PurityEst – Estimating Purity of Human Tumor Samples using Next-generation Sequencing Data

PurityEst

:: DESCRIPTION

PurityEst is a novel algorithm which infers the tumor purity level from the allelic differential representation of heterozygous loci with somatic mutations in a human tumor sample with a matched normal tissue using next-generation sequencing data.

::DEVELOPER

Xiaoping Su

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

PurityEst

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2265-6. doi: 10.1093/bioinformatics/bts365.
PurityEst: estimating purity of human tumor samples using next-generation sequencing data.
Su X, Zhang L, Zhang J, Meric-Bernstam F, Weinstein JN.

InfiniumPurify 1.3.1 – Predicting Tumor Purity from Methylation Microarray data

InfiniumPurify 1.3.1

:: DESCRIPTION

InfiniumPurify is a simple but effective method to estimate purities from the DNA methylation 450k array data.

::DEVELOPER

Yufang Qin <yfqin at shou.edu.cn>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX
R

:: DOWNLOAD

InfiniumPurify

:: MORE INFORMATION

Citation:

Qin Y, Feng H, Chen M, Wu H, Zheng X.
InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research.
Genes Dis. 2018 Feb 21;5(1):43-45. doi: 10.1016/j.gendis.2018.02.003. PMID: 30258934; PMCID: PMC6147081.

Predicting tumor purity from methylation microarray data.
Zhang N, Wu HJ, Zhang W, Wang J, Wu H, Zheng X.
Bioinformatics. 2015 Jun 25. pii: btv370.

ABSOLUTE 1.0 / HAPSEG – Estimate Purity/Ploidy and absolute copy-number and mutation data

ABSOLUTE 1.0 / HAPSEG

:: DESCRIPTION

The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.

HAPSEG is a probabilistic method to interpret bi- allelic marker data in cancer samples.

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX / Windows
R package

:: DOWNLOAD

ABSOLUTE , HAPSEG

:: MORE INFORMATION

Citation

Scott L Carter, et cl.
Absolute quantification of somatic DNA alterations in human cancer
Nature Biotechnology 30, 413–421 (2012) doi:10.1038/nbt.2203

Scott L. Carter, Matthew Meyerson & Gad Getz
Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping