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Ch. 20 - Recombinant DNA Technology
All textbooksKlug 12th EditionCh. 20 - Recombinant DNA TechnologyProblem 33
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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.

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?

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1
<span>Step 1: Understand the concept of Short Tandem Repeats (STRs). STRs are sequences of DNA where a short sequence of bases is repeated in tandem. The number of repeats can vary among individuals, making them useful for genetic differentiation.</span>
<span>Step 2: Learn about PCR (Polymerase Chain Reaction). PCR is a technique used to amplify specific DNA sequences, making it easier to analyze small amounts of DNA. In the context of STRs, PCR can be used to amplify the regions containing these repeats.</span>
<span>Step 3: Analyze how PCR reveals polymorphisms. By amplifying STR regions, PCR can produce DNA fragments of varying lengths depending on the number of repeats present in an individual's DNA. These differences in fragment length can be visualized using gel electrophoresis.</span>
<span>Step 4: Consider the application of these differences. The Department of Justice can use the variation in STR lengths to differentiate between individuals. This is particularly useful in forensic science for identifying individuals or establishing familial relationships.</span>
<span>Step 5: Explore the significance of the Y chromosome STRs. Since the Y chromosome is passed from father to son, Y-STRs can be used to trace paternal lineage and are particularly useful in cases where male-specific identification is needed.</span>

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Key Concepts

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

Short Tandem Repeats (STRs)

Short Tandem Repeats (STRs) are repeating sequences of DNA that vary in length among individuals. These polymorphic regions are highly variable, making them useful for genetic profiling. The number of repeats can differ between individuals, which allows for the identification of genetic differences that can be used in forensic analysis and paternity testing.
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Polymerase Chain Reaction (PCR)

Polymerase Chain Reaction (PCR) is a technique used to amplify specific DNA sequences, making millions of copies of a targeted region. This process involves repeated cycles of denaturation, annealing, and extension, allowing for the analysis of STRs even from small or degraded samples. PCR is crucial for detecting the variations in STRs that can distinguish between individuals.
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Forensic Applications of Y-STRs

Y-STRs are specific to the Y chromosome and are inherited paternally, making them particularly useful in forensic investigations involving male lineage. The U.S. Department of Justice can utilize the differences in Y-STR profiles to identify suspects, establish paternity, or resolve cases of sexual assault, where male DNA may be present. This database aids in matching DNA samples to individuals based on their unique STR patterns.
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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?

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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.

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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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?

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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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Textbook Question

There are a variety of circumstances under which rapid results using multiple markers in PCR amplifications are highly desired, such as in forensics, pathogen analysis, or detection of genetically modified organisms. In multiplex PCR, multiple sets of primers are used, often with less success than when applied to PCR as individual sets. Numerous studies have been conducted to optimize procedures, but each has described the process as time consuming and often unsuccessful. Considering the information given in Problem 30, why should multiplex PCR be any different than single primer set PCR in terms of dependability and ease of optimization?

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