) techniques used for identifying chromosomal imbalances?

Answer 15

comparative genomic hybridization (CGH) and SNP arrays

Question 16

Which chromosomal microarray analysis (CMA) is best at detecting copy-neutral loss of heterozygosity (LOH) and amplifications in the genome - CGH or SNP arrays?

Answer 16

SNP arrays