User: chloe.steen

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chloe.steen120
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Oslo
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Posts by chloe.steen

<prev • 24 results • page 1 of 3 • next >
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Matched normal necessary for Battenberg algorithm
... I am looking into using the [Battenberg algorithm][1] to infer subclonal copy number alterations in tumor samples. I was wondering whether it is necessary to have Affymetrix SNP6.0 array data for matched normal in order to use the algorithm, or is it enough with SNP6.0 data for tumor sample only. ...
clonality copy number snp written 9 weeks ago by chloe.steen120
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Comment: C: CNV detection from RNA-seq data
... Is [this the paper][1] you are referring to? [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123637/ ...
written 11 weeks ago by chloe.steen120
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Comment: C: Correcting for tumor purity in tumor evolution analysis
... > That said, there may be cases where you don't pick up the founding clone, especially when you're doing targeted or exome sequencing, or in tumors with very low mutation rates. That's an interesting thought. For my samples I have exome sequencing data of 300x depth. At such a high depth I would ...
written 11 months ago by chloe.steen120
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Correcting for tumor purity in tumor evolution analysis
... When you study the subclonality of a tumor, for example by using a tool like SciClone or PyClone, you have to adjust the frequencies of the mutations present in the tumor with the tumor content of the biopsy, aka the tumor purity. As far as I know, there are three methods for correcting for tumor p ...
genome sequencing written 12 months ago by chloe.steen120
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Comment: C: Only one cluster in multiple tumor phylogeny samples
... I used [samtools mpileup][1] and provided the list of positions based on the merged vcf files for the two samples. samtools mpileup -f myreferencefastafile.fasta -s merged_variants_file.txt path/to/bam/file.bam -o output.vcf -v -t DP4 DP4 is a tag to access the number of reads in the output file. ...
written 13 months ago by chloe.steen120
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Comment: C: Sciclone on exome sequencing data
... I still get some VAFs above 50%, and I think they occur in regions with no CN calls, which are assumed by sciClone to be equal 2. One way to exclude them would be to add these regions in the exclude file. But since sciClone already detects those regions, wouldn't it be easier to add an option "exclu ...
written 14 months ago by chloe.steen120
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Comment: C: Clonal Evolution Plot (figure 3d)
... I am using Clonevol, and it is giving me two or more models for the same patient, for example one with model probability of 0.49 and one with model probability 0.47. I only have two samples per patient. How to you choose the model when it gives several possible models. Is it enough to choose the on ...
written 14 months ago by chloe.steen120
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Comment: C: Only one cluster in multiple tumor phylogeny samples
... > Your variant lists need to be merged, such that you get readcounts for each variant in each bam, regardless of whether it was called or not. So what you are saying is that if I have 800 variants in the primary tumor, and 1000 in the relapse tumor, I have to merge them so that I end up with 100 ...
written 14 months ago by chloe.steen120
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Answer: A: CNV caller software
... ASCAT, FACETS, Theta, ABSOLUTE, ADTex, CopyCat, copynumber, depending on the type of data you have. I personally use ASCAT for array data, and it has been used in several articles as the gold standard to compare tools, and FACETS for exome sequencing, it was published this summer, and my first imp ...
written 14 months ago by chloe.steen120
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Comment: C: Sciclone on exome sequencing data
... Ok, that's what I did, but the reason I was unsure if it was the right to do is because I am still getting VAFs larger than 50%. I was expecting VAFs smaller or equal to 50% at most. Do you know what that can be due to? I am thinking that maybe there might be regions of LOH that were not included ...
written 14 months ago by chloe.steen120

Latest awards to chloe.steen

Popular Question 8 months ago, created a question with more than 1,000 views. For Sciclone on exome sequencing data
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Only one cluster in multiple tumor phylogeny samples

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