Simulation Results

Detection Statistics


            

            

              
Impact on Diversity Measurements

              

              

              

            

            

              
Detection by Clone Size

              

            

            

              
Sequencing Depth Effect

              
Compare different sequencing depths (1K to 1M reads):

              

            

            

              
Understanding the Simulation

              
Biological Context

              
Adaptive immune repertoires contain thousands to millions of unique clonotypes (T-cell or B-cell receptor sequences). A few clones undergo massive expansion (hyperexpanded), while most remain rare (singlets or small clones).

              
Clonality Bias

              
When sequencing depth is insufficient:

              
    
                
  • Hyperexpanded clones are almost always detected
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  • Rare clones are missed at high rates
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  • This makes repertoires appear MORE clonal than they truly are
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  • Diversity is systematically UNDERestimated
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Parameters

              
    
                
  • 
                  Power-law exponent (α):
                   Controls distribution shape. Higher α = steeper decline, more extreme inequality between large and small clones.
                
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                  Sequencing reads:
                   Total number of sequences obtained. Compare to total cells to assess sampling fraction.
                
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                  Minimum threshold:
                   Sequences appearing fewer than this many times are discarded (to filter sequencing errors). Higher thresholds increase bias against rare clones.
                
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Key Metrics

              
    
                
  • 
                  Richness:
                   Number of unique clones detected
                
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                  Shannon entropy:
                   Diversity measure accounting for abundance
                
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                  Clonality:
                   Inverse of normalized diversity (0=maximally diverse, 1=monoclonal)
                
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                  Gini coefficient:
                   Inequality measure (0=perfect equality, 1=maximum inequality)
                
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