18. Molecular Genetic Tools

Methods for Analyzing DNA

Open Question
Which of the examples of genetic testing below are prognostic tests? Which are diagnostic?

Genetic testing in a healthy teenager identifies an SNP correlated with autism.
Open Question
The frequencies of the four alleles contributed to the child by possible father F1 in Problem 7 are 0.18, 0.23, 0.13, and 0.14.Make a statement about the possible paternity of F1 based on this analysis.
Open Question
The frequencies of the four alleles contributed to the child by possible father F1 in Problem 7 are 0.18, 0.23, 0.13, and 0.14.Calculate the Combined Paternity Index (CPI) for the four genes in this analysis.
Open Question
Does genetic analysis by ASO testing allow for detection of epigenetic changes that may contribute to a genetic disorder? Explain your answer.
Open Question
In an inheritance case, a man has died leaving his estate to be divided equally between 'his wife and his offspring.' His wife (M) has an adult daughter (D), and they argue that they should split the estate equally. As a young couple, however, the man and his wife had a son that they gave up for adoption. Two men have appeared, each claiming to be the son of the couple and therefore entitled to a one-third share of the estate. The accompanying illustration shows the results of DNA analysis for five genes for the mother (M), her daughter (D), and the two claimants (S1 and S2).How many nonmaternal DNA bands are shared by D and S1? By D and S2?
Open Question
Maternal blood tests for three pregnant women revealed they would be having boys, yet subsequent ultrasound images showed all three were pregnant with girls. In each case Y chromosome sequences in each mother's blood originated from transplanted organs they had received from men! This demonstrates one dramatic example of a limitation of genetic analysis of maternal blood samples. What kind of information could have been collected from each mother in advance of these tests to better inform physicians prior to performing each test?
Open Question
Three independently assorting STR markers (A, B, and C) are used to assess the paternity of a colt recently born to a quarter horse mare. Blood samples are drawn from the mare, her colt, and three possible male sires (S₁, S₂, and S₃). DNA at each marker locus is amplified by PCR, and a DNA electrophoresis gel is run for each marker. Amplified DNA bands are visualized in each gel by ethidium bromide staining. Gel results are shown below for each marker.Calculate the PI and CPI based on these STR markers, using the following population frequencies: A₁₂ = 0.12,A₁₀ = 0.18;B₁₈ = 0.08,B₁₂ = 0.17;C₁₆ = 0.11,C₁₄ = 0.20.
Open Question
Three independently assorting STR markers (A, B, and C) are used to assess the paternity of a colt recently born to a quarter horse mare. Blood samples are drawn from the mare, her colt, and three possible male sires (S₁, S₂, and S₃). DNA at each marker locus is amplified by PCR, and a DNA electrophoresis gel is run for each marker. Amplified DNA bands are visualized in each gel by ethidium bromide staining. Gel results are shown below for each marker.Evaluate the data and determine if any of the potential sires can be excluded. Explain the basis of exclusion, if any, in each case.
Open Question
What is the main purpose of genome-wide association studies (GWAS)? How can information from GWAS be used to inform scientists and physicians about genetic diseases?
Open Question
Describe how the team from the J. Craig Venter Institute created a synthetic genome. How did the team demonstrate that the genome converted the recipient strain of bacteria into a different strain?
Open Question
In a control experiment, a plasmid containing a HindIII recognition sequence within a kanamycin resistance gene is cut with HindIII, re-ligated, and used to transform E. coli K12 cells. Kanamycin-resistant colonies are selected, and plasmid DNA from these colonies is subjected to electrophoresis. Most of the colonies contain plasmids that produce single bands that migrate at the same rate as the original intact plasmid. A few colonies, however, produce two bands, one of original size and one that migrates much less far down the gel. Diagram the origin of this slow band as a product of ligation.
Open Question
What advantages do cDNA libraries provide over genomic DNA libraries? Describe cloning applications where the use of a genomic library is necessary to provide information that a cDNA library cannot.
Open Question
The bacteriophage lambda genome can exist in either a linear form (see Figures 15.1 and 15.8) or a circular form.Diagram the resulting fragments as they would appear on an agarose gel after electrophoresis.
Open Question
To create a cDNA library, cDNA can be inserted into vectors and cloned. In the analysis of cDNA clones, it is often difficult to find clones that are full length—that is, many clones are shorter than the mature mRNA molecules from which they are derived. Why is this so?
Open Question
A hereditary disease is inherited as an autosomal recessive trait1. The wild-type allele of the disease gene produces a mature mRNA that is 1250 nucleotides (nt) long. Molecular analysis shows that the mature mRNA consists of four exons that measure 400 nt (exon 1), 320 nt (exon 2), 230 nt (exon 3), and 300 nt (exon 4). A mother and father with two healthy children and two children with the disease have northern blot analysis performed in a medical genetics laboratory. The results of the northern blot for each family member are shown here.Based on your analysis, what is the most likely molecular abnormality causing the disease allele?