TW201011107A - Method of determining susceptibility of myopia, method of screening myopia therapeutic agent, and method of assessing probability of response to a myopia therapeutic agent - Google Patents
Method of determining susceptibility of myopia, method of screening myopia therapeutic agent, and method of assessing probability of response to a myopia therapeutic agent Download PDFInfo
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201011107 六、發明說明: 【發明所屬之技術領域】 本發明係有關於一種檢測近視的方法,且特別有關於 一種利用檢測BICD1基因之單核苷酸多型性(SNP,single nucleotide polymorphism)來檢測近視及/或近視相關併發症 的方法。此外,本發明更有關於一種篩選治療或抑制近視 物質的方法。 ❹【先前技術】 近視係指在放鬆的情況下,平行於視轴的平行光線通 過眼球屈光系統的折射彙聚在視網膜前,屬於一種屈光不 正。近視的人在看遠處的物體時,不能在視網膜上清晰的 成像,使得影像聚焦於眼球的玻璃體中,而非視網膜上。 近視廣泛地存在於世界上,近視的治療與族群、性別 及年記有關(Invest Ophthalmol Vis Sci 1997;38:334-40 ; Optom Vis Sci 2001;78:234-9 ; J Formos Med Assoc 2001;100:684-91)。在美國,12至54歲的國民有25%的人 ❹罹患近視(Arch Ophthalmol 1983;101:405-7),且白人罹患 近視的比率(28.1%)高於非裔族群(19.4%)(Invest Ophthalmol Vis Sci 1997;38:334-40)。在所有的近視族群 中,高度近視(屈光度< -5.0 D)的比例可達27%至33%, 盛行率為 1.7%至 2°/〇(Arch Ophthalmol 1983;101:405-7)。 在世界上,台灣是屬於近視的高危險地區。若以屈光度< -6.0 D來作為高度近視,台灣的高度近視比例高於亞洲各 國,且在台灣有18%的男性學童及24%的女性學童罹患近 視(J Formos Med Assoc 2001;100:684-91),此比例甚至高201011107 VI. Description of the Invention: [Technical Field of the Invention] The present invention relates to a method for detecting myopia, and particularly relates to a single nucleotide polymorphism (SNP) for detecting BICD1 gene. Methods of myopia and/or myopia-related complications. Furthermore, the present invention is more related to a method of screening for treating or inhibiting myopia. ❹ [Prior Art] Myopia refers to the fact that in the case of relaxation, parallel rays parallel to the visual axis converge in front of the retina through the refraction of the eyeball refractive system, which is a kind of refractive error. When a person with myopia looks at a distant object, it cannot be clearly imaged on the retina, so that the image is focused on the vitreous of the eyeball, not on the retina. Myopia is widely present in the world, and the treatment of myopia is related to ethnicity, gender, and age (Invest Ophthalmol Vis Sci 1997; 38: 334-40; Optom Vis Sci 2001; 78: 234-9; J Formos Med Assoc 2001; :684-91). In the United States, 25% of people between the ages of 12 and 54 suffer from myopia (Arch Ophthalmol 1983; 101: 405-7), and the rate of whites suffering from myopia (28.1%) is higher than that of African-Americans (19.4%) (Invest Ophthalmol Vis Sci 1997; 38: 334-40). In all myopic populations, the proportion of high myopia (diopter < -5.0 D) is 27% to 33%, and the prevalence is 1.7% to 2 ° / 〇 (Arch Ophthalmol 1983; 101: 405-7). In the world, Taiwan is a high-risk area that belongs to myopia. If diopter < -6.0 D is used as high myopia, Taiwan has a higher proportion of high myopia than Asian countries, and 18% of male students and 24% of female students in Taiwan suffer from myopia (J Formos Med Assoc 2001;100:684 -91), this ratio is even higher
0911-A51298-TW 4 201011107 於新加坡年輕人的近比例(131%)(〇pt〇m Vis Sci 2001;78:234-9),在1995及2000年的全國調查中發現台 灣的近視盛行率仍持續增加。 高度近視可能會導致失明,例如,其與視網膜剝離、 黃斑點退化及青光眼有關。在美國所有的失明學童中有 5.6%與近視有關。雖然,近視可以藉由眼鏡、隱形眼鏡、 角膜矯正術及雷射屈光矯正手術(LASIK)治療或校正,但 上述方法皆無法抑制因近視併發症所造成視網膜剝離、黃 斑點退化及青光眼的產生。此外,過度使用隱形眼鏡(Curr 攀 Opin Ophthalmol 1998;9:66-71)、角膜矯正術(J Refract Surg 2003; 195247-9)及其他外科手術也可能會增加眼睛 產生併發症的風險。在美國,每年必須花費2億5千萬在 治療近視上(Arch Ophthalmol 1994;112:1526-30)。 目前已證實許多環境因子與近視有關,由雙胞胎研究 顯示近視與遺傳有顳著的關係,家族遺傳率估計在58%至 90%之間(Invest Ophthalmol Vis Sci 2001;42:1232-6 ; Genet Epidemiol 1988;5:171-81 ; Hum Hered 參 1991;41:151-6 ; Br J Ophthalmol 2001 ;85:1470-6)。實驗證 實家族病史是高度近視的重要原因(Invest Ophthalmol Vis Sci 2004;45:3446-52 ; Optom Vis Sci 1996;73:279-82 ; JAMA 1994;271:1323-7 ; Invest Ophthalmol Vis Sci 2002;43:3633-40 ; Optom Vis Sci 1999;76:387-92 ; Invest Ophthalmol Vis Sci 2004;45:2873-8)。然而,只有少許的 研究發現與近視相關的基因,但都無法得到大型資料的證 實。 因此,醫學上亟需要一種生物標的來作為檢測、治療 0911-A51298-TW 5 201011107 及減缓近視及其併發症的參考。 【發明内容】 本發明係提供一種決定一個體是否對近視具有感受 性的方法’包括:由該個體中獲得一生物樣本,以及測定 該生物樣本中的BICD1基因之至少一單核苷酸多型性 (SNP) ’其中該單核苷酸多型性的危險基因型存在,則表 示該個體對近視具有感受性。 本發明另提供一種筛選抑制或治療近視及/或近視相 _關併發症物質的方法,包括使一測試物質及一表現BICD1 基因之細胞相互接觸,以及篩選一物質,相較於一控制 組,該物質具有調控BICD1基因表現的能力。 本發明另提供一種評估一個體對一近視治療藥劑的 反應,包括測定一 BICD1基因之單核苷酸多型性,其中 帶有該單核苷酸多型性的某些基因型時,表示該個體對該 近視治療藥劑具有良好的反應(正反應)。 本發明更提供一種用於檢測近視感受性之套組,包括 _ 一或複數個試劑、一緩衝液、以及一酵素,用以偵測一或 複數個BICD1基因之單核皆酸多型性。 為了讓本發明之上述和其他目的、特徵、和優點能更 明顯易懂,下文特舉較佳實施例,並配合所附圖示,作詳 細說明如下: 【實施方式】 a在本,明一實施樣態中,本發明提供一種決定一個體 疋否易於罹患近視的方法,包括由一個體中獲得一生物樣 本’檢測此生物樣本中BICD1基因之至少一種SNP( single0911-A51298-TW 4 201011107 The proportion of young people in Singapore (131%) (〇pt〇m Vis Sci 2001; 78:234-9), found in the national surveys in 1995 and 2000, the prevalence of myopia in Taiwan is still Continued to increase. High myopia can cause blindness, for example, it is associated with retinal detachment, yellow spot degeneration, and glaucoma. 5.6% of all blind children in the United States are related to myopia. Although myopia can be treated or corrected by glasses, contact lenses, Orthokeratology, and Laser Refractive Surgery (LASIK), none of the above methods can inhibit retinal detachment, yellow spot degradation, and glaucoma due to myopia complications. . In addition, excessive use of contact lenses (Curr Opin Ophthalmol 1998; 9: 66-71), Orthokeratology (J Refract Surg 2003; 195247-9) and other surgical procedures may also increase the risk of complications in the eye. In the United States, it is necessary to spend 250 million to treat myopia each year (Arch Ophthalmol 1994; 112: 1526-30). Many environmental factors have been shown to be associated with myopia, and twin studies have shown a relationship between myopia and heredity. Family heritability is estimated to be between 58% and 90% (Invest Ophthalmol Vis Sci 2001; 42:1232-6; Genet Epidemiol 1988; 5: 171-81; Hum Hered 1971; 41: 151-6; Br J Ophthalmol 2001; 85: 1470-6). Experiments have confirmed that family history is an important cause of high myopia (Invest Ophthalmol Vis Sci 2004; 45: 3446-52; Optom Vis Sci 1996; 73: 279-82; JAMA 1994; 271:1323-7; Invest Ophthalmol Vis Sci 2002; : 3633-40; Optom Vis Sci 1999; 76: 387-92; Invest Ophthalmol Vis Sci 2004; 45: 2873-8). However, only a few studies have found genes associated with myopia, but no evidence of large data has been obtained. Therefore, medically, a biological standard is needed as a reference for detecting and treating 0911-A51298-TW 5 201011107 and slowing down myopia and its complications. SUMMARY OF THE INVENTION The present invention provides a method of determining whether a body is susceptible to myopia, comprising: obtaining a biological sample from the individual, and determining at least one single nucleotide polymorphism of the BICD1 gene in the biological sample. (SNP) 'The presence of a dangerous genotype of this single nucleotide polymorphism indicates that the individual is susceptible to myopia. The invention further provides a method for screening for inhibiting or treating myopia and/or myopia-related complications, comprising contacting a test substance and a cell expressing the BICD1 gene, and screening a substance compared to a control group This substance has the ability to regulate the expression of the BICD1 gene. The present invention further provides a method for assessing the response of a body to a myopia treatment agent, comprising determining a single nucleotide polymorphism of a BICD1 gene, wherein when the genotype of the single nucleotide polymorphism is present, The individual has a good response (positive reaction) to the myopia treatment agent. The invention further provides a kit for detecting myopia susceptibility comprising: one or a plurality of reagents, a buffer, and an enzyme for detecting mononuclear acid polymorphism of one or more BICD1 genes. The above and other objects, features, and advantages of the present invention will become more apparent and understood. In an embodiment, the present invention provides a method for determining whether a body is susceptible to myopia, comprising obtaining a biological sample from a body to detect at least one SNP of the BICD1 gene in the biological sample (single
0911-A51298-TW 201011107 nucleotide polymorphism)基因型,其中此SISfP基因型的 存在顯示該個體具近視感受性。此SNP基因型係擇自下 到所組成之族群:SNPsrs7966276、rsll51029、rs2650122 及rsl0771923。此基因型的變異可為一種BICD1基因序 列的改變’例如,可僅為單一核苷酸的改變,此改變可能 會改變編碼BICD1基因之胜肽,導致不同的轉譯或造成 基因轉錄功能受影響。 在本發明之決定是否帶有易於罹患近視及/或近視相 關併發症的基因型,可使用引子延伸法(例如,PinPoint 分析,Massextend™、SPC-SBE、或 GOOD 分析)、雜交法 (例如’ TaqMan分析、磁珠陣列(bead arry)、或SNP晶片)、 ligation(例如,組成式綠螢光轉移標誌(CFFr tagS)),以及 酵素切割(RFLP、Invader®分析),PCR-SSCP(單鏈構象多 態性)’ MRD(mismatch repair dection),BeadArray™,或 SNPlexTM。首先’由一個體中採集或收集一包含核苷酸 (DNA)之生物樣本。本發明所述之個體可為一哺乳動物, 較佳為一罹患近視及/或近視相關併發症的人類或個體。 β本發明之個體包括,但不限於,成人、幼童或嬰兒。本發 明之生物樣本可由任何具有染色體DNA之來源收集或分 離而得’所謂的來源包括血液、羊水、腦脊液、或皮膚、 肌肉、口腔黏膜、胎盤、腸胃道或其他器官之組織液。接 著’分析DNA樣本中是否有易造成近視之bicDI基因型 的存在。在本發明之一實施例中,BICD1基因型可藉由 TaqMaii技術進行鑑定。簡單地說,利用primer Express version 2.0設計PCR引子及TaqMan MGB探針,於 GeneAmp 9700熱反應槽及96孔盤中進行反應,並利用0911-A51298-TW 201011107 nucleotide polymorphism), wherein the presence of this SISfP genotype indicates that the individual has near vision sensitivity. This SNP genotype was selected from the following subgroups: SNPsrs7966276, rsll51029, rs2650122 and rsl0771923. The variation of this genotype may be a change in the sequence of a BICD1 gene', e.g., may be a single nucleotide change that may alter the peptide encoding the BICD1 gene, resulting in different translations or causing transcriptional function of the gene to be affected. In the present invention, whether a genotype susceptible to myopia and/or myopia-related complications is present, primer extension methods (for example, PinPoint analysis, MassextendTM, SPC-SBE, or GOOD analysis), hybridization methods (eg, ' TaqMan analysis, bead arry, or SNP wafers, ligation (eg, compositional green fluorescent transfer marker (CFFr tagS)), and enzyme cleavage (RFLP, Invader® analysis), PCR-SSCP (single chain) Conformation polymorphism) 'MRD (mismatch repair dection), BeadArrayTM, or SNPlexTM. First, a biological sample containing nucleotides (DNA) is collected or collected from one body. The subject of the present invention may be a mammal, preferably a human or individual suffering from myopia and/or myopia-related complications. Beta Individuals of the invention include, but are not limited to, adults, young children or infants. The biological sample of the present invention may be collected or isolated from any source having chromosomal DNA. The so-called source includes blood, amniotic fluid, cerebrospinal fluid, or tissue fluid of the skin, muscle, oral mucosa, placenta, gastrointestinal tract or other organs. Then, 'analyze the presence of bicDI genotypes in my DNA samples that are prone to myopia. In one embodiment of the invention, the BICD1 genotype can be identified by TaqMaii technology. Briefly, PCR primers and TaqMan MGB probes were designed using primer Express version 2.0, reacted in a GeneAmp 9700 thermal reaction cell and a 96-well plate, and utilized.
0911-A51298-TW 2010111070911-A51298-TW 201011107
ABI Prism 7500 序列债測系統及 ABI Prism 7500 SDS software version 1 .(H貞測及分析螢光強度。在另一實施例 中,可利用基因定型分析(genotyping)來鑑定SNP的基因 型,相關流程可參照Mutat Res 2005;573:70-82,可使用 Illumina BeadArray technology (Sentrix® Array Matrix) [Shen,2005 #135]來進行基因定型分析。簡單地說,將特 異的寡核普酸(allelic specific oligonucleotide)黏合至 DNA 上,藉由PCR放大,並利用Cy-3及Cy-5標定之引子進 行陣列式之雜交及及基因定型分析。在另一實施例中,可 ®使用商品化的基因晶片來鑑定BICD1基因中SNP的基因 型。例如,Affymetrix GeneChip® Human Mapping 500K 陣列套組包括二個陣列,每一個可分析約250,〇〇〇個 SNPs,藉由一般習知的方法進行雜交,並利用BRLMM clustering演算法分析基因型。 此外,若基因變異(多樣性)造成限制酶切位的產生或 消失,也可藉由限制酶的切割(消化)來鑑定BICD1基因 的各基因型。首先,以PCR放大生物樣本中之BICD1基 參因。接著進行一 RFLP分析。經切割的DNA片段可顯示 出特定BICD1基因型的存在與否,進而得知各基因型的 存在與否與近視的關係。在另一實施例中,可藉由序歹分 析(定序)來鑑定BICD1基因的各SNP基因型。首先利用 PCR或其他適當的方法放大BICD1基因或核苷酸,接 著,以一般習知的程序來分析BICD1核苷酸、BICD1核 苷酸片斷、BICD1基因體DNA、BICD1基因體DNa片斷 的序列,並分別比較上述核苷酸/核苷酸片斷或基因體 DNA/DNA片斷與已知BICD1基因序列的差異。若有上述ABI Prism 7500 Sequence Debt Measurement System and ABI Prism 7500 SDS software version 1. (H Measure and analyze fluorescence intensity. In another embodiment, genotyping can be used to identify SNP genotypes, related processes Refer to Mutat Res 2005; 573:70-82 for the analysis of genotyping using Illumina BeadArray technology (Sentrix® Array Matrix) [Shen, 2005 #135]. Simply put, specific oligonucleotides (allelic specific) The oligonucleotide is conjugated to DNA, amplified by PCR, and hybridized by Cy-3 and Cy-5 primers for array hybridization and genotyping analysis. In another embodiment, a commercially available gene chip can be used. To identify the genotype of the SNP in the BICD1 gene. For example, the Affymetrix GeneChip® Human Mapping 500K array kit consists of two arrays, each of which can analyze approximately 250, one SNPs, which are hybridized by conventional methods. The BRLMM clustering algorithm is used to analyze the genotype. In addition, if the gene mutation (diversity) causes the production or disappearance of the restriction enzyme cleavage site, it can also be cut by restriction enzymes. (Digestion) to identify each genotype of the BICD1 gene. First, PCR is used to amplify the BICD1 basal factor in the biological sample. Then an RFLP analysis is performed. The cleavage of the DNA fragment can indicate the presence or absence of a specific BICD1 genotype, and further The relationship between the presence or absence of each genotype and myopia is known. In another embodiment, each SNP genotype of the BICD1 gene can be identified by sequence analysis (sequencing). First, use PCR or other appropriate methods to amplify. BICD1 gene or nucleotide, followed by analysis of the sequence of BICD1 nucleotide, BICD1 nucleotide fragment, BICD1 gene DNA, BICD1 gene DNa fragment by a conventional procedure, and comparing the above nucleotides/nuclei The difference between the nucleotide fragment or the genomic DNA/DNA fragment and the known BICD1 gene sequence.
0911-A51298-TW 8 201011107 =的存在代表此個體對近視及/或近視相關併發症具 此技藝人士可依不同情況選用不同的方法來夢 制mcm基因的SNP,且此技藝人士可輕易地^並 施行上述方法或其他方法。 本發明中所述之“近視感受性”意指為當本發明之 SNP某-種基因型存在時,此個體容易於或不容易羅串近 視。本發明中所述之“低近視感受性,,意指為當本發明之 SNP某種基因型存在時,此個體不易罹患近視。本發明中 擊所述之“高近視感受性”意指為當本發明之册某種基 因型存在時’此個體容易罹患近視。在本發明之一實施例 中,當SNP rsl0771923有對偶基因G基因型,或sNp rsl151029有對偶基因T之基因型存在時,表示此個體較 容易罹患近視,其罹患近視的風險比其他基因型高至少 1.2倍。在本發明另一實施例中,當SNp rs7966276有對 偶基因A之基因型,其表示此個體較不容易罹患近視, 其惟患近視的風險比其他基因型低至少0 · 6倍。應注竟的 ❹是,此個體也會因其他因子,例如疾病或環境等而增加或 減少罹患近視的風險。 在本發明另一實施樣態中,本發明提供一種篩選可治 療近視及/或近視相關併發症的物質(候選藥物),包括將一 待測物質與一表現BICD1基因的細胞接觸,並篩選相較 於對照組(未接觸候選藥物之細胞)可調控BICD1基因的 物質。 BICD1基因之基因型(例如,SNP rs7966276、 rsll51029、rs2650122、及 rsl0771923)可用來做為尋找或 0911-A51298-TW 9 201011107 鑑定治療近視及/或近視相關併發症的生物標誌。此方法 是藉由篩選一可改變BICD1基因表現的物質。例如’將 一細胞曝露於一測試物質或一混合之測試物質組合物(依 序或同時),並分析此細胞BICD1基因的表現,比較未處 理以及經測試物質處理之細胞的BICD1基因表現。此測 試物質可為一已知或未知之化合物。測試物質包括,但不 限於,化合物、小分子藥物、聚聽類、核苦酸、蛋白質或 胜狀等。例如,此測試物質可為一小分子干擾RNA。在 本發明之一實施例中,此測試物質可藉由 SNP ® rsl0771923、SNP rsll51029 或 SNP rs7966276 的差異來 影響或調控BICD1基因,進而抑制或減緩近視及/或近視 相關併發症。 在本發明另一實施樣態中’本發明另提供一種治療、 抑制或減缓近視及/或近視相關併發症的方法,包括給予 一個體一有效量之近視治療劑(近視治療藥物),此治療劑 由上述方法獲得。 如上所述’藉由控制BICD1基因的表現或活性可抑 ®制或誘導近視及/或近視相關併發症。因此,候選藥物可 藉由調控BICD1基因的表現以達到治療或抑制近視及/近 視相關併發症。 在本發明另一實施樣態中,本發明更提供一種評估藥 物對治療近視效果的方法,包括分析BICD1基因的SNp ,因型,其中若該個體存在某一特之SNp基因型時,表 示此藥物可能對治療近視具有良好的反應。 在本發明之方法中’上述BICD1基因的基因標誌、(基 因型)可作為評估一個體對近視及/或近視相關併發症的0911-A51298-TW 8 201011107 = The presence of this individual represents a myopia and/or myopia-related complications. This artist can choose different methods to dream about the SNP of the mcm gene, and the skilled person can easily ^ And the above method or other methods are performed. "Myopia susceptibility" as used in the present invention means that the individual is susceptible to or not easy to be close when a certain genotype of the SNP of the present invention is present. The "low myopia susceptibility" as used in the present invention means that the individual is not susceptible to myopia when a certain genotype of the SNP of the present invention is present. The "high myopia susceptibility" as described in the present invention means When the genotype of the invention exists, the individual is prone to myopia. In one embodiment of the invention, when SNP rsl0771923 has a dual gene G genotype, or sNp rsl151029 has a dual gene T genotype, this is indicated Individuals are more prone to myopia, and their risk of developing myopia is at least 1.2 times higher than other genotypes. In another embodiment of the invention, when SNp rs7966276 has a genotype of dual gene A, it indicates that the individual is less prone to myopia, The risk of myopia is at least 0.6 times lower than other genotypes. It should be noted that this individual may also increase or decrease the risk of myopia due to other factors, such as diseases or the environment. In one embodiment, the present invention provides a substance (candidate drug) for screening for complications related to myopia and/or myopia, including a substance to be tested and a BICD1 group. The cells are contacted and screened for substances that regulate the BICD1 gene compared to the control group (cells not exposed to the drug candidate). The genotype of the BICD1 gene (eg, SNP rs7966276, rsll51029, rs2650122, and rsl0771923) can be used as a search or 0911-A51298-TW 9 201011107 Identify biomarkers for the treatment of myopia and/or myopia-related complications by screening for a substance that alters the expression of the BICD1 gene, such as 'exposed a cell to a test substance or a mixture The test substance composition (sequentially or simultaneously) is analyzed and the expression of the BICD1 gene of the cell is analyzed, and the BICD1 gene expression of the untreated and treated substance is compared. The test substance may be a known or unknown compound. Including, but not limited to, a compound, a small molecule drug, a poly-audio class, a nucleotide acid, a protein or a triumph, etc. For example, the test substance can be a small interfering RNA. In one embodiment of the invention, the test Substance can influence or regulate the BICD1 gene by the difference of SNP ® rsl0771923, SNP rsll51029 or SNP rs7966276 Preparing or slowing down myopia and/or myopia-related complications. In another embodiment of the invention, the invention further provides a method of treating, inhibiting or slowing the complications associated with myopia and/or myopia, comprising administering an effective one A myopia therapeutic agent (a myopia treatment drug) obtained by the above method. As described above, 'by controlling the performance or activity of the BICD1 gene can suppress or induce myopia and/or myopia-related complications. The drug can be used to treat or inhibit myopia and/or myopia-related complications by regulating the performance of the BICD1 gene. In another embodiment of the present invention, the present invention further provides a method for evaluating a drug for treating myopia, comprising analyzing an SNp of a BICD1 gene, a type, wherein the individual has a specific SNp genotype, indicating The drug may respond well to the treatment of myopia. In the method of the present invention, the gene marker (gene type) of the above BICD1 gene can be used as an evaluation of a body for myopia and/or myopia-related complications.
0911-A51298-TW 201011107 感受性。當一個體中存在著易罹患近視之SNP基因型時 (例如’ rsl0771923之對偶基因G,或SNP rsll51029之 對偶基因T),表示此個體可能對一近視治療藥物具有良 好反應。本發明所述之“良好反應,,意指與無此特定SNP 基因型之個體相較,此個體對於此近視治療藥物具有較佳 的反應,且此個體也較易於惟患近視及/或近視相關併發 症。 在本發明另一實施樣態中,本發明更提供一種套組, 可用於分析由一個體獲得之生物樣本,檢測此個體對近視 的感受性’此套組包括一或複數個試劑以偵測BICD1基 因中一或複數個SNP基因型。 本發明中所述之“套組”包括一或複數個SNp檢測 試劑,或以一或複數種型式存在之一或複數個SNp檢測 試劑(例如,生物試劑、容器、包裝的樣式)。本發明之 SNP檢測套組包括,但不限於,探針及引子組合(例如, TaqMan探針/引子組合)’核苷酸陣列/微陣列,以及包括 一或複數個探針、引子或其他檢測試劑的磁珠。本發明之 ❹套組可任意地包括各種電子裝置,例如,陣列(DNA晶片) 及微流體控制系統(“ lab-on-a-chip”系統)。本發明之套 組可不包含電子裝置’而包括—或複數個SNp檢測試劑。0911-A51298-TW 201011107 Sensitivity. When there is a SNP genotype that is susceptible to myopia in a body (for example, the dual gene G of 'rsl0771923, or the dual gene T of SNP rsll51029), this individual may have a good response to a myopia treatment. The "good response" of the present invention means that the individual has a better response to the myopia treatment drug than the individual without the specific SNP genotype, and the individual is also more susceptible to myopia and/or myopia. Related complication. In another embodiment of the present invention, the present invention further provides a kit for analyzing a biological sample obtained from a body and detecting the sensitivity of the individual to myopia. The set includes one or more reagents. To detect one or a plurality of SNP genotypes in the BICD1 gene. The "set" described in the present invention includes one or more SNp detection reagents, or one or a plurality of SNp detection reagents in one or more types ( For example, biological reagents, containers, packaging styles. The SNP detection kits of the invention include, but are not limited to, probe and primer combinations (eg, TaqMan probe/primer combinations) 'nucleotide arrays/microarrays, and A magnetic bead comprising one or more probes, primers or other detection reagents. The cartridge of the present invention can optionally include various electronic devices, such as arrays (DNA wafers) and microfluidic controls System ( "lab-on-a-chip" system) set of the present invention may comprise an electronic device 'and comprising - a plurality SNp or detection reagent.
SNP偵測套組一般包括一或複數個偵測試劑,及其他 必須成分(例如,緩衝液、酵素,例如DNA聚合酶或 iigases、鏈延伸核苷酸,例如,dNTP,以及Sanger_type DNA 疋序反應物,鏈終止核苷酸,正對照組序列,負對照組序 列及其類似物)以進行分析,例如,擴增及/或偵測一 SNp 核苷酸。本發明之套組更可包括一或複數個裝置以分析目The SNP detection kit typically includes one or more detection reagents, and other essential components (eg, buffers, enzymes such as DNA polymerase or iigases, strand extension nucleotides, eg, dNTPs, and Sanger_type DNA sequence reactions) , chain termination nucleotides, positive control sequences, negative control sequences and analogs thereof for analysis, for example, amplification and/or detection of an SNp nucleotide. The kit of the present invention may further comprise one or more devices for analyzing the mesh
0911-A51298-TW 201011107 標核苷酸的含量,比較目標核苷酸與一標準含量的差異, 以及包括使用說明書以說明如何使用此套組來偵測sNp 核苦酸。在本發明之-實施例中,本發明之套組包括所需 之所有試劑以偵測一或複數個SNp核苷酸。在本發明另 一實施列中’ SNP偵測套組為一種核苷酸陣列,或間隔陣 歹^compartmentaiized kits),如微流體控制系統/ “lab-on-a,chip” 系統。 任何適當的探針,例如對偶基因專一性探針,皆可用 於上述陣列(晶片)中,且每個探針或探針對可結合至不同 的對偶基因位置。聚核苷酸探針可利用光引導化學程序來 形成於特定的區域。每個DNA晶片可包括,例如,複數 個(上千至百萬個)獨立的核苷酸探針排列在微小化的格 子狀裝置上。較佳此複數個探針可結合至固狀的支持陣列 上。 /本發明中之套組可包括,例如一或複數個試劑,一缓 衝液,以及一酵素,用以檢測一或複數個BICD1的SNp 基因型態。此试劑中包括至少一物質用以區別及偵測SNp ⑩基因型,上述物質包括,但不限於,核苷酸序列,其可完 全與至少一 BICD1的SNP基因型之某一位置互補,一限 制酶(例如,内切酶)以鑑別一特定序列,一標定之引子或 一標定的偶基因專一性探針。在本發明一實施例中,本發 明用來檢測或診斷近視之套組可包括複數個引子,引子用 來擴增BICD1基因之一區域,此區域包括SNPs rs7966276、rsi151029、rs2650122、及/或 rsl0771923,當 偵測到具有高度近視感受性之SNP基因型時,表示此個 體為近視的高危險族群。引子可分別根據SNPs0911-A51298-TW 201011107 The content of nucleotides, the difference between the target nucleotide and a standard content, and the instructions for use to explain how to use this kit to detect sNp nucleotide. In an embodiment of the invention, the kit of the invention includes all of the reagents required to detect one or more SNp nucleotides. In another embodiment of the invention, the 'SNP detection kit is a nucleotide array, or a compartmentalized kits, such as a microfluidic control system/"lab-on-a, chip" system. Any suitable probe, such as a dual gene-specific probe, can be used in the array (wafer) described above, and each probe or pair of probes can bind to a different dual gene position. Polynucleotide probes can be formed in specific regions using light directing chemistry procedures. Each DNA wafer can include, for example, a plurality (thousands to millions) of individual nucleotide probes arranged on a miniaturized lattice device. Preferably, the plurality of probes can be bonded to a solid support array. The kit of the present invention may comprise, for example, one or more reagents, a buffer, and an enzyme for detecting the SNp genotype of one or more BICD1. The reagent includes at least one substance for distinguishing and detecting the SNp 10 genotype, and the substance includes, but is not limited to, a nucleotide sequence which is completely complementary to a position of at least one BINP1 SNP genotype, A restriction enzyme (eg, an endonuclease) is used to identify a particular sequence, a calibrated primer or a calibrated even gene-specific probe. In an embodiment of the invention, the kit for detecting or diagnosing myopia of the present invention may comprise a plurality of primers for amplifying a region of the BICD1 gene, including SNPs rs7966276, rsi151029, rs2650122, and/or rsl0771923. When a SNP genotype with high myopia sensitivity is detected, it indicates that the individual is a high-risk group of myopia. Primers can be based on SNPs
0911-A51298-TW 12 201011107 rs7966276、rsll51029、rs265〇122 及/或如〇77的 兩側的序列進行設計。此外,在分析個對偶基因的差異 後,可利用質譜儀、螢光或冷光來分析個對偶基因的差異。 【實施例】 1.基因篩選 /本實施例分別針對4000名受試者進行近視的研究。 此受試者大致可分為4類:(1)年輕的役男,(2)大學生,(3) 醫院人員,以及(4)眼科的臨床病人。若受試者一眼之屈 光度2-6.0D’且另一眼之屈光度€_4.〇1)則歸類為高度近 視,而若受試者其中視力較差之一眼的屈光度> _15 D, 則將此類受試當作對照組。所有受試者的年齡皆介於17 至45歲,且皆為華人。 在實施的第一步驟,使用Affymetrix GeneChip® Human Mapping 500K晶片組,每組包括2個晶片,每個 晶片可分析約25〇,〇〇〇個SNP(Nsp晶片可分析約262,000 個’ Sty晶片可分析238,000個)。為使DNA樣本維持於 ❿一適當的品質下’將所有DNA樣本的OD 260/280值控制 於1.7至2.0之間,且OD260/230值大於1.0,取約1.5 pg (30 μΐ of 50 ng/μΐ)的基因體DNA進行基因型分析,並利 用BRLMM algorithm以獲得基因定型分析結果。同時, 為降低誤差’所有的分析必須滿足以下條件:對每個SNP 至少90%的樣本判讀率(per sample call rate),每個檢體至 少90%的SNP判讀率(per SNP call rate),對每個SNP次 要對偶基因頻率至少在1%以上,以及滿足哈溫平衡(p > 0.001)。綜合上述結果,對SNPrs380619進行進一步的分 0911-A51298-TW 13 201011107 析。 接著利用 PLINK program (2m J i/ww Gewez1 2007;81:559-75)來計算基因型及對偶基因頻率,及進行 X2測試,以分析對偶基因、SNP基因型與高度近視之間 的關係。 為了在各種遣傳模式下分析基因型的關係,將所獲得 的基因定型分析數據置入顯性(dominant)、隱性(recessive) 及加成性(additive)模式,並進行trend測試。將包含各種 變因(性別及年齡)之基因效應導入迴歸分析中,並利用線 ®性回歸模式來分析各個SNP與屈光度的關係。由於屈光 度大於-3D的情況普遍發生於台灣人上,因此又將受試者 分為正常/中度近視(g-3D)以及高度近視(S -6D)二種, 並以邏輯迴歸(Logistic Regression)分析表現型。並利用 Hap-clustering 來分析單體型(haplotype)。 本實施例之初步分析顯示出10個最相關的SNPs,且 其中p值最小為0.0002。此10個SNPs分別位於染色體1、 2、4、6、12、16、17及21,且分別座落於不相鄰的位置。 ❹ 2.基因篩選之第二步驟 在本實施例的第二步驟,首先利用由晶片篩選出的10 個最相關的SNPs,並在每個SNP的前後端200 kb區域 當成是候選區域。在這10個區域我們選了 384個SNP, 在1536位受試者進行基因型鑑定。此1536位受試者之屈 光度分別< -6 D或> -1.5D。基因型鑑定是用Illumina BeadArray technology (Sentrix® Array Matrix) (Mutat Res 2005;573:70-82)的操作平台,此平台利用DNA會與對偶 0911-A51298-TW 14 201011107 基因特異性寡核苷酸黏合,並經由PCR程序放大。晶片 的雜交程序及基因定位分析分別利用經Cy-3及Cy-5標定 的引子所完成。每個SNP重複30次以計算最高的基因頻 率。 整體來看,在此第二步驟中的基因鑑定的成功率為 97.1%。我們發現最相關的SNP (rs7966276)位於染色體 12pll 的 BICD1 基因上,其 p 值< 1.13xUT04,且 BICD1 基因中其他的SNPs同樣具有高度的相關性(SNP rsll51029, p= 4.78xl0'4; SNP rs2650122, p= 3.65xl0'2; 參 SNPrsl0771923,p=2.70xl0·2)。 3.基因筛選之第三步驟 在第三步驟中,利用TaqMan技術(Applied Biosystems [ABI],Foster City,USA)來分析由第二步驟中所獲得之高 度相關的 SNPs。簡而言之,以 Primer Express version 2.0 設計PCR引子及TaqMan MGB探針,在96孔盤及 GeneAmp 9700 thermal cyclers反應槽中完成反應,並利 ❷用ABI Prism 7500序列偵測系統及ABI Prism 7500 SDS software version 1.0軟體來偵測及分析螢光強度。在此第 三步驟中,所有受試者不論其屈光度之DNA都進行SNP 基因型鑑定。 在第三步驟中,主要聚焦於BICD1基因,並以不同 的遺傳模式分析超過3000位受試者之SNP rsl0771923、 SNPrsll51029、及 SNPrs7966276 的基因效應,各個 SNP 的基因頻率如表一所示。參照表二,當rsl0771923的次 要對偶基因G具有加成效應(p = 〇.〇〇〇88,OR=1.22)或 0911-A51298-TW 15 201011107 rsll5H)29的次要對偶基因T具有顯性有害效應(d〇minant deleterious)時可在二種表現型(以g jo作為斟昭细 < -6D作為近視)中獲得最相關的結果,而snp^96627=6 與近視的相關性較其他二個SNPs來得低。當以近視度數 當成連續,數分析後,Λ 3個s卿s顯示出有意義的結 果,如表二所不。第1圖顯不SNp rsll51029對偶基因τ 之頻率與各屈光度的關係,橫軸代表屈光度。 表一、 對偶基因頻率及BICD1 基因定型型分析 rsl0771923 TS115102Q rs7966276 屈光度 樣本數 MAF 樣本數 MAF 樣本數 MAF ^ -3D 1305 0.375 0wu 0.211 1215 0.040 -3D 至-6 D 941 0.400 1148 0.228 953 0.027 ^ -6D 1027 0.423 1139 0.247 794 0.025 總合 3273 0.397 3917 0.226 2962 0.032 MAF(minor allele frequency):次要對偶基因頻率 表二、以邏輯迴歸分析二元特徵(正常/中度近視vs. 高度近視)________ _基因型_____OR (p值) lSf (〇/〇) N (%) N (%) 總合 力口顯瓦 隱Ε ΑΑ tsI 07719230911-A51298-TW 12 201011107 rs7966276, rsll51029, rs265〇122 and/or sequences on both sides of 〇77 are designed. In addition, after analyzing the differences in the dual genes, mass spectrometers, fluorescence, or luminescence can be used to analyze differences in the dual genes. [Examples] 1. Gene Screening / This example was conducted on 4,000 subjects for myopia. The subjects can be broadly divided into four categories: (1) young males, (2) college students, (3) hospital staff, and (4) ophthalmic clinical patients. If the subject has a diopter of 2-6.0D' and the other eye has a diopter of €_4.〇1), it is classified as high myopia, and if the subject has a poor visual power, the diopter of one eye is _15 D, then The class was tested as a control group. All subjects were between the ages of 17 and 45 and were all Chinese. In the first step of the implementation, the Affymetrix GeneChip® Human Mapping 500K chipset is used, each consisting of 2 wafers, each wafer can be analyzed for approximately 25 〇, one SNP (Nsp wafer can analyze approximately 262,000 ' Sty wafers Analysis of 238,000). In order to maintain the DNA sample at a suitable quality 'to control the OD 260/280 value of all DNA samples between 1.7 and 2.0, and the OD260/230 value is greater than 1.0, take about 1.5 pg (30 μΐ of 50 ng/ The genotype DNA of μΐ) was genotyped and the BRLMM algorithm was used to obtain the results of the genotyping analysis. At the same time, in order to reduce the error, all analyses must meet the following conditions: a per sample call rate of at least 90% for each SNP, and a per SNP call rate of at least 90% for each sample. The secondary gene frequency for each SNP is at least 1% above, and the Hwar equilibrium is satisfied (p > 0.001). Based on the above results, SNPrs380619 is further divided into 0911-A51298-TW 13 201011107. The PLINK program (2m J i/ww Gewez1 2007; 81:559-75) was then used to calculate the genotype and dual gene frequencies, and the X2 test was performed to analyze the relationship between the dual gene, SNP genotype and high myopia. In order to analyze genotype relationships in various deportation modes, the obtained genotyping analysis data was placed into dominant, recessive, and additive modes, and a trend test was performed. Gene effects including various variables (gender and age) were introduced into the regression analysis, and the relationship between each SNP and diopter was analyzed using a linear regression model. Since the diopter greater than -3D is common in Taiwanese, subjects are divided into normal/moderate myopia (g-3D) and high myopia (S-6D), and logistic regression (Logistic Regression) ) Analyze phenotypes. Hap-clustering was used to analyze the haplotype. The preliminary analysis of this example showed the 10 most relevant SNPs, and the p value was at least 0.0002. The 10 SNPs are located on chromosomes 1, 2, 4, 6, 12, 16, 17, and 21, respectively, and are located at non-adjacent locations. ❹ 2. Second step of gene screening In the second step of the present embodiment, the 10 most relevant SNPs screened by the wafer are first used, and the 200 kb region at the front and rear ends of each SNP is regarded as a candidate region. In these 10 regions, we selected 384 SNPs and genotypes were identified in 1536 subjects. The diopter of this 1536 subjects was < -6 D or > - 1.5D, respectively. Genotyping is performed using Illumina BeadArray technology (Sentrix® Array Matrix) (Mutat Res 2005; 573:70-82), which utilizes DNA to interact with the dual 0911-A51298-TW 14 201011107 gene-specific oligonucleotide Bonded and amplified by PCR program. The hybridization procedure and gene mapping analysis of the wafers were performed using primers calibrated with Cy-3 and Cy-5, respectively. Each SNP was repeated 30 times to calculate the highest gene frequency. Overall, the success rate of gene identification in this second step was 97.1%. We found that the most relevant SNP (rs7966276) is located on the BICD1 gene of chromosome 12pll with a p-value of 1.13xUT04, and other SNPs in the BICD1 gene are also highly correlated (SNP rsll51029, p= 4.78xl0'4; SNP Rs2650122, p= 3.65xl0'2; see SNPrsl0771923, p=2.70xl0·2). 3. Third Step of Gene Screening In the third step, TaqMan technology (Applied Biosystems [ABI], Foster City, USA) was used to analyze the SNPs obtained by the second step. Briefly, PCR primers and TaqMan MGB probes were designed with Primer Express version 2.0, and reactions were performed in 96-well plates and GeneAmp 9700 thermal cyclers, using ABI Prism 7500 sequence detection system and ABI Prism 7500 SDS. Software version 1.0 software to detect and analyze fluorescence intensity. In this third step, all subjects, regardless of their diopter DNA, were identified for SNP genotypes. In the third step, the BICD1 gene was mainly focused, and the genetic effects of SNP rsl0771923, SNP rsll51029, and SNP rs7966276 in more than 3,000 subjects were analyzed in different genetic models. The gene frequencies of each SNP are shown in Table 1. Referring to Table 2, when the minor dual gene G of rsl0771923 has an additive effect (p = 〇.〇〇〇88, OR=1.22) or 0911-A51298-TW 15 201011107 rsll5H)29, the minor dual gene T is dominant. In the case of detrimental effect (d〇minant deleterious), the most relevant results can be obtained in two phenotypes (g jo as 斟 细 & -6D as myopia), while snp^96627=6 is more relevant to myopia than other The two SNPs come low. When the number of myopia is continuous and the number is analyzed, Λ3 s s s show meaningful results, as shown in Table 2. Figure 1 shows the relationship between the frequency of the SNp rsll51029 dual gene τ and the diopter, and the horizontal axis represents the diopter. Table 1, dual gene frequency and BICD1 gene typing analysis rsl0771923 TS115102Q rs7966276 diopter sample number MAF sample number MAF sample number MAF ^ -3D 1305 0.375 0wu 0.211 1215 0.040 -3D to -6 D 941 0.400 1148 0.228 953 0.027 ^ -6D 1027 0.423 1139 0.247 794 0.025 total 3273 0.397 3917 0.226 2962 0.032 MAF (minor allele frequency): secondary dual gene frequency table 2. Logistic regression analysis of binary features (normal / moderate myopia vs. high myopia) ________ _ genotype _____OR (p value) lSf (〇/〇) N (%) N (%) Total joint force display tile concealed ΑΑ tsI 0771923
2-3 D ^-6 D 5091338(32.9) \)/ \—/ 1 7 1447.1049. 6 5 \»7 V-^ ο 4 8214.7917. 02 !·22 1.30 1.30 (0.00088) (0.0024) (0.021)2-3 D ^-6 D 5091338(32.9) \)/ \-/ 1 7 1447.1049. 6 5 \»7 V-^ ο 4 8214.7917. 02 !·22 1.30 1.30 (0.00088) (0.0024) (0.021)
rsl 151029 AA AT TTRsl 151029 AA AT TT
^ -3 D ^-6D 3 3 6 1 IX \—/ \7 5 4 84(5.70(6. \—y \ly 8 1 519(31.423(37. \—/ \J 7 ο 7 323·;£6· 10(664(5 !·22 1.30 1.21 (0.0017) (0.00088) (0.263)^ -3 D ^-6D 3 3 6 1 IX \—/ \7 5 4 84(5.70(6. \-y \ly 8 1 519(31.423(37. \—/ \J 7 ο 7 323·; £ 6· 10(664(5 !·22 1.30 1.21 (0.0017) (0.00088) (0.263)
rs7966276 TT AT AARs7966276 TT AT AA
2-3 D ^-6D \ϊ/' ο - 90(7.39(4.1 222.3)55.0)1 11(9275(9 4)3 .2(0 (00 94 〇·61 0.62 (0.0114) (0.0161)2-3 D ^-6D \ϊ/' ο - 90(7.39(4.1 222.3)55.0)1 11(9275(9 4)3 .2(0 (00 94 〇·61 0.62 (0.0114) (0.0161)
0911-A51298-TW 16 201011107 表三、以線性回歸模式分析屈光度 基因型 加成性 顯性 隱性 P値 βχ 100 Ρ値 BxlOO P値 BxlOO P値 rsl0771923 0.0128 48.4 0.0032 29.2 0.0115 35.4 0.0230 rsl 151029 0.020 46.9 0.0060 28.8 0.0060 29.6 0.181 rs7966276 0.022 -125.1 0.0060 -62.7 0.0077 -173.8 0.260 雖然本發明已以較佳實施例揭露如上,然其並非用以 限定本發明,任何熟習此技藝者,在不脫離本發明之精神 和範圍内,當可作些許之更動與潤飾,因此本發明之保護 範圍當視後附之申請專利範圍所界定者為準。0911-A51298-TW 16 201011107 Table 3. Analysis of diopter genotype-additive recessive P値βχ 100 Ρ値BxlOO P値BxlOO P値rsl0771923 0.0128 48.4 0.0032 29.2 0.0115 35.4 0.0230 rsl 151029 0.020 46.9 0.0060 28.8 0.0060 29.6 0.181 rs7966276 0.022 -125.1 0.0060 -62.7 0.0077 -173.8 0.260 Although the present invention has been disclosed in the above preferred embodiments, it is not intended to limit the invention, and any person skilled in the art without departing from the spirit of the invention In the scope of the invention, the scope of protection of the invention is defined by the scope of the appended claims.
參Reference
0911-A51298-TW 17 201011107 【圖式簡單說明】 第1圖顯示rsl 151029對偶基因T之頻率與各個屈光 度的關係。 【主要元件符號說明】 無00911-A51298-TW 17 201011107 [Simple description of the diagram] Figure 1 shows the relationship between the frequency of the rsl 151029 dual gene T and each diopter. [Main component symbol description] No 0
0911-A51298-TW 180911-A51298-TW 18
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CN102732607A (en) * | 2011-03-07 | 2012-10-17 | 四川省医学科学院(四川省人民医院) | Kit for detecting high myopia |
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