Deck 19: The Genetics of Cancer

Question 1

In genome analysis,presence of the Kozak signal is evidence of

A) enhancer sites.
B) splicing sites.
C) binding sites for core transcriptional machinery.
D) the start of a coding region.
E) polyadenylation.

Answer 1

D

Question 2

The lower limit for detection of deletions in human karyotypes is _________.

A) 50kb
B) 500kb
C) 5Mb
D) 50Mb
E) 500Mb

Answer 2

C

Question 3

What is the purpose of a ChIP-on-chip experiment?

A) Identify miRNAs and their mRNA targets.
B) Identify cis-elements to which a transcription factor binds.
C) Identify transcripts expressed in a genome-wide mutant collection.
D) Identify rare transcripts that are differentially expressed.
E) Identify repetitive DNA sequences on chromosomes.

Answer 3

B

Question 4

Which of the following is a conserved sequence motif that can help define eukaryotic promoters?

A) TGA
B) GATA box
C) splicing junction
D) polyadenylation signal
E) CAAT box

Question 5

To measure gene expression,DNA microarray probes can be designed to hybridize to

A) start codons.
B) introns.
C) promoter regions.
D) polyA tails.
E) 3'UTRs.

Question 6

Histone modifications do not affect

A) affinity of DNA for histones.
B) gene expression.
C) chromatin remodelling.
D) nucleosome structure.
E) RNA stability.

Question 7

You label cDNA from a tumour with a red fluorescent dye and you use a green dye to label cDNA from normal tissue.Upon microarray hybridization,you find a spot that has more fluorescent signal than the red signal.What is your conclusion?

A) Increased expression of the gene represented at the green spot is causally related to tumourgenesis.
B) Transcript of the gene represented at that green spot is less abundant in normal tissue than in the tumour.
C) Transcripts of all genes are more abundant in normal tissue than in the tumour.
D) Transcript of the gene represented at that green spot is more abundant in normal tissue than in the tumour.
E) Decreased expression of the gene represented at the green spot is causally related to tumourgenesis.

Question 8

Which of the following is not a feature that can be predicted by computational analysis of whole genome sequence?

A) rRNA
B) splicing acceptor
C) transcription rate
D) translation start
E) transcription start

Question 9

Which of the following statements about DNA microarrays is false?

A) They can be made of glass.
B) They involve DNA sequencing.
C) Expression is proportional to signal intensity.
D) Lasers are used in their analysis.
E) PCR is often used in their production

Question 10

DNA microarray probes are

A) made by labelling mRNA.
B) representative of the entire genome.
C) usually over 1kb in length.
D) complementary to cDNA.
E) radioactively labelled.

Question 11

Which of the following would be most difficult to detect using CGH?

A) 100kb duplications
B) inversions
C) aneuploidy
D) 100kb deletions
E) 50Mb deletions

Question 12

How are the probes for ChIP-on-chip different from probes made for gene expression analysis?

A) Arrays for ChIP-on-chip are made using probes based on intergenic regions.
B) Arrays for ChIP-on-chip are made using probes based on cDNAs.
C) Arrays for ChIP-on-chip are made using probes based on synthetic oligonucleotides
D) Arrays for ChIP-on-chip are made using probes based on rRNAs.
E) Arrays for ChIP-on-chip are made using probes based on miRNAs.

Question 13

A robotically produced DNA microarray for gene expression analysis contains

A) thousands of spots.Within each spot are millions of copies of a DNA sequence.Each spot contains DNA with a different sequence than every other spot on the array.
B) millions of spots.Within each spot are thousands of copies of a DNA sequence.Each spot contains DNA with a different sequence than every other spot on the array.
C) thousands of spots.Within each spot are millions of different DNA sequences.Each spot contains different DNA sequences than every other spot on the array.
D) millions of spots.Within each spot are thousands of different DNA sequences.Each spot is identical to every other spot on the array.
E) millions of spots.Within each spot are thousands of different DNA sequences.Each spot contains different DNA sequences than every other spot on the array.

Question 14

How is CGH used in studying or treating cancer?

A) Transcription factors that acts as tumour-suppressors can be identified by CGH.
B) Transcription factors that are more abundant in tumours can be identified by CGH.
C) Transcripts that are more abundant in tumours can be identified by CGH.
D) Trisomy 21 can be identified using CGH.
E) Deletions containing tumour-suppressor genes are often found in tumours and can be detected by CGH.

Question 15

Which of the following is not a use of the two-colour DNA microarray technique?

A) Shows which mRNAs are overexpressed in a mutant cell,compared to the case of a normal cell
B) Indicates which mRNAs are not being produced in either of two cell types
C) Allows identification of a cell's rarely expressed mRNAs (fewer than 10 copies per cell)
D) Shows which mRNAs are overexpressed in a normal cell,compared to the case of a mutant cell
E) Measures relative abundance of mRNA in two samples

Question 16

Which of the following is required in ChIP-on-chip but not when using a microarray to analyze transcript abundance?

A) fluorescent labels
B) an antibody
C) PCR
D) a microarray
E) hybridization

Question 17

How are the probes for CGH different from probes made for gene expression analysis?

A) Arrays for CGH are made using BAC probes.
B) Arrays for CGH are made using cDNA probes.
C) Arrays for CGH are made using synthetic oligonucleotide probes.
D) Arrays for CGH are made using PCR amplicon probes.
E) Arrays for CGH are made using miRNA probes.

Question 18

Probes for DNA microarrays are made using

A) RNA blotting
B) Southern blotting
C) PCR
D) Electrophoresis
E) DNA sequencing

Question 19

The population of mRNA expressed in a single cell or cell type is called

A) transcriptome.
B) genome.
C) proteome.
D) spliceosome.
E) orfeome.

Question 20

Which of the following is the correct sequence of events in sample preparation for microarray analysis?

A) RNA extraction,reverse transcription,differential labelling,hybridization
B) RNA extraction,reverse transcription,hybridization,differential labelling
C) reverse transcription,RNA extraction,differential labelling,hybridization
D) differential labelling,RNA extraction,reverse transcription,hybridization
E) RNA extraction,differential labelling,hybridization,reverse transcription

Question 21

Haplotypes are

A) genotypes of haploid organisms.
B) one half of a SNP genotype.
C) alleles made of the SNPs in a block of DNA.
D) genotypes made from gametic DNA.
E) ambiguous genotypes resulting from dominant markers.

Question 22

Antibodies specific to 5-methylcytosine can be used to precipitate DNA prior to array hybridization.

Question 23

Every ATG in the genome is a start codon.

Question 24

The control sample hybridized in ChIP-chip is random DNA.

Question 25

Almost all of a person's genetic diversity can be described using

A) CGH.
B) a detailed pedigree.
C) a karyotype.
D) tag SNPs.
E) cDNA microarrays.

Question 26

Hybridization is of little or no relevance to

A) CGH.
B) cDNA microarray analysis.
C) ChIP-chip analysis.
D) bisulfite sequencing.
E) PCR.

Question 27

ChIP-seq does not require a microarray for analysis.

Question 28

The control sample hybridized in CGH is haploid DNA.

Question 29

Which of these was a unique advantage that allowed DeCODE genetics to identify genes for dozens of human diseases?

A) ability to conduct high resolution linkage mapping with molecular markers
B) ability to perform integrate linkage mapping with CGH
C) access to detailed pedigrees of over 300,000 Icelandic citizens
D) a complete human genome sequence
E) access to health records for over 5,000 sets of identical twins in Britain

Question 30

Unlike pedigree analysis,genome wide association studies do not depend on __________ for gene mapping.

A) reliability of phenotypic information
B) availability of human DNA samples
C) molecular markers
D) knowing family relationships
E) control subjects

Question 31

The total number of SNPs identified in the human genome is approximately 50,000.

Question 32

The most efficient method for associating human SNPs with complex traits is

A) pedigree analysis.
B) genome wide association studies.
C) model organisms.
D) comparative genome hybridization.
E) whole genome sequencing.

Question 33

Housekeeping genes are usually either bright green or bright red in an expression microarray image.

Question 34

Bisulfite sequencing can be included under next-generation sequencing.

Question 35

Bisulfite sequencing relies on _______________ to detect ____________.

A) methylation of cytosine;methylated DNA
B) immunoprecipitation of methylated DNA;promoter regions
C) conversion of cysteine to uracil;unmethylated DNA
D) conversion of cytosine to uracil;unmethylated DNA
E) immunoprecipitation of promoter regions;methylated DNA

Question 36

The only molecule targeted for methylation in epigenetics is cytosine in CpG islands.

Question 37

In case of trisomy 21,the CGH signal ratio would be 3:1 (trisomic:control).

Question 38

Genotypes of approximately 50,000 SNPs can be done simultaneously using DNA microarrays.

Question 39

In many regions of the genome,95 percent or more of existing diversity is shared by just five to ten alternative haplotypes.

Question 40

Studies of the methylome are useful for __________.

A) high resolution karyotyping
B) identifying genome duplication
C) biomarker discovery
D) identifying modified histones
E) screening for small deletions

Question 41

What is a DNA microarray?

Question 42

Design an experiment to identify genes associated with cancer,using genome wide association studies.

Question 43

Design an experiment to identify genes associated with cancer,using comparative genome hybridization.

Question 44

Design an experiment to identify genes associated with cancer,using expression microarrays.

Question 45

Design an experiment to identify genes associated with cancer,using methylome analysis.

Question 46

Why are genome wide association studies (GWAS)preferable to traditional pedigree analysis for mapping genes associated with complex traits?