Key Lab of Forest Genetics and Biotechnology, Ministry of Education, College of Forestry,
Nanjing Forestry University, Nanjing 210037, China
Show less
文章历史+
出版日期
2016-08-18
发布日期
2016-08-18
摘要
外显子组测序主要包括3个步骤:目标序列的富集、DNA测序、生物信息学分析。笔者介绍了外显子组测序技术及其在遗传研究中的应用,分析了该技术的优势和不足,并对其应用前景进行了展望。与转录组和全基因组测序技术相比,外显子组测序在编码基因获取方面具有高效、准确、低成本的特点; 与全基因组关联分析技术(Genome-wide association analysis, GWAS)相比,能有效检测基因组中编码基因的稀有变异,但还不能检测到基因组水平上较大的结构性变异以及内含子区域的信息。目前,外显子组测序技术在人类单基因控制的遗传疾病和多基因控制的复杂疾病的分子机理研究中,能准确找到孟德尔遗传疾病致病基因; 在动植物上能成功检测到目标编码区的核苷酸变化。随着模式木本植物全基因组测序的完成,利用该技术可以加快对木本植物性别、林木抗逆性及生长等重要性状基因的定位,应用前景广阔。
Abstract
The exome sequencing mainly includes three steps: enriching the target region, DNA sequencing, bioinformatics analysis. The authors give a brief introduction on the exome sequencing technique and its application in genetic studies, discuss its advantages and disadvantages and propose its application prospect in future studies. Compared with the transcriptome and the whole genome sequencing techniques, it is more efficient, more time and labor saving in acquisition of large sequencing data of the encoding genes. Moreover, compared with Genome-wide association analysis(GWAS), it can effectively detect the rare variation in exonic DNA sequences. However, it can not detect the large structural variation and the information of introns in the genome level. At present, this technique can accurately find the Mendel disease-causing gene underlying both the single gene associated diseases and the multiple gene associated diseases in the molecular mechanism. It can also detect successfully the nucleotide variations in the target coding region in animal and plant genetic studies. With the completion of the pattern of woody plants genome sequencing, some important traits gene could be located by this technique, such as sex, plant resistance, growth etc. It will bring broad application prospects.
MA Qiuyue, DAI Xiaogang, LI Shuxian.
A review on exome sequencing technique[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2016, 40(04): 157-163 https://doi.org/10.3969/j.issn.1000-2006.2016.04.025
中图分类号：
Q78
{{custom_sec.title}}
{{custom_sec.title}}
{{custom_sec.content}}
参考文献
[1] Visscher P M, Brown M A, McCarthy M I, et al. Five years of GWAS discovery[J]. The American Journal of Human Genetics, 2012, 90(1): 7-24. Doi:10.1016/j.ajhg.2011.11.029.
[2] Cantor R M, Lange K, Sinsheimer J S. Prioritizing GWAS results: a review of statistical methods and recommendations for their application[J].The American Journal of Human Genetics, 2010, 86(1):6-22. Doi:10.1016/j.ajhg.2009.11.017.
[3] Stadler Z K, Vijai J, Thom P, et al. Genome-wide association studies of cancer predisposition[J]. Hematology Oncology Clinics of North America, 2010, 24(5): 973-996. Doi:10.1016/j.hoc.2010.06.009.
[4] Botstein D, Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease[J]. Nature Genetics, 2003, 33(3): 228-237. Doi:10.1038/ng1090.
[5] 姜海鸥,全庆丽,胡祥上,等. 全外显子组测序技术及其在遗传性耳聋研究中的应用[J]. 中华耳科学杂志, 2015, 13(1): 179-182.
Jiang H O, Quan Q L, Hu X S, et al. Whole exome sequencing and its application in genetic hearing loss research[J]. Chinese Journal of Otology, 2015, 13(1): 179-182.
[6] Zeitz C, Jacobson S G, Hamel C P, et al. Whole-Exome sequencing identifies LRIT3 mutations as a cause of autosomal-recessive complete congenital stationary night blindness[J]. The American Journal of Human Genetics, 2013, 92(1): 67-75. Doi:10.1016/j.ajhg.2012.10.023.
[7] Chen W J, Lin Y, Xiong Z Q, et al. Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia[J]. Nature Genetics, 2011, 43(12): 1252-1255. Doi: 10.1038/ng.1008.
[8] D'Ascenzo M, Meacham C, Kitzman J, et al.Mutation discovery in the mouse using genetically guided array capture and resequencing[J]. Mammalian Genome, 2009, 20(7): 424-436. Doi 10.1007/s00335-009-9200-y.
[9] Robert C, Fuentes-Utrilla P, Troup K, et al.Design and development of exome capture sequencing for the domestic pig(Sus scrofa)[J]. BMC Genomics, 2014,15:550. Doi: 10.1186/1471-2164-15-550.
[10] Saintenac C, Jiang D,Akhunov E D. Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome[J]. Genome Biology, 2011, 12(9): 88.
[11] Whitelaw C A, Barbazuk W B, Pertea G, et al.Enrichment of gene-coding sequences in Maize by genome filtration[J]. Science, 2003, 302: 2118-2120. Doi: 10.1126/science.1090047.
[12] Garber K. Fixing the front end[J]. Nature Biotechnology, 2008, 26(10): 1101-1104. Doi:10.1038/nbt1008-1101.
[13] Turner E H, Ng S B, Nickerson D A, et al. Methods for genomic partitioning[J]. Annual Review of Genomics and Human Genetics, 2009, 10: 263-284.Doi:10.1146/annurev-genom-082908-150112.
[14] Summerer D. Enabling technologies of genomie-scale sequence enrichment for targeted high-throughput sequencing[J]. Genomics, 2009, 94(6): 363-368. Doi: 10.1016/j.ygeno.2009.08.012.
[15] Mamanova L, Coffey A J, Scott C E, et al. Target-enrichment strategies for next-generation sequencing[J]. Nature Methods, 2010, 7: 111-118. Doi: 10.1038/nmeth.1419.
[16] Ku C S, Cooper D N, Polychronakos C, et al.Exome sequencing: dual role as a discovery and diagnostic tool[J]. Annals Neurology, 2012, 71(1): 5-14. Doi: 10.1002/ana.22647.
[17] Asan, Xu Y, Jiang H, et al. Comprehensive comparison of three commercial human whole-exome capture platforms[J]. Genome Biology, 2011, 12(9): R95. Doi: 10.1186/gb-2011-12-9-r95.
[18] Bodi K, Perera A G, Adams P S, et al. Comparison of commercially available target enrichment methods for next-generation sequencing[J]. Journal of Biomolecular Techniques, 2013, 24(2): 73-86. Doi: 10.7171/jbt.13-2402-002.
[19] Clark M J, Chen R, Lam H Y K, et al. Performance comparison of exome DNA sequencing technologies[J]. Nature Biotechnology, 2011, 29(10): 908-914. Doi:10.1038/nbt.1975.
[20] Chilamakuri C S R, Lorenz S, Madoui M A, et al. Performance comparison of four exome capture systems for deep sequencing[J]. BMC Genomics, 2014, 15(1):1-14. Doi: 10.1186/1471-2164-15-449.
[21] Sulonen A M, Ellonen P, Almusa H, et al. Comparison of solution-based exome capture methods for next generation sequencing[J]. Genome Biology, 2011,12(9): R94. Doi: 10.1186/gb-2011-12-9-r94.
[22] Droege M, Hill B. The Genome Sequencer FLXTM System-longer reads, more applications, straight forward bioinformatics and more complete data sets[J]. Journal Biotechnology, 2008, 136(1-2): 3-10.Doi:10.1016/j.jbiotec.2008.03.021.
[23] Hillier L W, Marth G T, Quinlan A R, et al. Whole-genome sequencing and variant discovery in C. elegans[J]. Nature Methods, 2008, 5(2): 183-188. Doi:10.1038/nmeth.1179.
[24] Hashimoto S, Qu W, Ahsan B, et al. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer[J]. PLoS One, 2009, 4(1): e4108. Doi: 10.1371/journal.pone.0004108.
[25] Rothberg J M, Leamon J H. The development and impact of 454 sequencing[J]. Nature Biotechnology, 2008, 26(10): 1117-1124. Doi: 10.1038/nbt1485.
[26] Bao R, Huang L, Andrade J, et al. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing[J]. Cancer Informatics, 2014:13(s2)67-82. Doi: 10.4137/CIN.S13779.
[27] Wu T D, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads[J]. Bioinformatics, 2010, 26(7):873-881. Doi: 10.1093/bioinformatics/btq057.
[28] Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools[J]. Bioinformatics, 2009, 25(16): 2078-2079. Doi:10.1093/bioinformatics/btp352.
[29] Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing[J]. Quantitative Biology, 2012, 1207:3907.
[30] Challis D, Yu J, Evani U S, et al. An integrative variant analysis suite for whole exome next-generation sequencing data[J]. BMC Bioinformatics, 2012, 13(1):8. Doi: 10.1186/1471-2105-13-8.
[31] Cingolani P, Platts A, Wang L L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3[J]. Fly(Austin), 2012, 6(2): 80-92. Doi:10.4161/fly.19695.
[32] Nam J Y, Kim N K D, Kim S C, et al. Evaluation of somatic copy number estimation tools for whole-exome sequencing data[J]. Briefings in Bioinformatics, 2016,17(2):185-192. Doi: 10.1093/bib/bbv055.
[34] Ng S B, Buckingham K J, Lee C, et al. Exome sequencing identifies the cause of a mendelian disorder[J]. Nature Genetics, 2010, 42(1): 30-35. Doi:10.1038/ng.499.
[35] Zhang X J. Exome sequencing greatly expedites the progressive research of Mendelian diseases[J]. Frontiers Medicine, 2014, 8(1): 42-57. Doi: 10.1007/s11684-014-0303-9.
[36] Boycott K M, Vanstone M R, Bulman D E, et al. Rare-disease genetics in the era of next-generation sequencing: discovery to translation[J]. Nature Review Genetics, 2013, 14(10): 68l-691. Doi:10.1038/nrg3555.
[37] Clayton-Smith J, O'SulliVan J, Daly S, et al. Whole exome-Sequencing identifies mutations in histone acetyltransferase gene KAT6B in individuals with the say-barber-biesecker variant of ohdo syndrome[J]. The American Journal of Human Genetics, 2011, 89(5): 675-681. Doi:10.1016/j.ajhg.2011.10.008.
[38] Walsh T, Shahin H, Elkan-Miller T, et al. Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82[J]. The American Journal of Human Genetics, 2010, 87(1): 90-94. Doi:10.1016/j.ajhg.2010.05.010.
[39] Caliskan M, Chong J X, Uricchio L, et al. Exome sequencing reveals a novel mutation for autosomal recessive non-syndromic mental retardation in the TECR gene on chromosome 19p13[J]. Human Molecular Genetics, 2011, 20(7): 1285-1289. Doi:10.1093/hmg/ddq569.
[40] Johnson J O, Mandrioli J, Benatar M, et al. Exome sequencing reveals VCP mutations as a cause of familial ALS[J]. Neuron, 2010, 68(5): 857-864. Doi:10.1016/j.neuron.2011.01.009.
[41] Bilgüvar K, Öztürk A K, Louvi A, et al. Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations[J]. Nature, 2010, 467: 207-210. Doi:10.1038/nature09327.
[42] Musunuru K, Pirruccello J P, Do R, et al. Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia[J]. The New England Journal of Medicine, 2010, 363(23): 2220-2227. Doi: 10.1056/NEJMoa1002926.
[43] Cosart T, Beja-Pereira A, Chen S Y, et al. Exome-wide DNA capture and next generation sequencing in domestic and wild species[J]. BMC Genomics, 2011, 12: 347. Doi: 10.1186/1471-2164-12-347.
[44] Bolon Y T, Haun W J, Xu W W, et al. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean[J]. Plant Physiology, 2011, 156(1): 240-253. Doi: 10.1104/pp.110.170811.
[45] Salmon A, Udall J A, Jeddeloh J A, et al. Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton[J]. Genes Genomes Genetics, 2012,2(8): 921-930. Doi: 10.1534/g3.112.003392.
[46] Mascher M T A, Richmond D J, Gerhardt A, et al. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond[J]. Plant Journal, 2013, 76(3): 494-505. Doi: 10.1111/tpj.12294.
[47] Klein C J, Botuyan M V, Wu Y, et al. Mutations in DNMT1cause hereditary sensory neuropathy with dementia and hearing loss[J]. Nature Genetics, 2011, 43(6): 595-600. Doi: 10.1038/ng.830.
[48] Biesecker L G. Exome sequencing makes medical genomics a reality[J]. Nature Genetics, 2010, 42(1): 13-14. Doi:10.1038/ng0110-13.
[49] Henry I M, Nagalakshmi M, Lieberman M C, et al. Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing[J]. Plant Cell, 2014, 26(4): 1382-1397. Doi:10.1105/tpc.113.121590.
[50] Brenchley R, Spannagl M, Pfeifer M, et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing[J]. Nature, 2012, 491: 705-710. Doi:10.1038/nature11650.
[51] Winfield M O, Wilkinson P A, Allen A M, et al. Targeted re-sequencing of the allohexaploid wheat exome[J]. Plant Biotechnology Journal, 2012, 10(6): 733-742. Doi: 10.1111/j.1467-7652.2012.00713.x.
PDF(1620082 KB)
