scholarly journals Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xinping Fan ◽  
Guanghao Luo ◽  
Yu S. Huang
Keyword(s):  
Copy Number ◽  
Bayesian Learning ◽  
Kernel Smoothing ◽  
Gaussian Mixture ◽  
Copy Number Alterations ◽  
Sequencing Data ◽  
Copy Numbers ◽  
Allele Specific ◽  
Tumor Sequencing ◽  
Low Coverage

Abstract Background Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. Results We introduce Accucopy, a method to infer total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy adopts many robust statistical techniques such as kernel smoothing of coverage differentiation information to discern signals from noise and combines ideas from time-series analysis and the signal-processing field to derive a range of estimates for the period in a histogram of coverage differentiation information. Statistical learning models such as the tiered Gaussian mixture model, the expectation–maximization algorithm, and sparse Bayesian learning were customized and built into the model. Accucopy is implemented in C++ /Rust, packaged in a docker image, and supports non-human samples, more at http://www.yfish.org/software/. Conclusions We describe Accucopy, a method that can predict both TCNs and ASCNs from low-coverage low-purity tumor sequencing data. Through comparative analyses in both simulated and real-sequencing samples, we demonstrate that Accucopy is more accurate than Sclust, ABSOLUTE, and Sequenza.

scholarly journals Estimating Mixture of Gaussian Processes by Kernel Smoothing

2013 ◽  
Author(s):  
Mian Huang ◽  
Runze Li ◽  
Hansheng Wang ◽  
Weixin Yao
Keyword(s):  
Gaussian Processes ◽  
Kernel Smoothing ◽  
Mixture Of Gaussian

Kernel Regression Estimation for Functional Data

2018 ◽  
Author(s):  
Frédéric Ferraty ◽  
Philippe Vieu
Keyword(s):  
Kernel Methods ◽  
Functional Data ◽  
Linear Functional ◽  
Kernel Smoothing ◽  
Kernel Regression ◽  
Functional Regression ◽  
Regression Estimation ◽  
Asymptotic Results ◽  
Kernel Regression Estimation ◽  
The Impact

This article provides an overview of recent nonparametric and semiparametric advances in kernel regression estimation for functional data. In particular, it considers the various statistical techniques based on kernel smoothing ideas that have recently been developed for functional regression estimation problems. The article first examines nonparametric functional regression modelling before discussing three popular functional regression estimates constructed by means of kernel ideas, namely: the Nadaraya-Watson convolution kernel estimate, the kNN functional estimate, and the local linear functional estimate. Uniform asymptotic results are then presented. The article proceeds by reviewing kernel methods in semiparametric functional regression such as single functional index regression and partial linear functional regression. It also looks at the use of kernels for additive functional regression and concludes by assessing the impact of kernel methods on practical real-data analysis involving functional (curves) datasets.

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