ctdna在给定的采样频率下计算预期的肿瘤检测大小。
ctdna的Python项目详细描述
循环肿瘤DNA
Python包（https://pypi.org/project/ctdna）计算从癌细胞到血流中的生物标志物的脱落及其在液体活检（小血样）中的分析。 可以从命令行运行包，也可以使用各种方法对自定义计算很重要。 下面提供了多个示例，可以从https://mybinder.org在浏览器中执行。 引用：Avanzini等人，A mathematical model of ctDNA shedding predicts tumor detection size，科学进步6:eabc4308（2020），出版。 有关更多技术细节，请参阅预印本Avanzini等人，bioRxiv（2020）：https://doi.org/10.1101/2020.02.12.946228 源代码位于https://github.com/reiterlab/ctdna。在
Releases
- ctdna 0.1.0 2020-05-06: Initial release of package.
- ctdna 0.1.1 2020-08-18: Added various examples and unittests. Added methods to calculate detection probabilities.
- ctdna 0.1.2 2020-11-16: Made example available at https://mybinder.org。在
Installation and Setup
- Easiest is to install Mini anaconda https://docs.conda.io/en/latest/miniconda.html，用
conda create -n ctdna python=3.6创建一个新的conda环境，并用conda activate ctdna激活它 - 使用
pip install ctdna安装ctdna包 - 使用
python -c 'import ctdna'测试安装 - 卸载包并使用
conda deactivate ctdna和conda remove --name ctdna --all删除conda环境
Manual
^{
- ^{
}: simulates the evolutionary dynamics of a tumor and its biomarkers over time - ^{
}: simulates the biomarker distribution at a given tumor size or tumor age - ^{
}: simulates the detection size of a growing tumor for repeated testing at a desired annual false positive rate or a specified p-value threshold - ^{
}: computes the ROC (receiver operating characteristic)
See ^{
Examples
- Use the interactive binder notebook at https://mybinder.org/v2/gh/reiterlab/ctdna/912b0958ef64d536185fdb2af33c71945db73287立即尝试该包。举例说明如何计算在直径为1、1.2、1.5和2cm的肿瘤中检测到特异性可操作突变的概率，其特异性为99%example.ipynb
- 模拟10种肿瘤生长和ctDNA脱落动力学：
ctdna dynamics -b 0.14 -d 0.13 -M 1e10 -n 10 - 为100名受试者模拟给定肿瘤大小的ctDNA:
ctdna distribution -b 0.14 -d 0.13 -n 100 -M 1e8 --q_d=1.4e-4 - 模拟先前模拟的肿瘤生长和脱落动力学的每月复发试验：
ctdna detection monthly -b 0.14 -d 0.13 -M 1e10 --panel_size 20 --n_muts 20 --annual_fpr 0.05 --seq_eff 0.5 --imaging_det_size 1e9 - 用CancerSEEK模拟以前模拟的肿瘤生长和脱落动力学的年度筛查：
ctdna detection annually -b 0.14 -d 0.136 -M 1e11 --panel_size 2000 --n_muts 1 --annual_fpr 0.01 --seq_eff 0.5 --diagnosis_size 2.25e10 - 用CAPPSeq模拟以前模拟的肿瘤生长和脱落动力学的年度筛选：
ctdna detection annually -b 0.14 -d 0.136 -M 1e11 --panel_size 300000 --n_muts 10 --pval_th 1.5e-7 --seq_eff 0.5 --diagnosis_size 2.25e10
Arguments
^{
} or ^{ }: birth rate of cancer cells ^{
} or ^{ }: death rate of cancer cells ^{
}: ctDNA shedding probability per cell death ^{
}: ctDNA shedding probability per cell birth ^{
}: ctDNA shedding probability per cell per day ^{
}: cfDNA half-life time in minutes ^{
}: size of blood sample tube (liters; default 0.015 l) ^{
}: sequencing panel size ^{
}: sequencing error rate per base-pair (default: 1e-5) ^{
}: sequencing efficiency, ie. fraction of the sampled molecules that are actually successfully sequenced (default: 0.5) ^{
}: number of clonal mutations in the cancer that are covered by the sequencing panel ^{
} or ^{ }: tumor detection size where biomarker level is evaluated or size where dynamics simulations are stopped ^{
} or ^{ }: simulations end when cancer reaches the given time ^{
}: approximate growth of tumor after this given threshold is reached ^{
} or ^{ }: output directory for files (default is defined in ^{ }) ^{
} Optional argument to fix the wildtype haploid genome equivalents (hGE) per plasma ml to the given number instead of sampling the plasma DNA concentration from a Gamma distribution with parameters specified in ^{ }
Detection mode
- ^{
}: Specifies desired annual false positive rate (1 - specificity) if test is repeated at the given frequency over a year - ^{
}: Instead of the desired annual false positive rate ^{ }, one can directly provide a p-value threshold that calls somatic point mutations in ctDNA
Authors: Stefano Avanzini & Johannes Reiter, Stanford University, https://reiterlab.stanford.edu
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