targetSeqView

targetSeqView detects structural variants within repetitive human genomic regions, particularly Immunoglobulin (Ig) and T-cell receptor (TCR) loci, by applying probability-based scoring to alignments from target-capture and whole-genome sequencing data.

Key Features:

• Probability-Based Scoring System: Quantifies the likelihood of true structural variants versus alignment artifacts to distinguish genuine SVs from false positives.
• Visualization Methodology: Provides visualization techniques to interpret complex variant and alignment patterns within repetitive sequences.
• Validation Across Experimental Designs: Validated using both target-capture sequencing and whole-genome sequencing datasets.
• Application to lymphoid and cell-line datasets: Tested on sequencing reads from primary lymphoid tumors, cancer cell lines, an EBV-transformed lymphoblast cell line, and whole-genome data from a lymphoblastoid cell line.

Scientific Applications:

• Repetitive-region structural variant detection: Enables accurate identification and interpretation of SVs in highly repetitive genomic loci such as Ig and TCR.
• Cancer genomics of lymphoid malignancies: Supports analysis of SVs in primary lymphoid tumors and related cancer cell lines to inform studies of disease mechanisms.

Methodology:

Implements probability-based scoring and visualization methods as an R package applied to alignments from target-capture and whole-genome sequencing.