Chapter 19, Problem 20P

Hepatocellular carcinoma is the most frequent form of liver cancer. In a patient with heritable hepatocellular carcinoma, formation of the tumor was associated with eight genetic alterations affecting two different oncogenes and three different tumor-suppressor genes. These alterations are:

i.	Mitotic recombination
ii.	A deletion of a chromosomal region
iii.	Trisomy
iv.	A duplication of a chromosomal region
v.	Uniparental disomy (see Fig. 20.24)
vi.	A point mutation
vii.	Another point mutation
viii.	Yet another point mutation

For parts a–c below, supply all possible correct answers from the preceding list. Remember that the majority of point mutations are loss-of-function mutations.

a.	Which of the mutations from the preceding list is likely to affect a proto-oncogene?
b.	Which of the mutations from the preceding list is likely to involve a tumor-suppressor gene?
c.	Which of the mutations from the preceding list involves copy-neutral loss-of-heterozygosity (that is, a loss-of-heterozygosity in which the genomes of the cancerous cells still have two copies of the gene in question, whether or not those copies are functional)?

Genomic DNA is prepared from normal white blood cells and from a biopsy of the tumor in this patient. These genomic DNAs are prepared as fluorescent probes that are each hybridized to an ASO microarray of polymorphisms in the human genome (review Figs. 11.16 and 11.17). The results for SNPs a–z on chromosomes 14, 15, 16, and 17 are shown in the accompanying figure. Red and orange represent different levels of fluorescence.

d.	Based on the microarray data, provide the most accurate localization of the first five types of genetic alterations in the list (i–v). For example, if an alteration involves markers a–e of chromosome 15, write 15a–e.
e.	As precisely as possible, indicate the location of the mitotic recombination event involved in the genesis of this cancer
f.	If these data allow you to map any of the three cancer-promoting point mutations, provide the most accurate mutation location(s) possible.
g.	Of all the genetic alterations i–viii, for which one do you see clear-cut evidence that the mutation or other event was inherited from a parent of the patient?
h.	For a tumor-suppressor gene to play a role in cancer, normally both of the copies in the tumor cells must be nonfunctional. For each of the three tumor-suppressor genes contributing to the cancer in this patient, provide a scenario explaining which two hits (i–viii in the list, with vi–viii equivalent) could be responsible, the order in which the hits must have occurred, and whether the hits in question could be inherited or could have occurred somatically.