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关联突变与用药部分逻辑代码实现

关联突变与用药部分逻辑代码实现

作者: 无话_ | 来源:发表于2022-12-23 17:04 被阅读0次

    项目地址
    https://github.com/user-tq/anvcivi

    直接用civic下载的文件进行简单的数据清洗,使用MANE下载的文件构造基因与转录本的字典(解决annovar的转录本问题),暂只考虑氨基酸改变完全匹配情况。最结果暂生成markdown,但由于markdown无法合并单元格,且未区分癌种,结果很长,实际分析后一两个位点突变就很多了。

    AA_match af
    0 NRAS:NM_002524:exon3:c.C181A:p.Q61K 0.017
    1 PIK3CA:NM_006218:exon2:c.G333C:p.K111N 0.027
    2 PIK3CA:NM_006218:exon21:c.A3140G:p.H1047R 0.03
    3 KIT:NM_000222:exon17:c.A2447T:p.D816V 0.021
    4 EGFR:NM_005228:exon18:c.G2155A:p.G719S 0.061
    5 EGFR:NM_005228:exon19:c.2235_2249del:p.E746_A750del 0.011
    6 EGFR:NM_005228:exon20:c.2296_2297insTGGCCAGCG:p.V769_D770insASV 0.02
    7 EGFR:NM_005228:exon20:c.C2369T:p.T790M 0.019
    8 EGFR:NM_005228:exon21:c.T2573G:p.L858R 0.012
    9 BRAF:NM_004333:exon15:c.T1799A:p.V600E 0.026
    10 KRAS:NM_004985:exon4:c.G436A:p.A146T 0.015
    11 KRAS:NM_004985:exon2:c.G38A:p.G13D 0.017
    12 KRAS:NM_004985:exon2:c.G35A:p.G12D 0.019
    13 MAP2K1:NM_002755:exon2:c.A167C:p.Q56P 0.068
    AA_match af disease drugs
    0 NRAS:NM_002524:exon3:c.C181A:p.Q61K 0.017 Neuroblastoma Binimetinib,Everolimus
    1 NRAS:NM_002524:exon3:c.C181A:p.Q61K 0.017 Skin Melanoma Vemurafenib
    2 NRAS:NM_002524:exon3:c.C181A:p.Q61K 0.017 Skin Melanoma Selumetinib
    3 NRAS:NM_002524:exon3:c.C181A:p.Q61K 0.017 Colorectal Cancer Chemotherapy,Cetuximab
    4 NRAS:NM_002524:exon3:c.C181A:p.Q61K 0.017 Colorectal Cancer Dactolisib,Selumetinib
    5 NRAS:NM_002524:exon3:c.C181A:p.Q61K 0.017 Lung Non-small Cell Carcinoma Trametinib,Selumetinib
    6 NRAS:NM_002524:exon3:c.C181A:p.Q61K 0.017 Ovary Serous Adenocarcinoma Trametinib
    7 PIK3CA:NM_006218:exon2:c.G333C:p.K111N 0.027 Her2-receptor Positive Breast Cancer Pictilisib
    8 PIK3CA:NM_006218:exon2:c.G333C:p.K111N 0.027 Her2-receptor Positive Breast Cancer Trastuzumab Emtansine

    结果太长略

    AA_match disease drugs evidence_statement
    0 NRAS:NM_002524:exon3:c.C181A:p.Q61K Neuroblastoma Binimetinib,Everolimus In-vitro study in 5 neuroblastoma cell lines (2 with NRAS Q61K mutation). The combination of mTOR and MEK Inhibitors synergistically blocked cell growth in NRAS mutant but not wild type cell lines. Single agent MEK inhibition (AZD6244/selumetinib, MEK162 or PD0325901) and single agent mTOR inhibition (Everolimus or AZD8055) also blocked cell growth in NRAS mutant cell lines, whereas single agent PI3K inhibitors or MEK Inhibitors in combination with PIK3CA/AKT inhibitors did not show synergistic effects.

    结果太长略

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