WO2021135072A1 - Probe and detection kit for detecting lung cancer driving gene mutation - Google Patents

Probe and detection kit for detecting lung cancer driving gene mutation Download PDF

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WO2021135072A1
WO2021135072A1 PCT/CN2020/094277 CN2020094277W WO2021135072A1 WO 2021135072 A1 WO2021135072 A1 WO 2021135072A1 CN 2020094277 W CN2020094277 W CN 2020094277W WO 2021135072 A1 WO2021135072 A1 WO 2021135072A1
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lung cancer
sequence
probe
probes
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李明定
杜文娟
赵俊生
王丹丹
张学文
徐怡
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浙江大学
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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Definitions

  • the invention relates to a cancer gene detection method, in particular to a probe and a detection kit for detecting lung cancer driving gene mutations.
  • the global incidence and mortality of lung cancer ranks first among all cancer types, and it is increasing year by year.
  • the global incidence of lung cancer accounts for 11.6% of the total cancer population, and the mortality rate accounts for 11.6% of the total cancer population. 18.4% of the total cancer population.
  • the incidence of lung cancer ranks first among all cancers, with an incidence of 787,000.
  • the incidence is relatively high; among women, the incidence of lung cancer is second only to breast cancer, ranking second.
  • the mortality rate of lung cancer in both men and women ranks first among cancer deaths, causing a serious burden on patients and society.
  • it has been discovered that human tumors are very different.
  • driver gene was introduced by Professor Wu Yilong, deputy dean of Guangdong Provincial People's Hospital at the Asian Cancer Conference in 2012. He pointed out that genes related to the occurrence and development of cancer can be called driver genes, which determine the main cause of this cancer.
  • driver gene we know which drugs can be used to combat it, and then we can carry out individualized treatment. It is precisely because of this huge change in concept that genetic testing and individualized treatment of tumors have attracted more and more attention, and they have developed rapidly in just a few years.
  • NGS Next Generation Sequencing
  • Illumina's Hiseq, Miseq, Nextseq series and Life's Ion Torrent TM series sequencers are mainly represented by Illumina's Hiseq, Miseq, Nextseq series and Life's Ion Torrent TM series sequencers. It is widely used in biological research, prenatal diagnosis, genetic diagnosis and treatment. However, cancer patients often carry a small piece of gene change or a single base change. If you choose whole genome sequencing, it will cause a waste of cost and bring a heavier economic burden to the patient.
  • the application of target sequence capture sequencing technology solves the above problems. This technology can customize the genomic region of interest into specific probes to hybridize with genomic DNA, enrich the DNA fragments of the target genomic region and then use second-generation sequencing Technology for sequencing.
  • this method Compared with traditional polymerase chain reaction (PCR) and gene chips, this method has high throughput and high accuracy, and can detect known and unknown genes at one time, and can effectively detect high-frequency mutations and low-frequency or even low-frequency mutations in samples. Ultra-low frequency mutation.
  • driver genes such as EGFR, KRAS, BRAF, MET, NRAS, PIK3CA, etc.
  • chemotherapeutic-related genes such as TP53 and UGT1A1.
  • Common targeted drugs are: EGFR target drug-gefitinib, erlotinib, icotinib, afatinib, osimertinib, AZD9291; MET target drug-Secure; BRAF target drug-Da Rafinis.
  • Chemotherapy drugs such as: irinotecan, 5-FU, capecitabine, platinum drugs, etc.
  • the most commonly used clinical gene mutation detection methods include Sanger sequencing technology, fluorescence in situ hybridization (FISH), amplification hindered mutation system technology (ARMS-PCR), fluorescent PCR technology, etc.
  • Sanger sequencing technology as the gold standard for genetic testing, is mainly used to find specific gene mutations related to diseases. It is difficult to complete the screening of large sample cases without clear candidate genes or with a large number of candidate genes. Fluorescence quantitative PCR detection of the target gene only needs to detect whether the sample has an amplification signal, which can detect small mutations, but the throughput is low.
  • ARMS-PCR technology can be used to detect known mutant genes, but it is not feasible for unknown mutant genes.
  • FISH technology uses several different colors of fluorescein alone or mixed-labeled probes for in situ hybridization, it can detect multiple genes at the same time, but it is still limited in the detection of a large number of sites.
  • the invention provides a probe and a detection kit for detecting lung cancer driving gene mutations. It can be combined to detect multiple mutations of lung cancer genes, which greatly saves patients' samples and waiting time for testing, provides a basis and guidance for individualized treatment of lung cancer patients, and can also monitor the efficacy and predict prognosis after treatment.
  • the purpose of the present invention is to provide a probe and a detection kit for detecting lung cancer driving gene mutations, including probes for BRAF, EGFR, KRAS, MET, NRAS and PIK3CA driving gene mutations and TP53 and UGT1A1 chemotherapeutic drugs related Gene probes, through the detection of these genes to achieve individualized treatment of lung cancer and predict prognosis,
  • the present invention provides a probe for detecting lung cancer driving gene mutations, including the following 6 groups of 248 probes:
  • BRAF driver mutation specific probe sequence its sequence is SEQ ID NO.1 to SEQ ID NO.3;
  • EGFR driver mutation specific probe sequence its sequence is SEQ ID NO.4 to SEQ ID NO.98;
  • KRAS driver mutation specific probe sequence its sequence is SEQ ID NO.99 to SEQ ID NO.148;
  • MET driver mutation specific probe sequence its sequence is SEQ ID NO.149 to SEQ ID NO.150;
  • NRAS driver mutation specific probe sequence its sequence is SEQ ID NO.151 to SEQ ID NO.193;
  • PIK3CA driver mutation specific probe sequence its sequence is SEQ ID NO.194 to SEQ ID NO.248;
  • TP53 specific probe nucleotide sequence its sequence is SEQ ID NO.249 to SEQ ID NO.272;
  • UGT1A1 specific probe sequence its sequence is SEQ ID NO.273 to SEQ ID NO.276.
  • the medication guidance program of the detection kit includes: BRAF, EGFR, KRAS, MET, NRAS, PIK3CA driving gene mutations and TP53 and UGT1A1 chemotherapy drug-related gene mutations.
  • BRAF BRAF
  • EGFR BRAF inhibitor dabrafenib
  • MEK inhibitor trametinib MEK inhibitor trametinib
  • BRAF G466V, G469A, Y472C and other non-V600E mutations may not be sensitive to current selective BRAF inhibitors.
  • Non-small cell lung cancer carrying EGFR activating mutations (such as exons 18, 19, 20 and 21) are sensitive to the first and second generation EGFR-TKIs.
  • Non-small cell lung cancer with EGFR T790M mutation may be resistant to the first and second generation EGFR-TKI, but sensitive to the third generation EGFR-TKI.
  • Non-small cell lung cancer carrying EGFR 20 exon insertion mutation may not be sensitive to existing EGFR-TKI.
  • Lung squamous cell carcinoma carrying EGFR amplification may be more sensitive to anti-EGFR antibody combined with chemotherapy vs. chemotherapy alone.
  • Non-small cell lung cancer with KRAS mutation may be resistant to current targeted therapies such as EGFR-TKI.
  • Advanced non-small cell lung cancer carrying variable splicing mutations in exon 14 of MET is sensitive to MET inhibitors.
  • Non-small cell lung cancer with high-level amplification of MET copy number may be sensitive to MET inhibitors.
  • Those with NRAS mutations may be sensitive to MEK inhibitors.
  • the rs1042522 locus of TP53 can predict the sensitivity to cisplatin, capecitabine, paclitaxel and oxaliplatin.
  • rs8175347 and rs4148323 of UGT1A1 can predict the risk of side effects to irinotecan.
  • the present invention also provides a detection kit for detecting lung cancer driving gene mutations, which includes the above-mentioned 6 groups of 248 probes and 2 groups of 28 probes.
  • the probe provided by the present invention has high specificity, good accuracy, and the minimum detection limit can reach 0.1%. It can provide medication basis for lung cancer patients who are looking for targeted therapy drugs; it can also change the treatment plan for lung cancer patients who have severe toxic side effects and drug resistance during the treatment process.
  • the form of the sample in the present invention is any form of tumor sample from which nucleic acid can be extracted.
  • whole blood samples are preferred, including but not limited to tissue samples, puncture samples, serum and plasma; and tissue samples include but not limited to paraffin-embedded tissue, Fresh tissue and frozen sectioned tissue.
  • genes related to lung cancer were screened from NCCN guidelines, COSMIC database, and drug-related databases.
  • the specific genes are as follows: BRAF, EGFR, KRAS, MET, NRAS, PIK3CA, TP53 and UGT1A1.
  • the probe sequence refers to SEQ ID NO.1-SEQ ID NO.276.
  • the method of constructing a library and hybridizing and capturing is adopted to verify the probes involved in the present invention, and the specific steps are as follows:
  • 1.3.2.2 Take 300ng of gDNA and add it to the interrupted tube, use 1x IDTE Buffer to make up to 80 ⁇ L, vortex to mix, and centrifuge for 1-3s.
  • Agilent 2200 detects the fragment size of the broken DNA (generally 200-300bp).
  • step 2.3.3 Place the 1.5mL centrifuge tube of step 2.3.2 on the magnetic stand and let it stand until the solution is completely clear. Aspirate and discard the supernatant, taking care to avoid attracting the magnetic beads.
  • step 2.5.3 Place the 1.5mL centrifuge tube of step 2.5.2 on the magnetic stand, and let it stand until the solution is completely clear. Discard the supernatant, taking care to avoid attracting the magnetic beads.
  • Hybridization Master Mix component Volume per reaction( ⁇ L) xGen 2X Hybridization Buffer 8.5 xGen Hybridization Buffer Enhancer 2.7 xGen Lockdown Panel or custom probes 4 Nuclease-Free Water 1.8 Total 17
  • step 4.2.2 Quickly transfer all the hybridized samples to the 0.2mL PCR tube containing Bead Resuspension Mix in step 4.1.4, pipette to mix and centrifuge.
  • the main quality control of the two patient samples is shown in Table 1: DNA quality evaluation and sequencing quality evaluation are both qualified, and the next step data analysis can be carried out.
  • the data analysis results of lung cancer patients and standard products are as follows:
  • the results of sequencing data analysis of another lung cancer patient showed that the genotype at the rs8175347 locus (*28) of the UGT1A1 gene was heterozygous, indicating that the use of irinotecan had a greater risk of side effects; the genotype at the rs1042522 locus of the TP53 gene was heterozygous.
  • the combined type suggests that the sensitivity of using cisplatin, capecitabine, paclitaxel, and oxaliplatin may be low.

Abstract

Disclosed in the present invention are a probe and a detection kit for detecting a lung cancer driving gene mutation. The probe comprises probes for BRAF, EGFR, KRAS, MET, NRAS and PIK3CA driving gene mutation, and probes for TP53 and UGT1A1 chemotherapy drug-related gene, and the total number of the probes is 276. The minimum detection limit of the probe provided by the present invention can reach 0.1%. The present invention can provide medication basis for lung cancer patients looking for targeted therapeutic drugs; and can also change therapeutic regimen for lung cancer patients experiencing severe toxic and side effects, drug resistance, and the like in the therapeutic process.

Description

用于检测肺癌驱动性基因突变的探针及检测试剂盒Probe and detection kit for detecting lung cancer driving gene mutation 技术领域Technical field
本发明涉及癌症基因检测方法,尤其涉及一种用于检测肺癌驱动性基因突变的探针及检测试剂盒。The invention relates to a cancer gene detection method, in particular to a probe and a detection kit for detecting lung cancer driving gene mutations.
背景技术Background technique
根据2018年世界癌症报告数据统计显示,全球肺癌的发病率和致死率在所有癌种中排首位,且逐年呈上升趋势,其中肺癌的全球发病率占癌症总发病人口的11.6%,致死率占癌症总发病人口的18.4%。在中国,肺癌的发病数位居所有癌症的榜首,发病数达78.7万。在男性中,发病比例较高;在女性中,肺癌的发病率仅次于乳腺癌,位居第二。但男女肺癌的死亡率均居癌症死亡榜首,对患者及社会造成了严重的负担。在临床肿瘤治疗过程中发现,人体肿瘤千差万别,即使是同一个部位的肿瘤,治疗效果和方法也应因人而异。此外,肿瘤的异质性高,即使是同一个人的同一部位的肿瘤也有可能包含了多种突变类型的肿瘤细胞,所以给临床治疗带来了很大的挑战。“驱动基因”这一名词的出现是在2012年亚洲肿瘤大会上,广东省人民医院副院长吴一龙教授提出的。他指出与癌症发生发展相关的基因可称为驱动基因,其决定了这个癌症的最主要原因。我们知道了驱动基因,就知道可以采用哪些药物来对抗它,就可以进行个体化治疗。也正是由于这种观念上的巨大改变,基因检测及肿瘤的个体化治疗越来越广泛的引起重视,短短几年之间发展飞速。According to the statistics of the 2018 World Cancer Report, the global incidence and mortality of lung cancer ranks first among all cancer types, and it is increasing year by year. Among them, the global incidence of lung cancer accounts for 11.6% of the total cancer population, and the mortality rate accounts for 11.6% of the total cancer population. 18.4% of the total cancer population. In China, the incidence of lung cancer ranks first among all cancers, with an incidence of 787,000. Among men, the incidence is relatively high; among women, the incidence of lung cancer is second only to breast cancer, ranking second. However, the mortality rate of lung cancer in both men and women ranks first among cancer deaths, causing a serious burden on patients and society. In the process of clinical tumor treatment, it has been discovered that human tumors are very different. Even if it is a tumor at the same site, the treatment effect and method should be different from person to person. In addition, the heterogeneity of tumors is high. Even tumors in the same part of the same person may contain tumor cells of multiple mutation types, which brings great challenges to clinical treatment. The term "driver gene" was introduced by Professor Wu Yilong, deputy dean of Guangdong Provincial People's Hospital at the Asian Cancer Conference in 2012. He pointed out that genes related to the occurrence and development of cancer can be called driver genes, which determine the main cause of this cancer. When we know the driver gene, we know which drugs can be used to combat it, and then we can carry out individualized treatment. It is precisely because of this huge change in concept that genetic testing and individualized treatment of tumors have attracted more and more attention, and they have developed rapidly in just a few years.
基因检测技术主要依赖于高通量测序仪,目前第二代测序(Next Generation Sequencing,NGS)平台主要以Illumina公司的Hiseq,Miseq,Nextseq系列及Life公司的Ion Torrent TM系列测序仪为代表,已被广泛应用于生物学研究、产前诊断、基因诊断和治疗方面。然而肿瘤患者往往携带的是一小片段基因的改变或单个碱基的改变,如果选择全基因组测序会造成成本的浪费,且给患者带来更沉重的经济负担。目标序列捕获测序技术的应用解决了上述问题,该技术可将感兴趣的基因组区域定制成特异性探针与基因组DNA进行杂交,将目标基因组区域的DNA片段进行富集后再利用第二代测序技术进行测序。这种方法与传统聚合酶链式反应(PCR)及基因芯片相比,通量高,准确度高,且可一次性检测已知和未知基因,可以有效检测到样本的高频突变及低频甚至超低频突变。 Gene detection technology mainly relies on high-throughput sequencers. At present, Next Generation Sequencing (NGS) platforms are mainly represented by Illumina's Hiseq, Miseq, Nextseq series and Life's Ion Torrent TM series sequencers. It is widely used in biological research, prenatal diagnosis, genetic diagnosis and treatment. However, cancer patients often carry a small piece of gene change or a single base change. If you choose whole genome sequencing, it will cause a waste of cost and bring a heavier economic burden to the patient. The application of target sequence capture sequencing technology solves the above problems. This technology can customize the genomic region of interest into specific probes to hybridize with genomic DNA, enrich the DNA fragments of the target genomic region and then use second-generation sequencing Technology for sequencing. Compared with traditional polymerase chain reaction (PCR) and gene chips, this method has high throughput and high accuracy, and can detect known and unknown genes at one time, and can effectively detect high-frequency mutations and low-frequency or even low-frequency mutations in samples. Ultra-low frequency mutation.
随着对肺癌基因层面的深入研究,越来越多的与肺癌相关的驱动基因被挖掘,进而开发出多种靶向特异基因突变的药物。目前已知驱动基因如EGFR、KRAS、BRAF、MET、NRAS、PIK3CA等等,还有化疗药的相关基因如TP53和UGT1A1等。常见靶向药物有:EGFR靶药 -吉非替尼、厄洛替尼、埃克替尼、阿法替尼、奥希替尼、AZD9291;MET靶药-赛可瑞;BRAF靶药-达拉非尼。化疗药物如:伊立替康、5-FU、卡培他滨、铂类药物等。With in-depth research on lung cancer genes, more and more driver genes related to lung cancer have been discovered, and a variety of drugs targeting specific gene mutations have been developed. Currently known driver genes such as EGFR, KRAS, BRAF, MET, NRAS, PIK3CA, etc., as well as chemotherapeutic-related genes such as TP53 and UGT1A1. Common targeted drugs are: EGFR target drug-gefitinib, erlotinib, icotinib, afatinib, osimertinib, AZD9291; MET target drug-Secure; BRAF target drug-Da Rafinis. Chemotherapy drugs such as: irinotecan, 5-FU, capecitabine, platinum drugs, etc.
目前,临床上最常用的基因突变检测方法有Sanger测序技术、荧光原位杂交技术(FISH),扩增阻碍突变系统技术(ARMS-PCR)、荧光PCR技术等。Sanger测序技术作为基因检测的金标准,主要用于寻找与疾病有关的特定的基因突变,难以完成没有明确候选基因或候选基因数量较多的大样本病例的筛查。荧光定量PCR检测目的基因仅需检测样本是否具有扩增信号即可,可检测微小突变,但通量低。ARMS-PCR技术可用于对已知突变基因进行检测,对未知突变基因不可行。FISH技术虽然采用几种不同颜色的荧光素单独或者混合标记的探针进行原位杂交,能同时检测多个基因,但在进行大量位点的检测仍然有限。At present, the most commonly used clinical gene mutation detection methods include Sanger sequencing technology, fluorescence in situ hybridization (FISH), amplification hindered mutation system technology (ARMS-PCR), fluorescent PCR technology, etc. Sanger sequencing technology, as the gold standard for genetic testing, is mainly used to find specific gene mutations related to diseases. It is difficult to complete the screening of large sample cases without clear candidate genes or with a large number of candidate genes. Fluorescence quantitative PCR detection of the target gene only needs to detect whether the sample has an amplification signal, which can detect small mutations, but the throughput is low. ARMS-PCR technology can be used to detect known mutant genes, but it is not feasible for unknown mutant genes. Although FISH technology uses several different colors of fluorescein alone or mixed-labeled probes for in situ hybridization, it can detect multiple genes at the same time, but it is still limited in the detection of a large number of sites.
本发明提供的一种用于检测肺癌驱动性基因突变的探针及检测试剂盒。可以联合检测肺癌多种基因的突变,大大节省了患者的样本和等待检测的时间,为肺癌患者的个体化治疗提供一种依据和指导,同时也可监测治疗后的疗效及预测预后。The invention provides a probe and a detection kit for detecting lung cancer driving gene mutations. It can be combined to detect multiple mutations of lung cancer genes, which greatly saves patients' samples and waiting time for testing, provides a basis and guidance for individualized treatment of lung cancer patients, and can also monitor the efficacy and predict prognosis after treatment.
发明内容Summary of the invention
本发明的目的在于提供一种用于检测肺癌驱动性基因突变的探针及检测试剂盒,包括BRAF、EGFR、KRAS、MET、NRAS和PIK3CA驱动性基因突变的探针及TP53和UGT1A1化疗药物相关基因的探针,通过对这些基因的检测实现肺癌的个体化治疗和预测预后,The purpose of the present invention is to provide a probe and a detection kit for detecting lung cancer driving gene mutations, including probes for BRAF, EGFR, KRAS, MET, NRAS and PIK3CA driving gene mutations and TP53 and UGT1A1 chemotherapeutic drugs related Gene probes, through the detection of these genes to achieve individualized treatment of lung cancer and predict prognosis,
本发明提供的一种用于检测肺癌驱动性基因突变的探针,包括下列6组共248条探针:The present invention provides a probe for detecting lung cancer driving gene mutations, including the following 6 groups of 248 probes:
BRAF驱动突变特异性探针序列:其序列为SEQ ID NO.1至SEQ ID NO.3;BRAF driver mutation specific probe sequence: its sequence is SEQ ID NO.1 to SEQ ID NO.3;
EGFR驱动突变特异性探针序列:其序列为SEQ ID NO.4至SEQ ID NO.98;EGFR driver mutation specific probe sequence: its sequence is SEQ ID NO.4 to SEQ ID NO.98;
KRAS驱动突变特异性探针序列:其序列为SEQ ID NO.99至SEQ ID NO.148;KRAS driver mutation specific probe sequence: its sequence is SEQ ID NO.99 to SEQ ID NO.148;
MET驱动突变特异性探针序列:其序列为SEQ ID NO.149至SEQ ID NO.150;MET driver mutation specific probe sequence: its sequence is SEQ ID NO.149 to SEQ ID NO.150;
NRAS驱动突变特异性探针序列:其序列为SEQ ID NO.151至SEQ ID NO.193;NRAS driver mutation specific probe sequence: its sequence is SEQ ID NO.151 to SEQ ID NO.193;
PIK3CA驱动突变特异性探针序列:其序列为SEQ ID NO.194至SEQ ID NO.248;PIK3CA driver mutation specific probe sequence: its sequence is SEQ ID NO.194 to SEQ ID NO.248;
还包括下列2组共28条探针:It also includes 28 probes in the following 2 groups:
TP53特异性探针核苷酸序列:其序列为SEQ ID NO.249至SEQ ID NO.272;TP53 specific probe nucleotide sequence: its sequence is SEQ ID NO.249 to SEQ ID NO.272;
UGT1A1特异性探针序列:其序列为SEQ ID NO.273至SEQ ID NO.276。UGT1A1 specific probe sequence: its sequence is SEQ ID NO.273 to SEQ ID NO.276.
以上特异性探针的序列具体如下:The sequence of the above specific probe is as follows:
1.BRAF驱动突变探针序列1. BRAF driver mutation probe sequence
Figure PCTCN2020094277-appb-000001
Figure PCTCN2020094277-appb-000001
Figure PCTCN2020094277-appb-000002
Figure PCTCN2020094277-appb-000002
2.EGFR驱动突变探针序列2. EGFR driver mutation probe sequence
Figure PCTCN2020094277-appb-000003
Figure PCTCN2020094277-appb-000003
Figure PCTCN2020094277-appb-000004
Figure PCTCN2020094277-appb-000004
Figure PCTCN2020094277-appb-000005
Figure PCTCN2020094277-appb-000005
Figure PCTCN2020094277-appb-000006
Figure PCTCN2020094277-appb-000006
Figure PCTCN2020094277-appb-000007
Figure PCTCN2020094277-appb-000007
Figure PCTCN2020094277-appb-000008
Figure PCTCN2020094277-appb-000008
Figure PCTCN2020094277-appb-000009
Figure PCTCN2020094277-appb-000009
3.KRAS驱动突变探针序列3. KRAS driver mutation probe sequence
Figure PCTCN2020094277-appb-000010
Figure PCTCN2020094277-appb-000010
Figure PCTCN2020094277-appb-000011
Figure PCTCN2020094277-appb-000011
Figure PCTCN2020094277-appb-000012
Figure PCTCN2020094277-appb-000012
Figure PCTCN2020094277-appb-000013
Figure PCTCN2020094277-appb-000013
4.MET驱动突变探针序列4. MET driver mutation probe sequence
Figure PCTCN2020094277-appb-000014
Figure PCTCN2020094277-appb-000014
5.NRAS驱动突变探针序列5. NRAS driver mutation probe sequence
Figure PCTCN2020094277-appb-000015
Figure PCTCN2020094277-appb-000015
Figure PCTCN2020094277-appb-000016
Figure PCTCN2020094277-appb-000016
Figure PCTCN2020094277-appb-000017
Figure PCTCN2020094277-appb-000017
Figure PCTCN2020094277-appb-000018
Figure PCTCN2020094277-appb-000018
6.PIK3CA驱动突变探针序列6. PIK3CA driver mutation probe sequence
Figure PCTCN2020094277-appb-000019
Figure PCTCN2020094277-appb-000019
Figure PCTCN2020094277-appb-000020
Figure PCTCN2020094277-appb-000020
Figure PCTCN2020094277-appb-000021
Figure PCTCN2020094277-appb-000021
Figure PCTCN2020094277-appb-000022
Figure PCTCN2020094277-appb-000022
Figure PCTCN2020094277-appb-000023
Figure PCTCN2020094277-appb-000023
7.TP53化疗药物基因探针7. TP53 chemotherapeutic drug gene probe
Figure PCTCN2020094277-appb-000024
Figure PCTCN2020094277-appb-000024
Figure PCTCN2020094277-appb-000025
Figure PCTCN2020094277-appb-000025
8.UGT1A1化疗药物基因探针8. UGT1A1 chemotherapeutic drug gene probe
Figure PCTCN2020094277-appb-000026
Figure PCTCN2020094277-appb-000026
Figure PCTCN2020094277-appb-000027
Figure PCTCN2020094277-appb-000027
该检测试剂盒的用药指导方案,包括:BRAF、EGFR、KRAS、MET、NRAS、PIK3CA驱动性基因突变及TP53和UGT1A1化疗药物相关基因突变的用药指导方案。(1)携带BRAF V600E突变的非小细胞肺癌对BRAF抑制剂达拉非尼联合MEK抑制剂曲美替尼敏感。但携带BRAF G466V、G469A、Y472C等非V600E突变的非小细胞肺癌可能对当前选择性BRAF抑制剂不敏感。(2)携带EGFR活化突变(如外显子18、19、20和21)的非小细胞肺癌对第一代和第二代EGFR-TKI敏感。携带EGFR T790M突变的非小细胞肺癌可能对第一代和第二代EGFR-TKI耐药,但对第三代EGFR-TKI敏感。携带EGFR20号外显子插入突变的非小细胞肺癌可能对现有EGFR-TKI都不敏感。携带EGFR扩增的肺鳞癌可能对抗EGFR抗体联合化疗VS单纯化疗更加敏感。(3)携带KRAS突变的非小细胞肺癌可能对EGFR-TKI等目前靶向治疗药物耐药。(4)携带MET14号外显子可变剪切突变的晚期非小细胞肺癌对MET抑制剂敏感。携带MET拷贝数高水平扩增的非小细胞肺癌可能对MET抑制剂敏感。(5)携带NRAS突变的可能对MEK抑制剂敏感。(6)携带PIK3CA基因突变(如外显子9和20),主要靶向药是brparlisib(BKM120)。如果PIK3CA发生激活突变,则可能对EGFR靶点、HER2靶点耐药,赫赛汀和易瑞沙、特罗凯效果欠佳。(7)TP53的rs1042522位点可预测对顺铂、卡培他滨、紫杉醇和奥沙利铂的敏感性。(8)UGT1A1的rs8175347和rs4148323可预测对伊立替康的毒副作用风险的高低。The medication guidance program of the detection kit includes: BRAF, EGFR, KRAS, MET, NRAS, PIK3CA driving gene mutations and TP53 and UGT1A1 chemotherapy drug-related gene mutations. (1) Non-small cell lung cancer with BRAF V600E mutation is sensitive to BRAF inhibitor dabrafenib combined with MEK inhibitor trametinib. However, non-small cell lung cancer carrying BRAF G466V, G469A, Y472C and other non-V600E mutations may not be sensitive to current selective BRAF inhibitors. (2) Non-small cell lung cancer carrying EGFR activating mutations (such as exons 18, 19, 20 and 21) are sensitive to the first and second generation EGFR-TKIs. Non-small cell lung cancer with EGFR T790M mutation may be resistant to the first and second generation EGFR-TKI, but sensitive to the third generation EGFR-TKI. Non-small cell lung cancer carrying EGFR 20 exon insertion mutation may not be sensitive to existing EGFR-TKI. Lung squamous cell carcinoma carrying EGFR amplification may be more sensitive to anti-EGFR antibody combined with chemotherapy vs. chemotherapy alone. (3) Non-small cell lung cancer with KRAS mutation may be resistant to current targeted therapies such as EGFR-TKI. (4) Advanced non-small cell lung cancer carrying variable splicing mutations in exon 14 of MET is sensitive to MET inhibitors. Non-small cell lung cancer with high-level amplification of MET copy number may be sensitive to MET inhibitors. (5) Those with NRAS mutations may be sensitive to MEK inhibitors. (6) Carrying PIK3CA gene mutations (such as exons 9 and 20), the main target drug is brparlisib (BKM120). If PIK3CA has an activating mutation, it may be resistant to EGFR and HER2 targets, and Herceptin, Iressa, and Tarceva are not effective. (7) The rs1042522 locus of TP53 can predict the sensitivity to cisplatin, capecitabine, paclitaxel and oxaliplatin. (8) rs8175347 and rs4148323 of UGT1A1 can predict the risk of side effects to irinotecan.
本发明还提供一种检测肺癌驱动性基因突变的检测试剂盒,包括:上述的6组共248条探针和2组共28条探针。The present invention also provides a detection kit for detecting lung cancer driving gene mutations, which includes the above-mentioned 6 groups of 248 probes and 2 groups of 28 probes.
本发明的有益效果是:本发明提供的探针特异性高,准确性好,最低检测限可达0.1%。可为寻找靶向治疗药物的肺癌患者提供用药依据;还可以为治疗过程中发生严重毒副作用、耐药等的肺癌患者更换治疗方案。The beneficial effects of the present invention are: the probe provided by the present invention has high specificity, good accuracy, and the minimum detection limit can reach 0.1%. It can provide medication basis for lung cancer patients who are looking for targeted therapy drugs; it can also change the treatment plan for lung cancer patients who have severe toxic side effects and drug resistance during the treatment process.
具体实施方式Detailed ways
下面通过具体实施例对本发明进行描述,应当指出的是下面实施例只用于对本发明的进一步说明,但并不能用作对本发明保护范围的限制,本领域的技术人员应当理解,基于本发明的技术前提下,做出的改进和变型也视为本发明的保护范围。The present invention is described below through specific examples. It should be noted that the following examples are only used to further illustrate the present invention, but cannot be used to limit the scope of protection of the present invention. Those skilled in the art should understand that based on the present invention Under the technical premise, improvements and modifications made are also regarded as the protection scope of the present invention.
本实施例中检测2例肺癌患者的新鲜全血样本及3种不同突变频率的标准品(0.1%、1%和5%)。本发明中样本的形式是可以提取核酸的任意形式的肿瘤样本,其中全血样本为优,包括但不限于组织样本,穿刺样本、血清和血浆;且组织样本包括但不限于石蜡包埋组织、新鲜组织和冰冻切片组织。In this example, fresh whole blood samples from 2 patients with lung cancer and 3 standard products with different mutation frequencies (0.1%, 1%, and 5%) were tested. The form of the sample in the present invention is any form of tumor sample from which nucleic acid can be extracted. Among them, whole blood samples are preferred, including but not limited to tissue samples, puncture samples, serum and plasma; and tissue samples include but not limited to paraffin-embedded tissue, Fresh tissue and frozen sectioned tissue.
本实施例中,与肺癌相关的基因筛选自NCCN指南、COSMIC数据库及药物相关数据库。具体基因如下:BRAF、EGFR、KRAS、MET、NRAS、PIK3CA、TP53和UGT1A1。探针序列参考SEQ ID NO.1-SEQ ID NO.276。In this example, genes related to lung cancer were screened from NCCN guidelines, COSMIC database, and drug-related databases. The specific genes are as follows: BRAF, EGFR, KRAS, MET, NRAS, PIK3CA, TP53 and UGT1A1. The probe sequence refers to SEQ ID NO.1-SEQ ID NO.276.
本发明采用建库杂交捕获的方法对本发明所涉及的探针进行验证,具体步骤如下:In the present invention, the method of constructing a library and hybridizing and capturing is adopted to verify the probes involved in the present invention, and the specific steps are as follows:
1样本的准备1 Sample preparation
1.1分离血浆和血细胞1.1 Separation of plasma and blood cells
将2例肺癌患者的新鲜全血样本分别离心3000rpm,5min,取上清至新的离心管中,再次将上清离心3000rpm,5min,取上清(血浆)保存于新的离心管中备用,做好标记(如不立即使用可放-20℃冻存)。Centrifuge the fresh whole blood samples of 2 patients with lung cancer at 3000 rpm for 5 minutes, and transfer the supernatant to a new centrifuge tube. Centrifuge the supernatant again at 3000 rpm for 5 minutes, and save the supernatant (plasma) in a new centrifuge tube for later use. Make a mark (if not used immediately, it can be stored at -20°C).
1.2 cfDNA的提取1.2 Extraction of cfDNA
严格按照磁珠法大体积游离核酸提取试剂盒说明书(天根,货号:DP710-01)从血浆中提取cfDNA,Qubit3.0检测浓度,无需进一步片段化。Strictly follow the instructions of the magnetic bead method large-volume free nucleic acid extraction kit (Tiangen, item number: DP710-01) to extract cfDNA from plasma, and Qubit3.0 to detect the concentration, without further fragmentation.
1.3 gDNA的提取和片段化1.3 Extraction and fragmentation of gDNA
1.3.1 gDNA的提取1.3.1 Extraction of gDNA
严格按照QIAamp DNA Blood Mini Kit(QIAGEN,货号:163026054)从血细胞中提取gDNA,Qubit3.0检测浓度,琼脂糖凝胶电泳检测DNA完整性。Strictly follow QIAamp DNA Blood Mini Kit (QIAGEN, article number: 163026054) to extract gDNA from blood cells, check the concentration by Qubit3.0, and check DNA integrity by agarose gel electrophoresis.
1.3.2 gDNA的片段化1.3.2 Fragmentation of gDNA
1.3.2.1提前打开打断仪,使其温度降至4℃。1.3.2.1 Turn on the interrupter in advance to reduce its temperature to 4°C.
1.3.2.2取300ng的gDNA加入到打断管中,使用1x IDTE Buffer补齐至80μL,涡旋混匀,瞬时离心1-3s。1.3.2.2 Take 300ng of gDNA and add it to the interrupted tube, use 1x IDTE Buffer to make up to 80μL, vortex to mix, and centrifuge for 1-3s.
1.3.2.3设置5(run 30s,stop 30s)×3次的程序进行打断。1.3.2.3 Set a program of 5 (run 30s, stop 30s) × 3 times to interrupt.
1.3.2.4 Agilent 2200检测打断后DNA的片段大小(一般为200-300bp)。1.3.2.4 Agilent 2200 detects the fragment size of the broken DNA (generally 200-300bp).
1.3.2.5将室温平衡30min后的
Figure PCTCN2020094277-appb-000028
AMPure XP Beads(磁珠)涡旋混匀后取144μL至新的1.5mL离心管中,做好标记。
1.3.2.5 After equilibrating at room temperature for 30 minutes
Figure PCTCN2020094277-appb-000028
AMPure XP Beads (magnetic beads) vortex and mix well, transfer 144μL to a new 1.5mL centrifuge tube, and mark it.
1.3.2.6将片段化后的产物转移至步骤1.3.2.5中的1.5mL离心管中,涡旋混匀,室温孵育5min。1.3.2.6 Transfer the fragmented product to the 1.5 mL centrifuge tube in step 1.3.2.5, vortex to mix, and incubate at room temperature for 5 min.
1.3.2.7将步骤1.3.2.6的1.5mL离心管置于磁力架,静置直至溶液完全澄清,吸弃上清,注意避免吸到磁珠。1.3.2.7 Place the 1.5 mL centrifuge tube from step 1.3.2.6 on the magnetic stand and let it stand until the solution is completely clear. Aspirate and discard the supernatant, taking care to avoid attracting the magnetic beads.
1.3.2.8加入200μL新鲜配制的80%乙醇,室温孵育30sec,吸弃上清。1.3.2.8 Add 200 μL of freshly prepared 80% ethanol, incubate at room temperature for 30 sec, and aspirate and discard the supernatant.
1.3.2.9重复1.3.2.8。1.3.2.9 repeat 1.3.2.8.
1.3.2.10将步骤1.3.2.9的1.5mL离心管微离心后静置于磁力架,吸弃残留溶液,开盖室温晾干直至乙醇完全挥发。1.3.2.10 Microcentrifuge the 1.5 mL centrifuge tube from step 1.3.2.9 and place it on a magnetic stand, aspirate the remaining solution, open the lid and dry at room temperature until the ethanol is completely evaporated.
1.3.2.11加入52μL NFW,涡旋混匀,室温孵育2min,置于磁力架,待溶液完全澄清后转移50μL上清至新的已标记好的0.2mL PCR管进入下一步反应。1.3.2.11 Add 52μL of NFW, vortex to mix, incubate at room temperature for 2min, place on a magnetic stand, after the solution is completely clear, transfer 50μL of supernatant to a new labeled 0.2mL PCR tube to enter the next reaction.
1.3.2.12取1μL用Qubit3.0检测浓度。1.3.2.12 Take 1μL and use Qubit3.0 to detect the concentration.
2文库构建2 Library construction
2.1末端修复和3'端加“A”2.1 End repair and 3'end with "A"
2.1.1取30ng cfDNA/40ng标准品,用NFW补齐至50μL,涡旋混匀并离心。2.1.1 Take 30ng cfDNA/40ng standard, make up to 50μL with NFW, vortex to mix and centrifuge.
2.1.2在0.2mL PCR Tube中配制以下反应体系:2.1.2 Prepare the following reaction system in 0.2mL PCR Tube:
组分Component 体积(μL)Volume (μL)
cfDNA/gDNAcfDNA/gDNA 5050
End Repair&A-Tailing BufferEnd Repair&A-Tailing Buffer 77
End Repair&A-Tailing Enzyme MixEnd Repair&A-Tailing Enzyme Mix 33
总体积total capacity 6060
2.1.3涡旋混匀,离心后进行以下反应:2.1.3 Vortex to mix well, and perform the following reactions after centrifugation:
Figure PCTCN2020094277-appb-000029
Figure PCTCN2020094277-appb-000029
2.2加Adapter2.2 add Adapter
2.2.1将上一步反应产物先离心,然后配制以下反应体系:2.2.1 Centrifuge the reaction product of the previous step, and then prepare the following reaction system:
组分Component 体积(μL)Volume (μL)
End Repair and A-Tailing Reaction ProductEnd Repair and A-Tailing Reaction Product 6060
NFWNFW 55
Ligation BufferLigation Buffer 3030
Duplex Seq Adapters(3μM)Duplex Seq Adapters(3μM) 55
DNA LigaseDNA Ligase 1010
总体积total capacity 110110
2.2.2涡旋混匀,离心后进行以下反应:2.2.2 Vortex to mix well, and perform the following reactions after centrifugation:
步骤step 反应温度temperature reflex 反应时间Reaction time
Adapter LigationAdapter Ligation 20℃20℃ 15min15min
HoldHold 4℃4℃
2.3连接后纯化2.3 Purification after connection
2.3.1将室温平衡30min后的
Figure PCTCN2020094277-appb-000030
AMPure XP Beads(磁珠)涡旋混匀后取88μL至新的1.5mL离心管中,做好标记。
2.3.1 After equilibrating at room temperature for 30 minutes
Figure PCTCN2020094277-appb-000030
AMPure XP Beads (magnetic beads) are vortexed and mixed, and 88μL is transferred to a new 1.5mL centrifuge tube and marked.
2.3.2将接头连接后的产物转移至步骤2.3.1中的1.5mL离心管中,涡旋混匀,室温孵育5min。2.3.2 Transfer the connected product to the 1.5 mL centrifuge tube in step 2.3.1, vortex to mix, and incubate at room temperature for 5 min.
2.3.3将步骤2.3.2的1.5mL离心管置于磁力架,静置直至溶液完全澄清,吸弃上清,注意避免吸到磁珠。2.3.3 Place the 1.5mL centrifuge tube of step 2.3.2 on the magnetic stand and let it stand until the solution is completely clear. Aspirate and discard the supernatant, taking care to avoid attracting the magnetic beads.
2.3.4加入200μL新鲜配制的80%乙醇,室温孵育30sec,吸弃上清。2.3.4 Add 200 μL of freshly prepared 80% ethanol, incubate at room temperature for 30 sec, and aspirate the supernatant.
2.3.5重复2.3.4。2.3.5 Repeat 2.3.4.
2.3.6将步骤2.3.5的1.5mL离心管微离心后静置于磁力架,吸弃残留溶液,开盖室温晾干直至乙醇完全挥发。2.3.6 Microcentrifuge the 1.5mL centrifuge tube in step 2.3.5 and place it on the magnetic stand, aspirate the remaining solution, open the lid and dry at room temperature until the ethanol is completely evaporated.
2.3.7加入22μL NFW,涡旋混匀,室温孵育2min,置于磁力架,待溶液完全澄清后转移20μL上清至新的已标记好的0.2mL PCR管。2.3.7 Add 22μL of NFW, vortex to mix, incubate at room temperature for 2min, place on a magnetic stand, after the solution is completely clear, transfer 20μL of supernatant to a new labeled 0.2mL PCR tube.
2.4 PCR扩增2.4 PCR amplification
2.4.1在0.2mL PCR Tube中,配制以下反应体系:2.4.1 Prepare the following reaction system in 0.2mL PCR Tube:
组分Component 体积(μL)Volume (μL)
2X KAPA HiFi HotStart ReadyMix2X KAPA HiFi HotStart ReadyMix 2525
UDI Primer Mix(5μM/Primer)UDI Primer Mix (5μM/Primer) 55
Adapter-ligated LibraryAdapter-ligated Library 2020
总体积total capacity 5050
2.4.2涡旋离心,离心后进行以下反应2.4.2 Vortex centrifugation, perform the following reactions after centrifugation
Figure PCTCN2020094277-appb-000031
Figure PCTCN2020094277-appb-000031
2.5 PCR产物纯化2.5 PCR product purification
2.5.1将室温平衡30min后的
Figure PCTCN2020094277-appb-000032
AMPure XP Beads(磁珠)涡旋混匀后取50μL至新的1.5mL离心管中,做好标记。
2.5.1 After equilibrating at room temperature for 30 minutes
Figure PCTCN2020094277-appb-000032
AMPure XP Beads (magnetic beads) vortex and mix well, take 50μL into a new 1.5mL centrifuge tube, and mark it.
2.5.2将PCR产物转移至步骤2.5.1中的1.5mL离心管中,涡旋混匀,室温孵育5min。2.5.2 Transfer the PCR product to the 1.5 mL centrifuge tube in step 2.5.1, vortex to mix, and incubate at room temperature for 5 min.
2.5.3将步骤2.5.2的1.5mL离心管置于磁力架,静置直至溶液完全澄清吸弃上清,注意避免吸到磁珠。2.5.3 Place the 1.5mL centrifuge tube of step 2.5.2 on the magnetic stand, and let it stand until the solution is completely clear. Discard the supernatant, taking care to avoid attracting the magnetic beads.
2.5.4加入200μL新鲜配制的80%乙醇,室温孵育30sec,吸弃上清。2.5.4 Add 200 μL of freshly prepared 80% ethanol, incubate at room temperature for 30 sec, and aspirate the supernatant.
2.5.5重复2.5.4。2.5.5 Repeat 2.5.4.
2.5.6将步骤2.5.5中的1.5mL离心管微离心后静置于磁力架,吸弃残留溶液,开盖室温晾干直至乙醇完全挥发。2.5.6 Microcentrifuge the 1.5mL centrifuge tube in step 2.5.5 and place it on the magnetic stand, aspirate the remaining solution, open the lid and dry at room temperature until the ethanol is completely evaporated.
2.5.7加入22μL NFW,涡旋混匀,室温孵育2min,置于磁力架,待溶液完全澄清后转移20μL上清至新的已标记好的1.5mL离心管中。2.5.7 Add 22μL of NFW, vortex to mix, incubate at room temperature for 2min, place on a magnetic stand, after the solution is completely clear, transfer 20μL of supernatant to a new labeled 1.5mL centrifuge tube.
2.5.8质检2.5.8 Quality Inspection
取1μL DNA文库溶液用Qubit荧光定量仪检测浓度。Take 1μL of DNA library solution and use Qubit Fluorometer to detect the concentration.
3杂交3 hybrids
3.1在1.5ml EP管中配置如下反应:3.1 Configure the following reaction in the 1.5ml EP tube:
Blocker componentBlocker component Volume per reaction(μL)Volume per reaction(μL)
Human Cot DNAHuman Cot DNA 55
xGen Blocking Oligos based on your library adaptersxGen Blocking Oligos based on your library adapters 22
3.2混合文库2ug,加至步骤3.1的混合液中。3.2 Mix 2ug of the library and add it to the mixed solution of step 3.1.
3.3真空抽干。3.3 Vacuum dry.
3.4配置下列体系于已真空干燥的样本EP管中3.4 Configure the following systems in the vacuum-dried sample EP tube
Hybridization Master Mix componentHybridization Master Mix component Volume per reaction(μL)Volume per reaction(μL)
xGen 2X Hybridization BufferxGen 2X Hybridization Buffer 8.58.5
xGen Hybridization Buffer EnhancerxGen Hybridization Buffer Enhancer 2.72.7
xGen Lockdown Panel or custom probesxGen Lockdown Panel or custom probes 44
Nuclease-Free WaterNuclease-Free Water 1.81.8
TotalTotal 1717
3.5振荡,离心,重复两次。3.5 Shake, centrifuge, and repeat twice.
3.6进行以下PCR反应程序:3.6 Carry out the following PCR reaction procedures:
Figure PCTCN2020094277-appb-000033
Figure PCTCN2020094277-appb-000033
Figure PCTCN2020094277-appb-000034
Figure PCTCN2020094277-appb-000034
4捕获。4 capture.
按照下表配置清洗buffer:Configure the cleaning buffer according to the following table:
Figure PCTCN2020094277-appb-000035
Figure PCTCN2020094277-appb-000035
按照下表配置Bead Resuspension MixConfigure Bead Resuspension Mix according to the following table
Bead Resuspension Mix componentBead Resuspension Mix component Volume per reaction(μL)Volume per reaction(μL)
xGen 2X Hybridization BufferxGen 2X Hybridization Buffer 8.58.5
xGen Hybridization Buffer EnhancerxGen Hybridization Buffer Enhancer 2.72.7
Nuclease-Free WaterNuclease-Free Water 5.85.8
TotalTotal 1717
4.1清洗链霉亲和素磁珠4.1 Cleaning streptavidin magnetic beads
4.1.1振荡混匀磁珠,按每个捕获50μL吸取磁珠至同一1.5mL EP管中。4.1.1 Shake and mix the magnetic beads, and draw 50μL of each captured magnetic beads into the same 1.5mL EP tube.
4.1.2按每个捕获加入100μL Bead Wash Buffer,用枪吹打10次以上,放于磁力架静置,直至完全澄清,弃去上清。4.1.2 Add 100μL of Bead Wash Buffer for each capture, blow with a gun more than 10 times, put it on the magnetic stand and let it stand until it is completely clarified, and discard the supernatant.
4.1.3重复4.1.2操作两次。4.1.3 Repeat 4.1.2 operation twice.
4.1.4加入已配置的Bead Resuspension Mix,按照每个捕获17μL,吹打混匀,移至0.2mL PCR管中。4.1.4 Add the configured Bead Resuspension Mix, capture 17 μL of each, pipette to mix, and transfer to a 0.2 mL PCR tube.
4.2捕获4.2 Capture
4.2.1探针杂交结束后,迅速将梯度PCR仪程序调至下表4.2.1 After the probe hybridization is over, quickly adjust the gradient PCR instrument program to the following table
Figure PCTCN2020094277-appb-000036
Figure PCTCN2020094277-appb-000036
4.2.2迅速将杂交后的样本全部转入步骤4.1.4中的含有Bead Resuspension Mix的0.2mL PCR管中,吹打混匀并离心。4.2.2 Quickly transfer all the hybridized samples to the 0.2mL PCR tube containing Bead Resuspension Mix in step 4.1.4, pipette to mix and centrifuge.
4.2.3将样本放入步骤4.2.1已设置好程序的PCR仪中,放置45min,每隔10-12min,取出快速振荡混匀,确保磁珠处于重悬状态。4.2.3 Put the sample into the PCR machine with the program set in step 4.2.1, place it for 45 minutes, and take out the rapid shaking and mix every 10-12 minutes to ensure that the magnetic beads are in a resuspended state.
4.3热洗4.3 Hot wash
4.3.1恒温仪65℃预热1X Wash Buffer 1和1X Stringent Wash Buffer至少15min。4.3.1 The thermostat warms up the 1X Wash Buffer 1 and 1X Stringent Wash Buffer at 65°C for at least 15 minutes.
4.3.2加入100μL预热的1X Wash Buffer 1至4.2.3的样本中,用枪快速吹打混匀,避免产生气泡。4.3.2 Add 100μL of preheated 1X Wash Buffer 1 to 4.2.3 samples, and quickly pipette and mix with a gun to avoid air bubbles.
4.3.3置于磁力架至澄清,弃上清,移除磁力架。4.3.3 Place on the magnetic stand until clarified, discard the supernatant, and remove the magnetic stand.
4.3.4加入150μL预热的1X Stringent Wash Buffer至样本,用枪快速吹打混匀,避免产生气泡。65℃孵育5min,置于磁力架至澄清,弃上清。4.3.4 Add 150μL of pre-heated 1X Stringent Wash Buffer to the sample, and quickly mix with a gun to avoid bubbles. Incubate at 65°C for 5 min, place on a magnetic stand until clear, and discard the supernatant.
4.3.5重复步骤4.3.4。4.3.5 Repeat step 4.3.4.
4.4室温洗4.4 Wash at room temperature
4.4.1向热洗步骤4.3.5中的样本加入150μL Wash Buffer 1,振荡离心。室温孵育2min,每30s振荡一次(不要太剧烈),确保磁珠处于重悬状态。4.4.1 Add 150μL Wash Buffer 1 to the sample in the hot wash step 4.3.5, and centrifuge with shaking. Incubate for 2min at room temperature, shake once every 30s (not too violently) to ensure that the magnetic beads are in a resuspended state.
4.4.2孵育结束后,微离心。置于磁力架1min,至澄清,弃上清。4.4.2 After the incubation, microcentrifuge. Place on the magnetic stand for 1 min, until clear, discard the supernatant.
4.4.3加入150μL Wash Buffer 2,振荡混匀。室温孵育2min,每30s振荡一次(不要太剧烈),确保磁珠处于重悬状态。4.4.3 Add 150μL Wash Buffer 2, shake and mix. Incubate for 2min at room temperature, shake once every 30s (not too violently) to ensure that the magnetic beads are in a resuspended state.
4.4.4孵育结束后,微离心。置于磁力架1min,至澄清,弃上清。4.4.4 After the incubation is over, microcentrifuge. Place on the magnetic stand for 1 min, until clear, discard the supernatant.
4.4.5加入150μL Wash Buffer 3,振荡混匀。室温孵育2min,30s振荡一次(不要太剧烈),确保磁珠处于重悬状态。4.4.5 Add 150μL Wash Buffer 3, shake and mix. Incubate for 2 minutes at room temperature, shake once for 30 seconds (not too vigorously) to ensure that the magnetic beads are in a resuspended state.
4.4.6孵育结束后,微离心。置于磁力架1min,至澄清,弃上清。4.4.6 After the incubation, microcentrifuge. Place on the magnetic stand for 1 min, until clear, discard the supernatant.
4.4.7用枪吸弃残余的Wash Buffer 3,移除磁力架。4.4.7 Use a gun to absorb the remaining Wash Buffer 3 and remove the magnetic stand.
4.4.8每个捕获加入20μL NFW,用枪吹打混匀,并转移至0.2mL PCR管中。4.4.8 Add 20μL NFW to each capture, mix well by pipetting with a gun, and transfer to a 0.2mL PCR tube.
5 PCR扩增和纯化5 PCR amplification and purification
5.1 PCR扩增5.1 PCR amplification
5.1.1在各个捕获中加入如下体系5.1.1 Add the following system to each capture
Amplification Reaction Mix componentAmplification Reaction Mix component Volume per reaction(μL)Volume per reaction(μL)
2X KAPA HiFi HotStart ReadyMix*2X KAPA HiFi HotStart ReadyMix* 2525
KAPA Primer mixKAPA Primer mix 55
5.1.2进行如下的PCR扩增5.1.2 Carry out the following PCR amplification
Figure PCTCN2020094277-appb-000037
Figure PCTCN2020094277-appb-000037
5.2 PCR产物纯化5.2 PCR product purification
5.2.1提前配置好80%乙醇,每个捕获需要250μL。5.2.1 Configure 80% ethanol in advance, 250μL is required for each capture.
5.2.2每个捕获加入75μL
Figure PCTCN2020094277-appb-000038
AMPure XP beads(AMP),用枪吹打混匀,室温孵育5-10min。置磁力架2-5min,至澄清,弃上清。
5.2.2 Add 75μL to each capture
Figure PCTCN2020094277-appb-000038
AMPure XP beads (AMP), mix well by pipetting and incubate at room temperature for 5-10min. Set the magnetic stand for 2-5 minutes until it is clear, and discard the supernatant.
5.2.3加入125μL 80%乙醇,室温静置1min,弃上清。5.2.3 Add 125 μL of 80% ethanol, let stand for 1 min at room temperature, and discard the supernatant.
5.2.4重复步骤5.2.3。5.2.4 Repeat step 5.2.3.
5.2.5室温干燥磁珠,大约1-3min。5.2.5 Dry the magnetic beads at room temperature for about 1-3 minutes.
5.2.6待磁珠干燥完毕,移除磁力架,加入22μL TE,吹打混匀。5.2.6 After the magnetic beads are dried, remove the magnetic stand, add 22μL TE, and mix by pipetting.
5.2.7室温孵育5min。置磁力架至澄清,转移20μL至新的1.5mL EP管中保存。5.2.7 Incubate at room temperature for 5 minutes. Set the magnetic stand until it is clear, and transfer 20 μL to a new 1.5 mL EP tube for storage.
5.2.8文库质检5.2.8 Library quality inspection
使用Qubit 3.0和Agilent 2200进行检测。Use Qubit 3.0 and Agilent 2200 for detection.
6.Nextseq上机测序。6. Nextseq on-machine sequencing.
7.数据分析结果7. Data analysis results
两位患者样本的主要质量控制如表1所示:DNA质量评估和测序质量评估均合格,可进行下一步数据分析。肺癌患者和标准品的数据分析结果如下:The main quality control of the two patient samples is shown in Table 1: DNA quality evaluation and sequencing quality evaluation are both qualified, and the next step data analysis can be carried out. The data analysis results of lung cancer patients and standard products are as follows:
(1)一位肺癌患者的测序数据分析结果显示:(1)检测到EGFR基因Exon 20存在c.2294T>G突变,导致所编码第765位上的缬氨酸(V)变为甘氨酸(G)。目前尚无专门针对该变异位点的药物,有被FDA或cFDA批准的该基因靶向药物。(2)UGT1A1基因的rs8175347位点基因型为杂合型,提示使用伊立替康的毒副作用风险较大(中性粒细胞减少症,腹泻,无力)。(1) The results of sequencing data analysis of a lung cancer patient showed that: (1) The c.2294T>G mutation in Exon 20 of the EGFR gene was detected, which caused the valine (V) at position 765 to be changed to glycine (G). ). At present, there are no drugs specifically targeting this mutation site, and there are gene-targeted drugs approved by the FDA or cFDA. (2) The genotype at the rs8175347 locus of the UGT1A1 gene is heterozygous, indicating that the use of irinotecan has a greater risk of side effects (neutropenia, diarrhea, weakness).
另外一位肺癌患者的测序数据分析结果显示:UGT1A1基因rs8175347位点(*28)基因 型为杂合型,提示使用伊立替康的毒副作用风险较大;TP53基因的rs1042522位点基因型为杂合型,提示使用顺铂、卡培他滨、紫杉醇、奥沙利铂的敏感性可能较低。The results of sequencing data analysis of another lung cancer patient showed that the genotype at the rs8175347 locus (*28) of the UGT1A1 gene was heterozygous, indicating that the use of irinotecan had a greater risk of side effects; the genotype at the rs1042522 locus of the TP53 gene was heterozygous. The combined type suggests that the sensitivity of using cisplatin, capecitabine, paclitaxel, and oxaliplatin may be low.
(2)三种标准品的检测结果如表2所示:等位基因频率分别为0.1%、1%和5%的已知突变位点均被检测出来。说明该检测试剂盒可以检测超低频突变的基因位点,最低检测限可达0.1%。(2) The test results of the three standard products are shown in Table 2: The known mutation sites with allele frequencies of 0.1%, 1%, and 5% were detected. It shows that the detection kit can detect the gene locus of ultra-low frequency mutation, and the minimum detection limit can reach 0.1%.
表1:Table 1:
Figure PCTCN2020094277-appb-000039
Figure PCTCN2020094277-appb-000039
表2:Table 2:
基因gene 已知突变位点Known mutation sites 预期的等位基因频率(%)Expected allele frequency (%) 检测的等位基因频率(%)Frequency of alleles detected (%)
EGFREGFR T790MT790M 5.05.0 4.74.7
EGFREGFR delE746-A750delE746-A750 5.05.0 1.81.8
EGFREGFR L858RL858R 5.05.0 3.93.9
EGFREGFR V769-D770insASVV769-D770insASV 5.05.0 3.03.0
PIK3CAPIK3CA E545KE545K 6.36.3 5.95.9
KRASKRAS G12DG12D 6.36.3 5.05.0
EGFREGFR T790MT790M 1.01.0 0.520.52
EGFREGFR delE746-A750delE746-A750 1.01.0 0.190.19
EGFREGFR L858RL858R 1.01.0 0.580.58
EGFREGFR V769-D770insASVV769-D770insASV 1.01.0 0.390.39
PIK3CAPIK3CA E545KE545K 1.31.3 0.250.25
KRASKRAS G12DG12D 1.31.3 0.250.25
EGFREGFR T790MT790M 0.10.1 0.00210.0021

Claims (2)

  1. 一种用于检测肺癌驱动性基因突变的探针,其特征在于,包括下列6组共248条探针:A probe for detecting lung cancer driving gene mutations, which is characterized in that it includes the following 6 sets of 248 probes:
    BRAF驱动突变特异性探针序列:其序列为SEQ ID NO.1至SEQ ID NO.3;BRAF driver mutation specific probe sequence: its sequence is SEQ ID NO.1 to SEQ ID NO.3;
    EGFR驱动突变特异性探针序列:其序列为SEQ ID NO.4至SEQ ID NO.98;EGFR driver mutation specific probe sequence: its sequence is SEQ ID NO.4 to SEQ ID NO.98;
    KRAS驱动突变特异性探针序列:其序列为SEQ ID NO.99至SEQ ID NO.148;KRAS driver mutation specific probe sequence: its sequence is SEQ ID NO.99 to SEQ ID NO.148;
    MET驱动突变特异性探针序列:其序列为SEQ ID NO.149至SEQ ID NO.150;MET driver mutation specific probe sequence: its sequence is SEQ ID NO.149 to SEQ ID NO.150;
    NRAS驱动突变特异性探针序列:其序列为SEQ ID NO.151至SEQ ID NO.193;NRAS driver mutation specific probe sequence: its sequence is SEQ ID NO.151 to SEQ ID NO.193;
    PIK3CA驱动突变特异性探针序列:其序列为SEQ ID NO.194至SEQ ID NO.248;PIK3CA driver mutation specific probe sequence: its sequence is SEQ ID NO.194 to SEQ ID NO.248;
    还包括下列2组共28条探针:It also includes 28 probes in the following 2 groups:
    TP53特异性探针核苷酸序列:其序列为SEQ ID NO.249至SEQ ID NO.272;TP53 specific probe nucleotide sequence: its sequence is SEQ ID NO.249 to SEQ ID NO.272;
    UGT1A1特异性探针序列:其序列为SEQ ID NO.273至SEQ ID NO.276。UGT1A1 specific probe sequence: its sequence is SEQ ID NO.273 to SEQ ID NO.276.
  2. 一种检测肺癌驱动性基因突变的检测试剂盒,包括:权利要求1所述的6组共248条探针和2组共28条探针。A detection kit for detecting lung cancer driving gene mutations, comprising: 6 sets of 248 probes in total and 2 sets of 28 probes in total according to claim 1.
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