Glossary

[1,2,3]  [A]  [B]  [C]  [D]  [E]  [F]  [G]  [H]  [I]  [J]  [K]  [L]  [M]  [N]  [O]  [P]  [Q]  [R]  [S]  [T]  [U]  [V]  [W]  [X]  [Y]  [Z]

A

ACT: Adrenocortical Carcinoma
Allele: One of two or more forms of a gene or genetic locus
AMBIGUOUS: For CNVs determined by WGS, these regions have ambiguous segment boundaries
AML: Acute Myeloblastoma
AMLM7: Acute megakaryoblastic leukemia
AMP: Amplification
AMPALL: iAmp21 ALL
API: Application Programming Interface

C

CBF: Core binding factor acute myeloid leukemia
Circos Plot: Circular representation of a complete genome
CNV: Copy number Variation
Coverage Plot: Graphic illustration of the number of reads/base position across a genome
CTX: Inter-chromosomal Translocation
CURATED: For CNVs determined by WGS or by SNP6 Array, these regions were reviewed to have good segment boundaries
CURATED_FOCAL: For CNVs determined by WGS, these regions were reviewed to have good segment boundaries and have been determined to be focal lesions and are overlapped by 5 or fewer genes

D

DAC: Data Access Committee evaluates applications for access to de-identified and anonymized genomic sequence data generated as a result of the PCGP activities
DEL: Deletion

E

EGA: The European Genome-phenome Archive (EGA) repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers
EPD: Ependymoma
ETP: Early T-cell precursor leukemia
ETV6ALL: ETV6-RUNX1 ALL
EXOME: .bam file from exome capture sequencing.
Exon: A nucleic acid sequence that is represented in the mature form of an RNA molecule, often a messenger RNA or a functional form of non-coding RNA such as rRNA or tRNA

F

Frameshift: A DNA mutation changing the ribosomal reading frame of the sequence leading to incorrect amino acid sequence or truncated proteins

G

GE: Gene expression

H

HGG: High Grade Glioblastoma
HYPO: Hypodiploid ALL

I

INDELs: Insertions and Deletions
INF: Infant Acute Lymphoblastic Leukemia
INS: Insertion
INV: Inversion
Isoform: A protein isoform is any of several different forms of the same protein produced from related genes or that arise from the same gene by alternative splicing or are caused by single-nucleotide polymorphisms or SNPs
ITX: Intra-chromosomal Translocation

L

LGG: Low Grade Glioblastoma

M

MB: Medulloblastoma
Missense: A point mutation in a gene in which a nucleotide is changed, resulting in a codon that codes for a different amino acid.

N

NBL: Neuroblastoma
Nonsense: A point mutation in a gene sequence that results in a premature stop codon, or a nonsense codon in the transcribed mRNA and in a truncated, incomplete, and usually non functional protein product
Number of Overlapping Genes: The # of overlapping genes means the number of genes that overlap the CNV. We do not determine the lesion affect and filter by this

O

OS: Osteosarcoma

P

PCGP: Pediatric Cancer Genome Project
PH-ALL: BCR-ABL1 ALL
PNG: Portable Network Graphics
Protein Paint: 2D visualization of amino acid sequences
PUTATIVE: For CNVs determined by SNP6, these regions were not reviewed

R

R: R is a programming language and software environment for statistical computing and graphics
RB: Retinoblastoma
Recurrence: The Recurrence cohort was not sequenced by Whole Genome Sequencing, but only targeted regions were sequenced. These regions are genes that were determined to be mutated in a significant amount of patients via Whole Genome Sequencing (the Discovery cohort).
RHB: Rhabdomyosarcoma

S

Sequencing Type: Describes the source of the sequencing file used in the analysis.
Silent: DNA mutations that do not result in a change to the amino acid sequence of a protein
SNP: Single nucleotide polymorphism
SNV: Single nucleotide variation
SUB: Singe nucleotide substitution (aka, SNP or SNV)
SV: Structural variation
SVG: Scalable Vector Graphics

T

T-ALL: T-cell ALL
TARGETED_SEQUENCING: .bam file from custom capture arrays or the trace file from Sanger sequencing.
Tier 1: Coding synonymous, nonsynonymous, splice site, and non-coding RNA variants
Tier 2: Conserved variants (cutoff: conservation score greater than or equal to 500 based on either the phastConsElements28way table or the phastConsElements17way table from the UCSC genome browser, and variants in regulatory regions annotated by UCSC annotation (Regulatory annotations included are targetScanS, ORegAnno, tfbsConsSites, vistaEnhancers, eponine, firstEF, L1 TAF1 Valid, Poly(A), switchDbTss, encodeUViennaRnaz, laminB1, cpgIslandExt)
Tier 3: Variants in non-repeat masked regions
TRANSLOCATION: Structural variation causing a gene fusion

U

UTR_3: Untranslated region at the 3-side of a coding sequence
UTR_5: Untranslated region at the 5-side of a coding sequence

W

WGS: Whole Genome Sequence

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