# Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination

## TL;DR

This study shows that microhomology in gene sequences significantly influences how immune system receptors are assembled in humans.

## Contribution

The paper demonstrates that germline-encoded microhomology affects trimming and ligation in V(D)J recombination using statistical analysis of TCRα repertoire data.

## Key findings

- Microhomology increases trimming and ligation probabilities during V(D)J recombination.
- Accounting for microhomology improves the accuracy of sequence annotation and event inference.
- The effects of microhomology are consistent across different receptor loci and sequence types.

## Abstract

V(D)J recombination generates the diverse B and T cell receptors essential for recognizing a wide array of antigens. This diversity arises from the combinatorial assembly of V(D)J genes and the junctional deletion and insertion of nucleotides. While previous in vitro studies have shown that microhomology—short stretches of sequence homology between gene ends—can bias the recombination process, the extent of microhomology’s impact in vivo, particularly in humans, remains unknown. In this paper, we assess how germline-encoded microhomology influences trimming and ligation during V(D)J recombination using statistical inference on previously published high-throughput TCRα repertoire sequencing data. We find that microhomology increases both trimming and ligation probabilities, making it an important predictor of recombination outcomes. These effects are consistent across other receptor loci and sequence types. Further, we demonstrate that accounting for germline microhomology effects significantly alters sequence annotation probabilities and rankings, highlighting its practical importance for accurately inferring the V(D)J recombination events that generated an observed sequence. Together, these results enhance our understanding of how germline-encoded microhomologous nucleotides shape the human V(D)J recombination process.

Graphical Abstract