JP2006087375A - Dna oligomer, gene marker and dna oligomer set for estimation of crisis of side effect in radiotherapy and method for estimating crisis of side effect - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a DNA oligomer, a gene marker, a DNA oligomer set (primer set for PCR (polymerase chain reaction)) and a DNA oligomer (primer for extension) for the estimation of the crisis of side effects in radiotherapy and capable of estimating the risk of the crisis of side effects in the radiotherapy of a cancer patient for the realization of an order-made radiotherapy, and to provide a method for estimating the crisis of side effects in radiotherapy. <P>SOLUTION: The DNA oligomer for the estimation of the crisis of side effects in radiotherapy can estimate the risk of the crisis of side effects in the radiotherapy of cancer by discriminating whether a specific base in a DNA base sequence is risk allele or non-risk allele and has at least 10-241 consecutive DNA base sequences containing a specific base in a specific DNA base sequence. <P>COPYRIGHT: (C)2006,JPO&NCIPI

Description

  The present invention relates to a DNA oligomer for predicting the occurrence of side effects in radiotherapy using a single nucleotide polymorphism of a gene as an index for determination, a genetic marker for predicting the occurrence of side effects using a DNA oligomer for predicting the occurrence of side effects in the radiotherapy, TECHNICAL FIELD The present invention relates to a DNA oligomer set (PCR primer) and DNA oligomer (elongation primer) for obtaining a DNA oligomer for predicting the occurrence of side effects and determining SNPs, and a method for predicting the occurrence of side effects using a DNA oligomer for predicting the occurrence of side effects in the radiotherapy. .

Cancer, which is said to affect about 500,000 people annually, is the number one cause of death for Japanese people, and overcoming it is a public desire.
Radiation therapy is one of the effective local therapies for cancer, but unlike surgery, it can be treated without excision of the lesion, so it is excellent in terms of preserving physical function and morphology. It can be said that it is a treatment method. In other words, since a scalpel is not put into the body like a surgical operation, the mental burden on the patient is light and the return to society after the operation is easy, so the QOL (Quality of Life) of the patient can be increased. There is an advantage, and it is a treatment method that is expected to be greatly developed in the future.

  In addition, the radiation treatment has a light burden on the patient and has an advantage that it can be applied to patients with complications and the elderly. Furthermore, in recent years, there has also been a stereotactic radiotherapy technique that can accurately determine the position, shape, and size of a lesion on three-dimensional coordinates based on image information such as CT and MRI, and concentrate the dose on the lesion. Has been established.

  In this way, radiation therapy is a very useful treatment method in the treatment of cancer, but there are serious side effects such as ulcers in the skin caused by irradiated radiation, complicated with intestinal perforation and pneumonia, In some cases, there are highly sensitive cancer patients who have to stop radiation therapy.

  Such a difference in sensitivity to radiation is considered to be related to a difference in DNA base sequence of each cancer patient. Such a difference in DNA base sequence is generally called polymorphism (polymorphism) and can be classified as follows. That is, (1) a polymorphism in which tens of bases from 1 to several tens of bases are deleted or inserted (insertion / deletion polymorphism), and (2) a sequence having 2 to tens of bases as one unit is repeated. Polymorphism (VNTR and microsatellite polymorphism), and (3) polymorphism in which one base is replaced with another base (single nucleotide polymorphism).

Among these, (3) single nucleotide polymorphism (SNP) is presumed to be present at a ratio of one place from several hundred base pairs to 1000 base pairs. There are thought to be between 10 and 10 million SNPs. And it is thought that this SNP has a strong influence on so-called “individuality” such as each person's face, personality, and responsiveness to pharmaceuticals (see Non-Patent Document 1).
Supervised by Kenichi Matsubara, Yoshiyuki Tsuji, edited by Yusuke Nakamura “Genomic Science of Post Sequence (1) SNP Gene Polymorphism Strategies”, Nakayama Shoten, 2nd and 3rd pages, published in June 2000

It is considered that the sensitivity to radiation is also greatly influenced by the difference in DNA base sequences of genes including SNPs. In other words, if it is possible to know in advance the degree of sensitivity of cancer patients to radiation by examining the DNA base sequence before radiation treatment, it is considered that tailor-made radiation therapy can be realized.
However, there has been little research on what genes are involved in radiation sensitivity and which SNPs affect radiation sensitivity. For this reason, it has been impossible to set an index for realizing tailor-made radiation therapy.

  The present invention has been made in view of the above problems, and in order to realize tailor-made radiotherapy, a DNA oligomer for predicting the onset of side effects in radiotherapy capable of predicting in advance the degree of sensitivity to radiation of cancer patients. Another object of the present invention is to provide a genetic marker, a DNA oligomer set (PCR primer set) and a DNA oligomer (extension primer), and a method for predicting the onset of side effects in radiation therapy.

  The inventors believe that if the SNP typing is performed mainly on cSNP (coding SNP), rSNP (regulatory SNP), and iSNP (intron SNP), the above-mentioned problems can be solved, and a customized radiotherapy can be realized. , Worked hard on research. As a result, after the radiotherapy, the DNA base sequence of the gene of the patient who developed side effects (hereinafter referred to as the onset group) and the patient who did not develop side effects or had a minor onset (hereinafter referred to as the non-onset group) As a result of the determination, it was possible to find a statistically significant difference between the appearance frequency of alleles in the onset group and the appearance frequency of alleles in the non-onset group, and completed the present invention. It came to do.

That is, the present invention provides [1] determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, and that side effects may occur in cancer radiotherapy. A DNA oligomer for prediction, which is a DNA base sequence represented by any one of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing, and contains at least 10 to 241 continuous DNA base sequences including the 121st base A radiation oligomer for breast cancer by determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele. A DNA oligomer for predicting that a side effect may occur in treatment, comprising SEQ ID NO: 1 in the sequence listing Sequence number 4, Sequence number 7, Sequence number 13, Sequence number 15, Sequence number 17, Sequence number 19, Sequence number 20, Sequence number 26, Sequence number 27, Sequence number 30, Sequence number 32, Sequence number 44, Sequence number 45, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, Sequence number 65, sequence number 67, sequence number 73, sequence number 74, sequence number 77, sequence number 78, sequence number 82, sequence number 85, sequence number 88, sequence number 90, sequence number 91, sequence number 94, sequence number 97, SEQ ID NO: 98, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 126, SEQ ID NO: 1 7, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 145, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 157, The DNA base sequence shown in SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 172, or SEQ ID NO: 173 contains the 121st base. A DNA oligomer for predicting the occurrence of side effects in radiation therapy, characterized by having a continuous DNA base sequence of at least 10 to 241; and [3] a specific base in the DNA base sequence is a risk allele or a non-risk allele By determining whether or not there are side effects in radiation therapy for cervical cancer A DNA oligomer for predicting that there is a possibility of developing, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 65, Sequence number 68, sequence number 70, sequence number 71, sequence number 72, sequence number 75, sequence number 76, sequence number 80, sequence number 83, sequence number 86, sequence number 89, sequence number 91, sequence number 93, sequence number 98, SEQ ID NO: 105, SEQ ID NO: 110, SEQ ID NO: 114, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 1 9, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 157, SEQ ID NO: 161, Or a DNA oligomer for predicting the onset of side effects in radiotherapy characterized by having at least 10 to 241 continuous DNA base sequence including the 121st base for the DNA base sequence shown in SEQ ID NO: 171; [4] It is a DNA oligomer for predicting that side effects may occur in prostate cancer radiotherapy by determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele. SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 0, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 73, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 84, SEQ ID NO: 87, SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 107, Sequence number 109, sequence number 111, sequence number 115, sequence number 116, sequence number 120, sequence number 122, sequence number 123, sequence number 124, sequence SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 151, SEQ ID NO: 156, SEQ ID NO: 158, SEQ ID NO: 160, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 168 Or a DNA oligomer for predicting the onset of side effects in radiation therapy, wherein the DNA base sequence represented by SEQ ID NO: 169 has at least 10 to 241 continuous DNA base sequence including the 121st base; ] To predict whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, so that side effects may occur at an early stage from the start of cancer radiotherapy DNA oligomer of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 7 in the sequence listing SEQ ID NO: 8, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, Sequence number 59, sequence number 60, sequence number 61, sequence number 64, sequence number 65, sequence number 66, sequence number 70, sequence number 71, sequence number 72, sequence number 73, sequence number 75, sequence number 76, sequence number 78, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 6, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 120, Sequence number 121, Sequence number 126, Sequence number 127, Sequence number 129, Sequence number 132, Sequence number 134, Sequence number 137, Sequence number 138, Sequence number 140, Sequence number 141, Sequence number 143, Sequence number 144, Sequence number 146, SEQ ID NO: 147, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, or a sequence A DNA oligomer for predicting the occurrence of side effects in radiation therapy, comprising a DNA base sequence represented by No. 171 and having at least 10 to 241 continuous DNA base sequences including the 121st base, and [6] DNA base By predicting whether a specific base in the sequence is a risk allele or a non-risk allele, it is possible to predict that side effects may occur at the stage of 3 months from the start of radiation therapy for cancer. A DNA oligomer, which is SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 48 No. 49, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 69, SEQ ID NO: 77, SEQ ID NO: 87, SEQ ID NO: 00, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, DNA base sequence shown in SEQ ID NO: 128, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, or SEQ ID NO: 170 A DNA oligomer for predicting the onset of side effects in radiotherapy characterized by having a continuous DNA base sequence of at least 10 to 241 including the 121st base, and [7] a specific base in the DNA base sequence is a risk By determining whether it is an allele or a non-risk allele, A DNA oligomer for predicting that a side effect may occur at a stage of 6 months from the start of radiation therapy of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39 , SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO: 57, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 63 SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 79, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: No. 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 102, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 139, SEQ ID NO: 142, SEQ ID NO: 155 The DNA base sequence represented by SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 172, or SEQ ID NO: 173 has a continuous DNA base sequence of at least 10 to 241 including the 121st base. By determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is possible to detect early onset of radiation therapy for breast cancer. DNA prediction for predicting that side effects may occur at this stage SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 32, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 65, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 98, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, Sequence number 117, Sequence number 127, Sequence number 132, Sequence number 137, Sequence number 138, Sequence number 140, Sequence number 143, Sequence number 147, Sequence number 157, Sequence number 160, Sequence number 162, Sequence number 163, Sequence number 165 or the DNA base sequence represented by SEQ ID NO: 167, comprising at least 10 to 241 consecutive sequences containing the 121st base A DNA oligomer for predicting the onset of side effects in radiotherapy characterized by having a DNA base sequence, and [9] determining whether a specific base in the DNA base sequence is a risk allele or a non-risk allele, A DNA oligomer for predicting that a side effect may occur at the stage of late 3 months from the start of radiation therapy for breast cancer, comprising SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 58, SEQ ID NO: 77, SEQ ID NO: 108, SEQ ID NO: 116, SEQ ID NO: 126, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 159, SEQ ID NO: 162, or SEQ ID NO: 170 About the DNA base sequence to be measured, including at least the 121st base, at least 10 to 241 consecutive A DNA oligomer for predicting the occurrence of side effects in radiotherapy characterized by having a DNA base sequence, and [10] determining whether a specific base in the DNA base sequence is a risk allele or a non-risk allele, A DNA oligomer for predicting that side effects may occur at the stage of late 6 months from the start of radiation therapy for breast cancer, comprising SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 30, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 67, SEQ ID NO: 74, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 97, SEQ ID NO: 172, or SEQ ID NO: 172 Concerning the DNA base sequence indicated by No. 173, at least 10 to 241 continuous DNA containing the 121st base A DNA oligomer for predicting the onset of side effects in radiotherapy characterized by having a base sequence, and [11] determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, A DNA oligomer for predicting that a side effect may occur at an early stage from the start of radiation therapy for cervical cancer, comprising SEQ ID NO: 2, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29 in the sequence listing, Sequence number 31, sequence number 34, sequence number 36, sequence number 43, sequence number 44, sequence number 52, sequence number 56, sequence number 60, sequence number 64, sequence number 65, sequence number 70, sequence number 71, sequence number 72, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 98 Sequence number 105, Sequence number 114, Sequence number 118, Sequence number 121, Sequence number 129, Sequence number 134, Sequence number 141, Sequence number 144, Sequence number 146, Sequence number 149, Sequence number 150, Sequence number 152, Sequence number 153, SEQ ID NO: 154, SEQ ID NO: 157, or a DNA base sequence represented by SEQ ID NO: 171 having a continuous DNA base sequence of at least 10 to 241 including the 121st base, and a side effect in radiation therapy The stage of 6 months from the start of radiation therapy for cervical cancer by determining whether a DNA oligomer for predicting the onset or [12] a specific base in the DNA base sequence is a risk allele or a non-risk allele DNA oligomers for predicting that side effects may occur in SEQ ID NO: 6, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 139, The DNA base sequence represented by SEQ ID NO: 142, SEQ ID NO: 155, or SEQ ID NO: 161 has a continuous DNA base sequence of at least 10 to 241 including the 121st base, and predicts the occurrence of side effects in radiotherapy Side effects occur at an early stage from the start of radiation treatment for prostate cancer by determining whether a specific base in a DNA oligomer or [13] DNA base sequence is a risk allele or a non-risk allele A DNA oligomer for predicting that there is a risk, SEQ ID NO: 5, SEQ ID NO: 8, Sequence number 24, sequence number 25, sequence number 28, sequence number 33, sequence number 48, sequence number 66, sequence number 81, sequence number 92, sequence number 96, sequence number 99, sequence number 102, sequence number 103, sequence number 120. The DNA base sequence shown in SEQ ID NO: 126, SEQ ID NO: 151, SEQ ID NO: 158, SEQ ID NO: 168, or SEQ ID NO: 169 has a continuous DNA base sequence of at least 10 to 241 including the 121st base. A radiotherapy for prostate cancer by determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele. DNA for predicting that side effects may occur at the stage of 3 months from the start It is a ligomer and is SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 55, SEQ ID NO: 69, SEQ ID NO: 87, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, Radiation therapy comprising a DNA base sequence represented by SEQ ID NO: 125, SEQ ID NO: 128, SEQ ID NO: 156, or SEQ ID NO: 160 having a continuous DNA base sequence of at least 10 to 241 including the 121st base In particular, DNA oligomers for predicting the occurrence of side effects in [15] DNA base sequences and specific bases in DNA base sequences A DNA oligomer for predicting that a side effect may occur at the stage of late 6 months from the start of radiation therapy for prostate cancer by determining whether it is a real or non-risk allele. Sequence number SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39, Sequence number 40, sequence number 47, sequence number 57, sequence number 73, sequence number 79, sequence number 84, sequence number 95, sequence number 96, sequence number 102, sequence number 107, sequence number 130, sequence number 131, sequence number 135, SEQ ID NO: 164 or the DNA base sequence shown in SEQ ID NO: 166, containing at least the 121st base and at least 10 to 241 consecutive In the DNA oligomer for predicting the onset of side effects in radiation therapy characterized by having a DNA base sequence, or in the DNA oligomer for predicting the onset of side effects in [16] above [1] to [15], a base other than the 121st base A DNA oligomer that is deleted, substituted or added, or a DNA oligomer having a complementary DNA base sequence thereof, for predicting the occurrence of side effects in radiation therapy, It is to provide.

  The present invention also provides [17] a DNA oligomer for predicting the occurrence of side effects according to any one of [1] to [16], or a DNA oligomer for predicting the occurrence of side effects, which is hybridized under stringent conditions. SEQ ID NO: 174 among genetic markers for predicting the onset of side effects in radiotherapy characterized by being a soybean DNA oligomer, and DNA oligomers having the DNA base sequence shown in SEQ ID NO: 174 to SEQ ID NO: 519 in [18] Sequence Listing A DNA oligomer set characterized in that two DNA oligomers are sequentially used as a set, [19] a DNA oligomer having a DNA base sequence shown in SEQ ID NO: 174 to SEQ ID NO: 519 of the sequence listing, or 1 or several bases are deleted, substituted or Of the DNA oligomer set according to [11], the DNA oligomer having the DNA base sequence shown in SEQ ID NO: 520 to SEQ ID NO: 692 in the sequence listing, or the DNA oligomer, The present invention provides a DNA oligomer characterized by deletion, substitution or addition of one or several bases.

Furthermore, the present invention includes the following steps (a) to (g), wherein the determination is performed using the DNA oligomer represented by any one of SEQ ID NO: 1 to SEQ ID NO: 173 in [21] Sequence Listing. A method for predicting the onset of side effects in radiation therapy, (a) a step of preparing a DNA sample based on a sample collected from a cancer patient scheduled to undergo radiation treatment, and (b) the step prepared in the step (a). A step of amplifying DNA based on a DNA sample to obtain a DNA product; (c) a step of performing an extension reaction using the DNA product amplified in the step (b) as a template to obtain a DNA oligomer as an extension product; d) a step of analyzing the DNA base sequence of the DNA oligomer obtained in the step (c), (e) a phase at the 121st position in the DNA base sequence of the DNA oligomer analyzed in the step (d). (F) an allele having a base verified in the step (e), a step of verifying the base to be compared with the 121st base of the DNA base sequence shown in any of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing (G) onset of side effects due to radiation in cancer patients scheduled to undergo radiation therapy based on the result of determination in step (f) A step of predicting the risk rate, [22] The DNA base sequence shown in any one of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing to be collated in the step (e) is used to predict the onset of side effects in radiation therapy for breast cancer. SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60 SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 126, SEQ ID NO: 127 , SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 1 45, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 172, Alternatively, using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 173 and predicting the occurrence of side effects in radiation therapy for cervical cancer, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 52, SEQ ID NO: 56 , SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: No. 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 98, SEQ ID NO: 105, SEQ ID NO: 110, SEQ ID NO: 114, SEQ ID NO: 118 , SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 139, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 152, SEQ ID NO: No. 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 157, SEQ ID NO: 161, or the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 171 is used to predict the onset of side effects in prostate cancer radiotherapy. SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, Sequence number 12, sequence number 14, sequence number 16, sequence number 18, sequence number 19, sequence number 21, sequence number 21, sequence number 24, sequence number 25, sequence number 28, sequence number 33, sequence number 35, sequence number 38, sequence number 39, SEQ ID NO: 40, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 73, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 84, Sequence number 87, sequence number 92, sequence number 95, sequence number 96, sequence number 99, sequence number 100, sequence number 101, sequence number 102, sequence number 103, sequence number 104, sequence number 107, sequence number 109, sequence number 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 151, SEQ ID NO: 156, SEQ ID NO: 158, SEQ ID NO: 160, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 168, or SEQ ID NO: 169 For predicting the occurrence of side effects in the early stage from the start of cancer radiotherapy using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, Sequence number 31, sequence number 32, sequence number 33, sequence number 34, sequence number 36, sequence number 43, sequence number 44, sequence number 45, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, Sequence number 73, sequence number 75, sequence number 76, sequence number 78, sequence number 80, sequence number 81, sequence number 86, sequence number 89, sequence number 90, sequence number 91, sequence number 92, sequence number 93, sequence number 94, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 117, SEQ ID NO: 118, Sequence number 120, sequence number 121, sequence number 126, sequence number 127, sequence number 129, sequence number 132, sequence number 134, sequence number 1 7, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, DNA oligomer DNA shown in SEQ ID NO: 154, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, or SEQ ID NO: 171 Regarding the occurrence of side effects at the stage 3 months after the start of cancer radiotherapy using the base sequence, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 69, SEQ ID NO: 77, SEQ ID NO: 87, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115 , SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: Regarding the prediction of the occurrence of side effects at the stage of 6 months from the start of cancer radiotherapy using the DNA base sequence of the DNA oligomer shown in No. 156, SEQ ID No. 159, SEQ ID No. 160, SEQ ID No. 162, or SEQ ID No. 170, SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, Sequence number 41, sequence number 42, sequence number 46, sequence number 47, sequence number 50, sequence number 51, sequence number 54, sequence number 57, sequence number 60, sequence number 62, sequence number 63, sequence number 67, sequence number 68, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 79, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 102, Sequence number 107, sequence number 110, sequence number 119, sequence number 130, sequence number 131, sequence number 135, sequence number 139, sequence number 142, sequence number 15 Using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 172, or SEQ ID NO: 173, for the prediction of the occurrence of side effects in the early stage from the start of radiation therapy for breast cancer, Sequence number SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 32, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 65, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 98, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 117, SEQ ID NO: 127, SEQ ID NO: 132, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 14 7. Side effects at the stage of 3 months from the start of radiation therapy for breast cancer using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 157, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, or SEQ ID NO: 167 For predicting the onset of the disease, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 58, SEQ ID NO: 77, SEQ ID NO: 108, SEQ ID NO: 116, SEQ ID NO: 126, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: Use of the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 159, SEQ ID NO: 162, or SEQ ID NO: 170 to predict the onset of side effects at the stage of 6 months from the start of radiation therapy for breast cancer For SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 30, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 67, SEQ ID NO: 74, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 97, SEQ ID NO: 172 Alternatively, using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 173 and predicting the onset of side effects in the early stage from the start of radiation therapy for cervical cancer, SEQ ID NO: 2, SEQ ID NO: 22, SEQ ID NO: 23 , SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 70, SEQ ID NO: No. 71, SEQ ID NO: 72, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 9 SEQ ID NO: 98, SEQ ID NO: 105, SEQ ID NO: 114, SEQ ID NO: 118, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 141, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: About the prediction of the onset of side effects in the stage 6 months from the start of radiation therapy for cervical cancer using the DNA base sequence of the DNA oligomer shown in No. 152, SEQ ID No. 153, SEQ ID No. 154, SEQ ID No. 157, or SEQ ID No. 171 SEQ ID NO: 6, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 139, SEQ ID NO: 139 The DNA base sequence of the DNA oligomer shown in No. 142, SEQ ID No. 155, or SEQ ID No. 161 For the prediction of the occurrence of side effects in the early stage from the start of radiation therapy for prostate cancer, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 48, SEQ ID NO: 66, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 96, SEQ ID NO: 99, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 120, SEQ ID NO: 126, SEQ ID NO: 151, SEQ ID NO: 158, SEQ ID NO: 168, Alternatively, using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 169 and predicting the onset of side effects at the stage 3 months later from the start of radiation therapy for prostate cancer, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10 SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, Sequence number 55, sequence number 69, sequence number 87, sequence number 100, sequence number 101, sequence number 104, sequence number 109, sequence number 111, sequence number 115, sequence number 116, sequence number 122, sequence number 123, sequence number 124, SEQ ID NO: 125, SEQ ID NO: 128, SEQ ID NO: 156, or using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 160 for predicting the onset of side effects at the stage of 6 months from the start of radiation therapy for prostate cancer, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39 SEQ ID NO: 40, SEQ ID NO: 47, SEQ ID NO: 57, SEQ ID NO: 73, SEQ ID NO: 79, SEQ ID NO: 84, SEQ ID NO: 9 The DNA base sequence of the DNA oligomer shown in SEQ ID NO: 96, SEQ ID NO: 102, SEQ ID NO: 107, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 164, or SEQ ID NO: 166 is used [ 21]. The method for predicting the onset of side effects in radiation therapy according to 21).

  By detecting a specific single nucleotide polymorphism (SNP) in the DNA base sequence of the gene using the DNA oligomer for predicting the onset of side effects or the gene marker for predicting the onset of side effects in the radiotherapy of the present invention, The risk rate of developing side effects can be predicted. Therefore, according to the present invention, it will contribute to the realization of the custom-made radiation therapy.

  Moreover, if the DNA oligomer set (PCR primer) of the present invention is used, DNA containing a specific single nucleotide polymorphism (SNP) is easily amplified based on a DNA sample prepared from a subject such as a cancer patient. be able to. Furthermore, if the DNA oligomer (extension primer) of the present invention is used, the base species of the specific SNP site can be easily determined. Therefore, it is possible to facilitate a method for predicting the risk rate of developing side effects due to radiation therapy.

  According to the side effect onset prediction method of the present invention, it is possible to predict the risk rate of developing side effects due to radiation from SNP information contained in a DNA sample collected from a cancer patient who is scheduled to perform radiotherapy. That is, it is possible to perform tailor-made radiation therapy.

  According to the present invention, for breast cancer, cervical cancer, and prostate cancer, the risk rate of developing side effects in each stage of early (less than 3 months), late 3 months, and late 6 months from the start of radiation therapy is determined in advance. It becomes possible to predict.

Hereinafter, although the best mode for carrying out the present invention will be described, the contents of the present invention are not limited to the contents described below.
[1. DNA oligomer (1) and genetic marker]
The “DNA oligomer for predicting the occurrence of side effects in radiation therapy” in the present invention comprises the 121st base in the DNA base sequences shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention. An oligonucleotide (DNA oligomer) having at least 10 to 241 bases.
However, in the present invention, it suffices to have a continuous DNA base sequence of 10 to 241 including the 121st base, and the length of the DNA base sequence is not particularly limited. That is, as described above, it may be a DNA oligomer having 10 bases or more and 241 bases or less, or may be one exceeding 241 bases. For example, if a DNA base sequence is present on the chromosome, a longer DNA oligomer (for example, a continuous 250 base DNA oligomer containing the 121st base, a 500 base DNA oligomer, or It goes without saying that even longer DNA oligomers) correspond to the DNA oligomers shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention.

In the present invention, the 121st base is a risk allele. “Risk allele” refers to a base in an allele (allele) of a person who is likely to develop a side effect (disorder) after radiation treatment at a specific SNP site, and an allele of a person who is less likely to develop a side effect This refers to an allele possessed by a base that is different from the base in it and that is likely to cause such side effects. Therefore, if the risk allele can be recognized by performing SNP typing, it is possible to predict the risk of developing side effects due to radiation therapy.
In addition, as long as it can recognize that it is the 121st base designated by this invention, the position in a DNA oligomer will not be limited. That is, the SNP site serving as the risk allele can be located in the middle of the DNA base sequence, and can also be located at the 5 ′ end or 3 ′ end.
In contrast, in a gene or chromosomal DNA containing a DNA base sequence that is identical or substantially identical to any one of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention, it is present at the SNP site corresponding to the risk allele In the present invention, an allele that is a base different from the risk allele is referred to as a “non-risk allele”.

  The DNA oligomer shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing (or information on the DNA base sequence) is obtained by determining whether a specific base in the DNA base sequence is a risk allele or a non-risk allele. It can be used to predict that side effects may occur in radiation therapy for cancer. In particular, it can be suitably used in the embodiments described in the following (1) to (14).

  (1) For predicting the occurrence of side effects in radiation therapy for breast cancer, SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, Sequence number 26, sequence number 27, sequence number 30, sequence number 32, sequence number 44, sequence number 45, sequence number 48, sequence number 49, sequence number 50, sequence number 51, sequence number 53, sequence number 54, sequence number 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 82, Sequence number 85, sequence number 88, sequence number 90, sequence number 91, sequence number 94, sequence number 97, sequence number 98, sequence number 106, sequence number 108, sequence number 11 , SEQ ID NO: 113, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: SEQ ID NO: 145, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 172 Or / and the DNA base sequence of the DNA oligomer represented by SEQ ID NO: 173 can be preferably used.

  (2) For predicting the occurrence of side effects in radiation therapy for cervical cancer, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, SEQ ID NO: SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 65 , SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, Sequence SEQ ID NO: 98, SEQ ID NO: 105, SEQ ID NO: 110, SEQ ID NO: 114, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 39, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 157, SEQ ID NO: 161, Alternatively and / or the DNA base sequence of the DNA oligomer represented by SEQ ID NO: 171 can be preferably used.

  (3) For predicting the occurrence of side effects in radiation therapy for prostate cancer, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, Sequence number 45, sequence number 47, sequence number 48, sequence number 55, sequence number 57, sequence number 66, sequence number 69, sequence number 73, sequence number 79, sequence number 81, sequence number 84, sequence number 87, sequence number 92, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 131 , SEQ ID NO: 135, SEQ ID NO: 151, SEQ ID NO: 156, SEQ ID NO: 158, SEQ ID NO: 160, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 168, and / or the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 169 is preferable Can be used.

  (4) For predicting the occurrence of side effects in the early stage from the start of radiation therapy for cancer, SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 32, Sequence number 33, sequence number 34, sequence number 36, sequence number 43, sequence number 44, sequence number 45, sequence number 48, sequence number 52, sequence number 56, sequence number 59, sequence number 60, sequence number 61, sequence number 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80 Sequence number 81, sequence number 86, sequence number 89, sequence number 90, sequence number 91, sequence number 92, sequence number 93, sequence number 94, sequence number 96, sequence number 98, sequence number 99, sequence number 102, sequence number 103, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO: 132, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 157, SEQ ID NO: 158 The DNA base sequence of the DNA oligomer shown in SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, and / or SEQ ID NO: 171 can be preferably used. .

  (5) About the prediction of the onset of side effects at the stage of late 3 months from the start of radiation therapy for cancer, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, Sequence number 21, Sequence number 33, Sequence number 45, Sequence number 48, Sequence number 49, Sequence number 53, Sequence number 55, Sequence number 58, Sequence number 69, Sequence number 77, Sequence number 87, Sequence number 100, Sequence number 101, SEQ ID NO: 104, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 156, SEQ ID NO: 159, No. 160, SEQ ID NO: 162 and / or, can be suitably used and the DNA sequence of the DNA oligomer shown in SEQ ID NO: 170.

  (6) For predicting the occurrence of side effects at the stage of 6 months from the start of radiation therapy for cancer, SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO: 57, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 67, SEQ ID NO: 68, Sequence number 73, sequence number 74, sequence number 79, sequence number 82, sequence number 83, sequence number 84, sequence number 85, sequence number 88, sequence number 95, sequence number 96, sequence number 9 , SEQ ID NO: 102, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 139, SEQ ID NO: 142, SEQ ID NO: 155, SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: The DNA base sequence of the DNA oligomer shown in No. 166, SEQ ID No. 172, and / or SEQ ID No. 173 can be preferably used.

  (7) For predicting the occurrence of side effects in the early stage from the start of radiation therapy for breast cancer, SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 26 SEQ ID NO: 27, SEQ ID NO: 32, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 65, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: SEQ ID NO: 98, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 117, SEQ ID NO: 127, SEQ ID NO: 132, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 147, SEQ ID NO: 157 DNA shown in SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, and / or SEQ ID NO: 167 The DNA nucleotide sequence of the oligomer can be preferably used.

  (8) For predicting the onset of side effects at the stage of late 3 months from the start of radiation therapy for breast cancer, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 58, SEQ ID NO: 77, SEQ ID NO: 108, sequence SEQ ID NO: 116, SEQ ID NO: 126, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 159, SEQ ID NO: 162, and / or the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 170 Can be suitably used.

  (9) Regarding the prediction of the occurrence of side effects in the stage of 6 months from the start of radiation therapy for breast cancer, SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 30, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO. SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 67, SEQ ID NO: 74, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 97, SEQ ID NO: 172, and / or DNA oligomer shown in SEQ ID NO: 173 The DNA base sequence can be preferably used.

  (10) For predicting the occurrence of side effects in the early stage from the start of radiation therapy for cervical cancer, SEQ ID NO: 2, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, Sequence number 36, sequence number 43, sequence number 44, sequence number 52, sequence number 56, sequence number 60, sequence number 64, sequence number 65, sequence number 70, sequence number 71, sequence number 72, sequence number 75, sequence number 76, SEQ ID NO: 80, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 98, SEQ ID NO: 105, SEQ ID NO: 114, SEQ ID NO: 118, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 141, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154 SEQ ID NO: 157 and / or, can be suitably used for DNA nucleotide sequence of the DNA oligomer shown in SEQ ID NO: 171.

  (11) For predicting the onset of side effects at the stage of 6 months from the start of radiation therapy for cervical cancer, SEQ ID NO: 6, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 139, SEQ ID NO: 142, SEQ ID NO: 155, and / or the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 161 is preferably used. Can do.

  (12) For predicting the occurrence of side effects in the early stage from the start of radiation therapy for prostate cancer, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 33 SEQ ID NO: 48, SEQ ID NO: 66, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 96, SEQ ID NO: 99, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 120, SEQ ID NO: 126, SEQ ID NO: 151, SEQ ID NO: 158, SEQ ID NO: 168 Or / and the DNA base sequence of the DNA oligomer represented by SEQ ID NO: 169 can be preferably used.

  (13) For predicting the onset of side effects at the stage 3 months after the start of radiation therapy for prostate cancer, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18 SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 55, SEQ ID NO: 69, SEQ ID NO: 87, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: The DNA base sequence of the DNA oligomer shown in SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 128, SEQ ID NO: 156, and / or SEQ ID NO: 160 is preferably used. be able to.

  (14) For predicting the occurrence of side effects in the stage of 6 months from the start of radiation therapy for prostate cancer, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 47, SEQ ID NO: 57, SEQ ID NO: 73, SEQ ID NO: 79, SEQ ID NO: 84, SEQ ID NO: The DNA base sequence of the DNA oligomer shown in SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 102, SEQ ID NO: 107, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 164, and / or SEQ ID NO: 166 is preferably used. be able to.

The DNA oligomer containing the risk allele used in the present invention can be used by appropriately setting an appropriate length as a continuous DNA oligomer of 10 to 241 bases containing the 121st base (risk allele).
For example, when such a DNA oligomer is used as a gene marker such as a labeled probe, for example, the length is preferably 20 to 200 bases, but may be 30 to 150 bases long, or 35 to 100 bases long. It can also be 200 bases or more. If an appropriate length is selected, specific hybridization can be performed, for example, a difference in electrophoretic mobility can be easily recognized, and SNP typing can be performed appropriately. On the other hand, if the number of bases is too small, nonspecific hybridization may occur, and if the number of bases is too large, it is difficult to make a difference in the migration degree, which is not suitable.

By analyzing / detecting the DNA oligomer described above, the present invention analyzes whether or not it has a genetic predisposition affecting the likelihood of side effects in radiation therapy, and from the results, side effects caused by radiation are analyzed. It was made to predict the risk of developing the disease.
Therefore, the analyzed DNA base sequence is compared with the DNA base sequence of any one of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing, and matches the risk allele specified in the present invention, or non- Whether it is a base sequence that is likely to cause side effects on radiation (onset group) or a base sequence that is less likely to cause side effects (non-onset group) by confirming whether it corresponds to a risk allele Can be determined. That is, it can be determined that a person having a risk allele has a genetic predisposition more likely to develop a side effect in radiation therapy than a person having a non-risk allele.

  Here, in the DNA oligomer according to the present invention, one or a plurality of bases other than the 121st base may be deleted, substituted or added, or a complementary strand thereof. That is, as long as it includes the SNP site specified in the claims and the sequence listing of the present invention, even if base substitution, deletion, insertion, etc. occur elsewhere, it is substantially the same or this DNA oligomer having a complementary DNA base sequence is equivalent to the DNA oligomer of the present invention.

Further, as such a DNA oligomer, DNA products replicated or amplified by various polymerases such as DNA polymerase, particularly heat-resistant polymerase (for example, Taq polymerase) can be preferably used.
And the DNA oligomer of this invention can be used conveniently in order to analyze directly the DNA base sequence which it has. For direct analysis of the DNA base sequence of this DNA oligomer, a conventionally known DNA sequencer, mass spectrometer or the like can be suitably used.
Moreover, the DNA oligomer of the present invention can be suitably used as a gene marker such as a so-called probe.

  When the DNA oligomer of the present invention is used as a gene marker, it is a gene marker (labeled probe) in which the end of the DNA base sequence or any base in the DNA base sequence is labeled with a fluorescent dye or a radioisotope. Is more preferable. If it is a marker gene marker, it can be easily detected by measuring fluorescence intensity and radiation dose. For example, it can be easily detected by exposing an X-ray film to fluorescence or exposure to radiation. It is also possible. For measurement of radiation dose and fluorescence intensity, a conventionally known radiation detection device, fluorescence measurement device, or the like can be suitably used. Further, if the fluorescent dye is labeled in this way, it can be appropriately analyzed by a DNA sequencer.

Examples of the radioisotope used for labeling include radioisotopes usually used such as ³² P and ³⁵ S. Examples of fluorescent dyes used for labeling include commonly used fluorescence such as FAM ^™ , Yakima Yellow ^™ , VIC ^™ , TAMRA ^™ , ROX ^™ , Cy3 ^™ , Cy5 ^™ , HEX ^™ , TET ^™ , and FITC. Mention may be made of pigments.

  As described above, the DNA oligomer for predicting the occurrence of side effects in radiotherapy according to the present invention can be suitably detected by directly analyzing the DNA base sequence or using the DNA oligomer as a gene marker. That is, SNP typing can be suitably performed. In general, “polymorphism” is defined as a change in the base present at a frequency of 1% or more in the population, but “polymorphism” in the present invention is not limited to this definition, Base changes of less than 1% are also included in the “polymorphism”.

[2. DNA oligomer set]
The DNA oligomers shown in SEQ ID NO: 174 to SEQ ID NO: 519 are preferably used as a DNA oligomer set in which two DNA oligomers are sequentially set from SEQ ID NO: 174.
If an appropriate one DNA oligomer set is appropriately selected from the DNA oligomer sets and used for amplification of DNA, any DNA oligomer shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing can be specifically amplified. Can do. In this DNA oligomer set, a DNA oligomer having a small sequence number corresponds to a forward primer, and a DNA oligomer having a large sequence number corresponds to a reverse primer. A portion sandwiched between sequences corresponding to these two types of primers is a target to be amplified by the PCR amplification reaction.

As described above, since the DNA oligomer set shown in SEQ ID NO: 174 to SEQ ID NO: 519 can be suitably used particularly when performing PCR (Polymerase Chain Reaction), the DNA oligomer set of the present invention is used for PCR amplification. It is preferable to use it as a primer set. Therefore, using this PCR amplification primer set, a DNA oligomer having a specific DNA base sequence, that is, a specific SNP site (121st position in the present invention) shown in SEQ ID NO: 1 to SEQ ID NO: 157 in the sequence listing A DNA oligomer containing a base is a specific SNP site.) Can be reliably and simply amplified.
Each DNA oligomer constituting this DNA oligomer set may be one in which one or several bases are deleted, substituted or added in the DNA base sequence of the DNA oligomer. In addition, DNA oligomers represented by SEQ ID NO: 174 to SEQ ID NO: 519 include DNA having about 10 bases such as an appropriate restriction enzyme recognition sequence (for example, “5′-ACGTTGGATG-3 ′” (SEQ ID NO: 693) as necessary. Oligomer) may be added to the 5 'upstream side of the DNA oligomer. The sequence added in this way has the effect of stabilizing the amplification reaction by PCR. The base sequence to be added is not limited to this, and any sequence can be used as long as it has the same effect.

[3. DNA oligomer (2)]
In addition, in the DNA oligomers shown in SEQ ID NO: 520 to SEQ ID NO: 692, the 3 ′ end is adjacent to the base that is a specific SNP site among the DNA oligomers shown in SEQ ID NO: 1 to SEQ ID NO: 174 of the sequence listing. Designed to do. Therefore, if such a DNA oligomer is enzymatically extended from one to several bases, the resulting DNA oligomer will have a different length depending on the polymorphism. In addition, this DNA oligomer can also be one in which one or several bases are deleted, substituted or added in the DNA oligomer.

  The DNA oligomer shown in SEQ ID NO: 520 to SEQ ID NO: 692 preferably has a length of 10 to 24 bases adjacent to the risk allele on the 3 ′ side, more preferably a length of 15 to 24 bases. More preferably, the length is 17 to 24 bases. The length can be appropriately changed depending on the GC content of the DNA oligomer, the hybridization conditions, and the like.

To add one to several bases enzymatically, for example, by using DNA polymerase, which is a DNA synthase, and dideoxynucleoside triphosphate (ddNTP), which is an analog of deoxynucleoside triphosphate (dNTP), A DNA oligomer having only one base extended can be obtained (one base primer extension method). Therefore, such a DNA oligomer can be suitably used for SNP typing for analyzing a base that is a risk allele.
In this way, for example, one of the alleles can be extended by 1 base and the other allele can be extended by 3 bases, so that the difference in length of the DNA product can be accurately detected by a mass spectrometer. Yes (MassEXTEND ^™ method, SEQUENOM). The number of bases to be extended is preferably designed for each SNP site so that the length is most efficiently different from the sequences before and after the polymorphic site of each SNP site.

[4. SNP typing]
As a technique for performing SNP typing, there are a technique based on primer extension, a technique based on hybridization, a technique based on DNA cleavage, a technique based on ligation, and the like.

(4-1. SNP typing method-1)
As a technique based on the primer extension, for example, the above-described single-base primer extension method (Syvanen, AC et al., Genomics, 8, 684-692 (1990)), and the MALDI-TOF / MS method (Ross) using the same. , P., et al. Nat Biotechnol, 16, 1347-1351 (1998); Buetow, KH et al., Proc Natl Acad Sci USA, 98, 581-584 (2001); SNP gene polymorphism strategy, Kenichi Matsubara・ Yoshiyuki Tsuji, Nakayama Shoten, pages 106-117), allele-specific primer extension method (Uggozzoli, L. et al., Genet Anal Tech Appl, 9, 107-112 (1992)), APEX (in the arrayed primer extension) method (Shumaker, JM et al., Hum Mutat, 7, 346-354 (1996)). Among these, the use of the MALDI-TOF / MS method is particularly preferable because it allows simple and large-scale sample SNP typing simultaneously.

This MALDI-TOF / MS (matrix assisted laser desorption ionization time-of-flight / mass spectrometry) method is capable of directly determining and comparing the DNA base sequences of DNA products obtained from DNA samples. Method.
The MALDI-TOF / MS method is one of the genotyping methods for processing a large amount of samples at a high speed as described above. In this method, a mass spectrometer that has been used in the field of biology / chemistry for a long time is applied to SNP typing. Since the method is based on a mass spectrometer, the basic principle is to determine the base sequence by matching the difference due to polymorphism with a molecular difference in some form and detecting the difference in mass of the molecule. That is, the MALDI-TOF / MS method combines a mass spectrometer and a primer extension method to determine a base difference at the SNP site.

  Specifically, first, a DNA sample is extracted from a cancer patient scheduled to undergo radiation therapy. At this time, DNA containing a base at a site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention is prepared by amplification using PCR or the like. Next, using the PCR product as a template, a genotyping primer (complementary to the base sequence from the base 1 'to the 3' side of the base corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing) A primer having a typical sequence, or a primer having a sequence complementary to the complementary strand in the case of a complementary strand of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing) Elongate one base. The PCR product used in this reaction is preferably purified to remove a primer for PCR amplification, and a genotyping primer (extended primer (shown in SEQ ID NO: 520 to SEQ ID NO: 692)). ) Usually preferably has a length of 15 bp or more. In addition, in the primer extension reaction, an excess of 10 times or more excess genotyping primer is usually added to the PCR product, but is not limited thereto. The conditions of the thermal cycle for performing PCR can be selected as appropriate, but conditions in which about 30 to 60% of the genotyping primers extend are suitable. For example, appropriate elongation efficiency can be obtained by performing about 25 times between two temperatures of 94 ° C. and 37 ° C. Next, the primer extension reaction product is spotted on a MALDI plate, and then mass measurement is performed to create a mass spectrogram. Then, the DNA base sequence is determined by analyzing the created mass spectrogram, and the base at the site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention has side effects on radiation. It is possible to discriminate between a case of a base sequence that is likely to develop (onset group) and a case of a base sequence that is less likely to develop side effects (non-onset group) by a single reaction.

  As described above, in the MALDI-TOF / MS method, a DNA base sequence can be directly determined using a mass spectrometer and SNP typing can be realized in a large amount and at a high speed. However, as a means for determining a DNA base sequence in the present invention. Is not limited to this. As a means for determining a DNA base sequence using a DNA sample, for example, SNP typing can also be performed by a DNA sequencer using a slab gel or a multicapillary.

(4-2. SNP typing method-2)
As a method based on hybridization, for example, TaqMan PCR method (Livak, KJ et al., PCR Methods Appl., 4, 357-362 (1995); SNP gene polymorphism strategy, Kenichi Matsubara, Yoshiyuki Tsuji, Nakayama Shoten Pp. 94-105).

Specifically, first, a DNA sample is extracted from a cancer patient scheduled to undergo radiation therapy. Then, a DNA oligomer (probe) for hybridizing to a DNA containing a base at a site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention selected in advance (SEQ ID NO: 1 of the sequence listing) To the 5 ′ end of any DNA oligomer of SEQ ID NO: 173 or its complementary strand). In the present invention, examples of the reporter fluorescent substance include FAM and VIC described above, but are not limited thereto. Further, a quencher substance is labeled at the 3 ′ end of the probe. In the present invention, the quencher substance is not particularly limited as long as it can quench the reporter fluorescence. Examples thereof include Dabcyl, BHQ1, BHQ2, Eclipse ^™ Dark Quencher, and ElleQuencher ^™ .
Next, a probe labeled with reporter fluorescence and a quencher substance for hybridizing to DNA containing a base at a site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention is used as radiation. Hybridize to DNA prepared from a cancer patient to be treated. Next, DNA containing a base at a site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention is amplified using a DNA polymerase having 5 '→ 3' exonuclease activity. As a result, the reporter fluorescence labeled portion of the nucleotide probe labeled with the reporter fluorescence and the quencher substance is cleaved, and the reporter fluorescence is released. In the present invention, Taq DNA polymerase can be preferably exemplified as a DNA polymerase having 5 ′ → 3 ′ exonuclease activity, but is not limited thereto. In this method, the released reporter fluorescence is then detected, and the emission of the reporter fluorescence is compared with a control. In this method, the base at the site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention is a base sequence (onset group) that is likely to cause side effects on radiation. SNP typing can be performed in a single reaction by using two types of nucleotide probes labeled with different reporter fluorescence depending on the case and the type of base sequence that is unlikely to cause side effects (non-onset group) It is.

(4-3. SNP typing method-3)
Other techniques based on hybridization include, for example, an allele specific oligonucleotide (ASO) hybridization method (Baner, J. et al., Nucleic Acids Res, 26, 5073-5078 (1998)). Can be mentioned.
That is, in order to detect only a mutation at a specific position, a DNA oligomer (gene marker) containing a base sequence that is considered to have a mutation is prepared in advance, and hybridization is performed with this DNA of a DNA sample. As a result, since the efficiency of hybridization is reduced when mutations are present, SNP can be detected by Southern blotting or a method that uses the property of quenching by intercalating a special fluorescent reagent into the hybrid gap. In addition, the type of base directly related to SNP can be determined by using the detected base sequence for a DNA sequencer or the like. Next, by comparing the determined base types, there is a type of base sequence that is likely to cause side effects due to radiation (onset group) or a type of base sequence that is less likely to cause side effects (non-onset group). SNP typing can be performed.

  In addition, examples of techniques based on DNA cleavage include the Invader method (Lyamichev, V. et al., Nat Biotechnol, 17,292-296 (1999); SNP gene polymorphism strategy, Kenichi Matsubara Yoshiyuki, Nakayama Shoten, pages 94-105).

Specifically, first, a DNA sample is extracted from a cancer patient scheduled to undergo radiation therapy. Then, a base sequence complementary to the base sequence 5 ′ from the base corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention selected in advance, and one base 3 of the base An allele probe that does not hybridize with the base sequence on the 3 'side from the base on the' side but has a base sequence (flap) complementary to a part of the base sequence of the invader probe described later is synthesized.
In addition, a base (arbitrary base) corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention is used as the 3 'end, and the base corresponding to the SNP site is 1 base 3' side. An invader probe having a sequence complementary to the base sequence on the 3 ′ side from this base is synthesized.
Next, these allele probe and invader probe are hybridized to the template DNA in the DNA sample. At this time, the base (arbitrary base) of the invader probe corresponding to the base corresponding to the SNP site of the DNA base sequence represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention is the template DNA, allele probe, Invade between. Using Cleavease (registered trademark), which is an enzyme having an endonuclease action for recognizing this invasion site and cleaving between the base of the allele probe corresponding to the site and the base on the 1st base 3 'side of the base, The flap part of the allele probe is cut and released. Next, the released flap is hybridized with a FRET (fluorescence resonance energy transfer) probe having a sequence complementary thereto and labeled with reporter fluorescence and a quencher substance. The FRET probe has a base sequence that can be complementarily bound by itself on the 5 'side. On the 3 ′ side, as described above, it has a complementary sequence to the flap. In addition, on the 5 ′ side that can be complementarily bound by itself, reporter fluorescence is labeled on the 5 ′ end, and a quencher substance is labeled on the 3 ′ side of the 5 ′ end. As a result of the hybridized 3 ′ terminal base of the released flap hybridizing to the FRET probe, the reporter fluorescence of the probe enters the labeled complementary binding site, thereby generating a structure recognized by Cleavease (registered trademark). . Therefore, in this method, the reporter fluorescence released by cleavage of the reporter fluorescent labeling portion by Cleavease (registered trademark) is measured, and the intensity of the measured fluorescence is compared, thereby making it possible to cause side effects due to radiation. SNP typing can be performed as to whether it has (onset group) or has a base sequence (non-onset group) that is less likely to cause side effects.

(4-4. SNP typing method-4)
As a technique based on ligation, for example, RCA (rolling circle amplification) can be cited (Lizardi, PM et al., Nat Genet, 19, 225-232 (1998); Magnus J., TECHNOLOGY DEVELOPMENT FOR GENOME AND POLYMORPHISM ANALYSIS, 23-24 (2003), Karolinska University Press, Stockholm, Sweden; SNP gene polymorphism strategy, Kenichi Matsubara, Yoshiyuki Tsuji, Nakayama Shoten, 118-127).
In the RCA method, a DNA polymerase that does not have 5 ′ → 3 ′ exonuclease activity under a specific condition continues to synthesize DNA over many laps while moving on a circular single-stranded DNA as a template. Thus, a long complementary strand DNA is synthesized.
Therefore, in the RCA method, alleles are identified by determining the presence or absence of DNA amplification by the RCA method. That is, a DNA oligomer that is a template for synthesis by DNA polymerase is linearized, and genomic DNA is used as a template for a ligation reaction. The SNP sites are set at the 3 ′ end and 5 ′ end of the linear DNA oligomer. Perform a ligation reaction. At this time, if the ligation is completed to form a circular single-stranded DNA, the RCA reaction proceeds and a long complementary strand DNA can be obtained. On the other hand, if the DNA oligomer is not ligated, it does not become circular single-stranded DNA, and the RCA reaction does not proceed. In order to perform such an RCA reaction, it is necessary to produce a single-stranded probe (padlock probe) that can anneal with genomic DNA and be circular.

  Specifically, first, a DNA base sequence consisting of bases of 10 to 20 bases around the SNP site (121st base) shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence table of the present invention is selected in advance. Keep it. Then, the 5 'end of a 10-20 base DNA oligomer 5' upstream of the SNP site is bound to the 3 'end of a single-stranded probe having a special sequence serving as a backbone. Then, the 3 ′ end of the DNA oligomer 3 ′ downstream of the SNP site is bound to the 5 ′ end of the single-stranded probe serving as the backbone. The DNA base sequence 5 ′ upstream of the SNP site used at this time matches the DNA base sequence shown in SEQ ID NO: 520 to SEQ ID NO: 692. In addition, the primer used as the scaffold of the DNA polymerase at the time of DNA synthesis is RCA primer having a DNA base sequence complementary to the backbone probe.

With such a configuration, such a padlock probe can be a probe whose SNP site becomes the 3 ′ end when it is made circular. That is, when complementary to a DNA sample (genomic DNA) prepared from a cancer patient to be subjected to radiation therapy, the SNP site bases hybridize with a single-stranded circular DNA probe by a ligation reaction. Therefore, as described above, the DNA polymerase synthesizes long complementary strand DNA using the circular single-stranded DNA as a template.
On the other hand, when the base of the SNP site is not complementary to the hybridizing genomic DNA, the ligation reaction does not occur and the circular single-stranded DNA cannot be synthesized, so that a long complementary DNA cannot be synthesized. Therefore, there is an advantage in that it can be easily confirmed whether or not it has the same base as the SNP site simply by confirming whether or not a long complementary strand DNA exists by electrophoresis or the like.
In addition, a primer (branch) having a DNA base sequence complementary to the complementary strand DNA synthesized by the DNA polymerase, that is, the same DNA base sequence as the circular single-stranded DNA, in the DNA synthesis reaction system described above. (Also referred to as a primer) can be combined with the synthesis system to increase the molecular weight of the DNA to be synthesized.

(4-5. Method of SNP typing-part 5)
Furthermore, as another SNP typing method used in the present invention, for example, a PCR-SSCP (single-strand conformation polymorphism) method (Genomics, 12, 139-146 (1992); Oncogene, 6, 1313-1318 (1991); PCR Methods Appl, 4, 275-282 (1995)).
This method is particularly convenient for screening a large number of DNA samples because it is relatively simple to operate and has the advantage of requiring a small amount of test sample. The principle is as follows. When a double-stranded DNA fragment is dissociated into single strands, each strand forms a unique higher order structure depending on the base sequence. When the dissociated DNA strand is electrophoresed in a polyacrylamide gel not containing a denaturing agent, single-stranded DNA having the same complementary strand length moves to a different position according to the difference in each higher-order structure. The higher-order structure of this single-stranded DNA also changes by substitution of a single base, and shows different mobility in polyacrylamide gel electrophoresis. Therefore, if the mobility by electrophoresis when the bases of the SNP sites are different is known in advance, SNP typing for single-stranded DNA can be performed by detecting the change in mobility.

Specifically, first, DNA containing a base at a site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention is amplified by PCR or the like. As a range to be amplified, a length of about 200 to 400 bp is usually preferable. The PCR reaction conditions can be performed, for example, by repeating heat denaturation at 94 ° C. for 40 seconds, annealing at 50 ° C. for 1 minute, and extension reaction at 72 ° C. for 2 minutes 30 times. It is not limited to this, and the conditions can be changed as appropriate.
In PCR, a PCR product can be labeled by using a primer labeled with the above-mentioned various radioisotopes, fluorescent dyes, biotin or the like. Alternatively, the PCR product can be labeled by adding a substrate base labeled with a radioisotope, a fluorescent dye, biotin or the like to the PCR reaction solution and performing PCR. Furthermore, labeling can also be performed by adding a substrate base labeled with a radioisotope, a fluorescent dye, biotin, or the like to the PCR product fragment using a Klenow enzyme or the like after the PCR reaction. In addition, as a primer used here, it is preferable to use the DNA oligomer set which consists of a DNA oligomer shown to sequence number 174 to sequence number 519 of a sequence table.
The fragment of the labeled PCR product thus obtained is denatured by applying heat or the like, and electrophoresis is performed using a polyacrylamide gel that does not contain a denaturing agent such as urea. At this time, by adding an appropriate amount (about 5 to 10%) of glycerol to the polyacrylamide gel, the conditions for separating the PCR product fragments can be improved. Moreover, although the electrophoresis conditions vary depending on the properties of each labeled PCR product, it is usually performed at room temperature (20 to 25 ° C.), and gives optimum mobility at temperatures up to 4 to 30 ° C. when preferable separation is not obtained. Review the temperature. After electrophoresis, the mobility of the labeled PCR product is analyzed by detecting a signal with an autoradiography using an X-ray film or a scanner for detecting fluorescence. When a band with a difference in mobility of the labeled PCR product is detected, this band is cut out directly from the gel, amplified again by PCR, and directly DNA sequenced to determine the presence of the mutation and the type of base. Can be confirmed. In addition, when the difference in mobility of the labeled PCR product depending on the base type of the SNP site is known, SNP typing can be easily performed by comparing with this.

(4-6. Method of SNP typing-6)
Furthermore, other SNP typing methods used in the present invention include, for example, a method using restriction fragment length polymorphism (RFLP) and a PCR-RFLP method.

Specifically, first, a DNA sample is extracted from a cancer patient scheduled to undergo radiation therapy. Here, in the site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention, when a restriction enzyme recognition site is changed by substitution of a base with SNP, restriction enzyme cleavage is performed. The length of the fragment changes. Therefore, SNP can be determined by comparing the size of the resulting DNA fragment between the onset group and the non-onset group.
That is, by amplifying a DNA sample containing this mutation by the PCR method and treating with each restriction enzyme, these mutations can be detected as a difference in mobility of bands after electrophoresis.
Alternatively, the chromosomal DNA is subjected to restriction enzyme treatment and then subjected to Southern blotting using a probe comprising a DNA oligomer represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention. The presence or absence can be detected.
In addition, the restriction enzyme used here can be suitably selected according to each mutation. In this method, in addition to chromosomal DNA, RNA prepared from cancer patients scheduled to undergo radiation therapy is converted to cDNA with reverse transcriptase, cut with restriction enzyme, and then subjected to Southern blotting. Is possible.
Thus, by detecting the presence or absence of SNP at the restriction enzyme recognition site, it has a base sequence of a type that tends to cause side effects due to radiation (onset group), or a type of base sequence that is less likely to cause side effects (non- SNP typing can be performed as to whether or not there is an onset group).

(4-7. Method of SNP typing-7)
As described above, the DNA oligomer having the DNA base sequence shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention and the information on the DNA base sequence are determined by directly decoding the DNA base sequence of the genomic DNA. In addition, it can be synthesized by a DNA synthesizer or the like and used as a probe for a DNA chip. A preferred example of using the DNA oligomers shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention as a probe for a DNA chip is a DNA chip for predicting the occurrence of side effects in radiation therapy.

Here, the DNA chip in the present invention refers to a DNA oligomer having a DNA base sequence shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing and containing a SNP site (probe for DNA chip) to be detected on a substrate. Aligned (arrayed) and fixed. Then, hybridization with the target DNA or target RNA fluorescently labeled on the substrate is performed, and the fluorescent signal on the DNA probe is detected. In a DNA chip, generally, a DNA oligomer fixed on a glass substrate serves as a probe, and a labeled DNA in a solution serves as a target. Therefore, the DNA oligomer fixed on the glass substrate is used as a DNA chip probe.
There are roughly two types of DNA chips, the Affymetrix method for synthesizing DNA on the glass surface and the Stanford method for mounting cDNA on the glass surface. Although it is preferable to use the Affymetrix method for SNP typing, the present invention is not limited to this, and the Stanford method can also be used.

Hereinafter, a DNA chip using DNA oligomers (DNA chip probes) represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention when an Affymetrix DNA chip is applied will be described.
The Affymetrix system combines photolithographic technology and light irradiation chemical synthesis to synthesize a DNA oligomer of about 20 to 25 bp having SNP sites shown in SEQ ID NO: 1 to SEQ ID NO: 173 on a glass substrate. A DNA chip on which the DNA oligomers shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention are immobilized can be prepared. Then, a fluorescently labeled cRNA is synthesized by in vitro transcription using a cDNA synthesized from the sample-derived DNA or a cDNA synthesized by reverse transcription from the sample-derived RNA as a template. Hybridization and measurement of fluorescence images with a dedicated scanner makes it easier to develop side effects due to radiation (onset group) or less likely to cause side effects ( SNP typing as to whether or not it has (non-onset group) can be performed.

  The DNA chip probe to be immobilized on the glass substrate can detect the base DNA polymorphism at the site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing. There is no particular limitation. That is, the DNA chip probe is, for example, a probe that hybridizes to a target DNA containing a base at a site corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing. If hybridization is possible, it is not necessary to be completely complementary to DNA containing a base corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing. These bases may be deleted, substituted or inserted. In the present invention, the length of the probe for a DNA chip to be bonded to the substrate is usually preferably 10 to 100 bp, more preferably 10 to 50 bp, and further preferably 15 to 25 bp.

  The hybridization reaction solution and reaction conditions in SNP typing using the DNA chip may vary depending on various factors such as the length of the nucleotide probe immobilized on the substrate, ie, bound to the complex or the probe for the DNA chip. It can be determined based on the melting temperature (Tm) of the target DNA. For example, stringent conditions of about “1 × SSC, 0.1% SDS, 37 ° C.” can be given as washing conditions after hybridization. The complementary strand that hybridizes with the DNA chip probe fixed to the DNA chip is preferably one that maintains the hybridized state with the target DNA even when washed under such conditions. Although it is not particularly limited, the more stringent conditions are about “0.5 × SSC, 0.1% SDS, 42 ° C.”, and the more stringent conditions are “0.1 × SSC, 0.1% SDS, A cleaning condition of about “65 ° C.” can be mentioned. In addition to this, it is possible to wash the hybridized DNA by appropriately changing the salt concentration such as NaCl and KCl and the temperature condition. For example, the salt concentration is 3M or less, 2.5M or less, 2M or less, 1.5M or less, more preferably 1M or less, 0.75M or less, 0.5M or less, which is a severe stringent condition. It can be appropriately selected from a salt concentration of 25 M or less and 0.1 M or less. Further, as the temperature condition, the temperature condition can be appropriately selected from at least about 15 ° C., about 20 ° C., about 25 ° C., and about 30 ° C., and more preferably stringent stringent conditions. It can be appropriately selected from the group consisting of at least 40 ° C, at least 40 ° C, at least 45 ° C, at least 50 ° C, at least 60 ° C, at least 70 ° C.

  As described above, a DNA oligomer having at least 10 bp containing a base corresponding to the SNP site represented by SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention and a DNA oligomer complementary thereto are used in SNP typing. It can be used as a probe (including a substrate on which the probe is immobilized) or a primer.

  When the DNA oligomer shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing of the present invention is used as a primer, the length is usually 10 to 241 bp, preferably 15 to 200 bp, more preferably 15 to 100 bp, and still more preferably Is 17-50 bp, most preferably 20-30 bp. When DNA oligomers are used as primers, it is preferable to use a DNA oligomer set using the DNA oligomers shown in SEQ ID NO: 174 to SEQ ID NO: 519 as a set and two in sequence starting from SEQ ID NO: 174. As long as it can be amplified including the SNP site (121st base) which is a risk allele, the DNA base sequence shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing is appropriately prepared. Can also be used. It is also possible to create a DNA oligomer set using sequences outside these sequences on the human chromosome.

When the DNA oligomer shown in SEQ ID NO: 1 to SEQ ID NO: 173 is used as a probe, the probe is the SNP site (121st base) shown by SEQ ID NO: 1 to SEQ ID NO: 173 of the present invention. If it hybridizes specifically with DNA containing the base of the site corresponding to, it is not particularly limited. It is preferable that the probe usually has a length of at least 15 bp.
The DNA oligomer of the present invention can be suitably prepared by, for example, a commercially available DNA synthesizer, but is not limited thereto, and is restricted from vectors having the DNA base sequence transformed and introduced into Escherichia coli or the like. It may be prepared as a double-stranded DNA fragment that can be obtained by enzyme treatment or the like.

[5. (Radiation used for radiation therapy)
In the present invention, X-rays, γ-rays, heavy particle beams, and electron beams can be suitably used as radiation that can be used for radiotherapy, but the present invention is not limited to these, and proton beams, neutron beams Such radiation can also be used.

[6. SNP information]
Information for performing SNP typing includes NCBI dbSNP (http://www.ncbi.nlm.nih.gov/SNP/), information on each gene described in various literature information, etc., and JSNP DB ( Information on SNPs was obtained from information registered at http://snp.ims.u-tokyo.ac.jp/).

[7. (Prediction method of side effects in radiation therapy)
Next, referring to FIG. 1, the DNA base sequence of a DNA sample prepared from a sample collected from a subject (cancer patient) is directly analyzed, and the DNA base of the DNA oligomer for predicting the occurrence of side effects in radiation therapy of the present invention is used. A side effect onset prediction method in radiation therapy for determining whether or not the SNP site (the 121st base) in the sequence matches will be described. FIG. 1 is a flowchart for explaining a method for predicting the occurrence of side effects in radiation therapy according to the present invention.

The method for predicting the occurrence of side effects in radiotherapy according to the present invention comprises the following steps (a) to (g), wherein determination is performed using the DNA oligomers shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing.
(A) a step of preparing a DNA sample based on a sample collected from a cancer patient scheduled to undergo radiation therapy (step S1);
(B) a step of amplifying DNA based on the DNA sample prepared in the step (a) to obtain a DNA product (step S2);
(C) a step of performing an extension reaction using the DNA product amplified in the step (b) as a template to obtain a DNA oligomer as an extension product (step S3),
(D) a step of analyzing the DNA base sequence of the DNA oligomer obtained in the step (c) (step S4),
(E) The base corresponding to the 121st position in the DNA base sequence of the DNA oligomer analyzed in the step (d) and the 121st base of the DNA base sequence shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing A step of collating with a base (step S5),
(F) A step of determining whether the allele having the base verified in the step (e) is a risk allele or a non-risk allele (step S6),
(G) A step of predicting an onset risk rate of side effects due to radiation in a cancer patient scheduled to undergo the radiation therapy from the result determined in the step (f) (step S7).

Hereafter, each process of the side effect onset prediction method in the radiotherapy of this invention is demonstrated in detail.
First, in the step (a), a DNA sample is prepared based on a sample collected from a cancer patient scheduled to undergo radiation therapy (step S1). At this time, it is preferable to use blood as the collected sample, but it is not limited thereto. For example, any sample containing DNA such as skin, oral mucosa, hair, tissue excised by surgery, etc. may be used. Anything can be used. If such a sample is used, a DNA sample such as chromosomal DNA can be suitably extracted.
In this process, in order to extract a DNA sample from blood (sample) collected from a cancer patient who is scheduled to undergo radiation therapy, it is preferable to use an automatic DNA extraction apparatus that automatically extracts DNA from blood. It is. This is because the time required for extracting a large amount of sample DNA can be saved and the operation is simple. When such an automatic DNA extraction apparatus is used, it is desirable to extract DNA using a standard protocol attached to the apparatus, but it is also possible to modify the protocol as appropriate.

As another simple method for extracting a DNA sample, the DNA sample may be extracted using a simple system or kit sold by each company.
Furthermore, another method for extracting DNA samples is to extract DNA samples by phenol-chloroform treatment and ethanol precipitation (BASIC METHODS IN MOLECULAR BIOLOGY 2nd EDITION, Davis et al., P.16-21). Is possible. In addition, purification of total RNA from samples collected from cancer patients as needed (guanidine isothiocyanate-cesium chloride ultracentrifugation method; BASIC METHODS IN MOLECULAR BIOLOGY 2nd EDITION, Davis et al., P.322-328) And isolation of poly A ⁺ -RNA (BASIC METHODS IN MOLECULAR BIOLOGY 2nd EDITION, Davis et al., Pages 344-349) and synthesis of cDNA based on these (synthesis of First-Strand cDNA; BASIC METHODS IN MOLECULAR BIOLOGY 2nd EDITION, Davis et al., P.515-522; ibid. P.136-137). Furthermore, it is also possible to use reagents, kits, etc. sold by each company for each of these operations.

  Next, in the step (b), DNA is amplified based on the DNA sample in the above step to obtain a DNA product (step S2). As a method for amplifying the DNA of the DNA sample in this step, the PCR method can be suitably used. As a primer used for PCR, for example, it is preferable to use a primer set for PCR amplification in which a set of DNA oligomers represented by SEQ ID NO: 174 to SEQ ID NO: 519 in the sequence listing is sequentially set from SEQ ID NO: 174. The PCR reaction conditions include, for example, heat denaturation at 94 ° C. for 2 minutes, heat denaturation at 94 ° C. for 40 seconds, annealing at 50 ° C. for 1 minute, and extension reaction at 72 ° C. for 2 minutes. It can be suitably shown that the final extension reaction for 5 minutes at 72 ° C. is performed after repeating the cycle 30 times, but the present invention is not limited to this, and the conditions can be changed as appropriate. . If the DNA product can be amplified without using the PCR method, DNA amplification may be performed using a DNA polymerase or the like.

  Next, in the step (c), an extension reaction is performed using the DNA product amplified in the above step as a template to obtain a DNA oligomer as an extension product (step S3). As an extension primer for analyzing the DNA base sequence used at this time, it is preferable to use DNA oligomers shown in SEQ ID NO: 520 to SEQ ID NO: 692 in the sequence listing of the present invention. The conditions for the extension reaction can be set and changed as appropriate, but are preferably the conditions specified in each extension kit.

Next, in the step (d), the DNA base sequence of the DNA oligomer subjected to the extension reaction in the above step is analyzed (step S4).
Here, as a method for analyzing the DNA base sequence of the DNA product, the MALDI-TOF / MS method, which is a method for directly analyzing the DNA base sequence described in detail above, can be preferably used, but is not limited thereto. The DNA base sequence can be analyzed, that is, SNP typing can be performed using the appropriate method described above.

Next, in the step (e), the base corresponding to the 121st position in the DNA base sequence of the DNA oligomer analyzed in the above step and the DNA base sequence shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing Is compared with the 121st base of (step S5).
In the next step (f), it is determined whether the allele having the base verified in the previous step is a risk allele or a non-risk allele (step S6).

  In this way, it is determined whether the base of the DNA product corresponding to the base at position 121 of the DNA base sequence shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing is a risk allele or a non-risk allele In consideration of the results and allele frequency at other SNP sites, the risk of developing side effects due to radiation is predicted in the next step (g) (Step S7).

  As mentioned above, the side effect onset prediction DNA oligomer, gene marker, DNA oligomer set, and side effect onset prediction method in radiation therapy according to the present invention have been described in detail, but the present invention is not limited to these contents. Needless to say, the present invention can be widely changed and modified without departing from the spirit of the present invention.

  For example, (1) at least one of a fluorescent dye, a radioactive isotope, a fluorescent dye luminescent enzyme, or a protein having an ability to bind to a specific substance as a gene marker for predicting the occurrence of side effects in radiation therapy of the present invention It can be set as the structure which added.

  For example, (2) a genetic marker for predicting the occurrence of side effects in radiation therapy of the present invention comprises a DNA oligomer having a DNA base sequence complementary to a risk allele and a DNA oligomer having a DNA base sequence complementary to a non-risk allele. Alternatively, a configuration in which different types of fluorescent dyes, radioisotopes, enzymes for emitting fluorescent dyes, or proteins having a binding ability with a specific substance are used can be used.

  The DNA oligomer for detection of the present invention is at least a DNA oligomer according to any one of claims 1 to 16 or claim 20 or a DNA oligomer set according to claim 18 or claim 19. One of the DNA oligomers can be configured such that a fluorescent dye, a radioisotope, an enzyme for emitting a fluorescent dye, or a protein capable of binding to a specific substance is added.

  For example, (3) the detection DNA oligomer of the present invention comprises a DNA oligomer having a DNA base sequence complementary to a risk allele and a DNA oligomer having a DNA base sequence complementary to a non-risk allele, of different types of fluorescence. A structure in which a dye, a radioisotope, an enzyme for emitting a fluorescent dye, or a protein having a binding ability with a specific substance is added thereto can be used.

  For example, (4) the method for predicting the onset of side effects in radiation therapy of the present invention includes the following steps (a) to (e) in which determination is performed using the DNA oligomers shown in SEQ ID NO: 520 to SEQ ID NO: 692. It is good also as a side effect onset prediction method in the radiotherapy characterized by this. (A) a step of preparing a DNA sample based on a sample collected from a cancer patient scheduled to undergo radiation therapy, (b) the DNA sample prepared in the step (a), and a sequence listing (C) a step of hybridizing with a DNA oligomer having the DNA base sequence shown in any one of SEQ ID NO: 520 to SEQ ID NO: 692, and (c) the DNA oligomer hybridized in the step (b) is alleleated using ddNTP. A step of performing a reaction that specifically extends one base, (d) a step of analyzing the base of the ddNTP of the DNA oligomer that is allele-specifically extended by one base in the step (c), (e) a step of (d) A step of collating the base of ddNTP analyzed in step 1 with the 121st base of the DNA oligomer represented by any one of SEQ ID NO: 1 to SEQ ID NO: 157 in the sequence listing (f Determining whether the allele having the base verified in the step (e) is a risk allele or a non-risk allele; (g) from the result determined in the step (f), The process of predicting the risk of developing side effects due to radiation in cancer patients scheduled to be performed.

  (5) The ddNTP may be added with a fluorescent dye, a radioisotope, a fluorescent dye luminescent enzyme, or a protein having a binding ability with a specific substance.

  Next, referring to the examples, the DNA oligomer for predicting the onset of side effects, gene marker, DNA oligomer set (PCR primer) and DNA oligomer (extension primer), and the method for predicting the onset of side effects in radiation therapy according to the present invention are described. This will be described more specifically.

  The study of SNPs to predict the risk of developing side effects includes (1) analysis of radiosensitive genes in cultured human cell lines and (2) analysis of radiosensitive genes in mouse strain differences. We conducted a survey and (4) performed a genetic statistical analysis related to the onset of side effects caused by radiation.

First, regarding [1] radiosensitive genes in human cell lines, there have been many reports on genes related to radiosensitivity. They focused on genes with specific functions, such as some DNA repair genes. In the present invention, these genes are also examined, but 21,000 types considered as genes or gene candidates from the analysis of the DNA base sequence information after the determination of the entire DNA base sequence of the human genome. , And commissioned to Agilent (CA, USA) to create oligo arrays with these gene-specific DNA sequences of 60 bases, and to search for genes that are uniquely effective for classification of radiation sensitivity. went.
First, dose-viability curves of 60 types of human cell lines were obtained, 32 cell lines with different sensitivities were selected, and gene expression profiles before and after X-ray irradiation were compared between the cells, and D ₁₀ , D _q , α / Genes effective for classifying cell lines were identified for each model parameter such as β, and used as radiation-sensitive gene candidates. These included genes thought to be involved in cell proliferation, cell cycle regulation, redox, DNA damage repair, and the like.

  Next, regarding the analysis of [2] mouse strain differences, damage / repair after irradiation in various organs such as the skin, lungs, intestinal tract, etc. for three strains of mice A / J, C3H / HeMs, and C57BL6J with different radiosensitivity. The process was determined (M. Iwakawa et al., Radiation Res., 44, 7-13 (2003)). At the same time, the gene expression profiles after irradiation in target organs were compared using a microarray, and gene groups thought to be related to strain differences were extracted. Then, human homologues of these genes were used as susceptibility gene candidates. This included signal transduction, apoptosis, and immune related genes.

[3] In the genetic statistical analysis related to the onset of side effects due to radiation, DNA base sequence information on polymorphic markers (SNP sites) on candidate genes is UCSC Genome Bioinformatics (version: UCSC Human April 2003 (http: / /genome.ucsc.edu/)), JSNP DB (http://snp.ims.u-tokyo.ac.jp/), dbSNP (http://www.ncbi.nlm.nih.gov/SNP/) Obtained from. We analyzed the polymorphism frequencies of these alleles using the healthy population we collected (the population with SNP alleles in the non-onset group), and selected alleles to be analyzed.
Next, SNP typing was performed on the group classified based on the determination of the occurrence of side effects due to radiation. The subjects of the study were 218 breast cancer patients who received informed consent to conduct the study from October 2001 to December 2003 and received blood and medical information, cervical cancer First, medical data analysis was performed on 57 patients and 71 prostate cancer patients, and stratification was performed for polymorphism frequency analysis. The incidence of side effects (disorders) due to radiation was targeted to skin disorders in breast cancer patients, bowel disorders (diarrhea) in cervical cancer patients, and bladder / urethral disorders (dysuria) in prostate cancer patients. Each disorder was classified into two groups according to the determination results in less than 3 months (early stage), 3 months (late 3 months stage), and 6 months (late 6 months stage) from the start of radiation therapy.

  Tables 1 to 18 show early stages from the start of radiation therapy for breast cancer patients, cervical cancer patients, and prostate cancer patients who have obtained informed consent to collect DNA and perform SNP typing. It is the table | surface which calculated | required statistically and calculated | required the allele frequency in the stage of late 3 months (it does not describe about cervical cancer) and the late 6 months stage. Each table shows the type of cancer, the time when the side effects (disorders) due to radiation therapy were confirmed, and the site to be investigated.

  That is, Tables 1 to 3 show the allele frequencies of the breast cancer patient group at the early stage from the start of radiation therapy for breast cancer, and Tables 4 and 5 show the allele frequencies of the breast cancer patient group at the stage of late 3 months from the start of radiation treatment. Tables 6 and 7 show the allele frequency of the breast cancer patient group at the stage of 6 months late from the start of radiation therapy for breast cancer, and Tables 8 to 11 show the children at the early stage from the start of radiation therapy for cervical cancer. Table 12 shows the allele frequency of the cervical cancer patient group, Table 12 shows the allele frequency of the cervical cancer patient group at the stage of 6 months from the start of radiation therapy for cervical cancer, and Tables 13 and 14 show the prostate cancer. Table 15 and Table 16 show the allele frequency of the prostate cancer patient group in the early stage from the start of radiation therapy of The allele frequency of prostate cancer patients in stage, and, Table 17 and Table 18 represent respectively the allele frequencies of prostate cancer patients from radiation therapy initiation of prostate cancer in stage of late 6 months.

And the A column to the J column of Table 1 to Table 18 show the following contents.
Column A: SNP ID and genotype registered in the public data bank (NCBI or JSNP (IMS-JST SNP)) assigned to each SNP, that is, the confirmed allele frequency. For breast cancer, skin disorders, cervical cancer for intestinal disorders, and prostate cancer for urethral disorders were investigated.
In the genotype shown here, the upper allele indicates a risk allele, and the lower allele indicates a non-risk allele. Here, for example, C / C and G / G are homozygotes of C (cytosine) and C (cytosine) and G (guanine) and G (guanine) in alleles, / G indicates a heterozygote of C (cytosine) and G (guanine).
In addition, regarding the time of confirming side effects due to radiation therapy, early means that the disorder was observed in less than 3 months after radiation treatment, and late 3 months means within 6 months after 3 months after radiation therapy. The late 6 months means that the disorder was observed after 6 months from the radiation treatment.

  Note that the risk alleles involved may be reversed depending on the failure of interest. For example, at the rs25661829 site shown in Table 1, the C / C allele is a risk allele in the early stage after radiation therapy for breast cancer, but in the late 6-month stage after radiation treatment for prostate cancer shown in Table 17, The T / T allele and the T / C allele are risk alleles. Since the functional analysis of genes has not been completed at present, it is difficult to explain the occurrence of such a phenomenon, but this result is obtained when statistical analysis is performed. This is because the difference between risk alleles and non-risk alleles is that the vector (that is, the direction of gene transcription / translation) may be reversed depending on the function of the gene or protein that is expressed, the onset site, and the timing. It is thought that the balance of the expression level of sucrose affects. In addition to rs2561829, rs48818 (see Tables 3 and 4), rs791041 (see Tables 2 and 17), rs704227 (see Tables 12 and 15), rs2283264 (see Tables 2 and 15) Table 17), rs73234 (see Tables 2, 9 and 14), rs518116 (see Tables 3 and 12), rs1171097 (see Tables 1 and 15), rs791040 (see Tables 2 and 17), rs1145720 (see Table 17) Tables 3 and 18), rs1144153 (see Tables 2 and 17), rs2267437 (see Tables 1 and 8 and 13), rs2270390 (see Tables 12 and 16), rs20728817 (see Tables 7 and 8) Is mentioned.

Column B: Shows the number of cases (n) in which a disorder was observed after radiotherapy and its grade (Grades 1 to 4).
Column C: Shows the number of cases (n) in which no disorder was observed (Grade 0) or the disorder was minor (Grade 1).
The degree of the side effect is Grade 0, 1, 2, 3, 4, indicating that the larger the number, the more serious the side effect. Determination of side effects in the early stage was in accordance with NCI / CTC (National Cancer Institute, Common Toxicity Criteria) which is an international criterion. Moreover, the determination with respect to the side effect (disorder) in the stage of 3 months and 6 months from the start of radiation therapy followed RTOG (Radiation Therapy Oncology Group) which is an international determination standard. In addition, items are selected from the acquired clinical information according to the type of cancer. For example, for breast cancer, age, smoking, drinking, complications, family history, TNM classification, pathological examination, chemotherapy, irradiation method, relapse / metastasis, etc. 38 items were analyzed and standardized, and cases that did not meet the conditions were excluded from the polymorphism frequency analysis.

Column D: Shows the P value by Fisher's exact test (direct probability). Statistically in biology, if the P value is 0.05 or less, they can be evaluated as having a significant difference. In the present invention, all the degrees of freedom are 1.
Column E: indicates the relative risk. Relative risk is also called risk ratio or risk rate, and has a factor (determined by each risk allele or a combination of these risk alleles is radiosensitive (ie, there is a risk of developing side effects) The risk of developing side effects (disorders) is determined to have no factors (mostly no side effects and radiation insensitivity (ie no risk of developing side effects)) ) Divided by the risk of developing side effects. This relative risk indicates that the higher the value, the higher the risk of developing side effects.
Column F: indicates a 95% confidence interval. In each table, since allele frequency of a part of the sample is “0”, there is data in which the relative risk level and the 95% confidence interval cannot be obtained (“−” in Table 1 to Table 18). ).

Column G: shows the SEQ ID NO of the DNA oligomer for predicting the occurrence of side effects in the radiotherapy of the present invention having a risk allele.
Column H: shows the sequence number of the DNA oligomer (forward primer) used in PCR.
Column I: shows the sequence number of the DNA oligomer (reverse primer) used for PCR.
A DNA oligomer set consisting of one set of SEQ ID NOs shown in the H and I columns at each SNP site can be used as a primer set for PCR amplification.

  J column: Shows the sequence number of the DNA oligomer (extension primer) used when SNP typing was performed. Among the extension primers of the present invention, those having the DNA base sequence of the strand in the same direction as the DNA oligomer shown in SEQ ID NO: 1 to SEQ ID NO: 173 and those having the DNA base sequence of the strand in the opposite direction There is. In the case of the extension primer which is a strand in the reverse direction, the base complementary to the base added 3 ′ downstream of this is the 121st base (risk allele) shown in any one of SEQ ID NO: 1 to SEQ ID NO: 173 It corresponds to.

  Specifically, for example, the SNP ID: rs1171097 shown at the top of Table 1 indicates that the skin of breast cancer patients in the early stage (less than 3 months) after the start of radiation therapy is damaged. The genotype of the C / C homozygote (shown as “genotype” in column A in Tables 1 to 18; the same applies hereinafter) is a risk allele. ing. In this SNP, the G / G homozygote and the C / G heterozygote are non-risk alleles (column A).

If we look in more detail, the skin damage was recognized early from the start of radiotherapy (Grade 1, 2, 3). The total number of breast cancer patients was 135 (column B), and no skin damage was found (Grade 0). ) The total number of breast cancer patients was 12 (column C).
Here, the number of breast cancer patients with skin disorders who had C / C homozygotes was 88, whereas the breast cancer patients with no skin disorders showed G / G The number of people who had homozygotes or C / G heterozygotes was 47 (column B).
On the other hand, in breast cancer patients with no skin disorder, the number of patients who had C / C homozygotes was 3, whereas in breast cancer patients with no skin disorder, G / G The number of people who had homozygotes or C / G heterozygotes was 9 (column C).

  As a result of statistical analysis of these results by Fisher's exact test, it was found that a breast cancer patient has a homozygote of a C / C homozygote and a G / G homozygote or a C / G heterozygote. A significant difference (P value = 0.01041) could be obtained from those having the zygote (column D). The relative risk of the risk allele was 1.15 (E column), and the 95% confidence interval was 1.02-1.30 (F column).

And, the SEQ ID NO in which the DNA base sequence of the DNA oligomer having such a risk allele is described is SEQ ID NO: 16 (column G), and among the PCR amplification primers used for the amplification of the DNA base sequence, The sequence number of the forward primer is SEQ ID NO: 188 (column H), and the sequence number of the reverse primer is SEQ ID NO: 189 (column I). And the sequence number of the extension primer used in order to determine the DNA base of this SNP site (risk allele) is sequence number 487 (J column).
As mentioned above, although the table | surface shown by this invention was demonstrated with an example, this is common to all the SNPs shown in Table 1 to Table 18.

Next, the SNP typing method performed in the present invention will be described. SNP typing is performed by DNA extraction, DNA amplification, and determination of the DNA base sequence by mass spectrometry. Hereinafter, SNP typing will be described in detail.
(Extraction of DNA sample)
First, after obtaining informed consent from cancer patients undergoing radiation therapy and healthy individuals, blood was collected and DNA was extracted. Cancer patients are categorized by cancer type, and less than 3 months (early stage), 3 months (late 3 months stage), 6 months (late 6 months stage) from the start of radiation therapy. The incidence of side effects was observed and the severity was evaluated (see Tables 1 to 18). In general, a disorder due to a side effect that develops in less than 3 months from the start of treatment is referred to as an early disorder, and a disorder due to a side effect that occurs after 3 months from the start of treatment is referred to as a late disorder.
And extraction of DNA from the blood extract | collected from each said cancer patient was performed by the standard protocol attached to this apparatus using NA-3000 made from Kurabo Industries.

(Primer selection and preparation)
Each forward primer, reverse primer, and extension primer used for SNP typing are based on the information on SNP described in [3] above, primer 3.0 (http://frodo.wi.mit.edu/cgi -bin / primer3 / primer3_www.cgi) was used to select an appropriate range as appropriate. Each primer was synthesized by consigning to SIGMA GENOSYS (Sigma Aldrich Japan) or PROLIGO (Proligo Japan).

(SNP typing)
SNP typing was performed by the MALDI-TOF / MS method using the extracted DNA sample. In addition, MassARRAY system made from SEQUENOM was used for the mass spectrometer. SNP typing by the MALDI-TOF / MS method is performed according to the following procedures (1) to (3).
(1) DNA amplification:
A DNA oligomer appropriately selected from the forward primer and reverse primer shown in SEQ ID NO: 174 to SEQ ID NO: 519 in order to amplify a target base sequence using a DNA sample PCR reaction was performed using the set.
The reaction conditions for PCR are as follows. 0.5 μl of 10 × HotStar Taq buffer, 0.2 μl of MgCl ₂ , 0.04 μl of 25 mM dNTP, 1.0 μl of each 1 μM PCR primer, 0.02 μl of HotStar Taq solution, 1.0 μl Of DNA solution (2.5 ng / μl) and 2.24 μl of pure water were added to prepare a total of 5 μl of PCR reaction solution.
This PCR reaction solution was dispensed into a 384 well plate, and a PCR reaction was performed with a thermal cycler using the following program. After activation of HotStar Taq polymerase at 95 ° C. for 15 minutes, (a) heat denaturation conditions of double-stranded DNA: 95 ° C. for 20 seconds, (b) annealing conditions: 56 ° C. for 30 seconds, (c) Elongation conditions: 55 cycles of the reaction performed in the order of (a) to (c) at 72 ° C. for 1 minute, and finally, the extension reaction is performed at 72 ° C. for 3 minutes.

(2) SAP reaction:
For the dephosphorylation of DNA, SAP (Shrimp Alkaline Phosphatase) reaction was performed. As the SAP reaction solution, 0.17 μl of hME buffer solution, 0.3 μl of SAP solution, and 1.53 μl of pure water were added to make the total amount of 2.0 μl of SAP reaction solution after the previous PCR reaction. The reaction is carried out at 37 ° C. for 20 minutes and then at 85 ° C. for 5 minutes.

(3) Elongation reaction:
Subsequently, PCR reaction was performed using the extension primers shown in SEQ ID NO: 520 to SEQ ID NO: 692. This is for determining the base type of the DNA to be the SNP. As the composition of the reaction solution, 0.2 μl of dNTP / ddNTP mix, 0.054 μl of 100 μM extension primer, 0.018 μl of Thermo Sequenase and 1.728 μl of pure water were added to make a total amount of 2.0 μl. The reaction solution was added to a reaction solution (7 μl) obtained by mixing the previous PCR reaction solution and the SAP reaction solution, and a PCR product for analyzing SNP was obtained by performing a PCR reaction under the following PCR reaction conditions. First, after thermal denaturation of the double-stranded DNA for 2 minutes at 94 ° C. with a thermal cycler, (a) thermal denaturation condition of the double-stranded DNA: 94 ° C. for 5 seconds, (b) annealing condition: 52 ° C. 55 cycles of the reaction performed in the order of (a) to (c) for 5 seconds, (c) elongation condition: 72 ° C. for 5 seconds.

(4) Desalting treatment:
Thereafter, 3 mg of SpectroCEAN as a desalting resin and 16 μl of pure water were added per 9 ml of the reaction solution, and the reaction solution was desalted by incubation at room temperature for 10 minutes.

(5) Mass spectrometry:
About 0.01 μl of the total 25 μl of SNP typing reaction solution thus obtained was spotted on a spectro chip for mass spectrometry, mass spectrometry was performed, and DNA oligomers shown in SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing were used. SNP typing of the risk allele (121st base) was performed.

(Clinical application)
The clinical application of the DNA oligomer, gene marker, DNA oligomer set, and side effect onset prediction method according to the present invention is as follows.
For example, after obtaining informed consent for DNA diagnosis from a cancer patient who is going to receive radiation therapy, DNA is extracted from a sample such as blood collected from the patient, and amplified using a DNA oligomer set. Analysis, determination of the base at the SNP site, and collation with the DNA base sequence of the DNA oligomer according to the present invention, or SNP typing using a fluorescently labeled gene marker. Based on the above-mentioned corresponding risk allele or combination of risk alleles, the risk rate of occurrence of side effects after radiation treatment of this cancer patient is calculated. Then, the radiotherapy doctor of the cancer patient appropriately uses the calculated risk factor as an index to appropriately carry out a treatment plan such as holding a QOL by utilizing it in a management plan after treatment for the cancer patient. be able to. Also, in dose-increasing clinical studies, measures such as avoiding patients with a high risk of developing side effects can be taken.

  Thus, by using the DNA oligomer, gene marker, DNA oligomer set, and side effect onset prediction method of the present invention, a scientific basis is provided for the risk of side effects due to radiation that currently has no means of prediction. It is possible to make predictions.

It is a flowchart for demonstrating the side effect onset prediction method in the radiotherapy of this invention.

Claims (22)

A DNA oligomer for predicting that a side effect may occur in cancer radiotherapy by determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele. ,
In radiation therapy, wherein the DNA base sequence shown in any one of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing has at least 10 to 241 continuous DNA base sequences including the 121st base DNA oligomer for predicting the occurrence of side effects. A DNA oligomer for predicting that a side effect may occur in breast cancer radiotherapy by determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele,
SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 30, SEQ ID NO: 32 SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 91 , SEQ ID NO: 94, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 26, SEQ ID NO: 127, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 145, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 151, 121 of the DNA base sequence shown in SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 172, or SEQ ID NO: 173 A DNA oligomer for predicting the onset of side effects in radiation therapy, comprising a continuous DNA base sequence of at least 10 to 241 containing the base of A DNA oligomer for predicting that side effects may occur in cervical cancer radiotherapy by determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele. There,
SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42 , SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 72 SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 98, SEQ ID NO: 105, SEQ ID NO: 110, SEQ ID NO: 114, SEQ ID NO: 118 , SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 139, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 144, SEQ ID NO: 46, the 121st base in the DNA base sequence shown in SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 157, SEQ ID NO: 161, or SEQ ID NO: 171 A DNA oligomer for predicting the onset of side effects in radiation therapy, comprising a continuous DNA base sequence of at least 10 to 241 comprising It is a DNA oligomer for predicting that side effects may occur in prostate cancer radiotherapy by determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele. And
SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 21 SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 55, SEQ ID NO: 55 SEQ ID NO: 57, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 73, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 84, SEQ ID NO: 87, SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 99, SEQ ID NO: 100 , SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 151, SEQ ID NO: 156, SEQ ID NO: 158 The DNA base sequence shown in SEQ ID NO: 160, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 168, or SEQ ID NO: 169 has a continuous DNA base sequence of at least 10 to 241 including the 121st base. A DNA oligomer for predicting the onset of side effects in radiation therapy. By predicting whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is possible to predict that side effects may occur at an early stage from the start of radiation therapy for cancer. A DNA oligomer,
SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24 SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 44 SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72 , SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 2, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, Sequence number 117, Sequence number 118, Sequence number 120, Sequence number 121, Sequence number 126, Sequence number 127, Sequence number 129, Sequence number 132, Sequence number 134, Sequence number 137, Sequence number 138, Sequence number 140, Sequence number 141, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167 Adverse drug occurrence prediction in radiotherapy characterized by having at least 10 to 241 consecutive DNA base sequences including the 121st base for the DNA base sequence shown in SEQ ID NO: 168, SEQ ID NO: 169, or SEQ ID NO: 171 DNA oligomer. By determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is predicted that a side effect may occur in the stage 3 months after the start of radiation therapy for cancer DNA oligomer for
SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 53 , SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 69, SEQ ID NO: 77, SEQ ID NO: 87, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, Sequence SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 156 1 for the DNA base sequence shown in SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, or SEQ ID NO: 170, The first base including side effects develop predictive DNA oligomer in radiotherapy, characterized in that it comprises a contiguous DNA sequence of at least 10 to 241. By determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is predicted that a side effect may occur at the stage of 6 months from the start of radiation therapy for cancer. A DNA oligomer for
SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19 SEQ ID NO: 30, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: SEQ ID NO: 54, SEQ ID NO: 57, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 79, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84 SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 102, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 130, No. 131, SEQ ID NO: 135, SEQ ID NO: 139, SEQ ID NO: 142, SEQ ID NO: 155, SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 172, or 121st of the DNA base sequence shown in SEQ ID NO: 173 A DNA oligomer for predicting the onset of side effects in radiation therapy, comprising a base and a continuous DNA base sequence of at least 10 to 241. DNA for predicting that side effects may occur at an early stage from the start of radiation therapy for breast cancer by determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele An oligomer,
SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 32, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 59 , SEQ ID NO: 61, SEQ ID NO: 65, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 98, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 117, Sequence SEQ ID NO: 127, SEQ ID NO: 132, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 147, SEQ ID NO: 157, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, or SEQ ID NO: For the DNA base sequence shown in 167, a continuous DNA base sequence of at least 10 to 241 including the 121st base Side effects develop predictive DNA oligomer in radiotherapy, characterized in that it comprises. By predicting whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is possible to predict that side effects may occur at the stage 3 months later from the start of radiation therapy for breast cancer A DNA oligomer of
Sequence number 48, sequence number 49, sequence number 53, sequence number 58, sequence number 77, sequence number 108, sequence number 116, sequence number 126, sequence number 133, sequence number 136, sequence number 145, sequence number 148 of a sequence table Radiation characterized by having a continuous DNA base sequence of at least 10 to 241 including the 121st base in the DNA base sequence shown in SEQ ID NO: 151, SEQ ID NO: 159, SEQ ID NO: 162, or SEQ ID NO: 170 DNA oligomer for predicting the occurrence of side effects in treatment. By predicting whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is possible to predict that a side effect may occur at a stage 6 months later from the start of radiation therapy for breast cancer A DNA oligomer of
SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 30, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 67, SEQ ID NO: 74, SEQ ID NO: 82 The DNA base sequence represented by SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 97, SEQ ID NO: 172, or SEQ ID NO: 173 has a continuous DNA base sequence of at least 10 to 241 including the 121st base. A DNA oligomer for predicting the onset of side effects in radiation therapy. By determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is predicted that side effects may occur at an early stage from the start of radiation therapy for cervical cancer DNA oligomer for
SEQ ID NO: 2, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60 , SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, Sequence SEQ ID NO: 98, SEQ ID NO: 105, SEQ ID NO: 114, SEQ ID NO: 118, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 141, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 152 The 121st base in the DNA base sequence shown in SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 157, or SEQ ID NO: 171 Including, side effects develop predictive DNA oligomer in radiotherapy, characterized in that it comprises a contiguous DNA sequence of at least 10 to 241. By determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, there is a possibility that side effects may occur at the stage of 6 months from the start of radiation therapy for cervical cancer. A DNA oligomer for prediction,
SEQ ID NO: 6, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 68, SEQ ID NO: 83, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 139, SEQ ID NO: 142 A DNA oligomer for predicting the onset of side effects in radiotherapy, characterized by having at least 10 to 241 continuous DNA base sequence containing the 121st base for the DNA base sequence shown in SEQ ID NO: 155 or SEQ ID NO: 161 . To predict whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, and that side effects may occur at an early stage from the start of radiation therapy for prostate cancer A DNA oligomer of
SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 48, SEQ ID NO: 66, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 96, SEQ ID NO: 99 SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 120, SEQ ID NO: 126, SEQ ID NO: 151, SEQ ID NO: 158, SEQ ID NO: 168, or SEQ ID NO: 169, the DNA base sequence represented by SEQ ID NO: 169 contains the 121st base, at least 10 A DNA oligomer for predicting the occurrence of side effects in radiation therapy, characterized by having a continuous DNA base sequence of ˜241. By determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is predicted that side effects may occur in the stage of late 3 months from the start of radiation therapy for prostate cancer A DNA oligomer for
SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 55, SEQ ID NO: 69 , SEQ ID NO: 87, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, Sequence For predicting the onset of side effects in radiotherapy, characterized by having at least 10 to 241 continuous DNA base sequences including the 121st base in the DNA base sequence shown in No. 128, SEQ ID No. 156, or SEQ ID No. 160 DNA oligomer. By determining whether a specific base in a DNA base sequence is a risk allele or a non-risk allele, it is predicted that a side effect may occur at the stage 6 months later from the start of radiation therapy for prostate cancer A DNA oligomer for
SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39 SEQ ID NO: 40, SEQ ID NO: 47, SEQ ID NO: 57, SEQ ID NO: 73, SEQ ID NO: 79, SEQ ID NO: 84, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 102, SEQ ID NO: 107, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: For predicting the onset of side effects in radiotherapy characterized by having at least 10 to 241 continuous DNA base sequences including the 121st base in the DNA base sequence shown in No. 135, SEQ ID No. 164, or SEQ ID No. 166 DNA oligomer.   The DNA oligomer for predicting the onset of side effects according to any one of claims 1 to 15, wherein one or several bases other than the 121st base are deleted, substituted or added, or a complementary thereof A DNA oligomer for predicting the occurrence of side effects in radiation therapy, which is a DNA oligomer having a DNA base sequence.   A DNA oligomer for predicting the occurrence of side effects according to any one of claims 1 to 16, or a DNA oligomer that hybridizes with this DNA oligomer for predicting the occurrence of side effects under stringent conditions. A genetic marker for predicting the onset of side effects in radiotherapy.   A DNA oligomer set comprising two DNA oligomers sequentially from SEQ ID NO: 174 as a set among DNA oligomers having DNA base sequences represented by SEQ ID NO: 174 to SEQ ID NO: 519 in the sequence listing.   The DNA oligomer having the DNA base sequence shown in SEQ ID NO: 174 to SEQ ID NO: 519 of the sequence listing, or one or several bases of the DNA oligomer are deleted, substituted or added, 11. A DNA oligomer set according to 11.   DNA oligomer having the DNA base sequence shown in SEQ ID NO: 520 to SEQ ID NO: 692, or a DNA oligomer characterized in that one or several bases of the DNA oligomer are deleted, substituted or added . A method for predicting the onset of side effects in radiation therapy, comprising the following steps (a) to (g), wherein the determination is performed using the DNA oligomer shown in any one of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing.
(A) A step of preparing a DNA sample based on a sample collected from a cancer patient scheduled to undergo radiotherapy (b) Amplifying DNA based on the DNA sample prepared in the step (a) And (c) a step of performing an extension reaction using the DNA product amplified in the step (b) as a template to obtain a DNA oligomer as an extension product (d) obtained in the step (c) Step (e) for analyzing the DNA base sequence of the DNA oligomer, the base corresponding to the 121st position in the DNA base sequence of the DNA oligomer analyzed in the step (d), and the sequence from SEQ ID NO: 1 in the sequence listing Step (f) of collating with the 121st base of the DNA base sequence shown in any of No. 173 The allele having the base collated in the step (e) is a risk allele or a non-risk allele A step of predicting one of step (g) the result of judgment in the step of the (f) determining the onset risk of side effects from radiation in cancer patients scheduled to the radiation treatment is enforced The DNA base sequence shown in any one of SEQ ID NO: 1 to SEQ ID NO: 173 in the sequence listing to be verified in the step (e) is:
For predicting the occurrence of side effects in radiation therapy for breast cancer, SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 26 of the Sequence Listing. SEQ ID NO: 27, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 58, SEQ ID NO: 58 SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 82, SEQ ID NO: 85 SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 145 , SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 172, or Using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 173,
For predicting the occurrence of side effects in radiation therapy for cervical cancer, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, SEQ ID NO: 36, Sequence number 37, sequence number 39, sequence number 41, sequence number 42, sequence number 43, sequence number 44, sequence number 46, sequence number 52, sequence number 56, sequence number 60, sequence number 64, sequence number 65, sequence number 68, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 83, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 98, SEQ ID NO: 105, SEQ ID NO: 110, SEQ ID NO: 114, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 139 SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 157, SEQ ID NO: 161, or SEQ ID NO: Using the DNA base sequence of the DNA oligomer represented by No. 171
For predicting the occurrence of side effects in radiation therapy for prostate cancer, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, sequence of the Sequence Listing SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 45 , SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 73, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 84, SEQ ID NO: 87, SEQ ID NO: 92, Sequence No. 95, SEQ ID NO: 96, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 107, SEQ ID NO: 09, SEQ ID NO: 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 131, Using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 135, SEQ ID NO: 151, SEQ ID NO: 156, SEQ ID NO: 158, SEQ ID NO: 160, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 168, or SEQ ID NO: 169,
For predicting the occurrence of side effects in the early stage from the start of cancer radiotherapy, SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, sequence SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33 , SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 64, Sequence No. 65, SEQ ID NO: 66, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: No. 81, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 102, SEQ ID NO: 103 , SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO: 129 SEQ ID NO: 132, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151 SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: Issue 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 167, SEQ ID NO: 168, using a DNA nucleotide sequence of the DNA oligomer shown in SEQ ID NO: 169 or SEQ ID NO: 171,,
Regarding the onset of side effects at the stage of 3 months from the start of cancer radiotherapy, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, SEQ ID NO: 21 SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 58, SEQ ID NO: 69, SEQ ID NO: 77, SEQ ID NO: 87, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: SEQ ID NO: 104, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 133 , SEQ ID NO: 136, SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 60, using the DNA nucleotide sequence of the DNA oligomer shown in SEQ ID NO: 162 or SEQ ID NO: 170,,
Regarding the onset of side effects at the stage of 6 months from the start of cancer radiotherapy, SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 10 SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO: 57, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 73 SEQ ID NO: 74, SEQ ID NO: 79, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 102, SEQ ID NO: 107, SEQ ID NO: 110, SEQ ID NO: 119, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 139, SEQ ID NO: 142, SEQ ID NO: 155, SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 166 Using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 172 or SEQ ID NO: 173,
For predicting the occurrence of side effects in the early stage from the start of radiation therapy for breast cancer, SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 32, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 65, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 98, Sequence number 106, Sequence number 112, Sequence number 113, Sequence number 117, Sequence number 127, Sequence number 132, Sequence number 137, Sequence number 138, Sequence number 140, Sequence number 143, Sequence number 147, Sequence number 157, Sequence number 160, DN of DNA oligomer shown in SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, or SEQ ID NO: 167 With a base sequence,
For predicting the onset of side effects at the stage of late 3 months from the start of radiation therapy for breast cancer, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 58, SEQ ID NO: 77, SEQ ID NO: 108, SEQ ID NO: 116, Using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 126, SEQ ID NO: 133, SEQ ID NO: 136, SEQ ID NO: 145, SEQ ID NO: 148, SEQ ID NO: 151, SEQ ID NO: 159, SEQ ID NO: 162, or SEQ ID NO: 170,
For predicting the occurrence of side effects in the stage of 6 months from the start of radiation therapy for breast cancer, SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 30, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO: 60, Using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 67, SEQ ID NO: 74, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 97, SEQ ID NO: 172, or SEQ ID NO: 173 ,
Regarding the prediction of the occurrence of side effects in the early stage from the start of radiation therapy for cervical cancer, SEQ ID NO: 2, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 34, SEQ ID NO: 36 , SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 75, SEQ ID NO: 76, Sequence SEQ ID NO: 80, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 98, SEQ ID NO: 105, SEQ ID NO: 114, SEQ ID NO: 118, SEQ ID NO: 121, SEQ ID NO: 129, SEQ ID NO: 134, SEQ ID NO: 141 , SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: Using a DNA nucleotide sequence of the DNA oligomer shown in 157 or SEQ ID NO: 171,,
For predicting the occurrence of side effects at the stage of 6 months from the start of radiation therapy for cervical cancer, SEQ ID NO: 6, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 46, SEQ ID NO. Using the DNA base sequence of the DNA oligomer shown in No. 68, SEQ ID No. 83, SEQ ID No. 110, SEQ ID No. 119, SEQ ID No. 139, SEQ ID No. 142, SEQ ID No. 155, or SEQ ID No. 161,
For predicting the onset of side effects in the early stage from the start of radiation therapy for prostate cancer, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 48, SEQ ID NO: 66, SEQ ID NO: 81, SEQ ID NO: 92, SEQ ID NO: 96, SEQ ID NO: 99, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 120, SEQ ID NO: 126, SEQ ID NO: 151, SEQ ID NO: 158, SEQ ID NO: 168, or SEQ ID NO: Using the DNA base sequence of the DNA oligomer represented by No. 169,
Regarding the prediction of the onset of side effects at the stage of late 3 months from the start of radiation therapy for prostate cancer, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 45, SEQ ID NO: 48, SEQ ID NO: 55, SEQ ID NO: 69, SEQ ID NO: 87, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 104, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 115, Using the DNA base sequence of the DNA oligomer shown in SEQ ID NO: 116, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 128, SEQ ID NO: 156, or SEQ ID NO: 160,
Regarding the prediction of the occurrence of side effects at the stage of 6 months from the start of radiation therapy for prostate cancer, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 19, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 47, SEQ ID NO: 57, SEQ ID NO: 73, SEQ ID NO: 79, SEQ ID NO: 84, SEQ ID NO: 95, The DNA base sequence of the DNA oligomer shown in SEQ ID NO: 96, SEQ ID NO: 102, SEQ ID NO: 107, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 135, SEQ ID NO: 164, or SEQ ID NO: 166 is used.
The method for predicting the onset of side effects in radiation therapy according to claim 21.

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