Allele-specific copy number detection | Whole-genome sequencing data analysis
Estimation of allele-specific copy number (ASCN), which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. Sequencing produces reads containing both alleles at heterozygous variant loci, and thus, like genotyping arrays, allows the disambiguation of ASCNs. Compared to genotyping arrays, next-generation sequencing can provide finer resolution in estimating ASCNs because each person has his/her own unique heterozygous variant loci that are not included in regular genotyping arrays.
Serves for dissection of genome-wide allele-specific copy number in tumors. ASCAT infers ASCAT (accurate genome-wide allele-specific copy number) profiles from single nucleotide polymorphism (SNP) array data to evaluate and adjust both tumor cell aneuploidy and non-aberrant cell admixture. The ASCAT profiles generated can be useful for interpretation of cancer genome sequencing data and for identification of changes varying in size from point mutations to complex rearrangements.
A bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid.
Normalizes allele-specific copy number estimates (ASCNs) from any technology and preprocessing method, without requiring matched normal. CalMaTe is a platform-independent multi-array method that controls single nucleotide polymorphism (SNP)-specific systematic variation by modeling the crosstalk between alleles in bi-allelic SNPs. The software was applied to the TCGA-ovarian cancer dataset. An add-on to the Aroma Project framework is also included in the package.
Allows users to find somatic allele-specific copy number changes in whole exome sequencing. FALCON-X consists of a model to estimate the allele-specific copy number at these heterozygous positions. It uses a modified Bayes information criterion to determine the number of signals. Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number.
Allows users to detect copy number aberrations (CAN) on cancer whole genome sequencing (WGS) data. ACEseq provides an automated platform without prior information requirement. The software can perform a wide range of features such as quality check or structure variants (SV) breakpoint inclusion. It authorizes to improve segmentation and to obtain quantitative metrics.
Leverages adjacent normal tissue from tumor biopsies. LumosVar has seven steps: (i) a set of unmatched control samples is analyzed for position quality scores, (ii) read counts and quality metrics are extracted from the tumor bams, (iii) quality scores are calculated for each candidate variant position, (iv) segmentation is performed, (v) allele specific copy number state for each segment is found, (vi) each candidate variant position is classified as somatic, germline heterozygous, or homozygous, and (vii) model parameters are optimized.
Evaluates the discordance between a given cell line sample to its reference sample according to the characterization of the Cancer Cell Line Encyclopedia (CCLE). Cell STRAINER allows users to exploit cell line copy number data to assess the strain genetic distance from the CCLE reference strain. This software intends to ease routine assessment of cell line diversification via a web application tool.