Why does clonotype diversity or clonal expansion not match expectations?

Answer:
TCR/BCR diversity is influenced by multiple biological factors and may not always reflect technical issues.

Common influencing factors:

• Age: Immune diversity generally decreases with age 

• Infections (viral, bacterial, parasitic):
  May induce clonal expansion of specific lymphocytes
  Examples: 
  • HIV → reduced TCR diversity 
  • EBV (especially in HIV patients) → further disruption 
  • HBV → reduced diversity with CD8+ clonal expansion 

• Tumors:
  Tumor antigens may drive immune activation and clonal expansion.
  Some hematological malignancies originate from clonal lymphocytes. 
• Transplantation:
  Immune system remodeling affects repertoire diversity.
  Stem cell transplantation may restore diversity. 
• Immunotherapy or vaccination:
  Alters T/B cell populations and repertoire composition. 

Recommendation: Interpret results in the context of clinical and biological background, and consider including biological replicates.