cytogenetic

Which of these is an example of cytogenetic mapping?
				A) Hybridization studies in Drosophila determined the location of the yellow gene, which influences body color, to be near the tip of the X chromosome.
				B) Karyotype analysis of humans with familial Down syndrome has identified a relatively small region of chromosome 21 containing genes that cause the Down phenotype.
				C) Analysis of the chromosomes of a transgenic strain of mice indicates that the transgene has been inserted into the short arm of chromosome 15.
				D) All of these.
				E) None of these.
			Feedback: Correct!
2	INCORRECT		Map units used in linkage mapping correlate with a specific number of base pairs.
				A) True
				B) False
			Feedback: Map units are a measure of recombination frequency between two genes or markers. Since recombination frequency at any given site varies across the chromosome, in some instances one map unit may represent a much longer physical segment of DNA than in other instances.
3	CORRECT		Cytologists can use which of the following to describe locations of a gene at a specific place on the chromosome?
				A) DNA sequence of a chromosomal region.
				B) Protein expression from a chromosomal region.
				C) Banding pattern of stained chromosomes.
				D) Comparison to markers located within a few thousand bp.
			Feedback: Correct!
4	INCORRECT		Cytogenetic mapping:
				A) Requires that the gene have been cloned if in situ hybridization is to be used.
				B) Is a high resolution method of gene localization.
				C) Can be used to determine relative order of genes located very close to each other.
				D) All of these.
				E) None of these.
			Feedback: Cytogenetic mapping is relatively low resolution.
5	INCORRECT		Which of the following questions could be easily answered by FISH?
				A) How often does recombination occur between the ebony and sepia loci in Drosophila?
				B) In a particular family affected with Becker muscular dystrophy, is the mutation due to a deletion of the entire gene?
				C) How large a piece of DNA would you need to clone in order to clone the group of human globin genes from chromosome 11?
				D) All of these.
				E) None of these.
			Feedback: Only B can be answered with cytogenetic mapping.
6	INCORRECT		In situ hybridization is done on fragments of specific chromosomes.
				A) True
				B) False
			Feedback: In situ hybridization for gene localization is typically done on intact chromosomes, often even in intact cells.
7	INCORRECT		Which of these is a key characteristic of a molecular marker?
				A) It is a known gene.
				B) It is located at a known site on the chromosome.
				C) It is only useful for linkage and physical mapping studies.
				D) None of these.
			Feedback: Markers are useful in all three types of gene mapping.
8	CORRECT		Changes in restriction enzyme sites can be used as polymorphic markers.
				A) True
				B) False
			Feedback: Correct!
9	CORRECT		A molecular marker which is amplified by PCR and is polymorphic by length is a(n):
				A) Restriction fragment length polymorphism (RFLP).
				B) Variable number of tandem repeats site (VNTR).
				C) Amplified fragment length polymorphism (AFLP).
				D) Single nucleotide polymorphism (SNP).
			Feedback: Correct!
10	INCORRECT		A polymorphism is:
				A) Any change in the DNA sequence.
				B) The most common variation of a gene or marker sequence.
				C) The least common variation of a gene or marker sequence.
				D) A variation of gene or marker sequence present in >1% of the population.
				E) None of these.
			Feedback: A polymorphism is present at relatively high frequency: >1%.
11	UNANSWERED		An AFLP is an example of a sequence tagged site.
				A) True
				B) False
12	UNANSWERED		Which of these statements regarding RFLP analysis is correct?
				A) RFLP analysis requires Southern blotting for detection of fragments.
				B) RFLPs can identify single base pair changes at any site in the chromosome.
				C) An RFLP typically produces several different alleles.
				D) All of these are correct.
				E) None of these are correct.
13	CORRECT		RFLPs are inherited in a simple Mendelian fashion and display codominance.
				A) True
				B) False
			Feedback: Correct!
14	INCORRECT		A monomorphic DNA segment is:
				A) A segment of DNA that exists in many forms in the population.
				B) A segment of DNA that controls a single gene function.
				C) A segment of DNA inherited in a dominant fashion.
				D) A segment of DNA shared by over 99% of the population.
				E) All of these.
			Feedback: Most people in the population are homozygous for a monomorphic DNA segment; dominance relationships require an understanding of at least two different alleles.
15	INCORRECT		Linkage mapping can determine the distance between which of the following pairs of DNA sequences?
				A) AFLPs and RFLPs.
				B) Two AFLPs.
				C) Two known genes.
				D) A known gene and any type of molecular marker.
				E) All of these.
			Feedback: Linkage mapping can determine the distance between any two unique and identifiable DNA sequences, including molecular markers and known genes.
The next set of questions all refer to the following situation: You have set up the following experiment to linkage map two RFLPs in pigs. For RFLP A, you can detect either a 5,000bp band or a 3,350bp band; for RFLP B you can detect either a 4,300bp band or a pair of bands of 2,300 and 2,000bp. Beginning with strains homozygous for different forms of each RFLP, you generate compound heterozygotes, which you then cross to pigs that are homozygous for the smaller forms of each RFLP. By analysis of several litters you get the following results: 52 individuals with 5,000bp and 4,300bp bands; 48 individuals with 5,000bp, 4,300bp, 3,350bp, 2,300bp, and 2,000bp bands; 11 individuals with 5,000bp, 4,300bp, 2,300bp, and 2,000bp bands; and 9 individuals with 5,000bp, 4,300bp, and 3,350bp bands.
16	INCORRECT		The reduced numbers of progeny with the pattern of (5,000bp, 4,300bp, 2,300bp, and 2,000bp bands) or (5,000bp, 4,300bp, and 3,350bp bands) indicates a selective disadvantage for these genotypes.
				A) True
				B) False
			Feedback: The reduced numbers of these progeny reflects the fact that they originate due to a crossover event between the two RFLP sites.
17	INCORRECT		What was the arrangement of the markers in the original parental strains?
				A) A: 5,000bp, B: 4,300bp and A: 3,350bp, B: 2,300/2000bp
				B) A: 5,000bp, B: 2,300/2,000bp and A: 3,350bp, B: 4,300bp
				C) A: 3,350bp, B: 4,300bp and A: 5,000bp, B: 4,300bp
				D) A: 3,350bp, B: 2,300/2000bp and A: 3,350bp, B: 2,300/2000bp
			Feedback: Of the original parents, one strain was homozygous for the large alleles of each RFLP and the other strain was homozygous for the smaller alleles of each RFLP.
18	INCORRECT		What is the distance between these two markers?
				A) 0.167mu.
				B) 0.20mu.
				C) 16.7mu.
				D) 20mu.
				E) None of these.
			Feedback: The distance between these markers is equal to the total recombinant progeny divided by the total progeny; converted to a percentage: ((11+9)/120)*100 = 16.7mu.
19	INCORRECT		Which of the following would be a reasonable use of an RFLP map?
				A) Identification of the exact location of an unknown gene along the chromosome.
				B) Description of the size of DNA fragment required to clone the region containing an unknown gene.
				C) Identification of the region in which an unknown gene is located.
				D) All of these.
				E) None of these.
			Feedback: RFLP maps are useful for linkage studies but cannot give exact physical locations of genes or markers.
20	INCORRECT		Which of these genetic markers is most likely to be highly polymorphic (have many different alleles)?
				A) An RFLP.
				B) A microsatellite.
				C) An SNP.
				D) All of these are equally polymorphic.
				E) None of these are likely to be polymorphic.
			Feedback: RFLPs can have two different alleles; SNPs can have up to four different alleles; microsatellites can have 50 or more different alleles.
21	INCORRECT		Why might use of microsatellites in genetic mapping studies be an advantage over RFLPs?
				A) Microsatellites are easier to detect.
				B) Microsatellites are more abundant than RFLPs.
				C) Microsatellites have more potential alleles than RFLPs.
				D) All of these.
				E) None of these.
			Feedback: This is an advantage of microsatellites.
22	CORRECT		Isolation of individual chromosomes can be used to map genes.
				A) True
				B) False
			Feedback: Correct!
23	INCORRECT		How are individual chromosomes identified in chromosome sorting techniques?
				A) Relative level of fluorescence when stained with a dye mixture.
				B) Level of charge relative to size.
				C) Size of the molecule.
				D) All of these.
				E) None of these.
			Feedback: Chromosomes should all have the same relative charge.
24	INCORRECT		Which of these describes a contig?
				A) A complete genomic library including overlapping clones.
				B) A complete mRNA library.
				C) A chromosome-specific library of overlapping clones.
				D) An ordered genomic library.
			Feedback: A contig is a group of overlapping clones, existing in hybrid vectors.
25	INCORRECT		What vector would be best suited for creating a contig of bovine (cattle) chromosome 10?
				A) λ?
				B) A plasmid.
				C) A YAc.
				D) Any of these.
				E) None of these.
			Feedback: Viral or plasmid vectors are limited in the size of inserts, so a very large number (perhaps 10s or 100s of thousands) of clones would be required to make up a contig.
26	CORRECT		Which of the following would not be a critical characteristic of a YAC vector?
				A) Telomeric sequences.
				B) A gene encoding a required structural protein.
				C) An origin of replication.
				D) A centromere.
				E) All of these are critical characteristics of a YAC.
			Feedback: Correct!
27	INCORRECT		After cytogenetic and linkage mapping, you have identified a relatively small area of a chromosome where your gene of interest is likely to reside. You decide to attempt to use a YAC contig to map the gene by positional cloning. How might you identify the clone that may contain the gene?
				A) The clone will also contain the nearest marker mapped by linkage analysis.
				B) The DNA sequence of the clone will contain an ORF (open reading frame).
				C) Cytological hybridization of the clone produces a different pattern than that of the nearest mapped marker.
				D) All of these.
				E) None of these.
			Feedback: Because of the low resolution of the technique, you would expect that cytological hybridization experiments would generate very similar patterns for many members of contig.
28	INCORRECT		Which of these is a reasonable use for the contigs and clones generated in the process of obtaining a physical map of the human genome?
				A) Correlation of physical and linkage map distances to determine recombination frequency.
				B) Identification of all the known alleles of a single disease-causing gene.
				C) Insertion into cells affected with genetic disease in the process of gene therapy.
				D) All of these.
				E) None of these.
			Feedback: Contigs and clones used for physical mapping are likely to have come from only one or at most a few individuals, and are far too large to be used directly in gene therapy.
29	INCORRECT		One of the goals of the Human Genome Project is to address ethical issues arising from use of the information gathered.
				A) True
				B) False
			Feedback: The Human Genome Project is the first major scientific initiative to have a portion of its funding earmarked to address the ethical, legal, and social implications of the project.
30	INCORRECT		Sequencing of genomes other than humans is potentially valuable because:
				A) Disorders of cellular function can be studied in relatively simple model systems.
				B) Comparison of gene sequences between different species can allow prediction of disease-causing mutations.
				C) Genes may have a similar function in other species, giving us a place to start with functional analysis of similar genes.
				D) None of these.
			Feedback: Genes with similar sequences are likely to have similar functions, providing a starting point for analysis. Eventually, once an understanding of gene function has been gained, a prediction of mutations that might cause disease is possible.