User: chloe.steen

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chloe.steen120
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Posts by chloe.steen

<prev • 24 results • page 2 of 3 • next >
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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 14 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 16 months ago by chloe.steen120
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Answer: A: Cancer CNV workflow
... First of all, Copy number Variation (CNV) are copy number variations present in normal cells. The ones you see in cancer cells are called Copy Number Aberrations (CNA). SNP6.0 array is probably the best platform to detect copy number aberrations. ASCAT is a very good software to detect copy number ...
written 17 months ago by chloe.steen120
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Answer: A: hg18 vs hg19 in SNP6.0 data
... I contacted Affymetrix directly, and they recommend to always use the latest version of the annotation file for the appropriate array. So for my case, that is the annotation file for GenomeWideSNP_6 Annotations, CSV format, Release 35 (313 MB, 4/30/15) (current latest release). The Annotation file ...
written 18 months ago by chloe.steen120
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Answer: A: Sciclone on exome sequencing data
... New question: Does sciClone calculate/take into account tumor percentage when calculating VAF? Is there a way to give it as input? The reason I ask if because my VAF plots are not scaled to tumor percentage, and it looks as though the VAF of a subclone increases between primary and relapse, but ...
written 19 months ago by chloe.steen120
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Answer: A: SciClone not numeric error
... You can try the following: 1. Make sure your variant allele frequency variable is a value between 0 and 100. 2. Convert the vaf variable into a numeric variable, and/or convert your file into a dataframe For example for sample 1: v1 <- data.frame(v1) v1$vaf <- as.numeric(v1$vaf) ...
written 19 months ago by chloe.steen120
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Answer: A: Measuring tumor heterogeneity
... I am not sure what kind of data you have, and I may have misunderstood your question, but here are anyway some tools that look at tumor heterogeneity, the clonality of the tumor and tumor purity, as well as evolutionary progression between several samples from the same patient. This list is probably ...
written 19 months ago by chloe.steen120
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Comment: C: hg18 vs hg19 in SNP6.0 data
... Thank you for your answer. I am not sure if I can use liftover with Genome-wide Human SNP6.0 array data, I don't have sequencing data. Do you have experience with using liftover on SNP6.0 data? ...
written 19 months ago by chloe.steen120
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hg18 vs hg19 in SNP6.0 data
... I have SNP6.0 data that were generated in 2010-2011. I use ASCAT to process them, and on the ASCAT website it is recommended to use PennCNV to create the LogR and BAF-files. In [ASCAT's protocol][1], they suggest using hg19 as build in the PennCNV procedure. I was wondering if anyone knows how usi ...
hg19 ascat hg18 penncnv snp6.0 written 19 months ago by chloe.steen120
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Comment: C: Sciclone on exome sequencing data
... I thought I would just include as a final comment in my post where I read about using ASCAT for WES in the Sciclone paper: > As with other tools [6], [11], [22], [30], regions of CNA and LOH are > provided as inputs after having been inferred from whole-exome > sequencing (WES, e.g., via A ...
written 19 months ago by chloe.steen120

Latest awards to chloe.steen

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