2. Briefly summarize the techniques that are shared in common in the analysis of RFLP and VNTR patterns.

3. What is the principal difference between RFLPs and VNTRs?

4. Which of the items in question 1 can be used effectively in linkage analysis? Why are the others less useful in such studies?

5. Site tagged sequences (STS) and RFLPs are both identified with annonymous probes. How do they differ from each other.

6. Explain why VNTRs are never dominant as genetic markers.

7. What is a contig and how is it used in genomic analysis?

8. What determines the maximum possible size of a contig?

9. What special advantages do YACs offer in genomic analysis? What does the acronym YAC stand for?

10. How many separate markers are needed to generate a physical map of the human genome with a marker spaced roughly every 100,000 base pairs?

11. What is the smallest number of contigs that the human genome can ultimately be described in terms of? (Hint: how many different pieces of DNA are needed to account for the entire human genome?) (Watch out for a couple of tricky aspects of this question!)

12. What remains to be done to understand a chromosomal DNA sequence after a complete contig of overlapping YACs has been assembled for that chromosome?

13. Distinguish between the bottom-up and the top-down approaches to genomic analysis in a manner that makes it clear you know what each is and how they differ.

14. DNA fingerprinting has become a widely used technique.

a. What is meant by DNA fingerprinting?

b. What types of markers are most commonly used for DNA fingerprinting?

c. Can this technique be used for species other than humans? Explain your answer.

d. Why is DNA fingerprinting frequently done on a DNA sample that has first been amplified by PCR?

e. How many different haplotypes do you expect the DNA fingerprint for an individual to contain for each marker examined?

f. How would your answer differ in part e if the sample has been amplified by PCR from a single sperm cell?

15. One of the problems of human genomic analysis is the large amount of DNA that must be dealt with.

a. Approximately how many base pairs of DNA are contained in the human nuclear genome?

b. Roughly how many YACs are needed to generate a series of contigs that represent the entire human genome? Include in your answer the average size of the cloned insert that you are assuming to be in each YAC.

c. How many lambda phage clones would be needed to generate a contig containing all of the DNA contained in one average sized YAC in part b?

d, If about 300 base pairs can be sequenced in an average sequencing run, how many separate sequencing runs would be needed as a minimum to cover the entire haploid human genome.