detecting LoH in cancer genomes

Question

[Bogdan]

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

Answer 1

[gaiusjaugustus]

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. http://biostats.bepress.com/mskccbiostat/paper29
2. Inferring copy number and genotype in tumour exome data. BMC Genomics 2014. http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-732
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. http://www.ncbi.nlm.nih.gov/pubmed/25319062
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. http://www.ncbi.nlm.nih.gov/pubmed/25883151
5. Markus Mayrhofer, Sebastian DiLorenzo and Anders Isaksson. Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue. Genome Biology 2013. https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-3-r24

[Bogdan]

thank you, all the information was very helpful !