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  • CNV-seq, to detect Copy Number Variation using next-generation sequencing

    CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

    more details at BMC Bioinformatics :
    Background DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. Results Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. Conclusion Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.


    The package is at

  • #2
    This may be really obvious but I'm trying to understand how to you decide which is ref and which is test. If I have 2 bam files generated by mapping Illumina reads from 2 individuals against the NCBI reference genome, does it mean either one can be ref or test?

    Comment


    • #3
      Detecting alignment collapse

      Hi,

      I want to check my genome sequence for collapsed, tandemly repeated genes. It seems to me that I could use software for detecting CNVs in that I am looking for significantly increased read depth. CNV-seq requires test and reference sequences, which makes sense to control for sequence-based noise in read depth however I only have my reference genome and one instance of Illumina data. Does anyone have any ideas?

      Adam

      Comment


      • #4
        Hi,

        I am trying to undertand how to build the file for CNV detection with sequence.
        I would like to know wich information is need it on the files.

        Do you have some examples?

        Comment


        • #5
          CNV-seq input file is DNA-seq or RNA-seq?

          Originally posted by xiechao View Post
          CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

          more details at BMC Bioinformatics :
          Background DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. Results Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. Conclusion Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.


          The package is at
          http://tiger.dbs.nus.edu.sg/cnv-seq
          Hi,I want to know:CNV-seq input file is DNA-seq or RNA-seq?

          Comment


          • #6
            Hi !

            My data are DNA-seq. But there are not from one Case-control study.

            I working on the human Chr 8. I use a reference sequence to simulate my DNA-seq. I just would like to know if some parameters that I modify on my simulation influence the CNV detection on my DNA-seq.

            Some ideas?

            Sergio

            Comment


            • #7
              Hello

              Did you already found how to detect the CNV with your data from non control case study?

              I am continuing seraching for a solution.

              Regards,

              Sergio

              Comment


              • #8
                Originally posted by louis7781x View Post
                Hi,I want to know:CNV-seq input file is DNA-seq or RNA-seq?
                Hi Louis,

                CNV-seq input consists in just two files (reference & test) with just two columns each.
                First column corresponds to the third column in a BAM file, that is the reference sequence name of the alignment (Chr1, Chr2, ..), the second column is the fourth column of a BAM file, that is the corresponding 1-based leftmost mapping position of that read. Input files can look like this:

                1 999
                1 1234
                1 23456
                1 25234

                Full explanation of the input, how to get it, how to run CNV-seq, etc:




                Jose Flores
                --
                J. Rodrigo Flores
                [email protected]
                Center for Genomic Sciences, UNAM, Mexico

                Comment


                • #9
                  Originally posted by roman.sergio View Post
                  Hello

                  Did you already found how to detect the CNV with your data from non control case study?

                  I am continuing seraching for a solution.

                  Regards,

                  Sergio
                  Hi Sergio,

                  With CNV-seq in mind and for non-control-case studies you can basically choose whatever reference you want. There might be some issues to worry about like what population the reference you choose come from? or what's the coverage .. It will depend on your purpose and the features of your sample to analyze.
                  I’ve seen some studies taking the health individual NA10851 from the 1000 genomes data as a control/reference.

                  ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/

                  Hope can help,
                  Jose Flores
                  --
                  J. Rodrigo Flores
                  [email protected]
                  Center for Genomic Sciences, UNAM, Mexico

                  Comment


                  • #10
                    Originally posted by jflores View Post
                    Hi Louis,

                    CNV-seq input consists in just two files (reference & test) with just two columns each.
                    First column corresponds to the third column in a BAM file, that is the reference sequence name of the alignment (Chr1, Chr2, ..), the second column is the fourth column of a BAM file, that is the corresponding 1-based leftmost mapping position of that read. Input files can look like this:

                    1 999
                    1 1234
                    1 23456
                    1 25234

                    Full explanation of the input, how to get it, how to run CNV-seq, etc:




                    Jose Flores
                    Thanks for your help,I want to know the input type because the coverage of DNA-seq and RNA-seq is different.So if I use RNA-seq aligned to ref genome and use output file bam to run CNV-seq,Does it apply to analyze copy number varivation?

                    Comment


                    • #11
                      Hi,

                      how to view the level of a gene in CNV-seq ?

                      Script :
                      samtools view Patient_test/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > test.hits
                      samtools view Patient_ref/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > ref.hits

                      perl cnv-seq.pl --test test.hits --ref ref.hits --genome chrom17

                      data <- read.delim("test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.minw-4.cnv")
                      cnv.print(data)
                      cnv.summary(data)
                      plot.cnv(data)
                      ggsave("sample.pdf")
                      [IMG]/home/labo/Sample1.pdf[/IMG]

                      Regards

                      Comment


                      • #12
                        Hi Tonio,

                        You can plot specific coordinates and try to infer from that if your gene of interest has or not gain/loss of copies.

                        Script :
                        samtools view Patient_test/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > test.hits
                        samtools view Patient_ref/Parsed_X/chr17.fa/bam/sorted.bam | perl -lane 'print "$F[2]\t$F[3]"' > ref.hits

                        perl cnv-seq.pl --test test.hits --ref ref.hits --genome chrom17

                        data <- read.delim("test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.minw-4.cnv"))
                        plot.cnv.chr(data, chromosome=NA, from=NA, to=NA)

                        ... For more options about plotting using CNV-seq you can have a look at the cnv.R file

                        Regards,

                        Rodrigo
                        --
                        J. Rodrigo Flores
                        [email protected]
                        Center for Genomic Sciences, UNAM, Mexico

                        Comment


                        • #13
                          Dear all,
                          I have a couple of questions regarding CNV-seq.
                          I am having a play around with some DNA sequencing that is from custom capture. I have analysed some BAM files using the program. Some work fine, but some file combinations come up with an error, which is strange as all the data has been produced and analysed in exactly the same way. The error is;

                          "Can't use an undefined value as an ARRAY reference at /share/apps/cnv-seq_1.0/bin/cnv-seq.pl line 204, <REF> line 6460211."

                          I think this is some kind of Perl script error??

                          Also does anyone have any experience of using capture data with CNV-seq? any advice would be greatly appreciated.

                          Thanks for you help

                          Comment


                          • #14
                            Dear xiechao,

                            I am trying to use CNV-seq for 36 length Read size simulated data. I am not detecting any CNV.
                            While for the same data with 76bp Read Length, CNV-seq detects CNV.

                            Is the read length hard coded in the script?

                            Is there a way to use CNV-seq on 36 length read data.

                            Thanking you,
                            pg

                            Comment


                            • #15
                              Originally posted by louis7781x View Post
                              Thanks for your help,I want to know the input type because the coverage of DNA-seq and RNA-seq is different.So if I use RNA-seq aligned to ref genome and use output file bam to run CNV-seq,Does it apply to analyze copy number varivation?
                              I have the same question too. It would be really great if someone can shed some light on it.

                              Comment

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