Method for assisting prediction of risk of occurrence of side effect of irinotecan

A method to prevent occurrence of one or more side effects of irinotecan when treating a patient with a cancer, comprising:

• determining whether the patient has a genetic predisposition to having side effects when treated with irinotecan by:
• obtaining or having obtained a biological sample from the patient with cancer;
• and
• performing or having performed a genotyping assay on the biological sample by following steps (i) to (iv);
• (i) performing an amplifying reaction using, as a template, genomic DNA of a biological sample collected from the patient with cancer to amplify a nucleic acid fragment containing a single nucleotide polymorphism site present at nucleotide 2459 of a nucleotide sequence encoding an EDEM3 gene as set forth in SEQ ID NO:
• 5 using polymerase chain reaction;
• (ii) performing a hybridization between a resulting nucleic acid fragment and at least a first probe to a wild type allele and at least a second probe to a variant type allele;
• wherein the first probe is to the wild type allele having T at position 2459, a complementary nucleotide sequence thereof having an A at position 2459, or both;
• and
• wherein the second probe comprises the single nucleotide polymorphism present at nucleotide 2459 of a nucleotide sequence encoding an EDEM3 gene as set forth in SEQ ID NO:
• 5 having a G at position 2459, a complementary nucleotide sequence thereof having a C at position 2459, or both;
• (iii) comparing an amount of nucleic acid fragment hybridized with the first and the second probes;
• and
• (iv) calculating a ratio between the first and the second probes;
• and
• determining if the patient is homozygous for the variant type allele, homozygous for the wild type allele, or heterozygous, and
• if the patient is homozygous for the wild type allele administering a cancer treatment other than irinotecan;
• or
• if the patient with cancer is homozygous or heterozygous for the variant type allele, administering irinotecan to the patient.

A method of treating a patient with a cancer, comprising:

• determining whether the patient has a genetic predisposition to having side effects when treated with irinotecan by:
• obtaining or having obtained a biological sample from the patient with cancer;
• and
• performing or having performed a genotyping assay on the biological sample by following steps (i) to (iv);
• (i) performing an amplifying reaction using, as a template, genomic DNA of the biological sample to amplify a nucleic acid fragment containing a single nucleotide polymorphism site present at nucleotide 2459 of a nucleotide sequence encoding an EDEM3 gene as set forth in SEQ ID NO:
• 5 using polymerase chain reaction;
• (ii) performing a hybridization between a resulting nucleic acid fragment and at least a first probe to a wild type allele and at least a second probe to a variant type allele;
• wherein the first probe is to the wild type allele having T at position 2459, a complementary nucleotide sequence thereof having an A at position 2459, or both;
• and
• wherein the second probe comprises the single nucleotide polymorphism present at nucleotide 2459 of a nucleotide sequence encoding an EDEM3 gene as set forth in SEQ ID NO:
• 5 having a G at position 2459, a complementary nucleotide sequence thereof having a C at position 2459, or both;
• (iii) comparing an amount of nucleic acid fragment hybridized with the first and the second probes;
• and
• (iv) calculating a ratio between the first and the second probes;
• determining if the patient is homozygous for the variant type allele, homozygous for the wild type allele, or heterozygous, and
• administering a cancer treatment other than irinotecan if the patient is homozygous for the wild type allele;
• or
• administering irinotecan to the patient if the patient with cancer is homozygous for the variant type allele or heterozygous.