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Table 2 Summary of the primary course of action likely to result from the molecular testing

From: Evaluation of ultra-deep targeted sequencing for personalized breast cancer care

Patient SNP or mutation (allelic fraction) Proposed action UDT-Seq advantagesa
AA1025 rs113993959 (Het) CFTR genetic counseling Germline
AA1090 CDKN2A-A85D (66%) CDK4/6 inhibitor  
FGFR1 amplification FGFR1/2 inhibitor CNA
AA1106 ERBB2-L755S (17%) Trastuzumab  
PTEN-frameshift (5%) PIK3CA inhibitor Depth
BRCA2-I1418T (4%) PARP inhibitor Depth
AA1204b PIK3CA-H1047R (26%) PIK3CA inhibitor Sensitivity
Her2 amplification Trastuzumab CNA
AA1222b Her2 amplification Trastuzumab CNA
AA1247b Her2 amplification Trastuzumab CNA
ERBB2-D769H (5%) Depth
AA1267 PIK3CA-H1047R (45%) PIK3CA inhibitor  
AA1277 rs80357508 (Het) BRCA1 genetic counseling Germline
FGFR2 amplification FGFR1/2 inhibitor CNA
AA948 PIK3CA-E545K (34%) PIK3CA inhibitor Sensitivity
AA952 PIK3CA-E545K (16%) PIK3CA inhibitor  
BRCA1-W306* (18%) PARP inhibitor  
BRCA1-E550K (13%)
JAK2-S131L (16%) JAK inhibitor  
JAK3-I386M (13%)
rs1801160 (Het) 5-FU toxicity Germline
AA957 PIK3CA-E542K (28%) PIK3CA inhibitor  
AA1515 PIK3CA-E545K (70%) PIK3CA inhibitor  
UCI1546879 PIK3R1-K204E (30%) PIK3CA inhibitor  
UCI1689380 RARA-337 T (14%) RARA inhibitor  
BRAF amplification Vemurafenib  
UCI1908503b PIK3CA-H1047R (40%) PIK3CA inhibitor  
Her2 amplification Trastuzumab CNA
UCI1951813 PIK3CA-E545K (7%) PIK3CA inhibitor Sensitivity
UCI2076630b Her2 amplification Trastuzumab CNA
UCI2224680 BRCA2-L1829F (2%) PARP inhibitor Depth
UCI2564879 PIK3R1-K204E (30%) PIK3CA inhibitor  
UCI2649875 AKT1-L52R (63%) AKT inhibitor  
FGFR1 amplification FGFR1/2 inhibitor CNA
UCI4216548 FGFR1-D683H (13%) FGFR1/2 inhibitor  
UCI8965412b Her2 amplification Trastuzumab CNA
ABL2 amplification Imatinib CNA
UCI1804937 rs1801160 (Het) 5-FU toxicity Germline
UCI2008866 rs1801160 (Het) 5-FU toxicity Germline
UCI3564897 PIK3CA amplification PIK3CA inhibitor CNA
  1. 5-FU, 5-fluorouracil; SNP, single nucleotide polymorphism. aDepth, accurate calls at low allelic fraction (<10%); sensitivity, accurate calls in heterogeneous samples; CNA, inference of copy number alterations; germline, inclusion of a matched germline DNA. bHer2-positive determined through standard of care.