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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.