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HomePIEDocumentation
diagnosis




HomePIEDocumentation
diagnosis




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EXPLORE CURATED DATA FROM ~ 9000 PEDIATRIC CANCER SAMPLES

DATA FACETS & TOOLS

VARIANTS



MUTATIONAL SIGNATURES



EXPRESSION



HISTOLOGY



PIE




CURATED DATA

The PeCan platform presents curated pediatric cancer genomics data including
variants, mutational signatures, and gene expression data in addition to
histological slide images* from ~9000 hematological, CNS, and non-CNS solid
tumor patient samples.

Data can be explored via a series of data facets containing both retrospective
and prospective study cohorts from St. Jude Children's Research Hospital and
other trusted institutions and research centers around the world.

*Note that a number of histological slide images are currently embargoed until
publication of the associated study.



CONTRIBUTING INSTITUTIONS


Variants


VARIANTS


EXPLORE CURATED VARIANTS VIA INTERACTIVE VISUALIZATIONS.

Perform exploratory research of variants in pediatric cancer subtypes via 5
custom interactive interfaces. Curated variants have been identified from
whole-genome, whole-exome and whole-transcriptome (RNA-seq) sequencing data from
5500 samples.

Explore Variants

FEATURES

ONCOPRINT

Variant landscape view summarizing variant presence and frequency across samples
for a given diagnosis subtype.

View Oncoprint

VARIANT PREVALENCE

Display of gene level variant type composition within a given diagnosis subtype.

View Variant Prevalence

GENOMEPAINT

A visualization tool that integrates whole-genome, whole-exome, transcriptome,
and epigenomic data of tumor samples.

View GenomePaint

PROTEINPAINT

Gene level display of variants presented on a protein domain view and scaled by
prevalence.

View ProteinPaint

VARIANT DETAILS

Individual customized variant pages displaying detailed associated genomic,
clinical, classification, and observed population frequency annotations.

Mutational Signatures


MUTATIONAL SIGNATURES


INVESTIGATE COSMIC SBS MUTATIONAL SIGNATURES AMONG PEDIATRIC CANCER SUBTYPES.

Use our tiered interface to observe COSMIC single base substitution (SBS)
mutational signatures identified across cancer subtypes and samples therein.

Explore Mutational Signatures

FEATURES

SUBTYPE HEATMAP

Observe COSMIC SBS signatures across pediatric cancer subtypes via an
interactive heatmap view - providing a gateway to further explore signatures
within each subtype and individual samples.

SAMPLE COHORT VIEW

View identified COSMIC SBS signatures in groups of samples grouped by cancer
subtype or subtypes with a specific mutational signature displayed as a barplot.

SAMPLE VIEW

View individual sample mutational profiles together with identified COSMIC SBS
signatures.

Expression


GENE EXPRESSION MAP-BASED


EXPLORE PEDIATRIC TUMOR SAMPLES WITHIN 2-DIMENSIONAL EXPRESSION LANDSCAPE MAPS.

Explore hematologic, CNS, and non-CNS solid tumor RNA-seq expression landscape
maps to select tumor samples of interest.

Explore Expression

FEATURES

PAN-CANCER EXPRESSION MAPS

Presenting interactive expression maps for each of hematologic, CNS, and non-CNS
solid tumor cancer subtypes derived from RNA-seq expression data.

SEARCH AND FILTER

Highlight samples of interest by performing keyword searches of sample id, tumor
subtype, cohort, subtype-biomarker etc. Alternatively, our interface enables
custom advanced filtering to display samples of interest.

SAMPLE VIEW AND LASSO

Hover over a sample on each expression map to view its metadata. Alternatively,
our lasso tool enables selection and listing of multiple samples and associated
metadata.

Histology


HISTOLOGY


EXPLORE, SEARCH AND FILTER HISTOLOGY SLIDE IMAGES OF PEDIATRIC SOLID TUMOR
SAMPLES.

Examine H&E histology slide images and associated clinical notes from a wide
variety of pediatric solid tumor subtypes.

Explore Histology

FEATURES

SEARCH AND FILTER

Select to view histology slide images via filtering on cancer subtype and/or
clinical metadata via our search navigation interface. In addition, images can
be searched by sampleID.

SLIDE VIEWER

Carefully examine slide images (zoom to 10x magnification) with our dynamic
high-resolution slide viewer (supported by OpenSeaDragon).

IMAGE SEARCH COMING SOON!

Upload your own slide and use our image search tool to identify similar images
within minutes!

PIE - Pathogenicity Information Exchange


PIE - PATHOGENICITY INFORMATION EXCHANGE


A VARIANT CLASSIFICATION AND INTERPRETATION SERVICE.

PIE automates annotations, classifies, and triages variants via our Medal
Ceremony pipeline. PIE also provides interactive variant pages with
visualization tools to support expert curation. Further, PIE supplies a
reference database of expert-vetted cancer-predisposing germline mutations.

Explore PIE

PeCanPIE was originally developed for pediatric cancer but can be easily
extended for use for non-pediatric cancers and non-cancer genetic diseases.

FEATURES

RUN PIE JOBS

Submit your VCF file or enter a single variant to run through our Medal Ceremony
pipeline.

ST. JUDE MEDAL CEREMONY

PIE implements our clinical Medal Ceremony pipeline - whereby variants within
disease-related genes are assigned a 'Gold', 'Silver', or 'Bronze' putative
pathogenicity class.

COLLABORATE

Invite team members to view the results of your PIE jobs - providing them with
full access to your processed data results.


NEED OUR ASSISTANCE?

Access our help guides – on how to cite us, who to contact for support, or to
learn more about each of the data facets or tools.

Visit Our Help Guides

GENOMIC AND PROTEOMIC DATA AND ANALYSIS RESOURCES FOR THE GLOBAL RESEARCH
COMMUNITY.

Genomics Platform

Sequencing Data and Analysis

Access and analyze the world's most comprehensive repositories of pediatric
cancer-related genomics data and analysis tools.

Access Data
Visualization Community

Interactive Figures

Create and share figures using St. Jude's unique genomic visualization tools
such as ProteinPaint and GenomePaint.

See Visualizations
Model Systems

Xenograft knowledge base

Access and analyze the world's most comprehensive repositories of pediatric
cancer-related genomics data and analysis tools.

Explore Models
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© Copyright 2023 St. Jude Children's Research Hospital , a not-for-profit,
section 501(c)(3).






SAMPLES

8540


SUBJECTS

7655


DIAGNOSIS SELECTION

HM
Hematologic Malignancy
ST
Solid Tumor
BT
Brain Tumor
GCT
Germ Cell Tumor
Brain TumorSolid tumorHematologic MalignancyGerm Cell TumorChoroid
PlexusEmbryonal, BrainEpendymomalGliomaMeningothelial
TumorNeuroepithelial/Glioneuronal TumorOther Brain TumorPinealSellarAdrenal
GlandBladder/Urinary TractBoneBowelEyeHead and NeckKidneyLiverLungOther Solid
TumorOvary/Fallopian TubePancreasPeripheral Nervous SystemSkinSoft
TissueThymusThyroidLymphoid NeoplasmMyeloid NeoplasmOther Hematologic
MalignancyMixed Germ Cell Tumor, BrainYolk Sac Tumor, BrainMixed Germ Cell
Tumor, TestisOvarian Germ Cell TumorYolk Sac Tumor, OvaryYolk Sac Tumor,
ParotidAtypical Choroid Plexus PapillomaChoroid Plexus CarcinomaChoroid Plexus
PapillomaAtypical Teratoid/Rhabdoid TumorEmbryonal Tumor, BrainEmbryonal Tumor
with Multilayered Rosettes, BrainMedulloblastomaPrimitive Neuroectodermal
TumorEpendymomal Tumor, AnaplasticAnaplastic Ependymoma, Posterior
FossaEpendymomal Tumor, NOSEpendymomal Tumor, Posterior FossaEpendymomal Tumor,
Spinal TumorEpendymomal Tumor, SupratentorialMixed Myxopapillary Anaplastic
Ependymoma, Spinal TumorMyxopapillary EpendymomaMyxopapillary Ependymoma, Fourth
VentricleMyxopapillary Ependymoma, Posterior FossaAstrocytoma, NOSDiffuse
GliomaEncapsulated GliomaGlioma, NOSMeningiomaAngiocentric GliomaCentral
NeurocytomaDesmoplastic Infantile AstrocytomaDesmoplastic Infantile
GangliogliomaGlioneuronal Neoplasm, NOSHigh-Grade Glioneuronal TumorHigh-Grade
Neuroepithelial TumorLow-Grade Glioneuronal TumorLow-Grade Neuroepithelial
TumorAcoustic NeuromaBrain Tumor, NOSCNS Ewing Sarcoma Family Tumor, CIC
alterationCIC-Rearranged Sarcoma, BrainHigh-Grade Calvarium SarcomaIntracranial
Mesenchymal Tumor, FET-CREBMiscellaneous Brain TumorPineal Anlage
TumorPineoblastomaPineocytomaPineal TumorPineal Parenchymal TumorPineal
Parenchymal Tumor of Intermediate DifferentiationPapillary Tumor of the Pineal
RegionCraniopharyngioma, Adamantinomatous TypeAdrenocortical
AdenomaAdrenocortical CarcinomaAdrenocortical Tumor, Uncertain Malignant
PotentialPheochromocytomaMalignant Rhabdoid Tumor of the BladderAneurysmal Bone
CystAtypical Osteocartilaginous LesionChondroblastomaChordomaChondroblastic
OsteosarcomaChondrosarcomaEwing SarcomaGiant Cell Tumor of BoneGiant Cell Tumor,
NOSMesenchymal ChondrosarcomaMyositis OssificansOsteoblastomaOsteoid
OsteomaOsteosarcomaOsteoblastic OsteosarcomaGastrointestinal Neuroendocrine
TumorGastrointestinal Stromal TumorInflammatory Myofibroblastic Stomach
TumorSignet Ring Cell Carcinoma of the StomachAdenoid Cystic Carcinoma of the
Lacrimal GlandRetinoblastomaAdenoid Cystic Carcinoma of the Salivary
GlandAdenomatoid Odontogenic TumorMucoepidermoid CarcinomaMyoepithelial
CarcinomaNasopharyngeal CarcinomaNeurothekeomaPleomorphic
AdenomaSialoblastomaSalivary Gland Anlage TumorClear Cell Sarcoma of
KidneyCongenital Mesoblastic NephromaRenal Epitheloid
AngiomyolipomaJuxtagliomerular Cell TumorJuvenile XanthogranulomaLow-Grade
Oncocytic Renal TumorRhabdoid Cancer, KidneyPapillary Renal Cell CarcinomaRenal
Cell CarcinomaWilmsWilms, BilateralHepatoblastomaHepatocellular CarcinomaHepatic
Focal Nodular HyperplasiaMalignant Rhabdoid Tumor of the LiverUndifferentiated
Embryonal Sarcoma of the LiverInflammatory Myofibroblastic Lung TumorCarcinoma,
NOSRhabdoid Tumor, NOSSolid Cancer of Unknown PrimaryMucinous Adenocarcinoma,
OvarianSex Cord Stromal TumorSertoli-Leydig Cell TumorPancreatic Neuroendocrine
TumorSolid Pseudopapillary Neoplasm of the PancreasGanglioneuroblastomaLow-Grade
Peripheral Nerve Sheath TumorMalignant Peripheral Nerve Sheath
TumorNeuroblastomaNeurofibromaNeuromuscular ChoristomaSchwannomaAtypical
NevusAtypical Spitzoid Melanocytic NeoplasmAtypical Spitzoid NeoplasmCongenital
Melanocytic NevusDermatofibrosarcoma ProtuberansMelanomaMelanocytic NevusNodular
Malignant MelanomaSquamous Cell Carcinoma, NOSCutaneous Melanoma,
CRTC1-TRIM11Spitzoid MelanomaNon-Rhabdomyosarcoma Soft Tissue
TumorRhabdomyosarcomaMalignant ThymomaNon-Invasive Follicular Thyroid Neoplasm
with Papillary Like Nuclear FeaturesNodular Thyroid HyperplasiaSpindle
Epithelial Tumor with Thymus-Like DifferentiationThyroid Gland Follicular
Adenoma with Papillary HyperplasiaFollicular Thyroid CancerHurthle Cell Thyroid
CancerMedullary Thyroid CancerPapillary Thyroid CancerAcute Lymphoblastic
Leukemia, NOSB-Cell Lymphoblastic LeukemiaNon-Hodgkin LymphomaT-Cell
Lymphoblastic LeukemiaAcute Myeloid LeukemiaChronic Myeloid
LeukemiaMyelodysplastic SyndromesMyeloproliferative NeoplasmsMyeloid
SarcomaTherapy Related Myeloproliferative NeoplasmAtypical Dendritic Cell
TumorAcute Leukemias of Ambiguous LineageAcute Undifferentiated LeukemiaAcute
Undifferentiated Leukemia, KMT2A rearrangementBlood Cancer of Unknown
PrimaryEosinophilia, NOSMixed Phenotype Acute Leukemia, T/Myeloid,
NOSRosai-Dorfman DiseaseAtypical Teratoid/Rhabdoid Tumor, SHH subgroupAtypical
Teratoid/Rhabdoid Tumor, TYR subgroupLarge Cell/Anaplastic
MedulloblastomaAnaplastic Medulloblastoma, Group 3Anaplastic Medulloblastoma,
Group 4Large Cell/Anaplastic Medulloblastoma, SHH subtypeDesmoplastic/Nodular
Medulloblastoma, SHH subtypeMedulloblastoma with Extensive Nodularity, SHH
subtypeMedulloblastoma, Group 3Medulloblastoma, Group 4Medulloblastoma, SHH
subtypeMedulloblastoma, WNT subtypeAnaplastic AstrocytomaAnaplastic
OligoastrocytomaDiffuse AstrocytomaDiffuse Intrinsic Pontine
GliomaGlioblastomaHigh-Grade Glioma,
NOSOligoastrocytomaOligodendrogliomaAnaplastic GangliogliomaAnaplastic
Pleomorphic XanthoastrocytomaDysembryoplastic Neuroepithelial
TumorGangliogliomaLow-Grade Glioma, NOSPilocytic AstrocytomaPilomyxoid
AstrocytomaPleomorphic XanthoastrocytomaAdenocarcinoma, NOSAngiomatoid Fibrous
HistiocytomaFibrosarcoma, AbdominalAlveolar Soft Part SarcomaBCOR SarcomaClear
Cell SarcomaDesmoid/Aggressive FibromatosisDesmoplastic Small Round Cell
TumorEpithelioid SarcomaEwing Sarcoma of Soft TissueFibromyxoid
SarcomaFibroblastic/Myofibroblastic TumorFibrous Umbilical PolypGiant Cell
FibroblastomaHigh Grade SarcomaInfantile FibrosarcomaInflammatory
Myofibroblastic TumorLipoblastomaLipofibromatosisLow-Grade Mesenchymal
NeoplasmLiposarcomaMyopericytomaParagangliomaRound Cell Sarcoma, NOSSarcoma,
NOSSpindle Cell NeoplasmSpindle Cell Sarcoma, NOSSerous cystadenomaSynovial
SarcomaUndifferentiated Round Cell SarcomaAlveolar RhabdomyosarcomaBotryoid Type
Embryonal RhabdomyosarcomaEmbryonal
RhabdomyosarcomaEctomesenchymomaRhabdomyosarcoma, NOSSpindle Cell
RhabdomyosarcomaSpindle Cell/Sclerosing RhabdomyosarcomaB-Cell Acute
Lymphoblastic Leukemia, BCR-ABL1B-Cell Acute Lymphoblastic Leukemia, BCR-ABL1
likeB-Cell Acute Lymphoblastic Leukemia, CRLF2 rearrangementB-Cell Acute
Lymphoblastic Leukemia, DUX4-IGHB-Cell Acute Lymphoblastic Leukemia, DUX4-IGH
likeB-Cell Acute Lymphoblastic Leukemia, ETV6-RUNX1B-Cell Acute Lymphoblastic
Leukemia, ETV6-RUNX1 likeB-Cell Acute Lymphoblastic Leukemia, HLF
rearrangementB-Cell Acute Lymphoblastic Leukemia, HyperdiploidyB-Cell Acute
Lymphoblastic Leukemia, HypodiploidyB-Cell Acute Lymphoblastic Leukemia,
iAMP21B-Cell Acute Lymphoblastic Leukemia, IGH-CEBPDB-Cell Acute Lymphoblastic
Leukemia, IKZF1 N159YB-Cell Acute Lymphoblastic Leukemia, KMT2A
rearrangementB-Cell Acute Lymphoblastic Leukemia, MEF2D rearrangementB-Cell
Acute Lymphoblastic Leukemia, MYC rearrangementB-Cell Acute Lymphoblastic
Leukemia, NOSB-Cell Acute Lymphoblastic Leukemia, NUTM1 rearrangementB-Cell
Acute Lymphoblastic Leukemia, PAX5 alterationB-Cell Acute Lymphoblastic
Leukemia, PAX5 P80RB-Cell Acute Lymphoblastic Leukemia, TCF3-PBX1B-Cell Acute
Lymphoblastic Leukemia, ZNF384 rearrangementB-Cell Acute Lymphoblastic Leukemia,
ZNF384 rearrangement likeAnaplastic Large Cell LymphomaAnaplastic Large Cell
Lymphoma, ALK PositiveBurkitt LymphomaB-Cell Lymphoblastic Lymphoma, BCR-ABL1
likeB-Cell Lymphoblastic Lymphoma, NOSB-Cell Lymphoblastic Lymphoma,
TCF3-HLFB-Cell Lymphoblastic Lymphoma, TCF3-PBX1Diffuse Large B-Cell Lymphoma,
NOSExtranodal Marginal Zone LymphomaFollicular LymphomaHigh-Grade B-Cell
Lymphoma, NOSMature B-Cell NeoplasmsT-Cell Lymphoblastic Lymphoma, LMO1
rearrangementT-Cell Lymphoblastic Lymphoma, NKX2 rearrangementT-Cell
Lymphoblastic Lymphoma, NOST-Cell Lymphoblastic Lymphoma, TAL1
rearrangementT-Cell Acute Lymphoblastic Leukemia, BCL11B rearrangementT-Cell
Acute Lymphoblastic Leukemia, HOXA activationT-Cell Acute Lymphoblastic
Leukemia, LMO2 activationT-Cell Acute Lymphoblastic Leukemia, NKX2
activationT-Cell Acute Lymphoblastic Leukemia, NOST-Cell Acute Lymphoblastic
Leukemia, SPI1 rearrangementT-Cell Acute Lymphoblastic Leukemia, TAL1
activationT-Cell Acute Lymphoblastic Leukemia, TAL2 activationT-Cell Acute
Lymphoblastic Leukemia, TLX1 activationT-Cell Acute Lymphoblastic Leukemia, TLX3
activationAcute Megakaryoblastic LeukemiaAcute Megakaryoblastic Leukemia,
CBFA2T3-GLIS2Acute Megakaryoblastic Leukemia, KMT2A rearrangementAcute
Megakaryoblastic Leukemia, RBM15-MKL1Acute Myeloid Leukemia, CBFA2T3-GLIS2Acute
Myeloid Leukemia, CBFB-MYH11Acute Myeloid Leukemia, Core Binding Factor,
NOSAcute Myeloid Leukemia, biallelic CEBPA alterationAcute Myeloid Leukemia,
DEK-NUP214Acute Myeloid Leukemia, ETS family rearrangementAcute Myeloid
Leukemia, GATA1 alterationAcute Myeloid Leukemia, HOX rearrangementAcute Myeloid
Leukemia, KAT6A rearrangementAcute Myeloid Leukemia, KMT2A rearrangementAcute
Myeloid Leukemia, MECOM rearrangementAcute Myeloid Leukemia, MNX1
rearrangementAcute Myeloid Leukemia, NOSAcute Myeloid Leukemia, NPM1
alterationAcute Myeloid Leukemia, NUP98 rearrangementAcute Myeloid Leukemia,
PICALM-MLLT10Acute Myeloid Leukemia, RBM15-MKL1Acute Myeloid Leukemia,
RUNX1-RUNX1T1Acute Myeloid Leukemia, RUNX1-RUNX1T1 likeAcute Myeloid Leukemia,
UBTF tandem duplicationAcute Myelomonocytic LeukemiaAcute Myelomonocytic
Leukemia, KMT2A rearrangementAcute Myelomonocytic Leukemia, NPM1 alterationAcute
Monoblastic/Monocytic Leukemia, KMT2A rearrangementAcute Promyelocytic Leukemia,
PML-RARAChronic Neutrophilic LeukemiaTherapy-Related Acute Myeloid
LeukemiaTherapy-Related Myelodysplastic SyndromeTherapy-Related Myeloid
NeoplasmBTSTHMGCTCHPLEMBBEPDYGLMMNGTNGLTOBTPINEALSELRADRNBLUTBONEBWLEYEHANKIDLIVLUNGOSTOVFTPANPNSSKNSTISTHYMTHYRLYMPHMYELOHMBMGCTBYSTMGCTOGCTOYSTYSTPACPPCPCCPPATRTEMBTETMRMBLPNETAPEAPEPFEPMTNOSEPMTPFEPMTSTEPMTSUMEPMSTMPEMPEFVMPEPFASTRDIFGENCGGNOSMNGANGLCNCDIADIGGLNOSHGGTHGNETLGGNTLGNETANMBTNOSCEFTCICCICRSBHGCSIMTFETCR...MBTPATPBLPINCPINTPPTPPTIDPTPRACPGACAACCACTUMPPHCMRTBABCAOSLCHBLCHDMCHOSCHSEWSGCTBGICTMCHSMOOBOOOSOSOSGINETGISTIMTSSSRCCACLGRBLACYCAOTMUCCMYECNPCNTKPADASBLSGATCCSKCMNEAMLJGCTJXGLGORTMRTPRCCRCCWTWTBHBHCCHFNHMRTLUESLIMTLCNOSRTNOSSCUPMAOSCSTSLCTPANETSPNGNBLLGPNSTMPNSTNBLNFIBNMCSCHWANASPZMNASPZNCMLNDFSPMELMLNNMMELSCCNOSSKCMCRTC...SPZMNRSTTRMSMTHYMNIFTPNTHPSETTLETFAPHTHFOTHHCTHMETHPAALLNOSBALLNHLTALLAMLCMLMDSMPNMSTMPNADCTALALAULAULKMT2ABCUPESOPMPALTNOSRDDATRTSHHATRTTYRAMBLAMBLNWSG...AMBLNWSG...AMBLSHHDMBLSHHMBENSHHMBLG3MBLG4MBLSHHMBLWNTAASTRAOASTDASTRDIPGGBHGGNOSOASTODGAGNGAPXADNTGNGLGGNOSPASTPMAPXAADNOSAFHAFIBSASPSBCSCCSDESDSRCTEPISESSTFMSFMTFUPGCFIBHGSIFSIMTLBLLFBRLGMNLIPOMPCPGNGRCSNOSSARCNOSSCNSCSNOSSCYSYNSURCSARMSBERMSERMSMEMRMSNOSSCRMSSCSRMSBALLBCRA...BALLBCRA...BALLCRLF...BALLDUX4...BALLDUX4...BALLETV6...BALLETV6...BALLHLFBALLHYPE...BALLHYPOBALLIAMP...BALLIGHC...BALLIKZF...BALLKMT2...BALLMEF2...BALLMYCBALLNOSBALLNUTM...BALLPAX5BALLPAX5...BALLTCF3...BALLZNF3...BALLZNF3...ALCLALCLALKPBLBLLBCRAB...BLLNOSBLLTCF3H...BLLTCF3P...DLBCLNOSEMZLFLHGBCLMBNTLLLMO1TLLNKX2TLLNOSTLLTAL1TALLBCL1...TALLHOXATALLLMO2TALLNKX2TALLNOSTALLSPI1TALLTAL1TALLTAL2TALLTLX1TALLTLX3AMKLAMKLCBFA...AMKLKMT2...AMKLRBM1...AMLCBFA2...AMLCBFBM...AMLCBFNO...AMLCEBPAAMLDEKNU...AMLETSAMLGATA1AMLHOXAMLKAT6AAMLKMT2AAMLMECOMAMLMNX1AMLNOSAMLNPM1AMLNUP98AMLPICAL...AMLRBM15...AMLRUNX1...AMLRUNX1...AMLUBTFAMMLAMMLKMT2...AMMLNPM1AMOLKMT2...APLPMLRA...CNLTAMLTMDSTMN
EpigeneticComing Soon
Histology549 samples
Expression3432 samples
Mutational Signatures1843 samples
Variants5467 samples