PIM2 - morinlab/LLMPP GitHub Wiki

bibliography: 'morinlab.bib' csl: 'NLM.csl' link-citations: true

PIM2

Overview

PIM2 is one of a number of genes affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.

History

%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
timeline
    title Publication timing
      2015-02-12 : Reichel : PMBL
      2017-10-10 : Reddy : DLBCL
2018-04-12 : Schmitz : DLBCL
2018-10-01 : Arthur : DLBCL

Relevance tier by entity

Entity	Tier	Description
	1	high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]
	1	aSHM target and high-confidence DLBCL gene[@reddyGeneticFunctionalDrivers2017; @schmitzGeneticsPathogenesisDiffuse2018a; @arthurGenomewideDiscoverySomatic2018]

Mutation incidence in large patient cohorts (GAMBL reanalysis)

Entity	source	frequency (%)
DLBCL	GAMBL genomes	3.44
DLBCL	Schmitz cohort	6.38
DLBCL	Reddy cohort	4.00
DLBCL	Chapuy cohort	3.85

Mutation pattern and selective pressure estimates

Entity	aSHM	Significant selection	dN/dS (missense)	dN/dS (nonsense)
BL	Yes	No	0.000	0.000
DLBCL	Yes	No	1.908	14.378
FL	Yes	No	0.000	62.405

aSHM regions

chr_name	hg19_start	hg19_end	region	regulatory_comment
chrX	48774756	48776255	TSS	active_promoter

View coding variants in ProteinPaint hg19 or hg38

View all variants in GenomePaint hg19 or hg38