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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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How to choose input SNPs for ASCAT? #178

Closed bounlu closed 3 months ago

bounlu commented 3 months ago

Hi,

Thanks for the great tool. I am wondering how to choose SNPs as the input for ASCAT for the sequencing data (if not using SNP array)? More specifically;

  1. How many SNPs are sufficient throughout the genome?
  2. How should the SNPs be distributed along the genome? i.e. in terms of window size, genomic region, ... ?
  3. Does the population-specificity / MAF of SNPs affect how ASCAT work?
zhangzhhcb commented 3 months ago

Hi, Thanks for your interests. To answer your questions:

  1. It is hard to say how many SNPs are sufficient. The density of SNPs matters to support the reliability of segments, so we prefer WES data with good coverage.
  2. The distribution of the SNPs depend on your data. If the sample is expected to have less copy number alternation, the less dense data may be good to catch up the major segments. However, if the sample is expected to have dramatic copy number alternations with more breakpoints across the chromosome, dense data is neccesary to increase the resolution of the results.
  3. MAF of SNPs should not affect a lot. The SNPs with low MAF may not present in the data and be excluded in the analysis, but if the data have enough SNPs to support segments, it shoulde be fine. If you need more details, please refer to the paper https://pubmed.ncbi.nlm.nih.gov/20837533/.
bounlu commented 3 months ago

Thank you very much for the helpful information.