Advanced Genetics - Moore Exam – Tuesday, October 26, 2010 Name______
Initial all pages. Show your work! I give partial credit, but only when I can tell what your intentions are.
1. Harry Butz is a human geneticist studying colon cancer in humans. Harry believes that there is a gene that conditions some individual humans to develop late on-set formation of cancerous colon polyps. From pedigree analyses, Harry believes that the allele for susceptibility (getting cancerous polyps) segregates in a dominant autosomal fashion. A pedigree in which this gene is segregating is shown below (black pedigree symbols indicate individuals who have been detected to have cancerous polyps):
Harry has identified two marker genes that he thinks might be linked to the polyp cancer gene (Marker A and Marker B in the figure above).
Which of the following statements are true about molecular markers shown in this figure? (circle any correct statements) (3 pts)
a. The molecular markers are segments of DNA that carry specific genes.
b. The molecular markers are individual segments of DNA that are located at specific locations in the genome.
c. It is possible to follow the transmission of the molecular markers by analyzing the physical phenotype of individuals (if allelic constitutions of the markers in the individuals are not known).
d. It is possible to follow the transmission of the molecular markers by analyzing the physical phenotype of individuals (if allelic constitutions of the markers in the individuals are known).
e. To be useful, the molecular markers must be polymorphic.
Do either Marker A or Marker B (or both) appear to be linked to the polyp cancer gene? If so, which? (4 pts)
Do any of the individuals in the pedigree appear to be recombinant? If so, circle them. (4 pts)
Estimate the percentage of recombination frequency in the pedigree (you don’t have to do the math). (2 pts)
Set up a LOD score equation using the formula and theta value of your choice (you don’t have to do the math). (4 pts)
Z (Q ) = log [(1 - Q )n-r Q r/ (1/2)n]
Z (Q) = (n - r) log [2 (1 - Q )] + r log (2 Q )
2. Harry decides to try to clone the gene responsible for the colon polyps and study it at a molecular level. Besides the markers shown above, Harry has investigated a number of other markers for linkage to the colon polyp trait by looking at many affected human families. Some of the information he has obtained is summarized in the table on the next page.
Which marker in the table could be Marker A analyzed above? Why? (2 pts)
Which marker do you think Harry should use to initiate a physical walk (i.e. for positional cloning) toward the polyp cancer gene? Why? (2 pts)
Theta ValuesMarker
Locus / Number of
informative
families / 0.01 / 0.05 / 0.1 / 0.2 / 0.3
Rect 1123 / 3 / -3.21 / -2.21 / -1.11 / -1.02 / -0.45
Rect 1314 / 4 / -2.00 / -1.55 / 0.05 / 0.17 / 1.44
Chyme 66 / 6 / 9.71 / 7.21 / 5.28 / 3.16 / 2.23
Pol 457 / 4 / -0.08 / 0.85 / 1.62 / 3.85 / 1.80
Pol 772 / 5 / 5.90 / 10.20 / 4.80 / 2.80 / 1.20
Fec 4537 / 2 / 1.38 / 1.45 / 1.33 / 1.21 / 0.56
Chyme 12 / 4 / 0.09 / 1.21 / 3.04 / 1.76 / 1.65
Pol 507 / 2 / -0.04 / 0.91 / 0.98 / 1.35 / 1.45
Fec 2201 / 3 / 2.40 / 1.90 / 1.20 / 0.80 / 0.20
Pol 333 / 5 / -1.90 / -1.45 / 0.01 / 0.12 / 2.44
3. Harry is also studying this disease in a mouse model. Here he has obtained an inbred mouse line that is segregating for what he thinks may be the same polyp cancer-causing gene and a marker with alleles A and B. In one backcross mouse population, Harry obtains the following results (C = polyp cancer allele, c = no cancer; A and B = marker alleles):
Genotype / Observed / Expected / Chi square / P value (df)CcAB / 42 / 23.5 / 14.56 / ------
CcBB / 12 / 23.5 / 5.63 / ------
ccAB / 5 / 23.5 / 5.63 / ------
ccBB / 35 / 23.5 / 14.46 / ------
Totals / 94 / 94 / 40.38
a. Is this a significant Chi square value? At what value? (3 pts) (See next page)
b. Set up the equation for the ccAB class in the table above. (3 pts)
C2 = å (O – E)2/E
c. What would Harry’s conclusion be from this result? (3 pts)
Chi Square Table
df / 0.995 / 0.99 / 0.975 / 0.95 / 0.90 / 0.10 / 0.05 / 0.025 / 0.01 / 0.0051 / --- / --- / 0.001 / 0.004 / 0.016 / 2.706 / 3.841 / 5.024 / 6.635 / 7.879
2 / 0.010 / 0.020 / 0.051 / 0.103 / 0.211 / 4.605 / 5.991 / 7.378 / 9.210 / 10.597
3 / 0.072 / 0.115 / 0.216 / 0.352 / 0.584 / 6.251 / 7.815 / 9.348 / 11.345 / 12.838
4 / 0.207 / 0.297 / 0.484 / 0.711 / 1.064 / 7.779 / 9.488 / 11.143 / 13.277 / 14.860
5 / 0.412 / 0.554 / 0.831 / 1.145 / 1.610 / 9.236 / 11.070 / 12.833 / 15.086 / 16.750
4. Before Harry begins his molecular cloning studies, he wants to assemble the materials he will need. He also will use a mouse model system to help isolate and characterize the gene. Which of the following materials are likely to be helpful to him? (Circle helpful ones.) (4 pts)
a. A cDNA library made from the liver of a human fetus.
b. An arrayed human genomic library in a BAC vector made from flow sorted chromosomes.
c. A mouse/ hamster somatic hybrid mapping panel.
d. A preparation of rat brain RNA.
e. A cDNA library made from adult human colon cells.
f. A cDNA library made from cancerous polyp cells.
5. Harry narrowed down the human genomic region where he thought his gene was located (he could still be far away). When he compared the locations of known genes on the linkage map of the region with the same genes on a physical map of the same region, he observed the following:
The maps are not identical because (3 pts):
a. There is no relationship between the position of the genes in a genetic map and their positions on the DNA.
b. Recombination frequencies per kb of DNA are not uniform throughout a chromosome.
c. The further apart two genes are, the more likely they are to recombine.
d. The closer two genes are, the more likely they are to recombine.
e. Some genes contain introns.
6. Which of the following statements are true about molecular markers on a physical map? (circle any correct statements) (3 pts)
a. The molecular markers are segments of DNA that carry specific genes.
b. The molecular markers are individual segments of DNA that are located at specific locations in the genome.
c. It is possible to follow the transmission of the molecular markers by analyzing the physical phenotype of individuals (if allelic constitutions of the markers in the individuals are not known).
d. It is possible to follow the transmission of the molecular markers by analyzing the physical phenotype of individuals (if allelic constitutions of the markers in the individuals are known).
e. To be useful, the molecular markers must be polymorphic.
7. By chromosome walking, Harry has reached the area of the human genome, on chromosome 3, where he thinks his gene of interest lies. The region is shown in the figure below. Unfortunately, there are at least three apparent genes in the region. Label the following in the figure: the chromosome arm; a BAC clone (or partial BAC clone); a gene; an intron in a gene; an exon in a gene. (5 pts)
8. Harry then tests the human genes in the region he has identified to determine which one might be the best candidate for the adult onset polyp cancer gene. One thing he does is northern analysis. From his analysis, which gene do you think is the best candidate? Why? (4 pts)
9. Harry used his newly identified human gene (let’s call it ColC), which mapped to human chromosome 3, as a probe on his mouse/hamster somatic cell line hybrid mapping panel (individual hybrid cell lines lose all but a few mouse chromosomes). Shown below are part of his results using four DNA clones to probe mouse/hamster hybrid cell tissue culture lines a-f, where + means the probe hybridized to a Southern blot of the DNA from that cell line. The mouse chromosomes present in each cell line are indicated by a + in the second part of the table. (8 pts)
CELL LINES
a / b / c / d / e / fProbe for ColC / + / + / - / - / - / -
Probe for VB6 / - / + / + / - / + / +
Probe for RJ776 / + / + / - / - / - / +
Probe for KLL89 / + / + / + / + / + / +
Mouse chromosome 3 / + / + / - / - / - / +
Mouse chromosome 16 / + / + / - / - / - / -
Mouse chromosome 17 / + / + / + / + / + / +
Mouse chromosome 22 / - / + / + / - / + / +
What is the chromosomal location of gene: ColC?_____ VB6?_____ RJ776? _____
KLL89? _____
Harry is married to the brilliant cytogeneticist Ona Thera. She produced a comparative map of human and mouse chromosomes as follows:
a. Do the mouse and human ColC genes map to the same chromosome? Why or why not? (2 pts)
b. What is the primary cytological event that probably led to the differences between the genic arrangements on human and mouse chromosomes? (2 pts)
10. Ona offered to do some cytological investigations for Harry (in humans) using his ColC probe, with other probes as controls. Their idea was to look at normal cells and cancerous polyp cells to see whether there were cytogenetic differences in normal and cancerous polyp cells and in the presence or absence of ColC.
The following FISH probes were made: one complementary to ColC; one to the Alu sequence (a highly repetitive sequence found throughout the genome); one to the entire chromosome 3; one to DudD, a nontranscribed gene; one to alphoid satellite sequences.
In an interphase chromosome preparation, which of the probes would hybridize to each of the following regions? (write the probe name after each region) (5 pts)
a. a heterochromatic area within each region, probably not on the periphery
b. to two regions, possibly in heterochromatic regions away from the periphery, of territories far from each other
c. all throughout all of the territories
d. to two entire territories, far from each other
e. to the periphery of two territories far from each other, or to loops extending from the territories
In a mitotic preparation, which of the probes would hybridize to each of the following regions? (write the probe name after each region) (5 pts)
a. the centromeres of all of the chromosomes
b. all along all of the chromosomes
c. on a single spot on each chromesome 3
d. on a single spot on two chromosomes somewhere else in the genome
e. to all of chromosome 3
11. A diploid mouse cell has 38 autosomes plus x and y. Some of the mice cancerous polyp cells had four sets of chromosomes. Which of the following terms should not be used to describe cells with for sets of chromosomes? (Circle) (3 pts)
a. polyploid
b. aneuploid
c. euploid
d. tetraploid
e. 4n
When a different polyp cell line was probed with a FISH probe specific for ColC, three spots were observed instead of the expected two. A second whole chromosome probe for chromosome 16 verified that the cell line contained three copies of chromosome 16. Which of the following terms should not be used to describe this cell line? (Circle) (3 pts)
a. polyploid
b. triploid
c. aneuploid
d. euploid
e. 2n + 1
f. Trisomy 16
12. Many things influence whether genes are transcribed and in what form. Label the individual diagrams on the next page that illustrate the following phenomena (8 pts):
a. Pervasive expression of RNA
b. Alternate splicing
c. Families of genes that duplicate and diverge
d. Exon shuffling
11. The diagram bellows shows ______in two configurations. Circle the region where the DNA most likely to be transcribed or replicated? (5 pts)
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