Molecular Oncology Almanac

Patient Report

Generated on: Feb 16 2021



Patient Information

Identifiers

Patient ID:   example
Tumor Barcode:   example_tumor_profile
Normal Barcode:   example_normal_profile

Disease

Code:   SKCM
Ontology:   Cutaneous Melanoma
Stage:   Metastatic

Metrics

Tumor Purity:   0.85
Tumor Ploidy:   4.02
Microsatellite Stability:   MSS

Actionability Report

About:

Variants and Features associated with Therapeutic Sensitivity

Predictive Implication Feature Type Feature Therapy & Rationale
FDA-Approved
Putatively Actionable
[More details]
Somatic Variant BRAF p.V600E (Missense) Dabrafenib + Trametinib
The U.S. Food and Drug Administration (FDA) granted approval to dabrafenib in combination with trametinib for the treament of patients with unresectable or metastatic melanoma (MEL) with BRAF V600E or V600K mutation, as detected by an FDA-approved test. [source]
[Preclinical evidence]
FDA-Approved
Investigate Actionability
[More details]
Germline Variant BRCA2 p.S1982fs (Frameshift) Talazoparib
The U.S. Food and Drug Administration (FDA) granted approval for talazoparib indicated for the treatment of adult patients with deleterious or suspected deleterious germline BRCA-mutated HER2-negative localy advanced or metastatic breast cancer. [source]
Guideline
Investigate Actionability
[More details]
Rearrangement COL1A1--CITED4 Fusion Imatinib
Imatinib has shown clinical activity against localized and metastatic DFSP tumors containing t(17;22)(q22;q13). [source]
[Preclinical evidence]
Clinical evidence
Investigate Actionability
[More details]
Somatic Variant MSH2 p.D887N (Missense) Pembrolizumab
Patients with defects in DNA mismatch repair genes may have enhanced sensitivity to immune checkpoint blockade. [source]

Variants and Features associated with Therapeutic Resistance

Predictive Implication Feature Type Feature Therapy & Rationale
Guideline
Putatively Actionable
[More details]
Somatic Variant BRAF p.V600E (Missense) Panitumumab
BRAF V600E makes response to panitumumab or cetuximab highly unlikely unless given with a BRAF inhibitor in metastatic colorectal cancer. [source]

Variants and Features associated with Prognostic Information

Predictive Implication Feature Type Feature Prognosis & Rationale
Guideline
Putatively Actionable
[More details]
Somatic Variant BRAF p.V600E (Missense) Not favorable
BRAF V600E alterations are associated with an unfavorable prognosis in MSI-low and microsatellite-stable patients. [source]
Guideline
Investigate Actionability
[More details]
Somatic Variant ZRSR2 p.N261I (Missense) Not favorable
NCCN guideline for Myelodysplastic Syndromes. [source]
Guideline
Investigate Actionability
[More details]
Somatic Variant STAG2 p.F467I (Missense) Not favorable
NCCN guideline for Myelodysplastic Syndromes. [source]
Inferential
Investigate Actionability
[More details]
Aneuploidy Not favorable
WGD was associated with adverse survival pan-cancer in patients with advanced disease and in cancers with heterogeneous clinical outcomes, even following the development of metastasis. [source]

Variants and Features that may be Biologically Relevant

Feature Type Features
Copy Number BLM Amplification, CTNNB1 Amplification, ERRFI1 Deletion, EWSR1 Amplification, JAK1 Deletion, TSC2 Deletion
Germline Variant BRAF p.R509* (Nonsense)
Microsatellite Stability Supporting variants: JAK1 Deletion, PRDM2 p.E282del (Deletion)
Mutational Signature COSMIC Signature (version 2) 7 (64%)
Somatic Variant NTRK2 p.H300Y (Missense), PDGFRB p.G674E (Missense)

Comparison of molecular profile to cancer cell lines

The Molecular Oncology Almanac compares the somatic variants, copy number alterations, and rearrangements present in this tumor
to identify similar cell lines and their corresponding therapeutic sensitivities to aid in treatment hypothesis generation.

The 5 most similar cancer cell lines, of 452 tested

Cell line name (CCLE) Sensitive therapies Clinically relevant features
SKHEP1_LIVER
[More details]
AGI-5198, SN-38 BRAF p.V600E, CDKN2A Deletion, CDKN2B Deletion, ERCC2 Missense, SMARCA4 Nonsense
G361_SKIN
[More details]
Bexarotene, Bryostatin 1, Dabrafenib, Refametinib ALK Missense, ALK Missense, BRAF Amplification, BRAF p.V600E, CDKN2A Deletion, EGFR Amplification, MET Amplification
IGR37_SKIN
[More details]
(5Z)-7-Oxozeaenol, CI-1040, Dabrafenib, ERK_2440, ERK_6604, PD0325901, PLX-4720, RAF_9304, Refametinib, Refametinib, SB52334, SB590885, Selisistat, Selumetinib, Trametinib AURKB Deletion, BRAF p.V600E, MLH3 somatic variant, TP53 Deletion, TP53 Frameshift
DU4475_BREAST
[More details]
ABT737, AS605240, AZ628, Ara-G, CI-1040, Dabrafenib, ERK_2440, ERK_6604, Entinostat, GSK1904529A, KIN001-236, LIMK1 inhibitor BMS4, LJI308, LY2109761, Mitoxantrone, Nutlin-3a (-), PD0325901, PLX-4720, Pevonedistat, Phenformin, Pilaralisib, RAF_9304, RO-3306, RU-SKI 43, Refametinib, Refametinib, SB590885, SCH772984, SL0101, SU11274, Selumetinib, Tozasertib, Trametinib, Ulixertinib, Ulixertinib, VX-11e, WEHI-539, XMD14-99 AR Missense, BRAF p.V600E, RB1 Deletion, SF3B1 somatic variant, STAG2 somatic variant
SKMEL5_SKIN
[More details]
FH535, IAP_7638, SB590885, UNC0642 BRAF p.V600E, CCND1 Amplification, CDKN2A Deletion, CDKN2B Deletion, PIK3CB somatic variant, SMARCA4 Frameshift, TET2 somatic variant

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Van Allen Laboratory    Dana-Farber Cancer Institute    Broad Institute of MIT & Harvard
Molecular Oncology Almanac