Table 2 Recovery of TCR V(D)J recombination reads from SKCM WXS files: proportions for barcodes representing ECM structural protein mutant AA adjacent to an MMP2-sensitive site

From: Potential MMP2-mediated availability of HLA binding, mutant ECM peptides reflects better melanoma survival rates and greater T-cell infiltrates

 

Fraction of total SKCM WXS with the indicated recombination read recovery

Fraction of WXS files, with the indicated recombination read recovery, representing barcodes with mutant AA adjacent to an MMP2-sensitive site

Fraction of WXS files, with the indicated recombination read recovery, representing barcodes with mutant AA NOT adjacent to an MMP2-sensitive site

Fraction of WXS files, with the indicated recombination read recovery, representing barcodes with mutant AA adjacent to a new MMP2-sensitive site (i.e., a site dependent on an adjacent mutant AA)

Fraction of WXS files, with the indicated recombination read recovery, representing barcodes with mutant AA adjacent to an MMP2-sensitive site but not including barcodes that have ONLY new MMP2-sensitive sites (which are sites dependent on an adjacent mutant AA)

TRA

0.605

0.644

0.572

0.705

0.632

TRB

0.554

0.588

0.510

0.588

0.589

Maximum possible WXS files

471

197

145

34

163

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