User: chloe.steen

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chloe.steen120
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Oslo
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1 year, 4 months ago
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c******@ifi.uio.no

Posts by chloe.steen

<prev • 22 results • page 1 of 3 • next >
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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 5 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 6 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 8 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 8 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 8 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 9 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 9 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 9 months ago by chloe.steen120
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Comment: C: Sciclone on exome sequencing data
... I see that in the paper you published in [Nature Communication][1] you write the following: > Variant allele fractions of all tier 1 variants were corrected for > purity by reducing the number of reference-supporting reads in > proportion to the purity of the sample. This effectively scal ...
written 9 months ago by chloe.steen120
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Working with sensitive personal data in bioinformatics
... Biological data from a person are considered as sensitive data. As bioinformaticians we are probably all at some point exposed to genomic data from someone else. For example, if you are working with cancer samples, usually you have the normal (blood) sample to substract for germline mutations. The ...
genome data ethics privacy written 11 months ago by chloe.steen120

Latest awards to chloe.steen

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Sciclone on exome sequencing data
Commentator 7 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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