Short Tandem Repeat Analysis — MCQs
Which of the following techniques can be used to detect single base pair substitutions?
Which of the following is the least suitable source for DNA extraction?
DNA fingerprinting was first used by Alec Jeffreys in a criminal case for detecting:
DNA fingerprinting is used for paternity testing and forensic identification of suspects. Which of the following is the most accurate description of DNA fingerprinting?
Which of the following are examples of trinucleotide repeat mutations?
34 week primigravida punjabi khatri comes with history of consanguineous marriage, with history of repeated blood transfusion to her sibling since 8 months of age. The first diagnostic test is -
The given karyotype is seen in which of the following syndromes?
In a macerated baby, the ideal sample for genetic analysis is obtained from:
The Takayama test is primarily used for what purpose?
DNA fingerprinting is based on possessing what in DNA?
Short Tandem Repeat Analysis Indian Medical PG Practice Questions and MCQs
Question 1: Which of the following techniques can be used to detect single base pair substitutions?
- A. FISH
- B. Southern blot
- C. PCR (Correct Answer)
- D. Restriction Fragment Length Polymorphism (RFLP)
Explanation: ***PCR (with sequencing or allele-specific methods)*** - **PCR-based techniques** are the most versatile methods for detecting single base pair substitutions (point mutations) - **Allele-specific PCR** can directly detect known point mutations by using primers specific to mutant or wild-type alleles - **PCR followed by Sanger sequencing** is the gold standard for identifying any single base pair substitution - **High-resolution melting (HRM) analysis** after PCR can detect mutations based on melting curve differences - PCR amplification is the foundation that enables these detection methods *FISH (Fluorescence in situ hybridization)* - FISH detects **large chromosomal abnormalities** such as aneuploidy, translocations, large deletions, and duplications - It visualizes chromosomal-level changes using fluorescent probes - **Not sensitive enough** to detect single base pair changes, as these are too small to visualize cytogenetically *Southern blot* - Southern blot detects **large DNA rearrangements**, insertions, deletions, or copy number variations - Analyzes restriction enzyme fragments separated by gel electrophoresis - **Generally cannot detect** single base pair substitutions unless they create or abolish a restriction enzyme recognition site - Even when applicable, PCR-based methods are more efficient and sensitive *Restriction Fragment Length Polymorphism (RFLP)* - RFLP can detect single base pair substitutions **only if** they create or abolish a **restriction enzyme recognition site** - Classic example: **Sickle cell mutation** (GAG→GTG in β-globin gene) abolishes an MstII restriction site - **Limited applicability** - can only detect the subset of point mutations that affect restriction sites - PCR-based methods are preferred as they can detect **any** single base pair substitution, not just those affecting restriction sites
Question 2: Which of the following is the least suitable source for DNA extraction?
- A. CSF (Correct Answer)
- B. Hair roots
- C. Semen
- D. Buccal mucosa
Explanation: ***CSF*** - **Cerebrospinal fluid (CSF)** contains a relatively **low number of cells**, making it a poor source for DNA extraction compared to other bodily fluids due to the scarcity of nuclear DNA. - While DNA can be extracted from CSF for specific diagnostic purposes (e.g., detection of pathogens), it is generally **not the preferred source** for DNA profiling or genetic studies due to the limited yield and potential for degradation. *Hair roots* - **Hair roots** (specifically the follicular tag) contain a significant number of **nucleated cells**, making them an excellent source for DNA extraction. - The DNA extracted from hair roots is often robust and sufficient for **forensic analysis** and genetic testing. *Semen* - **Semen** contains a high concentration of **sperm cells**, which are rich in nuclear DNA, making it a very good source for DNA extraction. - It is frequently used in **forensic investigations** and paternity testing due to its high DNA content. *Buccal mucosa* - **Buccal cells** scraped from the inside of the cheek provide a non-invasive and **abundant source of nucleated cells** for DNA extraction. - This method is widely used for genetic testing, **ancestry tracing**, and clinical diagnostics because of its ease of collection and high DNA yield.
Question 3: DNA fingerprinting was first used by Alec Jeffreys in a criminal case for detecting:
- A. Immigration purpose
- B. Disputed paternity
- C. Murder
- D. Rape (Correct Answer)
Explanation: ***Rape*** - **Alec Jeffreys** first applied DNA fingerprinting in 1986 to solve the **Narborough murders case** in Leicestershire, UK. - The technique was used to analyze **semen samples** from two rape-murder victims (1983 and 1986), linking them to a single perpetrator. - The **DNA evidence from semen** (sexual assault evidence) was the key forensic material that demonstrated the power of DNA fingerprinting in criminal investigation. - This led to the conviction of **Colin Pitchfork** in 1988, marking the first use of DNA profiling to solve a criminal case. *Immigration purpose* - While DNA fingerprinting is used for immigration cases to confirm family relationships, this was **not its initial application** by Jeffreys. - Its use in immigration came later, after its breakthrough in criminal forensics. *Disputed paternity* - Paternity testing is a common application of DNA fingerprinting, but it was **not the first criminal case** where Jeffreys demonstrated its utility. - The technique's power in establishing biological relationships was recognized after its initial use in criminal investigations. *Murder* - While the Narborough case did involve murders, the question focuses on what was **detected through DNA evidence**. - The DNA profiling was performed on **semen samples** (rape evidence), not on evidence directly proving murder. - The forensic breakthrough was in linking the sexual assault evidence to the perpetrator, which then solved the murder cases.
Question 4: DNA fingerprinting is used for paternity testing and forensic identification of suspects. Which of the following is the most accurate description of DNA fingerprinting?
- A. DNA is isolated from blood, skin, or sperm and its fragment size distribution is analyzed by gel electrophoresis
- B. DNA can be isolated from blood, skin, or sperm and analyzed for variable patterns of restriction fragments arising from tandemly repeated sequences (microsatellites) (Correct Answer)
- C. DNA is isolated from blood, skin, or sperm and hybridized with probes from the HLA locus to visualize HLA gene patterns
- D. DNA is copied from blood, skin, or sperm RNA using reverse transcriptase and analyzed for the pattern of complementary DNAs
Explanation: ***DNA can be isolated from blood, skin, or sperm and analyzed for variable patterns of restriction fragments arising from tandemly repeated sequences (microsatellites)*** - **DNA fingerprinting**, also known as **DNA profiling**, primarily relies on the analysis of highly variable regions of DNA, specifically **tandemly repeated sequences** like microsatellites or STRs (short tandem repeats). - These regions exhibit individual-specific variation in the number of repeats, which, when cut by **restriction enzymes**, produce fragments of varying lengths, generating a unique **restriction fragment length polymorphism (RFLP)** pattern. *DNA is isolated from blood, skin, or sperm and its fragment size distribution is analyzed by gel electrophoresis* - While **gel electrophoresis** is a part of the process to separate DNA fragments by size, this option is incomplete as it doesn't specify *what* fragments are being analyzed or *why* they differ between individuals. - The crucial aspect of DNA fingerprinting is the analysis of **variable short tandem repeats (STRs)** or **variable number tandem repeats (VNTRs)**, which generate these distinct fragment sizes. *DNA is isolated from blood, skin, or sperm and hybridized with probes from the HLA locus to visualize HLA gene patterns* - **HLA (Human Leukocyte Antigen)** typing is used for tissue matching in transplantation and for studying autoimmune diseases, but it is **not the primary method** for DNA fingerprinting in paternity or forensic cases. - While HLA genes are polymorphic, the specific patterns examined in DNA fingerprinting are typically **non-coding repetitive sequences** which are more variable and less complex to interpret for individual identification. *DNA is copied from blood, skin, or sperm RNA using reverse transcriptase and analyzed for the pattern of complementary DNAs* - **DNA fingerprinting** directly analyzes **genomic DNA**, not RNA. The process of reverse transcribing RNA into cDNA is typically used for studying gene expression. - **RNA is less stable** than DNA and does not contain the same highly variable **repetitive sequences** (like STRs or VNTRs) that are fundamental to DNA fingerprinting.
Question 5: Which of the following are examples of trinucleotide repeat mutations?
- A. Friedreich ataxia
- B. Fragile X syndrome
- C. Huntington's chorea
- D. All of the options (Correct Answer)
Explanation: ***All of the options*** - **Fragile X syndrome**, **Friedreich ataxia**, and **Huntington's chorea** are all well-known examples of genetic disorders caused by trinucleotide repeat expansions [1]. - The mutations involve an abnormal increase in the number of repetitions of a specific three-nucleotide sequence in the DNA [1]. *Fragile X syndrome* - This condition is caused by an expansion of the **CGG repeat** in the **FMR1 gene** on the X chromosome [1]. - The expansion leads to hypermethylation and silencing of the gene, impairing the production of fragile X mental retardation protein [1]. *Friedreich ataxia* - This is an autosomal recessive neurodegenerative disorder caused by an expansion of the **GAA repeat** in an intron of the **frataxin gene (FXN)**. - The repeat expansion interferes with transcription, leading to reduced frataxin protein levels. *Huntington's chorea* - This is an autosomal dominant neurodegenerative disorder caused by an expansion of the **CAG repeat** in the **huntingtin gene (HTT)**. - The expanded polyglutamine tract in the huntingtin protein leads to protein misfolding and neuronal damage, particularly in the striatum [1]. **References:** [1] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. Genetic Disorders, pp. 177-181.
Question 6: 34 week primigravida punjabi khatri comes with history of consanguineous marriage, with history of repeated blood transfusion to her sibling since 8 months of age. The first diagnostic test is -
- A. HPLC
- B. Bone marrow
- C. Blood smear
- D. Hb electrophoresis (Correct Answer)
Explanation: ***Hb electrophoresis*** - The patient's history of **consanguineous marriage**, a sibling requiring **repeated blood transfusions** since 8 months of age, and Punjabi Khatri ethnicity strongly suggest a **hemoglobinopathy**, likely **beta-thalassemia major or intermedia**. - **Hemoglobin electrophoresis** is the traditional gold standard for definitive diagnosis of various hemoglobin variants and thalassemia types, identifying and characterizing abnormal hemoglobin patterns (e.g., elevated HbF, HbA2). - It remains a primary diagnostic test for hemoglobinopathies, particularly useful for pattern recognition of various thalassemia syndromes. *HPLC* - **High-performance liquid chromatography (HPLC)** is an equally valid and increasingly preferred method for diagnosing hemoglobinopathies, offering automated, precise quantification of hemoglobin fractions (HbA, HbA2, HbF). - In modern practice, HPLC is often used as a first-line screening tool due to its accuracy, reproducibility, and ability to provide quantitative data crucial for thalassemia diagnosis. - Both HPLC and Hb electrophoresis are acceptable diagnostic approaches; the choice between them depends on laboratory availability and practice patterns. For this 2013 exam, Hb electrophoresis was considered the traditional first diagnostic test. *Blood smear* - A **peripheral blood smear** would show morphological changes like **microcytic hypochromic red blood cells**, **target cells**, **anisopoikilocytosis**, and **nucleated RBCs**, which are suggestive of thalassemia. - These findings are indicative but non-specific and require confirmatory tests like hemoglobin electrophoresis or HPLC to identify the specific hemoglobin disorder and establish a definitive diagnosis. *Bone marrow* - A **bone marrow** examination would show **erythroid hyperplasia** due to increased ineffective erythropoiesis in thalassemia but is an invasive procedure and not the initial diagnostic test for hemoglobinopathies. - It provides details about cellularity and maturation but does not directly identify hemoglobin abnormalities, making it unsuitable as the first diagnostic step in suspected hemoglobinopathies.
Question 7: The given karyotype is seen in which of the following syndromes?
- A. Angelman syndrome
- B. Fragile x syndrome
- C. Down syndrome (Correct Answer)
- D. Turner syndrome
Explanation: ***Correct: Down syndrome*** - The karyotype shows **trisomy 21** (47 chromosomes with an extra chromosome 21), which causes **Down syndrome**. - This is the most common chromosomal abnormality, with characteristic karyotype showing **three copies of chromosome 21**. - Clinical features include intellectual disability, characteristic facies, and congenital heart defects. *Incorrect: Angelman syndrome* - Caused by **deletion or mutation of UBE3A gene** on chromosome 15, not trisomy 21. - Shows normal chromosomal number (46 chromosomes), unlike the **47 chromosomes** seen in this karyotype. - Characterized by developmental delay, seizures, and happy demeanor. *Incorrect: Fragile X syndrome* - Results from **CGG repeat expansion** in the FMR1 gene on the X chromosome. - Typically shows **normal karyotype structure** (46 chromosomes), not the **extra chromosome 21** visible here. - Most common inherited cause of intellectual disability. *Incorrect: Cri du chat syndrome* - Caused by **deletion on chromosome 5p**, which would show as a **missing chromosomal segment**. - The karyotype would show **46 chromosomes with 5p deletion**, not **47 chromosomes with trisomy 21**. - Named for characteristic cat-like cry in infancy. *Incorrect: Turner syndrome* - Results from **missing X chromosome** (45,X karyotype) in females. - Shows **45 chromosomes total**, not the **47 chromosomes with extra chromosome 21** seen here. - Presents with short stature and ovarian dysgenesis.
Question 8: In a macerated baby, the ideal sample for genetic analysis is obtained from:
- A. Clotted fetal blood
- B. Placental Tissue (Correct Answer)
- C. Fibroblast from skin
- D. Fibroblast from Achilles tendon
Explanation: ***Placental Tissue*** - **Placental tissue** (chorionic villi) is preferred for genetic analysis in macerated fetuses because it is less susceptible to **autolysis** and **bacterial contamination** compared to fetal tissues. - The placenta often retains viable cells with intact DNA even when fetal tissues have significantly degraded, making it a more reliable source for **karyotyping** or **molecular genetic studies**. *Clotted fetal blood* - **Clotted fetal blood** from a macerated fetus is generally unsuitable due to significant **cellular degradation** and **DNA fragmentation** caused by autolysis. - The quality of DNA extracted from such a sample would likely be poor, leading to unreliable or unsuccessful genetic testing. *Fibroblast from skin* - While fibroblasts can be cultured from skin, obtaining a viable biopsy from a **macerated fetus** is challenging due to extensive **tissue degradation** and the high risk of **bacterial contamination**. - Successful culture and growth of fibroblasts would be unlikely given the compromised state of the fetal tissue. *Fibroblast from Achilles tendon* - Similar to skin, obtaining viable fibroblasts from the **Achilles tendon** of a macerated fetus is difficult due to widespread **autolysis** and **tissue degeneration**. - The degradation of cells in macerated fetuses significantly reduces the chances of culturing viable cells needed for genetic analysis from any fetal tissue, including tendons.
Question 9: The Takayama test is primarily used for what purpose?
- A. To determine the crystalline structure of a stain. (Correct Answer)
- B. To identify the species of origin of a stain.
- C. To perform blood grouping.
- D. None of the above.
Explanation: The **Takayama test** (also known as the **Haemochromogen crystal test**) is a microcrystalline test used for the confirmatory identification of blood. ### Why Option A is Correct The test involves treating a suspected bloodstain with Takayama reagent (containing glucose, sodium hydroxide, and pyridine). When heated, the pyridine reacts with the heme group of hemoglobin to form **pink, feathery, needle-shaped crystals** of pyridine haemochromogen. Therefore, the test's primary mechanism is the formation and observation of a specific **crystalline structure**, confirming the presence of hemoglobin. ### Why Other Options are Incorrect * **Option B:** Species of origin is determined using **serological tests** like the **Precipitin test** or Electrophoresis (e.g., Counter-immunoelectrophoresis), which rely on antigen-antibody reactions. * **Option C:** Blood grouping is typically performed using the **Absorption-Elution method** (Siracusa method) or the **Lattes Crust method** to identify ABO antigens or antibodies in dried stains. ### High-Yield Pearls for NEET-PG * **Confirmatory vs. Screening:** The Takayama test and Teichmann test are **confirmatory** for blood. Benzidine, Phenolphthalein (Kastle-Meyer), and Luminol are **presumptive/screening** tests. * **Takayama vs. Teichmann:** The Takayama test is generally preferred over the Teichmann (Haemin) test because it is more reliable, works better on old/weathered stains, and requires less heat. * **Reagent Components:** Remember the "Pyridine" in Takayama reagent; it is the key chemical that produces the characteristic pink crystals.
Question 10: DNA fingerprinting is based on possessing what in DNA?
- A. Constant tandem repeat
- B. Variable number tandem repeat (Correct Answer)
- C. Non-repetitive sequence
- D. Exon
Explanation: **Explanation:** DNA fingerprinting (DNA profiling) relies on the fact that while 99.9% of human DNA is identical, certain regions of non-coding DNA are highly polymorphic. The correct answer is **Variable Number Tandem Repeats (VNTRs)**, also known as minisatellites. These are short sequences of DNA (10–100 base pairs) that are repeated head-to-tail. The number of repeats varies significantly between individuals, creating a unique genetic "barcode" used for identification. **Analysis of Options:** * **B. Variable Number Tandem Repeat (Correct):** These serve as the molecular basis for RFLP (Restriction Fragment Length Polymorphism) and traditional DNA profiling because the length of these repetitive segments is inherited and unique to every individual (except monozygotic twins). * **A. Constant Tandem Repeat:** If repeats were constant across the population, they would provide no discriminatory power for forensic identification. * **C. Non-repetitive Sequence:** Most of the human genome consists of unique, non-repetitive sequences (genes). These do not show the high level of variation required to distinguish between two individuals. * **D. Exon:** Exons are the coding regions of DNA. They are highly conserved to maintain protein function; therefore, they lack the polymorphism needed for forensic profiling. **NEET-PG High-Yield Pearls:** * **Father of DNA Fingerprinting:** Sir Alec Jeffreys (World); Dr. Lalji Singh (India). * **STRs (Short Tandem Repeats):** Currently the "Gold Standard" in forensics. These are microsatellites (2–6 bp) that are easier to amplify via PCR than VNTRs. * **Mitochondrial DNA (mtDNA):** Used for maternal lineage and when samples are highly degraded (e.g., old bones/hair shafts). * **Specimen Choice:** Any nucleated cell can be used (Blood, Semen, Hair follicle, Skin). Mature RBCs cannot be used as they lack a nucleus.
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