分子倒置探针技术的研究进展及应用
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摘要
分子倒置探针技术是一项新发展起来的用于目标序列捕获的分子生物学技术,该技术通过设计特异的探针对已知的特定目的基因组序列进行捕获,将目标序列DNA富集后再利用芯片杂交或测序进行检测。此技术有助于研究人员对大样本中的基因组重要区域进行研究,避免了全基因组研究费用高、分析困难等问题。并且,分子倒置探针技术弥补了杂交捕获技术、PCR捕获技术等分子捕获手段的不足,为动植物及病原菌重要DNA片段的研究提供强有力的技术支持。目前,分子倒置探针技术广泛应用于单核苷酸多态性(SNP)分型、外显子测序、拷贝数变异、杂合性丢失、体细胞突变、DNA甲基化和可变剪接等方面的研究。由于其特异性强、重复性好、操作简单、费用低廉,并对DNA完整度要求不高,适用于福尔马林石蜡包埋样本分析等特点,分子倒置探针技术的应用越来越广泛。然而,分子倒置探针技术在探针设计及数据分析软件研发等方面仍存在一些不足,还需要进一步的优化完善。为促进相关领域学者全面了解该技术,综述了分子倒置探针技术的基本原理、发展历程、技术特点及在疾病研究领域的应用,讨论了分子倒置探针技术的价值及存在的问题。
Molecular inversion probe technology is a newly developed technique for capturing targeted sequences by designed specific probes,and the captured sequences is enriched for subsequent chip hybridization or sequencing detection. By this technology,researchers can study important genome regions in a large of samples and avoid the high cost and difficulties from genome-wide analysis. In addition,molecular inversion probe technology makes up for the shortages of molecular capture methods such as hybrid capture and PCR capture techniques,and will provide forceful technical support for the research of important DNA fragments of plants,animals and pathogens. Molecular inversion probe technology is currently being used in SNP genotyping,exon sequencing,copy number variation,loss of heterozygosity,somatic mutation,DNA methylation and alternative splicing,etc. Molecular inversion probe technology has been applied more and more broadly owing to its characteristics,such as strong specificity,fine repeatability,simple operation,low cost,low requirement for DNA integrity,and being adaptable to the analysis of formalin-paraffin-embedded samples. However,molecular inversion probe technology still needs to be improved in terms of probe design and data analysis software development. To promote a comprehensive understanding of this technology,here we review the principle,development process,technical characteristics,and the applications in disease research,as well as discuss its values and existing issues while applying molecular inversion probe technology.
Molecular inversion probe technology is a newly developed technique for capturing targeted sequences by designed specific probes,and the captured sequences is enriched for subsequent chip hybridization or sequencing detection. By this technology,researchers can study important genome regions in a large of samples and avoid the high cost and difficulties from genome-wide analysis. In addition,molecular inversion probe technology makes up for the shortages of molecular capture methods such as hybrid capture and PCR capture techniques,and will provide forceful technical support for the research of important DNA fragments of plants,animals and pathogens. Molecular inversion probe technology is currently being used in SNP genotyping,exon sequencing,copy number variation,loss of heterozygosity,somatic mutation,DNA methylation and alternative splicing,etc. Molecular inversion probe technology has been applied more and more broadly owing to its characteristics,such as strong specificity,fine repeatability,simple operation,low cost,low requirement for DNA integrity,and being adaptable to the analysis of formalin-paraffin-embedded samples. However,molecular inversion probe technology still needs to be improved in terms of probe design and data analysis software development. To promote a comprehensive understanding of this technology,here we review the principle,development process,technical characteristics,and the applications in disease research,as well as discuss its values and existing issues while applying molecular inversion probe technology.
引文
[1]黄建锋,肖华胜.目标序列捕获技术及其应用[J].生物产业技术, 2011(4):64-69.
[2]Nilsson M, Malmgren H, Samiotaki M, et al. Padlock probes:circularizing oligonucleotides for localized DNA detection[J].Science,, 1994, 265(5181):2085.
[3]Hardenbol P, Banér J, Jain M, et al. Multiplexed genotypingwith sequence-tagged molecular inversion probes[J]. NatureBiotechnology, 2003, 21(6):673-678.
[4]Ji H, Welch K. Molecular inversion probe assay for allelicquantitation[M]. Microarray Analysis of the Physical Genome:Methods and Protocols, 2009:67-87.
[5]Wang Y, Moorhead M, Karlin-Neumann G, et al. Analysis ofmolecular inversion probe performance for allele copy numberdetermination[J]. Genome Biology, 2007, 8(11):R246.
[6]Akhras MS, Unemo M, Thiyagarajan S, et al. Connector inversionprobetechnology:apowerfulone-primermultiplexDNAamplification system for numerous scientific applications[J].PLoS One, 2007, 2(9):e915.
[7]Turner EH, Lee C, Ng SB, et al. Massively parallel exon capture andlibrary-free resequencing across 16 genomes[J]. Nature Methods,2009, 6(5):315.
[8]Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accuratewhole human genome sequencing using reversible terminatorchemistry[J]. Nature, 2008, 456(7218):53.
[9]Porreca GJ, Zhang K, Li JB, et al. Multiplex amplification of largesets of human exons[J]. Nature Methods, 2007, 4(11):931.
[10]Hiatt JB, Pritchard CC, Salipante SJ, et al. Single moleculemolecular inversion probes for targeted, high-accuracy detection oflow-frequency variation[J]. Genome Research, 2013, 23(5):843-854.
[11]O'Roak BJ, Vives L, Fu W, et al. Multiplex targeted sequencingidentifiesrecurrentlymutatedgenesinautismspectrumdisorders[J]. Science, 2012, 338(6114):1619-1622.
[12]唱凯,贾双荣,潘锋,等.基于分子倒置探针的乙型肝炎病毒耐药基因单碱基突变检测技术的建立[J].中华检验医学杂志,2014(5):337-341.
[13]Carrascosa LG, Sina AAI, Palanisamy R, et al. Molecular inversionprobe-based SPR biosensing for specific, label-free and realtime detection of regional DNA methylation[J]. ChemicalCommunications, 2014, 50(27):3585-3588.
[14]Wang Y, Cottman ME, Schiffman JD. Molecular inversion probes:a novel microarray technology and its application in cancerresearch[J]. Cancer Genetics, 2012, 205(7):341-355.
[15]Wang T, Guo H, Xiong B, et al. De novo genic mutations amongaChineseautismspectrumdisordercohort[J].NatureCommunications, 2016, 7:13316.
[16]Kou HS, Wang CC. Molecular inversion probes equipped withdiscontinuous rolling cycle amplification for targeting nucleotidevariants:Determining SMN1 and SMN2 genes in diagnosis ofspinal muscular atrophy[J]. Analytica Chimica Acta, 2017,977:65-73.
[17]Ji H, Kumm J, Zhang M, et al. Molecular inversion probe analysisof gene copy alterations reveals distinct categories of colorectalcarcinoma[J]. Cancer Research, 2006, 66(16):7910-7919.
[18]Zhang J, Wang X, De Voer RM, et al. A molecular inversionprobe-based next-generation sequencing panel to detect germlinemutations in Chinese early-onset colorectal cancer patients[J].Oncotarget, 2017, 8(15):24533.
[19]Almendro V, Ametller E, García-Recio S, et al. The role of MMP7and its cross-talk with the FAS/FASL system during the acquisitionof chemoresistance to oxaliplatin[J]. PLoS One, 2009, 4(3):e4728.
[20]Yokoyama Y, Grünebach F, Schmidt SM, et al. Matrilysin(MMP-7)is a novel broadly expressed tumor antigen recognized by antigenspecific T cells[J]. Clinical Cancer Research, 2008, 14(17):5503-5511.
[21]Huo N, Ichikawa Y, Kamiyama M, et al. MMP-7(matrilysin)accelerated growth of human umbilical vein endothelial cells[J].Cancer Letters, 2002, 177(1):95-100.
[22]Beeghly-Fadiel A, Shu X, Long J, et al. Genetic polymorphisms inthe MMP-7 gene and breast cancer survival[J]. InternationalJournal of Cancer, 2009, 124(1):208-214.
[23]Thompson PA, Brewster AM, Kim-Anh D, et al. Selective genomiccopy number imbalances and probability of recurrence in earlystage breast cancer[J]. PLoS One, 2011, 6(8):e23543.
[24]Brewster AM, Thompson P, Sahin AA, et al. Copy numberimbalances between screen and symptom-detected breast cancersand impact on disease-free survival[J]. Cancer PreventionResearch, 2011, 4(10):1609.
[25]Johnson CE, Gorringe KL, Thompson ER, et al. Identification ofcopy number alterations associated with the progression of DCISto invasive ductal carcinoma[J]. Breast Cancer Research andTreatment, 2012, 133(3):889-898.
[26]HuwLY,O'brienC,PanditaA,etal.AcquiredPIK3CAamplification causes resistance to selective phosphoinositide3-kinase inhibitors in breast cancer[J]. Oncogenesis, 2013, 2(12):e83.
[27]Esserman LJ, Berry DA, Cheang MCU, et al. Chemotherapyresponse and recurrence-free survival in neoadjuvant breast cancerdepends on biomarker profiles:results from the I-SPY 1 TRIAL(CALGB 150007/150012;ACRIN 6657)[J]. Breast CancerResearch and Treatment, 2012, 132(3):1049-1062.
[28]Neveling K, Mensenkamp AR, Derks R, et al. BRCA testingby single-molecule molecular inversion probes[J]. ClinicalChemistry, 2017, 63(2):503-512.
[29]Brown LA, Kalloger SE, Miller MA, et al. Amplification of 11q13 inovarian carcinoma[J]. Genes, Chromosomes and Cancer, 2008,47(6):481-489.
[30]So WK, Cheng JC, Fan Q, et al. Loss of Sprouty2 in human highgrade serous ovarian carcinomas promotes EGF-induced E-cadherindown-regulation and cell invasion[J]. Febs Letters, 2015, 589(3):302-309.
[31]Weren RDA, Mensenkamp AR, Simons M, et al. Novel BRCA1and BRCA2 tumor test as basis for treatment decisions and referralfor genetic counselling of patients with ovarian carcinomas[J].Human Mutation, 2017, 38(2):226-235.
[32]Alexiev BA, Zou YS. Clear cell papillary renal cell carcinoma:a chromosomal microarray analysis of two cases using a novelMolecular Inversion Probe(MIP)technology[J]. PathologyResearch and Practice, 2014, 210(12):1049-1053.
[33]Kim WY, Kaelin WG. Role of VHL gene mutation in humancancer[J]. Journal of Clinical Oncology, 2004, 22(24):4991-5004.
[34]Hakimi AA, Reznik E, Lee CH, et al. An integrated metabolic atlasof clear cell renal cell carcinoma[J]. Cancer Cell, 2016, 29(1):104-116.
[35]Bitter T, Water C, Heuvel C, et al. Profiling of the metabolictranscriptome via single molecule molecular inversion probes[J].Scientific Reports, 2017, 7(1):11402.
[36]Xu R, Wei W, Krawczyk M, et al. Circulating tumour DNAmethylation markers for diagnosis and prognosis of hepatocellularcarcinoma[J]. Nature Materials, 2017, 16(11):1155.
[37]Andersen EF, Paxton CN, O'Malley DP, et al. Genomic analysis offollicular dendritic cell sarcoma by molecular inversion probe arrayreveals tumor suppressor-driven biology[J]. Modern Pathology,2017, 30(9):1321.
[38]Arnold A, Bahra M, Lenze D, et al. Genome wide DNA copynumber analysis in cholangiocarcinoma using high resolutionmolecular inversion probe single nucleotide polymorphismassay[J]. Experimental and Molecular Pathology, 2015, 99(2):344-353.
[39]Weren RDA, van der Post RS, Vogelaar IP, et al. Role of germlineaberrations affecting CTNNA1, MAP3K6 and MYD88 in gastriccancer susceptibility[J]. Journal of Medical Genetics, 2018:jmedgenet-2017-104962.
[40]Smyth DJ, Cooper JD, Bailey R, et al. A genome-wide associationstudy of nonsynonymous SNPs identifies a type 1 diabetes locusin the interferon-induced helicase(IFIH1)region[J]. NatureGenetics, 2006, 38(6):617-619.
[41]Bachmann-Gagescu R, Phelps IG, Dempsey JC, et al. KIAA0586 ismutated in Joubert syndrome[J]. Human Mutation, 2015, 36(9):831-835.
[2]Nilsson M, Malmgren H, Samiotaki M, et al. Padlock probes:circularizing oligonucleotides for localized DNA detection[J].Science,, 1994, 265(5181):2085.
[3]Hardenbol P, Banér J, Jain M, et al. Multiplexed genotypingwith sequence-tagged molecular inversion probes[J]. NatureBiotechnology, 2003, 21(6):673-678.
[4]Ji H, Welch K. Molecular inversion probe assay for allelicquantitation[M]. Microarray Analysis of the Physical Genome:Methods and Protocols, 2009:67-87.
[5]Wang Y, Moorhead M, Karlin-Neumann G, et al. Analysis ofmolecular inversion probe performance for allele copy numberdetermination[J]. Genome Biology, 2007, 8(11):R246.
[6]Akhras MS, Unemo M, Thiyagarajan S, et al. Connector inversionprobetechnology:apowerfulone-primermultiplexDNAamplification system for numerous scientific applications[J].PLoS One, 2007, 2(9):e915.
[7]Turner EH, Lee C, Ng SB, et al. Massively parallel exon capture andlibrary-free resequencing across 16 genomes[J]. Nature Methods,2009, 6(5):315.
[8]Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accuratewhole human genome sequencing using reversible terminatorchemistry[J]. Nature, 2008, 456(7218):53.
[9]Porreca GJ, Zhang K, Li JB, et al. Multiplex amplification of largesets of human exons[J]. Nature Methods, 2007, 4(11):931.
[10]Hiatt JB, Pritchard CC, Salipante SJ, et al. Single moleculemolecular inversion probes for targeted, high-accuracy detection oflow-frequency variation[J]. Genome Research, 2013, 23(5):843-854.
[11]O'Roak BJ, Vives L, Fu W, et al. Multiplex targeted sequencingidentifiesrecurrentlymutatedgenesinautismspectrumdisorders[J]. Science, 2012, 338(6114):1619-1622.
[12]唱凯,贾双荣,潘锋,等.基于分子倒置探针的乙型肝炎病毒耐药基因单碱基突变检测技术的建立[J].中华检验医学杂志,2014(5):337-341.
[13]Carrascosa LG, Sina AAI, Palanisamy R, et al. Molecular inversionprobe-based SPR biosensing for specific, label-free and realtime detection of regional DNA methylation[J]. ChemicalCommunications, 2014, 50(27):3585-3588.
[14]Wang Y, Cottman ME, Schiffman JD. Molecular inversion probes:a novel microarray technology and its application in cancerresearch[J]. Cancer Genetics, 2012, 205(7):341-355.
[15]Wang T, Guo H, Xiong B, et al. De novo genic mutations amongaChineseautismspectrumdisordercohort[J].NatureCommunications, 2016, 7:13316.
[16]Kou HS, Wang CC. Molecular inversion probes equipped withdiscontinuous rolling cycle amplification for targeting nucleotidevariants:Determining SMN1 and SMN2 genes in diagnosis ofspinal muscular atrophy[J]. Analytica Chimica Acta, 2017,977:65-73.
[17]Ji H, Kumm J, Zhang M, et al. Molecular inversion probe analysisof gene copy alterations reveals distinct categories of colorectalcarcinoma[J]. Cancer Research, 2006, 66(16):7910-7919.
[18]Zhang J, Wang X, De Voer RM, et al. A molecular inversionprobe-based next-generation sequencing panel to detect germlinemutations in Chinese early-onset colorectal cancer patients[J].Oncotarget, 2017, 8(15):24533.
[19]Almendro V, Ametller E, García-Recio S, et al. The role of MMP7and its cross-talk with the FAS/FASL system during the acquisitionof chemoresistance to oxaliplatin[J]. PLoS One, 2009, 4(3):e4728.
[20]Yokoyama Y, Grünebach F, Schmidt SM, et al. Matrilysin(MMP-7)is a novel broadly expressed tumor antigen recognized by antigenspecific T cells[J]. Clinical Cancer Research, 2008, 14(17):5503-5511.
[21]Huo N, Ichikawa Y, Kamiyama M, et al. MMP-7(matrilysin)accelerated growth of human umbilical vein endothelial cells[J].Cancer Letters, 2002, 177(1):95-100.
[22]Beeghly-Fadiel A, Shu X, Long J, et al. Genetic polymorphisms inthe MMP-7 gene and breast cancer survival[J]. InternationalJournal of Cancer, 2009, 124(1):208-214.
[23]Thompson PA, Brewster AM, Kim-Anh D, et al. Selective genomiccopy number imbalances and probability of recurrence in earlystage breast cancer[J]. PLoS One, 2011, 6(8):e23543.
[24]Brewster AM, Thompson P, Sahin AA, et al. Copy numberimbalances between screen and symptom-detected breast cancersand impact on disease-free survival[J]. Cancer PreventionResearch, 2011, 4(10):1609.
[25]Johnson CE, Gorringe KL, Thompson ER, et al. Identification ofcopy number alterations associated with the progression of DCISto invasive ductal carcinoma[J]. Breast Cancer Research andTreatment, 2012, 133(3):889-898.
[26]HuwLY,O'brienC,PanditaA,etal.AcquiredPIK3CAamplification causes resistance to selective phosphoinositide3-kinase inhibitors in breast cancer[J]. Oncogenesis, 2013, 2(12):e83.
[27]Esserman LJ, Berry DA, Cheang MCU, et al. Chemotherapyresponse and recurrence-free survival in neoadjuvant breast cancerdepends on biomarker profiles:results from the I-SPY 1 TRIAL(CALGB 150007/150012;ACRIN 6657)[J]. Breast CancerResearch and Treatment, 2012, 132(3):1049-1062.
[28]Neveling K, Mensenkamp AR, Derks R, et al. BRCA testingby single-molecule molecular inversion probes[J]. ClinicalChemistry, 2017, 63(2):503-512.
[29]Brown LA, Kalloger SE, Miller MA, et al. Amplification of 11q13 inovarian carcinoma[J]. Genes, Chromosomes and Cancer, 2008,47(6):481-489.
[30]So WK, Cheng JC, Fan Q, et al. Loss of Sprouty2 in human highgrade serous ovarian carcinomas promotes EGF-induced E-cadherindown-regulation and cell invasion[J]. Febs Letters, 2015, 589(3):302-309.
[31]Weren RDA, Mensenkamp AR, Simons M, et al. Novel BRCA1and BRCA2 tumor test as basis for treatment decisions and referralfor genetic counselling of patients with ovarian carcinomas[J].Human Mutation, 2017, 38(2):226-235.
[32]Alexiev BA, Zou YS. Clear cell papillary renal cell carcinoma:a chromosomal microarray analysis of two cases using a novelMolecular Inversion Probe(MIP)technology[J]. PathologyResearch and Practice, 2014, 210(12):1049-1053.
[33]Kim WY, Kaelin WG. Role of VHL gene mutation in humancancer[J]. Journal of Clinical Oncology, 2004, 22(24):4991-5004.
[34]Hakimi AA, Reznik E, Lee CH, et al. An integrated metabolic atlasof clear cell renal cell carcinoma[J]. Cancer Cell, 2016, 29(1):104-116.
[35]Bitter T, Water C, Heuvel C, et al. Profiling of the metabolictranscriptome via single molecule molecular inversion probes[J].Scientific Reports, 2017, 7(1):11402.
[36]Xu R, Wei W, Krawczyk M, et al. Circulating tumour DNAmethylation markers for diagnosis and prognosis of hepatocellularcarcinoma[J]. Nature Materials, 2017, 16(11):1155.
[37]Andersen EF, Paxton CN, O'Malley DP, et al. Genomic analysis offollicular dendritic cell sarcoma by molecular inversion probe arrayreveals tumor suppressor-driven biology[J]. Modern Pathology,2017, 30(9):1321.
[38]Arnold A, Bahra M, Lenze D, et al. Genome wide DNA copynumber analysis in cholangiocarcinoma using high resolutionmolecular inversion probe single nucleotide polymorphismassay[J]. Experimental and Molecular Pathology, 2015, 99(2):344-353.
[39]Weren RDA, van der Post RS, Vogelaar IP, et al. Role of germlineaberrations affecting CTNNA1, MAP3K6 and MYD88 in gastriccancer susceptibility[J]. Journal of Medical Genetics, 2018:jmedgenet-2017-104962.
[40]Smyth DJ, Cooper JD, Bailey R, et al. A genome-wide associationstudy of nonsynonymous SNPs identifies a type 1 diabetes locusin the interferon-induced helicase(IFIH1)region[J]. NatureGenetics, 2006, 38(6):617-619.
[41]Bachmann-Gagescu R, Phelps IG, Dempsey JC, et al. KIAA0586 ismutated in Joubert syndrome[J]. Human Mutation, 2015, 36(9):831-835.