Highest Resolution Technique for Detecting Chromosomal Alterations

Which one of the following techniques is of highest resolution for detection of chromosomal alterations?
A. PCR
B. CGH
C. G-banding
D. C-banding

Detecting chromosomal alterations is crucial for understanding genetic disorders, cancer development, and evolutionary biology. Several cytogenetic and molecular techniques are used to identify structural and numerical changes in chromosomes. However, these techniques vary significantly in resolution, sensitivity, and specificity. Understanding the differences between these methods helps researchers and clinicians choose the most effective approach for detecting chromosomal abnormalities.

Correct Answer:

The correct answer is (B) CGH (Comparative Genomic Hybridization).

What are Chromosomal Alterations?

Chromosomal alterations refer to changes in the structure or number of chromosomes. These changes can lead to genetic disorders, cancers, and developmental abnormalities. Chromosomal alterations are classified into:

• Structural Alterations:

  • Deletions
  • Duplications
  • Inversions
  • Translocations

• Numerical Alterations:

  • Aneuploidy (extra or missing chromosomes)
  • Polyploidy (extra sets of chromosomes)

Detecting these alterations requires high-resolution techniques to analyze chromosome structure and composition at the molecular level.

Comparison of Techniques for Chromosomal Alteration Detection

1. Polymerase Chain Reaction (PCR)

PCR is a molecular technique used to amplify specific DNA sequences.

How PCR Works:

• DNA is denatured at high temperature (95°C).
• Primers anneal to the target DNA sequence at 50–65°C.
• DNA polymerase extends the primers, synthesizing a new DNA strand at 72°C.

Strengths of PCR:

1  High sensitivity for detecting mutations and small deletions.
2  Fast and cost-effective.

Limitations of PCR:

• Low resolution for detecting large chromosomal alterations.
• Cannot identify balanced rearrangements or copy number variations.

2. Comparative Genomic Hybridization (CGH)

CGH is a high-resolution molecular cytogenetic technique used to detect copy number variations (CNVs).

How CGH Works:

• DNA from a test sample and a reference sample are labeled with different fluorescent dyes.
• The labeled DNA is co-hybridized to a metaphase chromosome or microarray slide.
• Differences in fluorescence intensity indicate gain or loss of chromosomal material.

Strengths of CGH:

1  High resolution for detecting deletions, duplications, and amplifications.
2  Genome-wide analysis.
3 Useful for identifying small chromosomal alterations missed by other techniques.

Limitations of CGH:

• Cannot detect balanced rearrangements (e.g., translocations, inversions).
• Expensive and technically demanding.

3. G-Banding (Giemsa Banding)

G-banding is a classical cytogenetic technique used to visualize chromosomal structure.

How G-Banding Works:

• Chromosomes are stained with Giemsa dye.
• Dark and light bands represent AT- and GC-rich regions, respectively.

Strengths of G-Banding:

1 Detects large structural changes.
2  Useful for karyotyping and diagnosing aneuploidy.

Limitations of G-Banding:

• Low resolution (~5–10 Mb).
• Cannot detect small deletions or duplications.

4. C-Banding

C-banding is used to stain constitutive heterochromatin regions, primarily around centromeres.

How C-Banding Works:

• Chromosomes are treated with acid and alkaline solutions before staining with Giemsa.
• Only heterochromatic regions (centromeres) are stained.

Strengths of C-Banding:

1 Useful for identifying centromeric rearrangements.
2 Effective for studying satellite DNA.

Limitations of C-Banding:

• Extremely low resolution.
• Limited to centromeric regions only.

Why CGH is the Highest Resolution Technique

1. CGH provides high resolution (up to 1 kb in array-based CGH).
2 It detects small chromosomal alterations that cannot be seen with G-banding or C-banding.
3 Genome-wide analysis allows for comprehensive profiling of chromosomal changes.

Why Other Options Are Incorrect:

• (A) PCR – High sensitivity but low resolution for large chromosomal changes.
• (C) G-Banding – Detects large alterations but lacks fine detail.
• (D) C-Banding – Limited to centromeric regions and low resolution.

Comparison of Resolution and Applications

Importance of CGH in Molecular Biology

CGH has revolutionized chromosomal analysis by offering:
1. High resolution for genome-wide analysis.
2. Detection of microdeletions and duplications.
3. Application in cancer genomics, prenatal diagnosis, and genetic disorders.

Conclusion

Among PCR, CGH, G-banding, and C-banding, Comparative Genomic Hybridization (CGH) provides the highest resolution for detecting chromosomal alterations. CGH is particularly effective for detecting copy number variations and small structural abnormalities. While PCR and banding techniques have specific applications, CGH remains the most powerful tool for high-resolution chromosomal analysis.