USMLE Step 1 Quiz: Genetic Testing And Diagnostics
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Genetic Testing And DiagnosticsQuestion 1 of 20

In a molecular genetics laboratory, a technician is preparing a labeled, single-stranded DNA molecule. This molecule is designed to be complementary to a specific gene sequence on a chromosome. It will be used in an experiment to visualize the location of that gene within a cell nucleus.

The fundamental principle that allows this DNA 'probe' to bind specifically to its target sequence on the chromosome is known as which of the following?

Hybridization
Translation
Reverse transcription
Polymerization
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USMLE Step 1 Quiz

USMLE Step 1 Quiz: Genetic Testing And Diagnostics

Practice Genetic Testing And Diagnostics in USMLE Step 1 with focused quiz questions that help you check what you know, review explanations, and build confidence with test-style prompts.

What this quiz covers

This quiz focuses on Genetic Testing And Diagnostics, giving you a quick way to practice the rules, question types, and explanations that matter most for USMLE Step 1.

How to use this quiz

Try each quiz question before looking at the correct answer. Use the explanations to review missed ideas, then come back to similar questions until the pattern feels familiar.

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Question 1

In a molecular genetics laboratory, a technician is preparing a labeled, single-stranded DNA molecule. This molecule is designed to be complementary to a specific gene sequence on a chromosome. It will be used in an experiment to visualize the location of that gene within a cell nucleus.

The fundamental principle that allows this DNA 'probe' to bind specifically to its target sequence on the chromosome is known as which of the following?

  1. Hybridization (correct answer)
  2. Translation
  3. Reverse transcription
  4. Polymerization

Explanation: Hybridization is the process by which a single-stranded nucleic acid molecule (DNA or RNA) anneals to its complementary sequence through hydrogen bonds between the bases. This principle of specific base pairing (A with T, G with C) is the foundation for techniques like FISH, Southern blotting, Northern blotting, and microarrays, where a labeled probe is used to detect a target sequence.

Question 2

A geneticist is studying a large family affected by a rare, autosomal dominant form of early-onset dementia. The causative gene is unknown. To identify the chromosomal location of the gene, the researcher genotypes all family members, both affected and unaffected, for hundreds of polymorphic DNA markers spread across the genome. The goal is to find markers that are consistently inherited along with the disease.

This research method, which tracks the co-segregation of a genetic marker and a disease phenotype within a family, is best described as which of the following?

  1. Linkage analysis (correct answer)
  2. Genome-wide association study (GWAS)
  3. Cytogenetic analysis
  4. Case-control study

Explanation: Linkage analysis is a method used to map a disease-causing gene to a specific chromosomal region by studying its inheritance pattern alongside known genetic markers in large families. Markers that are physically close to the disease gene on a chromosome tend to be inherited together (i.e., they are 'linked') and will not assort independently. GWAS is a population-based study to find common variants associated with common diseases, not for mapping rare single-gene disorders in families.

Question 3

A 28-year-old woman of Ashkenazi Jewish descent undergoes carrier screening before trying to conceive. The test is a targeted mutation analysis for the three most common mutations causing Tay-Sachs disease in her ethnic group. The result is reported as negative.

Which of the following is the most accurate interpretation to provide to the patient?

  1. She has zero risk of being a carrier for Tay-Sachs disease.
  2. She should have an enzyme assay instead, as DNA testing is unreliable.
  3. Her risk of being a carrier is significantly reduced, but a small residual risk remains. (correct answer)
  4. She and her partner can have a child with Tay-Sachs disease.

Explanation: Targeted mutation analysis only screens for a specific set of common mutations. A negative result means the person does not carry any of the mutations tested, which significantly lowers their risk. However, it does not rule out the possibility that they could be a carrier of a rare, untested mutation in the same gene. Therefore, a small residual risk of being a carrier always remains after a negative targeted screening test.

Question 4

A newborn presents with multiple congenital anomalies. A physician orders a standard G-banded karyotype, which is reported as 46,XY. Despite the normal karyotype, the physician still suspects a genetic cause, such as cystic fibrosis, which is caused by mutations in the CFTR gene.

The normal karyotype result rules out a large structural or numerical chromosomal abnormality but cannot detect which of the following?

  1. Trisomy 18
  2. A large deletion of the short arm of chromosome 5
  3. A single-gene point mutation (correct answer)
  4. A balanced reciprocal translocation

Explanation: A karyotype provides a low-resolution, microscopic view of the chromosomes. It is excellent for detecting aneuploidy (abnormal chromosome number), such as trisomy 18, and large structural changes like major deletions or translocations. However, its resolution is far too low to detect changes within a single gene, such as a point mutation, a small deletion, or an insertion, which require molecular techniques like DNA sequencing.

Question 5

A 45-year-old man is evaluated for a 2-year history of involuntary, jerky movements and a progressive decline in cognitive function. His father had similar symptoms and died in his late 50s. On neurologic examination, he has chorea and impaired executive function. A diagnosis of Huntington disease is suspected, which is caused by an expansion of a CAG trinucleotide repeat in the HTT gene.

Which of the following molecular diagnostic techniques is most appropriate to confirm the diagnosis by determining the number of CAG repeats in the HTT gene?

  1. Karyotyping
  2. Polymerase chain reaction (PCR) with fragment analysis (correct answer)
  3. Western blotting
  4. Enzyme-linked immunosorbent assay (ELISA)

Explanation: Huntington disease is a trinucleotide repeat disorder. Polymerase chain reaction (PCR) is used to amplify the region of the HTT gene containing the CAG repeat. The size of the resulting DNA fragment, which is proportional to the number of repeats, can then be accurately determined by fragment analysis (e.g., capillary electrophoresis). This is the standard method for diagnosing such disorders. Karyotyping is used for large chromosomal abnormalities. Western blotting detects proteins, not gene repeats. ELISA detects antigens or antibodies.

Question 6

A newborn infant presents with a cleft palate, a heart murmur consistent with a ventricular septal defect, and hypocalcemia causing tetany. The constellation of findings raises suspicion for DiGeorge syndrome, which is typically caused by a microdeletion at chromosome 22q11.2.

Which of the following genetic tests is the most specific and sensitive method for detecting this microdeletion?

  1. G-banded karyotype
  2. Fluorescence in situ hybridization (FISH) (correct answer)
  3. Serum calcium measurement
  4. Y-chromosome analysis

Explanation: DiGeorge syndrome is a classic microdeletion syndrome. The deletion at 22q11.2 is typically too small to be visualized on a standard G-banded karyotype. Fluorescence in situ hybridization (FISH) uses a DNA probe specific to the 22q11.2 region, which will fail to bind if the region is deleted, making it the gold standard for diagnosis. Serum calcium is a biochemical finding, not a genetic test. Y-chromosome analysis is irrelevant.

Question 7

A couple has a child with intellectual disability, a flat facial profile, upslanting palpebral fissures, and a single transverse palmar crease. A cytogenetic analysis is performed on the child's lymphocytes, and the report shows a karyotype of 47,XX,+21.

This result is most consistent with a diagnosis of Down syndrome due to which of the following mechanisms?

  1. Meiotic nondisjunction (correct answer)
  2. Robertsonian translocation
  3. Somatic mosaicism
  4. Uniparental disomy

Explanation: The karyotype 47,XX,+21 indicates that the child, a female, has 47 chromosomes in total, with an extra copy of chromosome 21. This is the classic karyotype for trisomy 21 (Down syndrome). The most common cause (approximately 95% of cases) is the failure of chromosome 21 to segregate properly during meiosis in a parent (meiotic nondisjunction), leading to a gamete with an extra chromosome 21. Robertsonian translocation would result in 46 chromosomes. Mosaicism would show two cell lines. Uniparental disomy would result in 46 chromosomes.

Question 8

A newborn screening test for cystic fibrosis is positive. The infant is of Northern European descent. Confirmatory genetic testing is planned to screen for the most common mutation in the CFTR gene, the ΔF508 mutation, which is a specific 3-base pair deletion.

Which of the following molecular techniques is most suitable for rapidly detecting this specific known mutation?

  1. Allele-specific oligonucleotide (ASO) hybridization (correct answer)
  2. Whole genome sequencing
  3. Northern blotting
  4. Chromosomal microarray

Explanation: Allele-specific oligonucleotide (ASO) hybridization uses probes that bind specifically to either the wild-type or the mutant DNA sequence. This makes it an ideal, rapid, and cost-effective method for screening for a known, common point mutation or small deletion like ΔF508. Whole genome sequencing is unnecessarily broad and expensive for this purpose. Northern blotting analyzes RNA, not the DNA mutation itself. Chromosomal microarray detects copy number variants, not small deletions within a gene.

Question 9

A molecular biologist is performing Sanger sequencing to determine the exact nucleotide sequence of a gene implicated in a familial cancer syndrome. The reaction mixture includes a DNA template, a specific primer, DNA polymerase, and a mix of deoxynucleoside triphosphates (dNTPs).

The termination of DNA synthesis at specific nucleotide positions during Sanger sequencing is achieved through the incorporation of which of the following?

  1. Ribonucleoside triphosphates (rNTPs)
  2. Dideoxynucleoside triphosphates (ddNTPs) (correct answer)
  3. Methylated cytosine bases
  4. Reverse transcriptase

Explanation: Sanger sequencing, also known as the chain-termination method, relies on the use of dideoxynucleoside triphosphates (ddNTPs). These molecules lack the 3'-hydroxyl group required for the formation of a phosphodiester bond. When a ddNTP is incorporated into the growing DNA strand by DNA polymerase, synthesis is terminated. This creates a set of DNA fragments of different lengths, which allows the sequence to be determined.

Question 10

A 5-year-old boy presents with progressive proximal muscle weakness and calf pseudohypertrophy. His serum creatine kinase level is markedly elevated. A muscle biopsy is performed to investigate for Duchenne muscular dystrophy, which is caused by a frameshift mutation in the dystrophin gene leading to a nonfunctional, absent protein.

Which of the following laboratory techniques would be most appropriate to determine if the dystrophin protein is absent in the patient's muscle tissue?

  1. Southern blot
  2. Northern blot
  3. Western blot (correct answer)
  4. Chromosomal microarray

Explanation: The question specifically asks about the presence or absence of a protein. Western blotting is the technique used to separate proteins by size via gel electrophoresis, transfer them to a membrane, and then use a specific antibody (in this case, anti-dystrophin) to detect the protein of interest. Absence of a band would confirm the diagnosis. Southern blot analyzes DNA, Northern blot analyzes RNA, and chromosomal microarray analyzes for DNA copy number variations.

Question 11

A 10-year-old boy is evaluated for intellectual disability, a long face with prominent ears, and macroorchidism. His family history is notable for a maternal uncle with similar features. Fragile X syndrome, a trinucleotide repeat disorder affecting the FMR1 gene on the X chromosome, is suspected.

Molecular analysis of the FMR1 gene promoter in this patient is most likely to show which finding?

  1. A missense point mutation
  2. Extensive DNA hypermethylation (correct answer)
  3. A large chromosomal deletion
  4. Histone acetylation

Explanation: Fragile X syndrome is caused by a large expansion of a CGG trinucleotide repeat in the 5' untranslated region of the FMR1 gene. When the number of repeats exceeds 200 (a full mutation), the CpG islands in the promoter region become hypermethylated. This methylation silences the gene, preventing transcription of FMR1 mRNA and production of the FMRP protein. Histone acetylation is associated with gene activation, not silencing.

Question 12

A laboratory technician is preparing a polymerase chain reaction (PCR) to amplify a specific segment of the beta-globin gene to test for sickle cell anemia. The master mix contains a thermostable DNA polymerase, sequence-specific primers, buffer, and the patient's genomic DNA.

Which of the following components must also be included in the reaction mixture to serve as the building blocks for the newly synthesized DNA strands?

  1. Deoxyribonucleoside triphosphates (dNTPs) (correct answer)
  2. Reverse transcriptase
  3. DNA ligase
  4. RNA polymerase

Explanation: PCR is an in vitro method for DNA synthesis. The DNA polymerase enzyme requires a supply of monomer units to build the new DNA strands. These building blocks are the four deoxyribonucleoside triphosphates: dATP, dCTP, dGTP, and dTTP, collectively known as dNTPs. Reverse transcriptase synthesizes DNA from an RNA template. DNA ligase joins DNA fragments. RNA polymerase synthesizes RNA from a DNA template.

Question 13

A 3-year-old boy is evaluated for global developmental delay and multiple congenital anomalies. A standard G-banded karyotype analysis was performed and reported as normal (46,XY). Because a submicroscopic chromosomal abnormality is still suspected as the cause of the patient's condition, the geneticist recommends further testing.

Which of the following tests offers the highest resolution for detecting genome-wide copy number variants, such as microdeletions and microduplications?

  1. Fluorescence in situ hybridization (FISH)
  2. Chromosomal microarray analysis (CMA) (correct answer)
  3. Southern blotting
  4. Repeat G-banded karyotyping

Explanation: Chromosomal microarray analysis (CMA) is the recommended first-tier genetic test for individuals with unexplained developmental delay or congenital anomalies. It can detect copy number variants (gains or losses of DNA segments) at a much higher resolution than a karyotype, identifying submicroscopic abnormalities. FISH is a targeted test for a specific region, not a genome-wide scan. Southern blotting is not used for this purpose. Repeating the low-resolution karyotype would be unhelpful.

Question 14

A 15-year-old boy presents with slowly progressive muscle weakness. A muscle biopsy is performed, and genetic testing confirms a diagnosis of Becker muscular dystrophy (BMD), caused by an in-frame deletion in the dystrophin gene. This type of mutation results in the production of a truncated but partially functional dystrophin protein. A Western blot is performed on the muscle biopsy sample.

Compared to a sample from a healthy individual, the Western blot from this patient is most likely to show a protein band that is:

  1. Normal in position and intensity
  2. Shifted to a lower apparent molecular weight (correct answer)
  3. Completely absent
  4. Increased in intensity

Explanation: Becker muscular dystrophy results from mutations that allow for the production of a smaller, internally deleted, but still partially functional dystrophin protein. On a Western blot, which separates proteins by size, this truncated protein will migrate further down the gel than the full-length protein from a healthy control. This results in a band at a lower apparent molecular weight. An absent band is characteristic of Duchenne muscular dystrophy.

Question 15

A pregnant woman undergoes chorionic villus sampling (CVS) for prenatal diagnosis of a genetic condition. To ensure the accuracy of the result, the laboratory must rule out contamination of the fetal sample with maternal cells from the uterus or placenta.

Which of the following molecular techniques is most commonly used to detect maternal cell contamination in a fetal DNA sample?

  1. Enzyme activity assay
  2. Analysis of polymorphic short tandem repeats (STRs) (correct answer)
  3. G-banded karyotyping of the mother
  4. Mitochondrial DNA sequencing

Explanation: Analysis of highly variable short tandem repeats (STRs) is a form of DNA fingerprinting. The fetal sample should contain one allele from the mother and one from the father at each STR locus. If the fetal sample's STR profile shows more than one maternal allele, or a signal intensity ratio that is skewed towards the maternal alleles, it indicates maternal cell contamination. The other methods are not suitable for this specific quality control purpose.

Question 16

A 39-year-old woman, who is 12 weeks pregnant, receives a report from her non-invasive prenatal testing (NIPT). The test, which analyzes cell-free fetal DNA in the maternal blood, indicates a high risk for trisomy 21. She is very anxious and asks about the next step.

Which of the following is the most appropriate recommendation for this patient?

  1. Repeat the NIPT to confirm the result
  2. Proceed with pregnancy termination based on this result
  3. Undergo diagnostic testing via amniocentesis or CVS (correct answer)
  4. Reassurance that the test is likely a false positive

Explanation: Non-invasive prenatal testing (NIPT) is a highly accurate screening test, but it is not diagnostic. A high-risk result must be confirmed with a diagnostic test that directly analyzes fetal cells. The options for definitive diagnosis are invasive procedures such as chorionic villus sampling (CVS) in the first trimester or amniocentesis in the second trimester. Clinical decisions, such as pregnancy termination, should only be made after a confirmed diagnostic result.

Question 17

A 1-year-old infant is diagnosed with Angelman syndrome, characterized by developmental delay, seizures, and an unusually happy demeanor. This disorder is caused by a lack of expression of the maternal copy of the UBE3A gene, located in the imprinted region of chromosome 15q11-13. The most common cause is a deletion of the maternal 15q11-13 region.

Which of the following diagnostic tests is most effective for confirming the diagnosis by detecting the abnormal DNA methylation pattern characteristic of Angelman syndrome, regardless of whether it is caused by a deletion or uniparental disomy?

  1. Standard G-banded karyotype
  2. Methylation-specific PCR (correct answer)
  3. Sanger sequencing of the UBE3A gene
  4. Serum UBE3A protein levels

Explanation: Angelman and Prader-Willi syndromes are classic imprinting disorders. The genes in this region are differentially methylated depending on their parental origin. Regardless of the underlying cause (maternal deletion, paternal uniparental disomy, or an imprinting center defect), Angelman syndrome results in an abnormal, exclusively paternal methylation pattern. Methylation-specific PCR is designed to detect these parent-of-origin-specific methylation patterns and is therefore a key diagnostic test.

Question 18

A 50-year-old patient presents to a clinic with jaundice and fatigue. The physician suspects hepatitis C infection. To confirm the diagnosis and quantify the amount of virus in the blood, a sample is sent to the laboratory for molecular testing.

Given that the hepatitis C virus is an RNA virus, which of the following is the most sensitive and specific laboratory test to detect and quantify the viral load?

  1. Southern blot
  2. ELISA for hepatitis C antibodies
  3. Viral culture
  4. Quantitative reverse transcription PCR (qRT-PCR) (correct answer)

Explanation: Quantitative reverse transcription PCR (qRT-PCR) is the standard method for detecting and quantifying RNA viruses like hepatitis C. The viral RNA is first converted to cDNA by reverse transcriptase, and then the cDNA is amplified and quantified by PCR. This method is extremely sensitive and specific. ELISA for antibodies indicates exposure but not necessarily active infection. Viral culture is difficult and slow for HCV. Southern blot detects DNA, not RNA.

Question 19

A 4-year-old boy shows signs of Duchenne muscular dystrophy (DMD), including a positive Gowers' sign. Approximately 65% of DMD cases are caused by large intragenic deletions of one or more exons in the dystrophin gene. The geneticist orders an initial test to screen for such deletions.

Which of the following molecular diagnostic techniques is specifically designed to detect deletions and duplications of multiple exons simultaneously and is a common first-line test for DMD?

  1. Multiplex ligation-dependent probe amplification (MLPA) (correct answer)
  2. Sanger sequencing of the entire gene
  3. G-banded Karyotyping
  4. Northern blotting

Explanation: Multiplex ligation-dependent probe amplification (MLPA) is a semiquantitative PCR-based method designed to determine the copy number of up to 50 different DNA sequences in a single reaction. It is highly effective for detecting exon-level deletions and duplications, making it a standard first-line test for disorders like DMD where such mutations are common. Sanger sequencing is better for point mutations, and karyotyping cannot resolve intragenic changes. Northern blotting assesses mRNA levels.

Question 20

A 30-year-old woman is a known carrier of the X-linked recessive disorder hemophilia A. She has normal coagulation studies and is asymptomatic. Her physician explains that this is due to random X-inactivation, a process where one of the two X chromosomes in each female somatic cell is transcriptionally silenced. To better understand her carrier status and potential risk of symptoms, the physician wants to study the pattern of X-inactivation in her hematopoietic cells.

Analysis of which of the following would provide the most direct assessment of the X-inactivation pattern in this patient?

  1. G-banded karyotype analysis
  2. DNA methylation status of X-linked gene promoters (correct answer)
  3. Mitochondrial DNA copy number
  4. Telomere length analysis

Explanation: X-inactivation is an epigenetic process that involves transcriptional silencing of one X chromosome through DNA methylation. The inactive X chromosome undergoes extensive hypermethylation of CpG islands in gene promoter regions. Analyzing the methylation patterns of X-linked genes can determine which X chromosome (normal vs. mutant allele) is preferentially inactivated in different cell populations, explaining why this carrier remains asymptomatic despite having one defective copy of the coagulation factor gene.