Number of Discovery (WGS) Patients/Sequences by Disease

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Sequence~and Analysis~Completed (362): (362, 56.47%) 362
~Public (165): (165, 25.74%) 165
Published (115): (115, 17.95%) 115
362
NBL~(42, 6.55%) 42
ACT~(8, 1.25%) 8
EPD~(22, 3.43%) 22
PHALL~(9, 1.41%) 9
INF~(22, 3.43%) 22
RHB~(13, 2.03%) 13
CBF~(17, 2.65%) 17
HGG~(15, 2.34%) 15
OS~(17, 2.65%) 17
115
362
165
LGG (38,5.92%) 38
~RB~(4,0.63%) 4
~MB~(37,5.77%) 37
AMLM7 (4,0.63%) 4
HYPO (20,3.12%) 20
T-ALL (12,1.87%) 12
ERG (24, 3.74%) 24
ETV (50, 7.79%) 50
HYPO (2, 0.32%) 2
BALL (49, 7.64%) 49
INF (4, 0.63%) 4
HYPER (39, 6.08%) 39
CPC (4, 0.63%) 4
EWS (35, 5.46%) 35
MEL (5, 0.78%) 5
E2A (33, 5.15%) 33
RB (11, 1.72%) 11
PHALL (26, 4.05%) 26
ACT (12, 1.87%) 12
OS (15, 2.34%) 15
HGG (20, 3.12%) 20
NBL (16, 2.5%) 16
EPD (17, 2.65%) 17
165
115
362
165
115
Click on Disease(s) displayed under Published section to see the associated data
Click on the Thumbnail image to pause the slide.
What's New

June 5, 2013

  • Enables user to Download all the selected Circos Plots or Coverage Plots as one zip file
  • Enables user to export the dynamically generated pie chart for each column in PNG/ SVG format
  • Analysis Tab: Fixed the Excel view to show only 245 donors with appropriate message where it exceeds the Excel limits based on number of columns
What's New
Protein Paint

Protein Paint Tool

The Protein Paint Tool allows you to create your own custom protein paints. You can add, edit, or delete domains generated from GenBank database. You can also add, edit, or delete mutations and their locations within the protein of interest.

Protein Paint
Gene Search

Gene Search

Gene Search allows you to view Protein Paint, 3D structure, and data associated with a gene in published PCGP patients.

Gene Search
Protein Structure

Protein Structure

If a 3D structure exists, a model is displayed, which actively encourages users to evaluate the general location, surrounding environment, and potential loss of interactions from a missense mutation. A user has the ability to manipulate the molecule through the website or download the structure file to their local computer.

Protein Structure
PCGP Germline Variant

PCGP Germline Variant Search

This tool searches chromosomes for SNPs at specific positions within published PCGP patients.

PCGP Germline Variant
Matrix Plot

Matrix Plot

The Matrix Plot enables you to visualize genomic alterations and the pathways in which they are found.

Matrix Plot
Coverage Plot

Coverage Plot

The Coverage Plot displays the distributions of genomic coverage (excluding sequencing gaps) across all chromosomes, comparing the matched germline and disease samples.

Coverage Plot
CNV Summary

Genomic Alterations Summary

The Genomic Alterations Summary depicts copy number changes, single nucleotide variations, structural variations, and gene expressions for patients with specified diseases.

CNV Summary
Sample Circos

Circos Plot

The Circos Plot depicts a comprehensive overview of a genome showing chromosomal rearrangements, copy number changes, loss-of-heterozygosity, SNVs, INDELs, and gene fusions.

Sample Circos
Gene Expression

Gene Expression

Boxplots display gene expression data categorized by disease subtype or by copy number change status on a gene level basis. Customize the display by selecting different data transformations and subtypes.

Gene Expression
Please cite the Pediatric Cancer Genome Project as follows:
St. Jude Children's Research Hospital - Washington University. Pediatric Cancer Genome Project. 19 Apr 2014.

Export in BibTeX format

  1. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas.
    Jinghui Zhang, Gang Wu, et al. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat. Genet.
  2. The genetic landscape of hypodiploid acute lymphoblastic leukemia.
    Holmfeldt L, et al. The genetic landscape of hypodiploid acute lymphoblastic leukemia. Nat. Genet. 2013
  3. Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing.
    Parker M, et al. Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing. Genome Biol. 2013
  4. An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia.
    Gruber TA, et al. An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. Cancer Cell. 2012; 22(5):683-697
  5. Novel mutations target distinct subgroups of medulloblastoma.
    Robinson G, et al. Novel mutations target distinct subgroups of medulloblastoma. Nature. 2012; 488(7409):43-48
  6. The pediatric cancer genome project.
    Downing JR, et al. The pediatric cancer genome project. Nat. Genet. 2012; 44(6):619-622
  7. Association of age at diagnosis and genetic mutations in patients with neuroblastoma.
    Cheung NK, Zhang J, et al. Association of age at diagnosis and genetic mutations in patients with neuroblastoma. JAMA. 2012; 307(10):1062-1071
  8. Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas.
    Wu G, et al. Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat. Genet. 2012; 44(3):251-253
  9. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.
    Zhang J, et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature. 2012; 481(7380):157-163
  10. A novel retinoblastoma therapy from genomic and epigenetic analyses.
    Zhang J, et al. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature. 2012; 481(7381):329-334
  11. CREST maps somatic structural variation in cancer genomes with base-pair resolution.
    Wang J, et al. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat. Methods. 2011; 8(8):652-654

Data Overview

Disease Sequences Discovery Cohort Recurrence Cohort
Patient
Count
SNV Indel CNV SV Patient
Count
SNV Indel CNV SV
T-cell ALLData dbGaP 15 232 21 154 147 89 113 96 722 n/a
RetinoblastomaData EGA 4 24 1 60 44 4 n/a 4 n/a n/a
MedulloblastomaData EGA 37 901 30 5494 454 56 99 13 5721 n/a
Hypodiploid ALLData EGA 31 650 53 582 164 95 208 30 1608 n/a
Low Grade GliomaData EGA 38 90 5 100 62 110 26 2 14176 n/a
Acute megakaryoblastic leukemiaData EGA 14 81 6 22 15 42 n/a n/a n/a n/a
Adrenocortical CarcinomaLink EGA 8 - - - - - - - - -
BCR-ABL1 ALLLink EGA 9 - - - - - - - - -
Core binding factor AMLLink EGA 17 - - - - - - - - -
EpendymomaLink EGA 22 - - - - - - - - -
High Grade GlioblastomaLink EGA 16 - - - - - - - - -
Infant ALLLink EGA 22 - - - - - - - - -
NeuroblastomaLink EGA 42 - - - - - - - - -
OsteosarcomaLink EGA 17 - - - - - - - - -
RhabdosarcomaLink EGA 13 - - - - - - - - -

Data Data available on Explore Links Links to publicly available sequences

Note: All the counts are based on assembly version HG19

Minor Release Date: December 27, 2013, Major Release Date: Apr 11, 2013 Help

PCGP Explore - What's New

Click here to view Release Notes
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