全外顯子組測序?qū)ふ襏sher綜合征致病基因位點(diǎn)
發(fā)布時(shí)間：2018-08-20 20:06
【摘要】：目的尋找患有先天性耳聾及視網(wǎng)膜變性同胞姐弟的致病基因位點(diǎn)。方法應(yīng)用全外顯子捕獲測序技術(shù),對人類基因組上1%的基因編碼區(qū)進(jìn)行捕獲,體外進(jìn)行擴(kuò)增,并在hiseq2500高通量測序儀上進(jìn)行并行測序,運(yùn)用生物信息學(xué)方法分析測序數(shù)據(jù)與測序質(zhì)量,并計(jì)算外顯子區(qū)的覆蓋度與測序深度,使用主流的數(shù)據(jù)分析流程GATK檢測變異位點(diǎn),并使用Annovar對位點(diǎn)進(jìn)行注釋,采用最新的致病位點(diǎn)算法pVAAST分析排序致病位點(diǎn),分析致病位點(diǎn)在數(shù)據(jù)庫中的頻率、危害性及保守性,一代測序驗(yàn)證位點(diǎn)在家系中是否共分離。結(jié)果1.一家四口全外顯子測序數(shù)據(jù)都在10G以上,80%的堿基測序質(zhì)量在Q30以上;2.對外顯子區(qū)域測序深度分析,平均測序深度在110X以上,99%區(qū)域大于10X;3.pVAAST分析顯示MYO7A基因的兩個(gè)位點(diǎn)為最可能致病基因;4.MYO7A兩位點(diǎn)在公共數(shù)據(jù)庫中均未見報(bào)導(dǎo),其中一個(gè)位點(diǎn)c.5994GA為無義突變,使蛋白翻譯提前終止,另一位點(diǎn)c.849+2TC在剪切位點(diǎn)附近,該位點(diǎn)經(jīng)scSNV算法評估影響外顯子剪切;5.通過PhastCons算法評估兩個(gè)位點(diǎn)均非常保守,一代Sanger測序驗(yàn)證,父母各攜帶一個(gè)位點(diǎn)雜合子,姐弟為復(fù)合雜合突變,符合隱性遺傳傳遞模式。結(jié)論應(yīng)用全外顯子測序技術(shù)尋找到一個(gè)Usher綜合征核心家系的兩個(gè)MYO7A致病位點(diǎn),為臨床進(jìn)行核心家系的遺傳致病位點(diǎn)鑒定提供了有義的探索。
[Abstract]:Objective to search for the genetic loci of siblings with congenital deafness and retinal degeneration. Methods A total exon capture and sequencing technique was used to capture 1% of the coding region of the human genome and amplify it in vitro. Parallel sequencing was performed on a hiseq2500 high throughput sequencing apparatus. The sequence data and quality were analyzed by bioinformatics method, and the coverage and sequencing depth of exon region were calculated. GATK was used to detect the mutation sites, and Annovar was used to annotate the sites. The latest pathogenetic loci algorithm (pVAAST) was used to analyze the sequence of pathogenicity loci. The frequency, harmfulness and conservatism of the pathogenicity loci in the database were analyzed. A generation of sequencing was used to verify whether the loci were coisolated at home. Result 1. The total exon sequencing data of four members of a family were all above 10G and 80% of the base sequence quality was above Q30. The analysis of exon region sequencing depth showed that the average sequencing depth was above 110X and 99% was more than 10XG 3.pVAAST analysis showed that the two loci of MYO7A gene were the most likely pathogenetic gene. The two loci of MYO7A were not reported in the public database. One locus, c.5994GA, was a nonsense mutation, resulting in early termination of protein translation, and another locus, c.849 2TC, was located near the shear site. The site was evaluated by scSNV algorithm for the effect of exon shearing. The PhastCons algorithm was used to evaluate the two loci. The results of Sanger sequencing showed that each parent carried one heterozygote and the sibling was a compound heterozygous mutation, which was in accordance with the recessive transmission pattern. Conclusion two MYO7A pathogenicity loci of a nuclear family with Usher syndrome were found by using total exon sequencing technique, which provides a meaningful exploration for clinical identification of genetic pathogenicity sites in nuclear families.
【學(xué)位授予單位】：天津醫(yī)科大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2017
【分類號】：R764.43;R774.1
本文編號：2194843
[Abstract]:Objective to search for the genetic loci of siblings with congenital deafness and retinal degeneration. Methods A total exon capture and sequencing technique was used to capture 1% of the coding region of the human genome and amplify it in vitro. Parallel sequencing was performed on a hiseq2500 high throughput sequencing apparatus. The sequence data and quality were analyzed by bioinformatics method, and the coverage and sequencing depth of exon region were calculated. GATK was used to detect the mutation sites, and Annovar was used to annotate the sites. The latest pathogenetic loci algorithm (pVAAST) was used to analyze the sequence of pathogenicity loci. The frequency, harmfulness and conservatism of the pathogenicity loci in the database were analyzed. A generation of sequencing was used to verify whether the loci were coisolated at home. Result 1. The total exon sequencing data of four members of a family were all above 10G and 80% of the base sequence quality was above Q30. The analysis of exon region sequencing depth showed that the average sequencing depth was above 110X and 99% was more than 10XG 3.pVAAST analysis showed that the two loci of MYO7A gene were the most likely pathogenetic gene. The two loci of MYO7A were not reported in the public database. One locus, c.5994GA, was a nonsense mutation, resulting in early termination of protein translation, and another locus, c.849 2TC, was located near the shear site. The site was evaluated by scSNV algorithm for the effect of exon shearing. The PhastCons algorithm was used to evaluate the two loci. The results of Sanger sequencing showed that each parent carried one heterozygote and the sibling was a compound heterozygous mutation, which was in accordance with the recessive transmission pattern. Conclusion two MYO7A pathogenicity loci of a nuclear family with Usher syndrome were found by using total exon sequencing technique, which provides a meaningful exploration for clinical identification of genetic pathogenicity sites in nuclear families.
【學(xué)位授予單位】：天津醫(yī)科大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2017
【分類號】：R764.43;R774.1
【參考文獻(xiàn)】
相關(guān)期刊論文 前1條
1 Wei Zhai;Xin Jin;Yan Gong;Ling-Hui Qu;Chen Zhao;Zhao-Hui Li;;Phenotype of Usher syndrome type Ⅱ assosiated with compound missense mutations of c.721 C>T and c.1969 C>T in MYO7A in a Chinese Usher syndrome family[J];International Journal of Ophthalmology;2015年04期
，本文編號：2194843
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