Table 3.

Summary of significant oncogenomic findings across all specimens analyzed for patients 1 to 5

PatientOncogenomic findingsMechanisms for rapalog response
1R1R2R3
PI3K/Akt/mTORSomatic mutationsComplete functional
pathway alterationsTSC1 frameshift (c.932delC)XXloss of TSC1
TSC1 nonsense (Q527*)X
CNA
Heterozygous loss of Chr 9XXX
Other pertinentSomatic mutations
genomic alterationsVHL nonsense (E94*)XXX
PBRM1 missense (E991D)XXX
CNA
Heterozygous loss of Chr 3pXXX
2R1R2R3M1
PI3K/Akt/mTORSomatic mutationsComplete functional
pathway alterationsTSC1 frameshift (c.1738delAT)XXXXloss of TSC1
CNA
Heterozygous loss of Chr 9XXXX
Other pertinentSomatic mutations
genomic alterationsVHL missense (H115N)XXXX
TP53 missense (R273H)XXXX
CNA
3R1R2R3R4
PI3K/Akt/mTORSomatic mutationsmTOR activation
pathway alterationsmTOR missense (Q2223K)XX±mutation/complete
TSC1 nonsense (Q781*)XXfunctional loss of TSC1
CNA
Heterozygous loss of Chr 9XX
Other pertinentSomatic mutations
genomic alterationsVHL frameshift (c.635delGA)XXXX
BAP1 splice (G220_splice)XX±
BAP1 splice (Q85_splice)XX
CNA
Heterozygous loss of Chr 3pXXXX
4R1M1
PI3K/Akt/mTORSomatic mutationsUnclear
pathway alterationsNone
CNA
None
Other pertinentSomatic mutations
genomic alterationsVHL missense (L118P)XX
PBRM1 frameshift (c.4019delTCACTGCTGAA)XX
CNA
Heterozygous loss of Chr 3pXX
5R1
PI3K/Akt/mTORSomatic mutationsUnclear
pathway alterationsNone
CNA
Heterozygous loss of Chr 9X
Other pertinentSomatic mutations
genomic alterationsNone
CNA
None