CNAsim：改进了单细胞拷贝数谱和肿瘤 DNA-seq 数据的模拟。

CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors.

机构信息

Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, United States.

Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, United States.

出版信息

Bioinformatics. 2023 Jul 1;39(7). doi: 10.1093/bioinformatics/btad434.

DOI:10.1093/bioinformatics/btad434

PMID:37449891

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10363024/

Abstract

SUMMARY

CNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumors. CNAsim can be used to efficiently generate single-cell copy number profiles for thousands of simulated tumor cells under a more realistic error model and a broader range of possible CNA mechanisms compared with existing simulators. The error model implemented in CNAsim accounts for the specific biases of single-cell sequencing that leads to read count fluctuation and poor resolution of CNA detection. For improved realism over existing simulators, CNAsim can (i) generate WGD, whole-chromosomal CNAs, and chromosome-arm CNAs, (ii) simulate subclonal population structure defined by the accumulation of chromosomal CNAs, and (iii) dilute the sampled cell population with both normal diploid cells and pseudo-diploid cells. The software can also generate DNA-seq data for sampled cells.

AVAILABILITY AND IMPLEMENTATION

CNAsim is written in Python and is freely available open-source from https://github.com/samsonweiner/CNAsim.

摘要

CNAsim 是一款用于改进肿瘤单细胞拷贝数改变 (CNA) 数据模拟的软件包。与现有模拟器相比，CNAsim 可以在更现实的误差模型和更广泛的可能 CNA 机制下，高效地为数千个模拟肿瘤细胞生成单细胞拷贝数谱。CNAsim 中实现的误差模型考虑了导致读取计数波动和 CNA 检测分辨率差的单细胞测序的特定偏差。为了在现有模拟器的基础上提高真实性，CNAsim 可以 (i) 生成 WGD、全染色体 CNA 和染色体臂 CNA，(ii) 模拟由染色体 CNA 积累定义的亚克隆群体结构，以及 (iii) 用正常二倍体细胞和假二倍体细胞稀释采样细胞群体。该软件还可以为采样细胞生成 DNA-seq 数据。