What is the Lesser Allele Fraction (LAF), and where can I find it?

The allele fraction for alleles at a heterozygous site in a diploid portion of the genome should be 50% each, but due to heterogeneity, loss of heterozygosity (LOH), and copy number variation, the allele fraction of each allele may be greater or less than 50%. The Lesser Allele Fraction (LAF) is the fraction of the sample containing the allele that is present in ≤ 50% of the sample. Therefore, the range of LAF values is 0 to 0.5. The LAF is similar to “B-allele frequency” estimates from microarray genotyping data, but captures the fraction of the less abundant allele/haplotype rather than the fraction of an arbitrary allele at each locus.

Single-sample LAF estimates are provided for all genomes. These calculations apply to 100 kb windows and are based on the read counts of each allele at all fully-called loci within the window. Paired-sample LAF estimates are provided for tumor (non-baseline) samples submitted to the Cancer Sequencing Service. Paired-sample LAF calculations apply to 100 kb windows and are based on allele read counts in the tumor at loci that are called heterozygous in the matched normal (baseline) sample. LAF measurements are provided in several output files, including masterVarBeta, all cnvSegments and cnvDetails files, the vcfBeta and somaticVcfBeta files, and all Circos plots.

For more information, see How do I interpret the Lesser Allele Fraction (LAF)?


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