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Table 3 Genomic alterations detected in patient and corresponding PDX by next generation sequencing using the OCCRA gene panel (Lorentzian et al., 2019)

From: PDX models reflect the proteome landscape of pediatric acute lymphoblastic leukemia but divert in select pathways

  Disease Type Sample Origin OCCRA panel NGS
1 B-ALL Dx Primary  
B-02-Dx ETV6-RUNX1 fusion
SNV: SUZ12 lys690fs, 0.03
PDX  
B-02-Dx-PDXb ETV6-RUNX1 fusion
CNV: SOCS2 (0.83), TET2 (0.97)
2 B-ALL R1 Primary  
B-05-R1 SNV: ARID1A (Gln563Ter, 0.33), KRAS (Lys117Arg, 0.35)
PDX  
B-05-R1-PDX SNV: ARID1A Gln563Ter (0.49), KRAS Lys117Arg( 0.52)
CNV: FASLG (3.67), CDKN2A (0.85), CDKN2B (0.96)
3 B-ALL R3 Primary  
B-06-R3 SNV: JAK1 (Val658Phe, 0.48)
CNV: CDKN2A (0.07), CDKN2B (0.07), PTCH1(0.79), EBF1(1.0)
PDX  
B-06-R3-PDXb SNV: JAK1 (Val658Phe, 0.99)
CNV: CDKN2A (0), CDKN2B (0), PTCH1 (0.76), EBF1 (1.0)
4 B-ALL R3 Primary  
B-07-R3 SNV: KRAS Gln61His (0.13)
CNV: CDKN2A (0.52), RB1 (0.85), P53 (1.37)
PDX  
B-07-R3-PDXa SNV: KRAS Gln61His (0.4)
CNV: CDKN2A (0.33), RB1 (0.22), P53 (1.1)
5 T-ALL Dx Primary  
T-02-Dx STIL-TAL1 fusion
SNV: PTEN (Leu247fs, 0.2)
PDX  
T-02-Dx-PDX STIL-TAL1 fusion
6 T-ALL Dx Primary  
T-01-Dx CNV: CDKN2A (0.6)
PDX  
T-01-Dx-PDX CNV: CDKN2A (0.03)