Supplementary Tables Table S1: Datasets, Data Portals and Repositories Relevant for Precision Oncology



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Supplementary Tables

Table S1: Datasets, Data Portals and Repositories Relevant for Precision Oncology

Name

Reference

URL

Data Sources

Datasets

TCGA: The Cancer Genome Atlas

[1]

http://cancergenome.nih.gov




ICGC: International Cancer Genome Consortium

[2]

https://dcc.icgc.org




CCLE: Cancer Cell Line Encylopedia

[3]

https://portals.broadinstitute.org/ccle/home

SNV, CNA, gene expression in cancer cell lines

Project Achilles

[4]

https://portals.broadinstitute.org/achilles

shRNA knockdowns of CCLE cell lines

CTD^2: Cancer Target Discovery and Development




https://ocg.cancer.gov/programs/ctd2




TARGET: Therapeutically Applicable Research To Generate Effective Treatments




https://ocg.cancer.gov/programs/target




Data portals, repositories, and clouds

COSMIC

[5]

http://cancer.sanger.ac.uk/cosmic

TCGA, ICGC, others

cBioPortal

[6]

http://www.cbioportal.org/

TCGA, ICGC, CCLE, others

FireBrowse




http://firebrowse.org/

TCGA

SynLethDB

[7]

http://histone.sce.ntu.edu.sg/SynLethDB/

Genetic interactions

BioXpress

[8]

https://hive.biochemistry.gwu.edu/tst/bioxpress/

GE pan cancer database

Genomic Data Commons




https://gdc.cancer.gov/

TCGA, TARGET

Cancer Genomics Cloud Pilot (SevenBridges)




http://www.cancergenomicscloud.org/

TCGA

Cancer Genomics Cloud (Institute for Systems Biology)




http://cgc.systemsbiology.net/




FireCloud




https://software.broadinstitute.org/firecloud/




Table S2: Select List of Computational Methods Relevant for Precision Oncology

Approach

Method

Reference

Notes

Cluster-of-clusters

CoCA

[9]

Multi-view, incomplete data

Dimensionality reduction

MCIA

[10]

Multi-view




MFA

[11]

Multi-view




MEREDITH

[12]


Multi-view




rMKL-DR

[13]

Multi-view

Patient similarity networks

SNF

[14]



Multi-view, incomplete data




NBS

[15]




Mutation impact

PolyPhen

[16]







SIFT

[17, 18]







MutationAssessor

[19]




Hotspots

NMC

[20]







iPAC

[21]







MutationAligner

[22]

Coding and non-coding regions




Hotspots

[23]







Oncodrive-FML

[24]

Coding and non-coding regions




3D Hotspot

[25]




Significantly mutated genes

MutSig, MutSigCV, MutSigCV2

[26]







MuSiC

[27]







Oncodrive-FM

[28]







20/20 rule

[29]




Copy number target selection

GISTIC

[30]







GISTIC2

[31]







Oncodrive-CIS

[32]




Mutually exclusive mutations

RME

[33]







Dendrix

[34]







Multi-Dendrix

[35]







muex

[36]







CoMEt

[37]







WeSME

[38]







WExT

[39]




Network

PRINCE

[40]







EnrichNet

[41]







HotNet

[42, 43]







VarWalker

[44]







DawnRank

[45]

Personalized, single-patient level




HotNet2

[46]




Pathways

PathScan

[47]




Progression

ct-cbn

[48]

Gene-based




H-CBN

[49]

Pathway-based




TiMEx

[50]

Gene-based, mutual exclusivity







[51]

Pathway-based, mutual exclusivity




PathTiMEx

[52]

Pathway-based, mutual exclusivity

Supervised mutual exclusivity

REVEALER

[53]







LOBICO

[54]




Integrated mutual exclusivity

MEMo

[55]

Network and mutual exclusivity




DriverNet

[56]







Mutex

[57]

Network and mutual exclusivity




MEMCover

[58]

Network and mutual exclusivity







[59]

GO, mutual exclusivity and gene expression







[60]

Network




C3

[61]

Gene expression and mutual exclusivity

Crowd-sourced annotations

DoCM

[62]







CIVIC

[63]







MAGI

[64]




Clinical descriptions of mutations

PMKB




https://pmkb.weill.cornell.edu/




PCT




https://pct.mdanderson.org/#/home

Unsupervised discovery of genetic interactions

DAISY

[65]







underMutExSL

[66]










[67]

Subtype-specific

Supervised discovery of genetic interactions




[68]







Mashup

[69]










[70]

Subtype-specific

Mutation signatures




[71, 72]

Non-negative matrix factorization




EMu

[73]







SomaticSignatures

[74]







pmsignatures

[75]







signeR

[76]




Tumor composition

ABSOLUTE

[77]







THetA

[78]







ISOpure

[79, 80]

Individual gene expression profile




DeMix

[81]

Individual gene expression profile




PyClone

[82]







THetA2

[83]







Clomial

[84]

Multi-sample




SciClone

[85]

Multi-sample

Tumor phylogeny from bulk sequencing

TrAp

[86]







recBTP

[87]







PhyloSub

[88]

Multi-sample




AncesTree

[89]

Multi-sample




PhyloWGS

[90]

Multi-sample




BitPhylogeny

[91]

Multi-sample, DNA methylation




LICHeE

[92]

Multi-sample




CITUp

[93]

Multi-sample




SPRUCE

[94]

Multi-sample

Tumor phylogeny from single-cells




[95]







FISHtrees

[96]

FISH







[97]

Does not use reference genome




SCITE

[98]







OncoNEM

[99]




Forests (progression)

SCUnmix

[100]




Table S3: Select List of Relevant Analyses of Cancer “Omics” Data

Cancer Types

Reference

Notes

Glioblastoma


[101]

Molecular subtypes and intratumor heterogeneity

Prostate

[102]

Drivers and actionable mutations

Colorectal

[103]

Predict response to therapy from lymphocyte count

Breast

[104]

Predict response to therapy from gene expression signatures

Thyroid

[105]

Multi-sample sequencing

Esophageal

[106]

Multi-sample sequencing, spatial intratumor heterogeneity

Glioblastoma

[107]

Longitudinal samples, response to therapy

Liver

[108]

Evidence of non-Darwinian tumor evolution

Pan-cancer

[109]

Patterns of tumor purity

Kidney

[110]

Convergent evolution in single tumor

Ovarian

[111]

Longitudinal, spatially-distinct tumor sequencing

Glioma

[112]

Tumor evolution in response to therapy

Lung (non-small cell)

[113]; [114, 115]

Description of TRACERx study; results from the first 100 patients

Myeloma

[116]

Tumor heterogeneity and drivers, response to therapy

Colorectal

[117]

Mechanisms of resistance to EGFR inhibitors

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Directory: cms -> attachment
attachment -> Combined antegrade-retrograde recanalization of a completely obstructed esophagus. All authors have no conflicts of interest. We will be discussing a 76-year-old woman with htn
attachment -> Ocular manifestations of the Johanson-Blizzard syndrome
attachment -> Supplementary Material, File 2
attachment -> Supplemental Table S4: Genes Tested in Detail
attachment -> Radiofrequency ablation is a treatment option for early stages of verrucous esophageal carcinoma
attachment -> Supplementary Table gene expression of tyrosine kinases and phosphatases during disease
attachment -> Successful removal of an esophageal submucosal tumor by submucosal tunneling endoscopic resection technique. This is a 32-year-old male with a history of dysphagia
attachment -> Supplemental data
attachment -> Supplementary Table 1: Enriched genes in early mitosis
attachment -> Supplemental material expedition trials mri data acquisition


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