Copy number measurement device, computer readable medium, copy number measurement method and gene panel

A non-transitory computer-readable medium storing a copy-number measurement program to cause a computer to function as:

• a position identification unit to map a plurality of tumor sample reads which are a plurality of reads obtained from a tumor sample involving a cancer cell, to a human genome sequence, and identify, for each target gene, a target position, which is a genome position of a base, the genome position having changed with respect to the human genome sequence;
• a frequency calculation unit to calculate a variant allele frequency for each target position of each target gene;
• a distance calculation unit to calculate, for each target gene, a feature distance equivalent to a difference between a variant allele frequency corresponding to a peak density and a reference variant allele frequency in a density distribution indicating a density of a number of mapping reads with respect to the variant allele frequency, the number of mapping reads being a number of tumor sample reads mapped to respective target positions in the target gene;
• a coefficient calculation unit to calculate a correction coefficient being used for correcting a copy number of each target gene in the tumor sample, using the feature distance of each target gene;
• and
• a copy-number calculation unit to calculate a copy number of each target gene in the cancer cell using the copy number of each target gene in the tumor sample and the correction coefficient.

A copy-number measurement method comprising:

• by a position identification unit, mapping a plurality of tumor sample reads which are a plurality of reads obtained from a tumor sample involving a cancer cell to a human genome sequence, and identifying, for each target gene, a target position which is a genome position of a base, the genome position having changed with respect to the human genome sequence;
• by a frequency calculation unit, calculating a variant allele frequency for each target position of each target gene;
• by a distance calculation unit, calculating, for each target gene, a feature distance equivalent to a difference between a variant allele frequency corresponding to a peak density and a reference variant allele frequency in a density distribution indicating a density of a number of mapping reads with respect to the variant allele frequency, the number of mapping reads being a number of tumor sample reads mapped to respective target positions in the target gene;
• by a coefficient calculation unit, calculating a correction coefficient being used for correcting a copy number of each target gene in the tumor sample, using the feature distance of each target gene;
• and
• by a copy-number calculation unit, calculating a copy number of each target gene in the cancer cell using the copy number of each target gene in the tumor sample and the correction coefficient.