New feature - LOH data

Loss of heterozygosity (LOH) is a phenomenon frequently observed in cancer genomes where the selective pressure to keep only the susceptible gene product from one allele removes the other healthy allele from the pool; In this context, copy neutral - loss of heterozygosity (CN-LOH) is commonly observed in haematological malignancies (O’keefe et al., 2010 and Mulligan et al., 2007). To Progenetix oncogenomic resource, comprising of nearly 800 cancer types (by NCIt classification) as of 2021, we expanded the new feature of LOH in our data collection, in addition to the total copy number, to open the door for the analysis of frequency and impact of this phenomenon.

Update 2021-01-28:

LOH variants can now be queried through the Search and Beacon+ interfaces, either as specific variants or together with deletions.

Please be aware that in contrast to the “complete for chromosomes 1-22” DUP and DEL calls, LOH is only determined for a subset of samples and therefore will be underreported in the statistics section.


O’Keefe, Christine, Michael A. McDevitt, and Jaroslaw P. Maciejewski. “Copy neutral loss of heterozygosity: a novel chromosomal lesion in myeloid malignancies.” Blood 115.14 (2010): 2731-2739. Mullighan, Charles G., et al. “Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia.” Nature 446.7137 (2007): 758-764.

@qingyao 2021-01-14
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