Cassis: Detection of genomic rearrangement breakpoints

Using Cassis to identify breakpoints in the genomes of Homo sapiens and Mus musculus

     The package Cassis was used for the comparison of the genomes of the species Homo sapiens (reference genome) and Mus musculus.

1 - Input data

     To execute this comparison, we obtained all necessary information from the Ensembl Genome Brower site (Build 57).

     The Build 57 was released in March 3rd, 2010 and contains information about the Homo sapiens assembly GRCh37 (released in February 2009) and about the Mus musculus assembly NCBI m37 (released in April 2007).

  1. FASTA sequences

    The FASTA sequences of the chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 and X of the Homo sapiens and of the chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 and X of the Mus musculus were downloaded from the Ensembl FTP site:


    We downloaded the FASTA files which contains the chromosome sequences after being processed by RepeatMasker (dna_rm).
    All files are renamed according to the pattern: [chromosome_name].fasta (Example: 1.fasta, 2.fasta, X.fasta, etc.)

  2. Orthologous genes

    The list of orthologous genes was produced with data obtained through the Biomart tool. We downloaded the list of all orthologous genes which can be found between Homo sapiens and Mus musculus and the list of all Mus musculus genes. We processed these two lists with the script util/createOne2OneTable.pl (available in the Cassis package) to produce a TSV (Tab Separated Values) file containing all one-to-one orthologous genes.
    Download the list of one-to-one orthologous genes


2 - Results

     The list of 15,047 pairs of one-to-one orthologous genes was processed by the package Cassis.

     In the first step of the method, Cassis identified a total of 369 breakpoints. In the second step, these breakpoints were submitted to the segmentation process.

     Table 1 shows the minimum, maximum, mean and median breakpoint length before and after the segmentation process. It also shows the number of breakpoints which received status 1 or 0 (respectively, passed or failed in the statistical test that evaluates the significance of the segmentation).

Table 1: Minimum, maximum, mean and median breakpoint length before and after the segmentation
Description N Before segmentation [length in bp] After segmentation [length in bp]
Min Max Mean Median Min Max Mean Median
All breakpoints 369 1 32,752,838 771,401 244,568 21 5,133,352 201,251 52,986
Status = 1 365 1 32,752,838 775,512 244,568 21 5,133,352 203,057 53,262
Status = 0 4 79,048 1,031,931 396,243 236,998 2,069 72,226 36,459 35.771

     Of the 365 breakpoints which were classified with status 1, a total of 25 breakpoints had their length increased after the segmentation. Table 2 shows the minimum, maximum, mean and median length of these breakpoints, before and after the segmentation process.

Table 2: Minimum, maximum, mean and median length of the 25 breakpoints which had their length increased after the segmentation
Description N Before segmentation [length in bp] After segmentation [length in bp]
Min Max Mean Median Min Max Mean Median
Length (after) ≥ Length (before) 25 1 5,115,573 282,827 34,067 1,539 5,133,352 311,471 51,645

     A total of 340 breakpoints were classified with status 1 and had their length decreased after the segmentation process. Table 3 shows the minimum, maximum, mean and median length of these breakpoints, before and after the segmentation process.

Table 3: Minimum, maximum, mean and median length of the 340 breakpoints which had their length decreased after the segmentation
Description N Before segmentation [length in bp] After segmentation [length in bp] Length reduction [%]
Min Max Mean Median Min Max Mean Median Min Max Mean Median
Length (after) < Length (before) 340 303 32,752,838 811,739 256,577 21 4,860,908 195,085 54,883 0.31 99.99 62.26 71.20

     Figure 1 shows the histogram of the differences of the breakpoint lengths, before and after the segmentation step, for the 358 breakpoints which were classified with status 1.

Figure 1: Histogram of the breakpoint size differences between "before" and "after" the refinement step of Cassis.
(7 values larger than 5 Mbp have been removed for the purpose of readability)

3 - Download