多重置换扩增方法在无创性产前基因诊断中的应用

目的探讨多重置换扩增（multiple displacement amplification，MDA）方法应用到杜氏肌营养不良（Duchenne muscular dystrophy，DMD）的无创性产前基因诊断中的可行性。方法对12例孕7～25周的孕妇外周血用Pcreoll不连续密度梯度离心初步富集、甩片后，用Kleihauer抗酸染色法标记胎儿有核红细胞。显微操作法获取阳性细胞后，进行多重置换扩增，得到的全基因组扩增产物直接作为模板进行性别鉴定及短串联重复序列连锁分析检测，验证有核红细胞的来源，同时进行DMD的无创性产前基因诊断。结果经多重置换扩增后的产物进行琼脂糖电泳，显示片段长度大于15kb。应用多重置换扩增方法对12例孕有DMD高风险患儿的孕妇进行了无创性产前基因诊断，诊断结果与引产或产后反馈相一致。结论多重置换扩增能从微量模板中扩增出大量均一、完整的胎儿基因组序列，确保了无创性产前基因诊断结果的准确性。     

多重置换扩增——一种新的全基因组扩增技术

全基因组扩增技术用于扩增大量的DNA以满足遗传检测的需要。在高通量的遗传分型中,处理有限的临床样本的基因组DNA,一直是个瓶颈问题。一种新方法—多重置换扩增,能高度忠实的复制整个基因组DNA,扩增出10–100 kb大小的片段,能提供大量均一完整的全基因组序列。MDA是一种简单、有效的方法,非常适用于遗传研究,法医学和临床诊断的需要。     

两种全基因组扩增方法用于微量检材STR基因座分型比较

目的 应用多重置换扩增(MDA)技术和改进型扩增前引物延伸（IPEP）技术对法医学微量DNA进行全基因组扩增,比较两种方法的STR分型效果及法医学应用价值。 方法 用MDA、IPEP方法分别对不同模板量DNA进行扩增,扩增产物用实时荧光定量PCR技术定量、用AmpFLSTR® Identifiler®试剂盒检测基因型。 结果 MDA方法可对模板DNA增加103～106倍,IPEP方法可增加25～310倍。为获得完整准确的分型结果,MDA最低需1ng基因组DNA,IPEP最低需0.05ng基因组DNA。当基因组DNA为0.01ng～0.1ng时,IPEP产物、MDA产物的平均基因座检出数均高于未经全基因组扩增的DNA,其中IPEP产物的平均基因座检出数高于MDA产物。 结论 MDA方法、IPEP方法均可提高微量检材的STR分型效果。MDA方法的产量高于IPEP方法;IPEP方法的灵敏度高于MDA方法,且对微量DNA的STR分型效果优于MDA方法,因此更适于法医学痕量DNA检测。     

少量细胞模板下多重置换扩增技术的保真度评估

目的 应用单核苷酸多态性(single nucleotide polymorphism,SNP)芯片,检测以少量细胞(1～10个)为模板的多重置换扩增(multiple displacement amplification,MDA)产物的保真度.方法 结合10K 2.0 SNP芯片平台与MDA,以纤维母细胞系GM02732(47,XY,+18)作为模板,共分6组进行实验,其中A组与B组分别为阳性对照组(细胞gDNA)与阴性对照组(无模板MDA);C～F组为实验组,分别以1、2、5和10个细胞为模板进行MDA扩增,产物与芯片杂交,检测并比较各组产物的基因组覆盖率、等位基因杂合性缺失(loss of heterozygosity,LOH)率以及等位基因脱扣(allele dropout,ADO)率.结果 阴性对照组的MDA产物与gDNA序列有3.2%的重叠.随着起始模板从单细胞提升至10细胞,MDA产物的基因组覆盖率从86.4%逐步上升至96.4%,平均LOH率和ADO率则逐渐下降,各组之间比较差异均有统计学意义(P<0.05).结论 多重置换扩增技术是一种高效而可靠的全基因组扩增方法 ,随着模板细胞的增加,MDA产物的保真度可获得明显的改善.10K 2.0 SNP芯片可快速准确地在全基因组水平对DNA扩增产物进行保真度分析,但应注意区分LOH中的ADO和等位基因优势扩增,以避免产生误差.     

多重连接探针扩增技术及其应用

多重连接探针扩增是一种建立在PCR技术七的新型相对定量检测技术,该技术具有高效率、高分辨率、操作简便、设备要求低等诸多优势,目前已被广泛应用于基因片段缺失与重复、点突变及甲基化检测等相关疾病的分子生物学研究.其与基因芯片结合而建立的多重连接探针扩增微阵列芯片技术不但真正具备了高通量的检测能力,还使该技术的可靠性获得了很大的提高.本文就多重连接探针扩增的技术方法 、应用进展及目前还存在的局限性作一综述.     

一种新的核酸扩增技术--网状分枝扩增方法

网状分枝扩增方法(RAM)是利用环形寡核脱氧核苷酸探针进行的核酸扩增方法.环形探针与靶序列结合后,在连接酶的作用下闭合成环形,然后以闭合的环形探针为模板,通过引物的延伸、置换而达到指数级扩增.本文对RAM的创立和发展、基本原理和方法、特点以及应用前景进行综述.     

单细胞水平检测von Hippel-Lindau病基因突变的实验研究

目的建立单细胞水平检测vonHippel-Lindau病基因(VHL)突变的实验方法。方法单个淋巴细胞基于多重置换扩增(multiple displacement amplification,MDA)的全基因组扩增后进行常规PCR后测序和实时荧光定量PCR,结合各荧光的终点变化判断对应的等位基因存在与否。结果MDA后单细胞扩增效率为90.91%,污染率为0;通过测序,患者VHL等位基因的脱扣率为26.67%,诊断正确率为73.33%;通过结合相应荧光的终点变化判断患者VHL基因的等位基因的脱扣率为16.67%,正确率为83.33%。结论单细胞MDA后常规PCR后测序及实时荧光定量PCR能够特异、准确地检测单个淋巴细胞的VHL基因型,两者的联合应用有助于提高检测的准确性。     

X-连锁慢性肉芽肿病的植入前遗传学检测

目的 采用多重置换扩增结合单体型分析及致病基因检测进行X-连锁慢性肉芽肿病的植入前遗传学检测。方法 利用位于CYBB基因两侧的16个短串联重复序列位点对一个X-连锁慢性肉芽肿病的家系构建单体型进行分析。活检的胚胎细胞通过多重置换扩增技术进行全基因组扩增，利用扩增产物检测具有多态性的STR位点与CYBB基因，同时采用位点Amel进行性别诊断。结果 对一个家系共进行了2个周期的PGT，家系分析结果显示7个STR位点具有多态性。共对16个胚胎进行了诊断，均获得诊断结果，诊断效率为100%，其中8个为正常胚胎，1个为携带者，7个为异常胚胎。全基因组扩增成功率100%，后续PCR成功率为99.3%(143/144),ADO率为14.0%(6/43)。先后进行了三次胚胎移植，末次移植后获得单胎妊娠，最终足月顺产一个不携带致病基因的健康男婴。结论 基于多重置换扩增产物对短串联重复序列进行连锁分析结合致病基因检测可对X连锁慢性肉芽肿病进行准确且有效的植入前遗传学检测。     

引物延伸预扩增结合简并引物PCR在单细胞比较基因组杂交分析染色体异常中的应用

目的 建立一种可信的单细胞全基因组扩增(whole genome amplification.WGA)技术,结合比较基因组杂交(comparative genomic hybridization,CGH)分析单细胞的染色体拷贝数变化,探讨其在胚胎植入前遗传学诊断(preimplantation genetic diagnosis,PGD)中的应用前景.方法 采用引物延伸预扩增结合简并核苷酸引物PCR(primer extension preamplification with degenerate oligonucleotide primed-PCR,PEP-DOP-PCR)的方法,扩增12个已知核型的单细胞标本(包括5个绒毛标本、4个干细胞标本和3个淋巴细胞标本)和4个经PGD检测发现染色体异常的单卵裂球标本,将扩增产物标记红色荧光染料后,与标记绿色荧光染料的正常DNA等量混匀,与正常中期分裂相进行比较基因组杂交分析.同时,应用单纯的简并寡核苷酸引物-PCR(DOP-PCR)扩增10个单细胞DNA,标记后进行CGH分析.比较两种单细胞全基因组扩增方法的扩增效率及随后用于CGH分析染色体拷贝数时的准确性.结果 所有的单细胞采用PEP-DOP-PCR扩增时,均能获得稳定均匀的PCR产物,片段大小范围在100～1000 bp之间,集中分布于400 bp左右的区域,CGH分析结果显示染色体拷贝数变化与其它技术检测的结果一致.而10个单纯的DOP-PCR扩增只有6个标本成功,扩增产物进行CGH分析时,杂交信号不均匀,有2个显示与其它技术分析的结果不一致.结论 PEP-DOP-PCR技术能有效地扩增单细胞的全基因组DNA,其扩增产物可应用CGH技术成功检测单个细胞的染色体拷贝数变化,而单纯的DOP-PCR技术易于出现扩增失败、扩增产物杂交后信号不均一的缺点.PEP-DOP-PCR全基因组扩增结合CGH技术在胚胎植入前遗传学诊断中有良好的应用前景.     

利用基因芯片对少量细胞进行非整倍体检测的影响因素分析

目的 评估利用微阵列-比较基因组杂交技术检测少量细胞非整倍体的准确率及相关影响因素.方法 结合10K 2.0单核苷酸多态性(SNP)基因分型芯片平台与多重置换扩增技术(MDA),计算并比较扩增模板为1～10个细胞时各染色体拷贝数分析的准确率,评估影响芯片平台的拷贝数准确率的有关因素及其对染色体拷贝数异常的实际分辨率.结果 使用MDA-DNA作参照时,拷贝数分析的准确率[(79.3±2.9)%～(100.0±1.7)%]高于使用gDNA作参照时的准确率[(66.7±3.4)%～(89.5±3.3)%](P<0.001).随着模板增加至10细胞,芯片可在1 M平滑化处理的同时获得94%的分析准确率.对于单细胞MDA产物,缺失型非整倍体具有比获得型非整倍体更高的分析准确率[1C组(71.9±4.1)%～(95.5～2.0)%;1C-sDel-4组(81.4±3.7)%～(99.6±2.8)%],各组间差异均有统计学意义(P<0.01).结论 10K 2.0 SNP基因分型芯片平台结合多重置换扩增技术可有效对少量细胞进行非整倍体检测,选择MDA-DNA作为参照是提高分析准确率的最关键因素,而增加细胞模板与提升分析中的平滑化参数(即降低芯片的分辨率要求)也有助于改善拷贝数准确率,在同样的条件下,芯片更容易准确检出缺失型非整倍体.     

Use of multiple displacement amplification in the investigation of human papillomavirus physical status

BACKGROUND AND AIMS: The investigation of human papillomavirus (HPV) physical status in pre-invasive cervical lesions has been restricted by the small amounts of tissue available for study. Multiple displacement amplification (MDA), a phi29 DNA polymerase based whole genome amplification technique, has the potential to help resolve this problem by yielding large amounts of high molecular weight DNA from tiny starting quantities. METHODS: Firstly, a comparison was made of restriction endonuclease fragment patterns of DNA from seven different HPV types and corresponding MDA products. Secondly, E6/E7 and LCR sequencing data from HPV16 recombinant plasmid and MDA copy DNA were correlated. Thirdly, DNA and MDA products from cervical cell lines (CaSki, HeLa, and SiHa that contain integrated HPV) and an invasive cervical carcinoma were analysed by Southern blot hybridisation. Fourthly, MDA product from CaSki cell DNA mixed with HPV18-plasmid DNA was tested for the demonstration of both episomal and integrated HPV. Finally, MDA products from HPV16 positive abnormal cervical cytological samples were assayed for integration by Southern blot hybridisation. RESULTS: DNA templates and MDA products yielded analogous data. Episomal and integrated HPV DNA were successfully detected by Southern blot assay of the cell line/HPV-plasmid model, and in MDA products of clinical samples. CONCLUSIONS: These data show that MDA has considerable potential to assist in the investigation of HPV physical status; abundant (>40 microg) DNA can be generated with high fidelity from minuscule (50 ng) starting quantities, and both episomal and integrated HPV DNA are distinguishable in MDA products from solid tumours and cytological materials.     

Assessment of multiple displacement amplification for polymorphism discovery and haplotype determination at a highly polymorphic locus, MC1R

The identification of common genetic variants such as single nucleotide polymorphisms (SNPs) in the human genome has become central in human population genetics and evolution studies, as well as in the study of the genetic basis of complex traits and diseases. Crucial for the accurate identification of genetic variants is the availability of high quality genomic DNA (gDNA). Since popular sources of gDNA (buccal cells, lymphocytes, hair bulb) often do not yield sufficient quantities of DNA for molecular genetic applications, whole genome amplification methods have recently been introduced to generate a renewable source of double-stranded linear DNA. Here, we assess the fidelity of one method, multiple displacement amplification (MDA), which utilizes bacteriophage Phi29 DNA polymerase to generate amplified DNA from an original source of gDNA, in a representative SNP discovery and genetic association study at the melanocortin 1 receptor (MC1R) locus, a highly polymorphic gene in humans involved in skin and hair pigmentation. We observed that MDA has high fidelity for novel SNP discovery and can be a valuable tool in generating a potentially indefinite source of DNA. However, we observed an allele amplification bias that causes genotype miscalls at heterozygous sites. At loci with multiple polymorphic sites in linkage disequilibrium, such as at MC1R, this bias can create a significant number of heterozygote genotype errors that subsequently misrepresents haplotypes.     

Multiple displacement amplification to create a long-lasting source of DNA for genetic studies

In many situations there may not be sufficient DNA collected from patient or population cohorts to meet the requirements of genome-wide analysis of SNPs, genomic copy number polymorphisms, or acquired copy number alternations. When the amount of available DNA for genotype analysis is limited, high performance whole-genome amplification (WGA) represents a new development in genetic analysis. It is especially useful for analysis of DNA extracted from stored histology slides, tissue samples, buccal swabs, or blood stains collected on filter paper. The multiple displacement amplification (MDA) method, which relies on isothermal amplification using the DNA polymerase of the bacteriophage phi29, is a recently developed technique for high performance WGA. This review addresses new trends in the technical performance of MDA and its applications to genetic analyses. The main challenge of WGA methods is to obtain balanced and faithful replication of all chromosomal regions without the loss of or preferential amplification of any genomic loci or allele. In multiple comparisons to other WGA methods, MDA appears to be most reliable for genotyping, with the most favorable call rates, best genomic coverage, and lowest amplification bias.     

Multiple displacement amplification on single cell and possible PGD applications

Multiple displacement amplification (MDA) is a technique used in the amplification of very low amounts of DNA and reported to yield large quantities of high-quality DNA. We used MDA to amplify the whole genome directly from a single cell. The most common techniques used in PGD are PCR and fluorescent in-situ hybridization (FISH). There are many limitations to these techniques including, the number of chromosomes diagnosed for FISH or the quality of DNA issued from a single cell PCR. This report shows, for the first time, use of MDA for single cell whole genome amplification. A total of 16 short tandem repeats (STRs) were amplified successfully with a similar pattern to the genomic DNA. Furthermore, allelic drop out (ADO) derived from MDA was assessed in 40 single cells by analysing (i) heterozygosity for a known beta globin mutation (IVSI-5 C-G) and by studying (ii) the heterozygous loci present in the STRs. ADO turned out to be 10.25% for the beta globin gene sequencing and 5% for the fluorescent PCR analysis of STRs. Moreover, the amplification accuracy of MDA permitted the detection of trisomy 21 on a single cell using comparative genome hybridization-array. Altogether, these data suggest that MDA can be used for single cell molecular karyotyping and the diagnosis of any single gene disorder in PGD.     

Multiple displacement amplification improves PGD for fragile X syndrome

We report an improvement in the PGD test for fragile X syndrome (FXS). Recently, multiple displacement amplification (MDA) has been reported to yield large amounts of DNA from single cells. Taking into account this technique, we developed a new PGD test for FXS, enabling combined analysis of linked polymorphic markers with the study of the non-expanded CGG repeat. Single cell amplification efficiency was first assessed on single lymphocytes. Amplification rate of the different markers ranged from 85 to 95% with an allele drop-out (ADO) rate comprised between 7 and 34%. Using this test, eight PGD cycles were carried out for six couples, and 37 embryos were analysed after preliminary MDA. Amplification rate was increased by this technique from 41 to 66% so that embryos with no results were rarer (14 versus 45% without MDA). Reliability of the test was considerably improved by combining direct with indirect genetic analysis. Furthermore, in cases of fully expanded alleles too large to be amplified by PCR, this test gives an internal amplification control. Embryonic transfers were carried out in all but one PGD cycles. One biochemical and one clinical pregnancy resulted, and a healthy child was born. This single diagnosis procedure could be suitable to most patients carrying FXS.     

Mutation and haplotype analysis for Duchenne muscular dystrophy by single cell multiple displacement amplification

Duchenne muscular dystrophy (DMD) is an X-linked recessive genetic disorder with mutational heterogeneity. The scarcity of DNA from single cells in preimplantation genetic diagnosis (PGD) for DMD limits comprehensive genetic testing. Multiple displacement amplification (MDA) is reported to generate large amounts of template and give the most complete coverage and unbiased amplification to date. Here, we developed mutation and haplotype analysis in conjunction with gender determination on MDA products of single cells providing a generic approach that widens availability of PGD for female carriers with varied mutations. MDA amplified with 98.5% success for single lymphocytes and 94.2% success for single blastomeres, which was evaluated on 60 lymphocytes and 40 blastomeres. A total of six commonly mutant exons, eight short tandem repeat markers within dystrophin gene and amelogenin were incorporated into subsequent singleplex PCR assays. The mean allele dropout rate was 9.0% for single lymphocytes and 25.5% for single blastomeres. None of the blank controls gave a positive signal. Genotyping of each pedigree for three families provided 2-3 fully informative alleles per dystrophin haplotype besides specific mutant exons and amelogenin. We suggest that this approach is reliable to identify non-carrier female embryos other than unaffected male embryos and reduce the risk of misdiagnosis.     

Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources

The promise of whole genome amplification (WGA) is that genomic DNA (gDNA) quantity will not limit molecular genetic analyses. Multiple displacement amplification (MDA) and the OmniPlex PCR-based WGA protocols were evaluated using 4 and 5 ng of input gDNA from 60 gDNA samples from three tissue sources (mouthwash, buffy coat, and lymphoblast). WGA DNA (wgaDNA) yield and genotyping performance were evaluated using genotypes determined from gDNA and wgaDNA using the AmpFlSTR Identifiler assay and N = 49 TaqMan SNP assays. Short tandem repeat (STR) and SNP genotyping completion and concordance rates were significantly reduced with wgaDNA from all WGA methods compared with gDNA. OmniPlex wgaDNA exhibited a greater reduction in genotyping performance than MDA wgaDNA. Reduced wgaDNA genotyping performance was due to allelic (all protocols) and locus (OmniPlex) amplification bias leading to heterozygote and locus dropout, respectively, and %GC sequence content (%GC) was significantly correlated with TaqMan assay performance. Lymphoblast wgaDNA exhibited higher yield (OmniPlex), buffy coat wgaDNA exhibited higher STR genotyping completion (MDA), whereas mouthwash wgaDNA exhibited higher SNP genotyping discordance (MDA). Genotyping of wgaDNA generated from < or = 5 ng gDNA, e.g., from archaeological, forensic, prenatal diagnostic, or pathology samples, may require additional genotyping validation with gDNA and/or more sophisticated analysis of genotypes incorporating observed reductions in genotyping performance.