Table A1.
TP53 status determined by ddPCR and NGS analyses in a subset of retrospective and prospective FFPE samples.
| Sample | IHC (%) | ddPCR FFPE-DNA * |
NGS FFPE-DNA | ddPCR/NGS Combined Data |
||||
|---|---|---|---|---|---|---|---|---|
| Sequence Change | Exon | VAF | Varsome Prediction |
|||||
| 1 | GR001 | 0 | Del | c.104del/p.Leu35CysfsTer9 | 4/11 | 0.1917 | Pathogenic | Del/disruptive |
| 2 | GR004 | 0 | Not-del | c.637C>T/p.Arg213Ter | 6/11 | 0.1918 | Pathogenic | Not-del/disruptive |
| c.524G>A/p.Arg175His | 5/11 | 0.0143 | Pathogenic | |||||
| 3 | GR008 | 0 | Del | c.158G>A/p.Trp53Ter | 4/11 | 0.4982 | Pathogenic | Del/disruptive |
| 4 | GR016 | 0 | Del | c.830del/p.Cys277PhefsTer68 | 8/11 | 0.0769 | Likely pathogenic | Del/disruptive |
| 5 | GR022 | 0 | Del | c.916C>T/p.Arg306Ter | 8/11 | 0.4483 | Pathogenic | Del/disruptive |
| 6 | GR028 | 0 | Del | c.159G>A/p.Trp53Ter | 4/11 | 0.3838 | Pathogenic | Del/disruptive |
| c.161dup/p.Thr55HisfsTer2 | 4/11 | 0.3810 | Likely pathogenic | |||||
| 7 | GR034 | 0 | Del | c.949C>T/p.Gln317Ter | 9/11 | 0.2632 | Pathogenic | Del/disruptive |
| c.587G>A/p.Arg196Gln | 6/11 | 0.0121 | Pathogenic | |||||
| 8 | GR050 | 0 | Del | c.724_731del/p.Cys242ArgfsTer19 | 7/11 | 0.3852 | Likely pathogenic | Del/disruptive |
| 9 | GR062 | 0 | Not-del | wt | - | - | - | Not-del/wt |
| 10 | G016 | 0 | Del | c.637C>T/p.Arg213Ter | 6/11 | 0.2537 | Pathogenic | Del/disruptive |
| 11 | G036 | 0 | Del | wt | - | - | - | Del/wt |
| 12 | G069 | 0 | Del | c.326del/p.Phe109SerfsTer14 | 4/11 | 0.3125 | Likely pathogenic | Del/disruptive |
| c.532C>G/p.His178Asp | 5/11 | 0.0455 | Pathogenic | |||||
| c.476C>G/p.Ala159Gly | 5/11 | 0.0455 | Pathogenic | |||||
| 13 | GR010 | 1 | Del | wt | - | - | - | Del/wt |
| 14 | GR049 | 2 | Del | wt | - | - | - | Del/wt |
| 15 | G043 | 2 | Not-del | wt | - | - | - | Not-del/wt |
| 1 | G048 | 5 | Not-del | wt | - | - | - | Not-del/wt |
| 2 | G049 | 5 | Del | c.1040C>G/p.Ala347Gly | 10/11 | 0.0909 | VUS | Del/IF |
| 3 | GR061 | 10 | Not-del | c.799C>T/p.Arg267Trp | 8/11 | 0.1754 | Pathogenic | Not-del/IF |
| 4 | G070 | 10 | Del | c.706T>C/p.Tyr236His | 7/11 | 0.1111 | Pathogenic | Del/IF |
| c.542G>A/p.Arg181His | 5/11 | 0.1000 | Pathogenic | |||||
| 5 | GR029 | 15 | Del | c.1146del/p.Lys382AsnfsTer40 | 11/11 | 0.2198 | Pathogenic | Del/disruptive |
| 6 | G077 | 15 | Del | wt | - | - | - | Del/wt |
| 7 | GR033 | 20 | Not-del | wt | - | - | - | Not-del/wt |
| 8 | G020 | 20 | Del | wt | - | - | - | Del/wt |
| 9 | G039 N5 | 20 | Not-del | c.902del/p.Pro301GlnfsTer44 | 8/11 | 0.0135 | Pathogenic | Not-del/disruptive |
| 10 | G068 | 20 | Del | c.524G>A/p.Arg175His | 5/11 | 0.4552 | Pathogenic | Del/IF |
| 11 | G021 | 25 | Not-del | wt | - | - | - | Not-del/wt |
| 12 | G074 | 25 | Not-del | wt | - | - | - | Not-del/wt |
| 13 | G075 | 30 | Not-del | c.652_654dup/p.Val218dup | 6/11 | 0.0476 | Pathogenic | Not-del/IF |
| 14 | GR002 | 40 | Not-del | c.856G>A/p.Glu286Lys | 8/11 | 0.1479 | Pathogenic | Not-del/IF |
| c.772G>T/p.Glu258Ter | 7/11 | 0.0118 | Pathogenic | |||||
| c.400T>C/p.Phe134Leu | 5/11 | 0.0784 | Pathogenic | |||||
| 15 | GR043 | 60 | Del | c.713G>A/p.Cys238Tyr | 7/11 | 0.0633 | Pathogenic | Del/IF |
| 1 | A564 | 75 | Del | c.326T>G/p.Phe109Cys | 4/11 | 0.6904 | Pathogenic | Del/IF |
| 2 | G002 | 75 | Not-del | c.818G>A/p.Arg273His | 8/11 | 0.2280 | Pathogenic | Not-del/IF |
| 3 | G064 | 75 | Del | c.1024C>G/p.Arg342Gly | 10/11 | 0.7143 | VUS | Del/IF |
| c.380C>T/p.Ser127Phe | 5/11 | 0.4000 | Pathogenic | |||||
| c.310del/p.Gln104ArgfsTer19 | 4/11 | 0.0417 | Pathogenic | |||||
| 4 | G045 | 75 | Not-del | c.524G>A/p.Arg175His | 5/11 | 0.4444 | Pathogenic | Not-del/IF |
| c.482C>G/p.Ala161Gly | 5/11 | 0.1000 | Likely pathogenic | |||||
| c.532C>T/p.His178Tyr | 5/11 | 0.0909 | Pathogenic | |||||
| 5 | G072 | 75 | Del | c.455C>T/p.Pro152Leu | 5/11 | 0.0580 | Pathogenic | Del/IF |
| 6 | A577 | 80 | Del | c.451C>T/p.Pro151Ser | 5/11 | 0.6603 | Pathogenic | Del/IF |
| 7 | A573 | 80 | Del | c.703_705del/p.Asn235del | 7/11 | 0.1329 | Pathogenic | Del/IF |
| 8 | G024 | 85 | Del | c.770T>A/p.Leu257Gln | 7/11 | 0.5581 | Pathogenic | Del/IF |
| c.950A>G/p.Gln317Arg | 9/11 | 0.0321 | VUS | |||||
| 9 | GR037 | 90 | Del | c.623A>T/p.Asp208Val | 6/11 | 0.4687 | Likely pathogenic | Del/IF |
| 10 | GR054 | 90 | Del | c.700T>G/p.Tyr234Asp | 7/11 | 0.7577 | Pathogenic | Del/IF |
| 11 | GR075 | 90 | Del | c.524G>A/p.Arg175His | 5/11 | 0.1948 | Pathogenic | Del/IF |
| 12 | G013 | 90 | Not-del | c.809T>C/p.Phe270Ser | 8/11 | 0.6015 | Pathogenic | Not-del/IF |
| 13 | G025 | 90 | Del | c.817C>T/p.Arg273Cys | 8/11 | 0.0900 | Pathogenic | Del/IF |
| 14 | G039 N10 | 90 | Del | c.733G>A/p.Gly245Ser | 7/11 | 0.5567 | Pathogenic | Del/IF |
| 15 | G042 | 90 | Del | c.808T>G/p.Phe270Val | 8/11 | 0.6376 | Pathogenic | Del/IF |
| 16 | G050 | 90 | Not-del | c.528C>G/p.Cys176Trp | 5/11 | 0.1842 | Pathogenic | Not-del/IF |
| 17 | G054 | 90 | Del | c.638G>T/p.Arg213Leu | 6/11 | 0.5130 | Pathogenic | Del/IF |
| 18 | GR084 | 95 | Not-del | c.722C>T/p.Ser241Phe | 7/11 | 0.4765 | Pathogenic | Not-del/IF |
| 19 | GR063 | 98 | Del | c.818G>A/p.Arg273His | 8/11 | 0.2513 | Pathogenic | Del/IF |
| 20 | GR078 | 98 | Del | c.638G>A/p.Arg213Gln | 6/11 | 0.3137 | Pathogenic | Del/IF |
| 21 | GR086 | 98 | Not-del | c.742C>T/p.Arg248Trp | 7/11 | 0.4335 | Pathogenic | Not-del/IF |
* ddPCR assay maps in exon eight targeting a region between the positions 17:7669643 and 7669765, as declared by the producer and according to hg19 reference genome. IHC—immunohistochemistry; FFPE—formalin-fixed, paraffin-embedded; NGS—next-generation sequencing; ddPCR—droplet digital PCR; VAF—variant allele frequency; del—deleted; IF—inframe; wt—wild-type; VUS—variant of uncertain significance.