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Ch. 20 - Recombinant DNA Technology
Chapter 19, Problem 33

The U.S. Department of Justice has established a database that catalogs PCR amplification products from short tandem repeats of the Y chromosome (Y-STRs) in humans. The database contains polymorphisms of five U.S. ethnic groups (African-Americans, European Americans, Hispanics, Native Americans, and Asian-Americans) as well as the worldwide population.

For forensic applications, the probability of a 'match' for a crime scene DNA sample and a suspect's DNA often culminates in a guilty or innocent verdict. How is a 'match' determined, and what are the uses and limitations of such probabilities?

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<span>Step 1: Understand the concept of Y-STRs. Y-STRs are short tandem repeats found on the Y chromosome, which are used in forensic analysis because they are passed from father to son without recombination, making them useful for tracing paternal lineage.</span>
<span>Step 2: Learn how a 'match' is determined. In forensic DNA analysis, a 'match' is determined by comparing the Y-STR profile from a crime scene sample to that of a suspect. If the profiles are identical, it suggests that the DNA could have come from the suspect or a paternal relative.</span>
<span>Step 3: Explore the use of probability in determining a 'match'. The probability of a 'match' is calculated based on the frequency of the Y-STR profile in a given population. A low probability indicates that the profile is rare, strengthening the evidence that the suspect's DNA matches the crime scene sample.</span>
<span>Step 4: Consider the uses of Y-STR analysis. Y-STR analysis is used in forensic investigations to identify male individuals, especially in cases where mixed DNA samples are present, such as sexual assault cases.</span>
<span>Step 5: Understand the limitations of Y-STR analysis. One limitation is that Y-STRs cannot distinguish between male relatives who share the same paternal lineage. Additionally, the probability of a 'match' does not prove guilt, as it only indicates the likelihood of the DNA profile occurring in the population.</span>

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

PCR and Y-STRs

Polymerase Chain Reaction (PCR) is a technique used to amplify specific DNA sequences, making it easier to analyze genetic material. Y-chromosome Short Tandem Repeats (Y-STRs) are specific regions on the Y chromosome that vary among individuals and can be used for male lineage tracing. In forensic science, analyzing Y-STRs helps in identifying male DNA in mixed samples, particularly in sexual assault cases.
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Probability of a Match

The probability of a match in forensic DNA analysis refers to the likelihood that a DNA profile from a crime scene sample corresponds to that of a suspect. This is calculated using statistical methods that consider the frequency of specific alleles in the population. A higher probability indicates a stronger likelihood of a match, which can significantly influence legal outcomes, such as determining guilt or innocence.
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Limitations of DNA Evidence

While DNA evidence is powerful, it has limitations. Factors such as sample contamination, degradation, and the presence of mixed DNA profiles can affect the accuracy of results. Additionally, the interpretation of statistical probabilities can be complex, and a high match probability does not guarantee that a suspect is the perpetrator, as coincidental matches can occur in large populations.
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Related Practice
Textbook Question

In humans, congenital heart disease is a common birth defect that affects approximately 1 out of 125 live births. Using reverse transcription PCR (RT-PCR) Samir Zaidi and colleagues [(2013) Nature 498:220.223] determined that approximately 10 percent of the cases resulted from point mutations, often involving histone function. To capture products of gene expression in developing hearts, they used oligo(dT) in their reverse transcription protocol.

How would such a high %T in a primer influence annealing temperature?

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Textbook Question

In humans, congenital heart disease is a common birth defect that affects approximately 1 out of 125 live births. Using reverse transcription PCR (RT-PCR) Samir Zaidi and colleagues [(2013) Nature 498:220.223] determined that approximately 10 percent of the cases resulted from point mutations, often involving histone function. To capture products of gene expression in developing hearts, they used oligo(dT) in their reverse transcription protocol.

Compared with oligo(dT) primers, a pool of random sequence primers requires a trickier assessment of annealing temperature. Why?

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Textbook Question

In humans, congenital heart disease is a common birth defect that affects approximately 1 out of 125 live births. Using reverse transcription PCR (RT-PCR) Samir Zaidi and colleagues [(2013) Nature 498:220.223] determined that approximately 10 percent of the cases resulted from point mutations, often involving histone function. To capture products of gene expression in developing hearts, they used oligo(dT) in their reverse transcription protocol.

If one were interested in comparing the quantitative distribution of gene expression in say, the right and left side of a developing heart, how might one proceed using RT-PCR?

314
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Textbook Question

The U.S. Department of Justice has established a database that catalogs PCR amplification products from short tandem repeats of the Y chromosome (Y-STRs) in humans. The database contains polymorphisms of five U.S. ethnic groups (African-Americans, European Americans, Hispanics, Native Americans, and Asian-Americans) as well as the worldwide population.

Given that STRs are repeats of varying lengths, for example (TCTG)₉₋₁₇ or (TAT)₆₋₁₄, explain how PCR could reveal differences (polymorphisms) among individuals. How could the Department of Justice make use of those differences?

239
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Textbook Question

The U.S. Department of Justice has established a database that catalogs PCR amplification products from short tandem repeats of the Y chromosome (Y-STRs) in humans. The database contains polymorphisms of five U.S. ethnic groups (African-Americans, European Americans, Hispanics, Native Americans, and Asian-Americans) as well as the worldwide population.

Y-STRs from the nonrecombining region of the Y chromosome (NRY) have special relevance for forensic purposes. Why?

281
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Textbook Question

The U.S. Department of Justice has established a database that catalogs PCR amplification products from short tandem repeats of the Y chromosome (Y-STRs) in humans. The database contains polymorphisms of five U.S. ethnic groups (African-Americans, European Americans, Hispanics, Native Americans, and Asian-Americans) as well as the worldwide population.

What would be the value of knowing the ethnic population differences for Y-STR polymorphisms?

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