3. Which of the items in question 2 can be used effectively for genetic linkage analysis? Why are the others less useful in such studies?

4. Which of the items in question 2 can be used effectively in physical mapping? Explain why methods that cannot be used for genetic mapping can be used for physical mapping.

5. Site tagged sequences (STS) and RFLPs are both frequently 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 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. 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? Include in your answer the average size of cloned insert that you are assuming to be in each lambda phage clone (see pages 265-266 if you need help with this quesiton).

d. How many of the lambda phage clones from part c would be needed to contain the complete human genome?

e, 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.

16. Describe the use of somatic cell hybridization for the assignment of genes to specific human chromosomes. How are the individual human chromosomes identified in such studies?

17. How many human chromosomes are there? How many linkage groups do they represent? (Think carefully about the second part before you answer!)

18. Describe the use of chromosome banding in genetic research.

19. Explain how linkage to an RFLP defined by an annonymous probe can be used to assign a human disease gene to a specific chromosome.

20. What techniques are being used to identify functional genes among the huge excess of non-coding DNA in the human genome.

21. What remains to be determined after a genomic sequence has been shown to be transcribed and translated before a specific genetic function can be assigned to it.

22. Describe the process of chromosome walking, including what it is used for.

23. How does chromosome jumping differ from chromosome walking? What is the advantage of chromosome jumping? How is it accomplished?

24. What is the approximate number of base pairs represented by a map distance of one centimorgan in the human genome. Can this coversion factor also be used for other species? Explain your answer.