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

## Overview

Mutations in this gene were first described in DLBCL in 2013[@zhangGeneticHeterogeneityDiffuse2013] and by the same group in a subsequent study.[@reddyGeneticFunctionalDrivers2017] It remains in Tier 2 because other exome and genome-wide studies of DLBCL did not reproduce this observation. 



## Relevance tier by entity

|Entity|Tier|Description                              |
|:------:|:----:|-----------------------------------------|
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@mottokIntegrativeGenomicAnalysis2019]|
|![DLBCL](images/icons/DLBCL_tier2.png) |2   |relevance in DLBCL not firmly established[@zhangGeneticHeterogeneityDiffuse2013]|

## Mutation incidence in large patient cohorts (GAMBL reanalysis)

|Entity|source        |frequency (%)|
|:------:|:--------------:|:-------------:|
|DLBCL |GAMBL genomes |2.49         |
|DLBCL |Schmitz cohort|1.91         |
|DLBCL |Reddy cohort  |2.20         |
|DLBCL |Chapuy cohort |2.14         |

## Mutation pattern and selective pressure estimates

[[include:dnds_JAK1.md]]




## JAK1 Hotspots

| Chromosome |Coordinate (hg19) | ref>alt | HGVSp | 
 | :---:| :---: | :--: | :---: |
| chr1 | 65301158 | C>A | G1097V |

[[include:browser_JAK1.md]]

## Expression
![](images/gene_expression/JAK1_by_pathology.svg)
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->

[[include:mermaid_JAK1.md]]

## References