Copy number variation analysis - `squenza`

Sequenza CNV Analysis

Sequenza 包括在 Python 中实现的2步预处理步骤，及第3步在 R 中操作并得到：

depth ratio
cellularity
ploidy

最后将结果绘制成图。

Step 1: Pre-processing – Walking the Genome 基因组步移

The first pre-processing step is run on the final normal and tumour mapped data (BAM files) in order to walk the genome in a pileup format (automatically generated by samtools).

This first step finds high quality sites in the genomes and extracts their depth and genotype in the normal genome and calculates the variant alleles and allele frequencies in the tumour genome.

This output has one line for each position in the BAMs and includes information on the position, depths, allele frequencies, zygosity, GC in the location.

Step 2: Perform Binning 数据合并

The binning step takes the rows of genomic positions and compresses them down to 1 row for every 200 rows previously. This massively reduces the file size and processing time in the third step.

Step 3: Running Sequenza Algorithms and Plotting Results

这一步用R实现。

Sequenza Analysis Results and Visualisation

Cellularity estimate

One of the first and most important estimates that Sequenza provides is the tumour cellularity.

tumour cellularity 说明了肿瘤细胞在肿瘤基因组中的百分比，其分析是基于 BAF (B Allele Frequency) 及基因组的 depth ratio.

由 sequenza 分析得到的 cellularity 结果一般是在 *model_fit.pdf.

直接拿jimmy大神给的结果文件看一眼，长这样：

cellularity: 35%, 即肿瘤组织中细胞的占比
ploidy: 4.2, 代表基因组被扩增的程度

ploidy: the amount of DNA per tumour cell, expressed as multiples of haploid genomes.

https://www.crick.ac.uk/research/labs/peter-van-loo/software>
The ploidy of cancer cells refers to the amount of DNA they contain.
- If there's a normal amount of DNA in the cells, they are said to be diploid. These cancers tend to grow and spread more slowly.
- If the amount of DNA is abnormal, then the cells are called aneuploid. These cancers tend to be more aggressive. (They tend to grow and spread faster.)
https://www.cancer.org/cancer/breast-cancer/understanding-a-breast-cancer-diagnosis/ploidy-and-cell-proliferation.html
sd.BAF: 0.13, 即BAF的标准差，表示未发生大片段的杂合性丢失 ( long losses of heterozygosity).

Loss of heterozygosity (LOH) is a cross chromosomal event that results in loss of the entire gene and the surrounding chromosomal region.

The loss of heterozygosity is a common occurrence in cancer, where it indicates the absence of a functional tumor suppressor gene in the lost region. However, many people remain healthy with such a loss, because there still is one functional gene left on the other chromosome of the chromosome pair. The remaining copy of the tumor suppressor gene can be inactivated by a point mutation, leaving no tumor suppressor gene to protect the body. Loss of heterozygosity does not imply a homozygous state (which would require the presence of two identical alleles in the cell).

https://en.wikipedia.org/wiki/Loss_of_heterozygosity#Breast_Cancer_and_BRCA1/2

CNV inferences

*genome_view.pdf 文件查看基因组拷贝数，推断CNV.

This file contains three “pages” of copy number events through the entire genomic block.

The first page shows copy numbers of the A (red) and B (blue) alleles,

The second page shows overall copy number changes, and

The third page shows the B allele frequency and depth ratio through genomic block.

以单个染色体为单位查看：