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Protocols

PCGP specifications

Information


Unique identifier OMICS_29843
Name PCGP
Alternative name Pediatric Cancer Genome Project
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainers


  • person_outline James Downing
  • person_outline William Evans

Publication for Pediatric Cancer Genome Project

PCGP citations

 (10)
library_books

Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes

2018
PMCID: 5943605
PMID: 29743561
DOI: 10.1038/s41419-018-0600-3

[…] The detailed clinical and omics data of patients with leukaemia collected in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) program and Pediatric Cancer Genome Project (PCGP) provide excellent resources for exploring the mechanisms involved in somatic cell alterations, , . A metadata summary of 1781 patients from the consortium reveal […]

call_split

The critical role that STAT3 plays in glioma initiating cells: STAT3 addiction in glioma

2018
Oncotarget
PMCID: 5955139
PMID: 29774125
DOI: 10.18632/oncotarget.25188
call_split See protocol

[…] in RNAse- and DNAse-free distilled water (Life Technologies). Sequences derived from total RNA paired end 100 bp sequences were mapped to the hg19 genome with the STRONGARM pipeline developed for the PCGP project [] which employs bwa [] and STAR [] aligners. Transcript level data was counted using HTSEQ []. Transcript level log2FPKM (log2(FPKM +0.5)) was calculated and used to define log fold-chan […]

call_split

HNRNPH1 is required for rhabdomyosarcoma cell growth and survival

2018
Oncogenesis
PMCID: 5833419
PMID: 29362363
DOI: 10.1038/s41389-017-0024-4
call_split See protocol

[…] cing (RNA-seq) with an Illumina HiSeq 2500 (Illumina, San Diego, CA). Resultant stranded paired-end 100-bp sequences were mapped to the hg19 human genome with the STRONGARM pipeline developed for the Pediatric Cancer Genome Project and counted with HTSEQ. Statistical testing to determine differential expression was performed in R by using the voom and limma packages. By using our rnapeg in-house t […]

library_books

Genome wide segregation of single nucleotide and structural variants into single cancer cells

2017
BMC Genomics
PMCID: 5702214
PMID: 29178827
DOI: 10.1186/s12864-017-4286-1

[…] taken from a child that was diagnosed with acute lymphoblastic leukemia. We first performed whole genome, exome, and RNA sequencing to characterize the somatic variants in that sample as part of the Pediatric Cancer Genome Project [, ]. In that patient, we identified 51 putative somatic SNVs and 40 SVs (Fig. , Additional file : Table S1, Additional file : Table S2). We then performed microfluidic […]

library_books

Exome sequencing analysis of murine medulloblastoma models identifies WDR11 as a potential tumor suppressor in Group 3 tumors

2017
Oncotarget
PMCID: 5630286
PMID: 29029386
DOI: 10.18632/oncotarget.19642

[…] Genomic DNA was extracted from mouse Shh and Wnt spontaneously occurring tumors and G3 orthotopic MBs using the Qiagen DNAeasy kit. DNA samples were submitted to the Pediatric Cancer Genome Project Validation Lab for exome sequencing. Paired end sequencing reads have been mapped to mouse reference genome mm9 assembly. The mapping statistics was obtained from ‘samt […]

library_books

Cancer Genomics: Large Scale Projects Translate into Therapeutic Advances

2016
PLoS Med
PMCID: 5189932
PMID: 28027296
DOI: 10.1371/journal.pmed.1002209

[…] from a tissue site–specific and a pan-cancer perspective. This huge body of genomic information generated by The Cancer Genome Atlas (TCGA), The International Cancer Genome Consortium (ICGC), and The Pediatric Cancer Genome Project has contributed significantly to our understanding of individual cancer types. There has, importantly, also been a huge expansion of technical advances, including devic […]

Citations

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PCGP institution(s)
St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project, Memphis, TN, USA; Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA; St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project, St. Louis, MO, USA; The Genome Institute at Washington University, St. Louis, MO, USA; Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA; Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA; Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
PCGP funding source(s)
Supported by The St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project, American Lebanese Syrian Associated Charities (ALSAC) of St. Jude Children’s Research Hospital, an NCI Cancer Center support grant (P30 CA021765), the US National Institutes of Health (NIH; U01 GM 92666 and R37 CA36401), the Washington University in St. Louis and a grant from the NHGRI (U54 HG003079).

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