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HNRNPU.md
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| 1 | +# HNRNPU |
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| 2 | +## History |
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| 3 | + |
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| 4 | +```mermaid |
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| 5 | +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
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| 6 | +timeline |
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| 7 | + title Publication timing |
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| 8 | + 2017-10-10 : Reddy : DLBCL |
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| 9 | + 2019-09-26 : Panea : BL |
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| 10 | +``` |
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| 11 | +## Relevance tier by entity |
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| 12 | + |
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| 13 | +|Entity|Tier|Description | |
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| 14 | +|:------:|:----:|--------------------------| |
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| 15 | +| |1-a | aSHM target and high-confidence BL gene | |
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| 16 | +| |1-a | aSHM target and high-confidence DLBCL gene| |
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| 17 | + |
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| 18 | +||1|high-confidence BL gene| |
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| 19 | +||1|high-confidence DLBCL gene| |
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| 20 | +## Mutation incidence |
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| 21 | + |
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| 22 | +|Entity|source |frequency (%)| |
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| 23 | +|:------:|:---------------------:|:-------------:| |
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| 24 | +|BL |GAMBL genomes+capture|5.77 | |
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| 25 | +|BL |Thomas cohort |6.40 | |
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| 26 | +|BL |Panea cohort |8.90 | |
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| 27 | +|DLBCL |GAMBL genomes |2.49 | |
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| 28 | +|DLBCL |Schmitz cohort |3.40 | |
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| 29 | +|DLBCL |Reddy cohort |2.40 | |
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| 30 | +|DLBCL |Chapuy cohort |3.42 | |
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| 31 | + |
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| 32 | +## Mutation pattern |
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| 33 | + |
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| 34 | +|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)| |
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| 35 | +|:------:|:----:|:---------------------:|:----------------:|:----------------:| |
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| 36 | +|BL |Yes |Yes |1.081 |27.052 | |
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| 37 | +|DLBCL |Yes |No |1.712 | 0.000 | |
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| 38 | +|FL |Yes |No |4.865 |31.056 | |
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| 39 | + |
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| 40 | +## aSHM regions |
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| 41 | + |
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| 42 | +|chr_name|hg19_start|hg19_end |region |regulatory_comment| |
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| 43 | +|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:| |
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| 44 | +|chr1 |245023502 |245029083|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A245023502%2D245029083)|NA | |
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| 45 | + |
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| 46 | +View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU_protein_hg38.html) |
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| 47 | + |
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| 48 | + |
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| 49 | + |
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| 50 | +View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU_hg38.html) |
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| 51 | + |
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| 52 | + |
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| 53 | + |
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| 54 | + |
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| 55 | +## References |
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| 56 | +1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
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| 57 | +2. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |