Question: detecting LoH in cancer genomes
gravatar for Bogdan
7 months ago by
Palo Alto, CA, USA
Bogdan530 wrote:

Dear all,

when analyzing whole genome sequences for the loss of heterozygozity (LoH) regions, what algorithms would you recommend to use ?

thank you, and happy holidays, and a Merry Christmas !

-- bogdan

loh • 370 views
ADD COMMENTlink modified 7 months ago by gaiusjaugustus110 • written 7 months ago by Bogdan530
gravatar for gaiusjaugustus
7 months ago by
United States
gaiusjaugustus110 wrote:

I've only worked with SNP data for LOH, but have suggested the following publications for allele-specific copy number analysis. Hopefully someone else can lend some experience with these or other methods. Good luck!

  1. Shen, Ronglai and Seshan, Venkatraman, "FACETS: Allele-Specific Copy Number and Clonal Heterogeneity Analysis Tool Estimates for High-Throughput DNA Sequencing" (May 2016).Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series. Working Paper 29.
  2. Inferring copy number and genotype in tumour exome data. BMC Genomics 2014.
  3. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol. 2015 Jan;26(1):64-70. doi: 10.1093/annonc/mdu479. Epub 2014 Oct 15.
  4. Allele-specific copy-number discovery from whole-genome and whole-exome sequencing. Nucleic Acids Res. 2015 Aug 18;43(14):e90. doi: 10.1093/nar/gkv319. Epub 2015 Apr 16.
  5. Markus Mayrhofer, Sebastian DiLorenzo and Anders Isaksson. Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue. Genome Biology 2013.
ADD COMMENTlink written 7 months ago by gaiusjaugustus110

thank you, all the information was very helpful !

ADD REPLYlink written 7 months ago by Bogdan530
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