Real-time PCR for prenatal and preimplantation genetic diagnosis of monogenic diseases

The provision of prenatal diagnosis requires the highest standards in laboratory practice to ensure an accurate result. In preimplantation genetic diagnosis protocols additionally have to address the need to achieve an accurate result from 1 to 2 cells within a limited time. Emerging protocols of "non-invasive" prenatal diagnosis, which are based on analysis of free fetal DNA in the circulation of the pregnant mother, also have to achieve a result from a limited quantity of fetal DNA against a high background of maternal free DNA. Real-time PCR uses fluorescent probes or dyes and dedicated instruments to monitor the accumulation of amplicons produced throughout the progress of a PCR reaction. Real-time PCR can be used for quantitative or qualitative evaluation of PCR products and is ideally suited for analysis of nucleotide sequence variations (point mutations) and gene dosage changes (locus deletions or insertions/duplications) that cause human monogenic diseases. Real-time PCR offers a means for more rapid and potentially higher throughput assays, without compromising accuracy and has several advantages over end-point PCR analysis, including the elimination of post-PCR processing steps and a wide dynamic range of detection with a high degree of sensitivity. This review will focus on real-time PCR protocols that are suitable for genotyping monogenic diseases with particular emphasis on applications to prenatal diagnosis, non-invasive prenatal diagnosis and preimplantation genetic diagnosis.     

The genetic screening of preimplantation embryos by comparative genomic hybridisation

Comparative genomic hybridization (CGH) is an indirect DNA-based test which allows for the accurate analysis of aneuploidy involving any of the 24 types of chromosomes present (22 autosomes and the X and Y sex chromosomes). Traditionally, embryos have been screened using fluorescence in situ hybridization (FISH)--a technique that was limited in the number of chromosomes able to be identified in any one sample. Early CGH reports on aneuploidy in preimplantation embryos showed that any of the 24 chromosomes could be involved and so FISH methods were going to be ineffective in screening out abnormal embryos. Our results from routine clinical application of array CGH in preimplantation genetic diagnosis (PGD) patients confirm previous reports on patterns of chromosomal contribution to aneuploidy. The pregnancy outcomes following embryo transfer also indicate that despite the requirement to freeze embryos, rates are encouraging, and successful ongoing pregnancies can be achieved.     

荧光原位杂交探针应用于平衡易位t（1，6）（q42；p23）胚胎植入前诊断的研究

背景：染色体相互易位在人群中比较常见,下一代常常产生相同或不同的易位,易导致容易流产,而植入前诊断方法之一的CGH难以检测到相互易位,因此原位杂交（FISH）依然是解决诊断相互易位的有力手段。目的：通过设计个体化的FISH探针,制备探针,并在卵裂球单细胞水平进一步验证探针的准确性,为筛选正常核型的囊胚进行植入奠定技术基础,为个体化的FISH探针植入前诊断提供应用研究基础。方法：通过设计1 q和6p平衡易位探针,进行探针标记,再采用患者和正常人核型验证探针质量,通过荧光原位杂交技术进一步检测正常人受精后的卵裂球中1q 和6p平衡易位对易位染色体状态。结果：3个卵接球裂均呈现单个完整细胞核,荧光原位杂交中各细胞核均有清晰明亮的杂交信号。信号数分别为2。均为正常胚胎,可以考虑进一步对该易位患者进行卵裂球进行诊断,上述研究对个体化的易位探针的应用研究提供了研究基础。     

Comparison of PCR-RFLP with allele-specific PCR in genetic testing for spinal muscular atrophy

PCR-based methods for the detection of homozygous deletion of exon 7 of the SMN1 gene have been widely used in genetic testing for spinal muscular atrophy (SMA). We compared the most commonly used PCRrestriction fragment length polymorphism (PCR-RFLP) assay with an allele-specific PCR method, evaluating their potential application in direct testing, prenatal prediction, and preimplantation diagnosis, in terms of a range of DNA amounts used in such testing. We showed that PCR-RFLP could identify the SMN1 exon 7 by amplifying 10 pg of genomic DNA, and could differentiate SMN1 from SMN2 at the 100-pg DNA level (DraIdigested SMN2 fragments served as an internal control for PCR efficiency). In contrast, allele-specific PCR for SMN1, despite some advantages in a rapid preimplantation diagnosis, quickly lost its specificity when 100 pg of genomic DNA was used. In addition, the absence of a SMN1 fragment at the 10-pg DNA level may be due to a PCR amplification failure, and, thus, it is difficult to interpret without a proper internal control. Our data indicate that PCR-RFLP can be used for most diagnostic purposes, whereas the use of allelespecific PCR may be considered with caution under certain circumstances.     

PID in der Reproduktionsmedizin

Preimplantation genetic diagnosis in assisted reproduction Preimplantation genetic diagnosis (PGD) describes the biopsy of one or more cells of an in vitro fertilized embryo and its genetical analysis before the transfer of the embryo into the uterus. Since the modification of the Embryonenschutzgesetz a PGD can be lawfully performed in Germany. Several diagnostic methods can be performed: FISH for the detection of maternal translocations on polar bodies, at the moment the most applied the array‐CGH for the screening of aneuploidies and the detection of translocations and also in the case of monogenic diseases PCR followed by sequencing. In the near future next generation sequencing will possibly replace all mentioned methods.     

FISH在人类未受精卵染色体异常分析中的应用

分子细胞遗传学的主要技术代表———荧光原位杂交 (FISH)是用荧光标记的依靠探针杂交原理在细胞核中或染色体上显示某一特定核酸序列的位置 ,并可进行相对定量分析 .它广泛应用于遗传病的诊断、产前诊断、肿瘤遗传学、进化遗传学研究和基因定位等领域 ,随着辅助生殖技术的进展 ,将在植入前胚胎遗传学诊断 (PGD)、生殖细胞 (卵母细胞和精子 )染色体异常的研究方面发挥更大的用途 .它是联系分子遗传学和细胞遗传学之间的桥梁 .     

Comparision of the sensitivity of detection of bacteria in human blood using classic culture methods and molecular techniques: PCR and FISH

Blood infections are one of the major problems of the contemporary medical care. Their detection depends strongly on sensitivity of the used microbiological methods. Widely applied classical techniques based on blood cultivation are time consuming and less sensitive. Therefore, it is necessary to search for new molecular tools to detect bacteria in blood directly taken from patient, like as PCR or FISH. In this paper we have proved that both PCR and FISH show very high sensitivity but due to various limitations their procedures need for further standardization before future application to routine diagnosis of blood infections.     

Prenatal diagnosis of tetrasomy 18p using multiplex fluorescent PCR and comparison with a variety of techniques

We report genetic characterization of isochromosome 18p using a combination of cytogenetic and molecular genetic methods, including multiplex fluorescent PCR. The patient was referred for chorionic villus sampling (CVS) due to advanced maternal age and maternal anxiety. The placental karyotype was 47,XX,+mar, with the marker having the appearance of a small supernumerary isochromosome. Because differentiating between isochromosomes and other structural rearrangements is normally very difficult, a variety of genetic tests including fluorescence in situ hybridization (FISH), PCR, and multiplex fluorescent PCR were undertaken to determine chromosomal origin and copy number and, thus, allow accurate diagnosis of the corresponding syndrome. FISH determined that the marker chromosome contained chromosome 18 material. PCR of a variety of short tandem repeats (STRs) confirmed that there was at least one extra copy of the maternal 18p material. However, neither FISH nor PCR could accurately determine copy number. Multiplex fluorescent PCR (MF-PCR) of STRs simultaneously determined that: (1) the marker included 18p material; (2) the marker was maternal in origin; (3) allele copy number indicated tetrasomy; and (4) contamination of the sample could be ruled out. Results were also rapid with accurate diagnosis of the syndrome tetrasomy 18p possible within 5 hours.     

Uses and limitations of two molecular cytogenetic techniques for the study of arrested embryos obtained through assisted reproduction technology

We studied chromosomal abnormalities in arrested embryos produced by assisted reproductive technology with fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) in order to determine the best technique for evaluating chromosomal aneusomies to be implemented in different situations. We examined individual blastomeres from arrested embryos by FISH and arrested whole embryos by CGH. All of the 10 FISH-analyzed embryos gave results, while only 7 of the 30 embryos analyzed by CGH were usable. Fifteen of the 17 embryos were chromosomally abnormal. CGH provided more accurate data for arrested embryos; however, FISH is the technique of choice for screening in preimplantation genetic diagnosis, because the results can be obtained within a day, while the embryos are still in culture.     

优生与遗传咨询的临床研究

总结本室优生遗传咨询门诊万例病例资料,应用细胞学方法、荧光原位杂交法和分子遗传学PCR方法检出外周血染色体异常率10.30%（555/5390）,产前诊断核型异常率为6.68%（145/2171）,胎停育绒毛核型异常率45.16%（28/62）,总检出率为9.55%;PCR检测178例,正常人155例,患者23例;FISH结果：性别Y检测5例,21-三体征检测6例,均阳性。传统细胞学方法为染色体病诊断不可替代的重要手段;分子遗传学PCR方法及FISH检测方便、快速、精确,值得推广;遗传咨询,遗传病检测及产前诊断,对降低患儿出生率具有重大意义。 Clinical Research of Genetic Counseling WANG Shu-yu,WANG Su-gui,REN Guo-qing,JIA Chan-wei,MA Yan-min,XUE Hong Capital Medical University Beijing OB/GYN Hospital,Beijing 100006,China Abstract:To supply reliable materials for the assessment of recurrence risk,prenatal diagnosis and the supervision of high risk persons,we analyzed 10811 patients with the methods of cytogenetics,fluorescent in situ hybridization and molecular genetic PCR methods.The result of cytogenetics:there were 555 abnormal karyotypes of peripheral blood on 5390 cases (10.30%);In 2171 patients who asked for prenatal diagnosis,145 abnormal karyotypes were found (6.68%);We also karyotyped chorionic villous cells of 62 patients with spontaneous abortion and found 28 abnormal karyotypes (45.16%).The PCR results of 23 patients with Down's syndrome were all positive while the results of 155 normal persons were all negative.The method of cytogenetics is very important for diagnosis of abnormal karyotypes;Molecular genetic methods by PCR and FISH are quick,convenient and applicable way. Key words：genetic counseling; prenatal diagnosis; karyotypes abnormal; molecular genetics     

Preimplantation genetic diagnosis: applications for molecular medicine.

Preimplantation genetic diagnosis is an alternative to prenatal diagnosis for the detection of genetic disorders. Tests are conducted on single cells biopsied from embryos before they are implanted, allowing the selection of unaffected embryos before a pregnancy has been established. Thus, the issue of pregnancy termination is circumvented. The use of preimplantation genetic diagnosis might have a significant impact on in vitro fertilization success rates as well as allowing the diagnosis of inherited disease.     

Comparative study of MLPA-FISH to determine DNA copy number alterations in neuroblastic tumors

Neuroblastoma tumor cells show complex combinations of genetic aberrations, and to date many different methods have been used for their detection. To apply genome-wide techniques, such as Multiplex Ligation-dependent Probe Amplification (MLPA), in routine diagnosis their validation is appropriate and necessary. DNA copy number alterations in 129 cases of neuroblastic tumors were detected using MPLA, and the results validated by Fluorescence In Situ Hybridization (FISH) (MYCN gene, 1p36, 11q and 17q). Kappa index values showed very good concordance between the two techniques in detecting homogeneous MYCN amplification (1); 11q deletion (0.908) and 17q gain (0.922). The validation results showed that MLPA is a highly efficient technique for diagnosis based on the genetic aberrations in relevant regions in neuroblastoma, showing a high concordance with FISH.     

Specific detection of Arcobacter and Campylobacter strains in water and sewage by PCR and fluorescent in situ hybridization

The aim of this study was to evaluate PCR and fluorescent in situ hybridization (FISH) techniques for detecting Arcobacter and Campylobacter strains in river water and wastewater samples. Both 16S and 23S rRNA sequence data were used to design specific primers and oligonucleotide probes for PCR and FISH analyses, respectively. In order to assess the suitability of the methods, the assays were performed on naturally and artificially contaminated samples and compared with the isolation of cells on selective media. The detection range of PCR and FISH assays varied between 1 cell/ml (after enrichment) to 10(3) cells/ml (without enrichment). According to our results, both rRNA-based techniques have the potential to be used as quick and sensitive methods for detection of campylobacters in environmental samples.     

Reliability of detecting rRNA sequences of Chlamydia trachomatis with fluorescence in situ hybridization without amplification

OBJECTIVE: To use fluorescence in situ hybridization (FISH) using ribosomal RNA (rRNA) oligonucleotide probes as the target nucleic acid for the detection of Chlamydia trachomatis. STUDY DESIGN: Suitable sequences selected from the rRNA sequence of C trachomatis were labeled with a fluorescent dye and used in FISH for detecting chlamydial inclusion bodies and/ or elementary bodies in paraformaldehyde-fixed urogenital swab samples. The sensitivity and specificity of the FISH assay were compared with those of the polymerase chain reaction (PCR) using plasmid primers. Positive known C trachomatis-infected McCoy cells were used as positive controls. Urogenital swab specimens that were C trachomatis negative on culture and PCR were used as negative controls. RESULT: Among the 128 samples included in the study, FISH was positive in 28 (21.8%) and PCR in 33 (25.7%). A significant correlation was found between the 2 detection methods. Results of PCR and FISH were consistent in 115 of the 128 samples (R = 0.89). Thirteen samples showed discordant results. Of these, 9 FISH negative samples were PCR positive and 4 FISH positive samples were PCR negative. CONCLUSION: FISH was a highly specific and fairly sensitive technique for detecting C trachomatis. Signal amplification techniques and use of different fluorophores may further increase the sensitivity of this technique.     

Fish-on-a-chip: a sensitive detection microfluidic system for alzheimer's disease

Microfluidics has become an important tool in diagnosing many diseases, including neurological and genetic disorders. Alzheimer's disease (AD) is a neurodegenerative disease that irreversibly and progressively destroys memory, language ability, and thinking skills. Commonly, detection of AD is expensive and complex. Fluorescence in situ hybridization (FISH)-based microfluidic chip platform is capable of diagnosing AD at an early stage and they are effective tools for the diagnosis with low cost, high speed, and high sensitivity. In this review, we tried to provide basic information on the diagnosis of AD via FISH-based microfluidics. Different sample preparations using a microfluidic chip for diagnosis of AD are highlighted. Moreover, rapid innovations in nanotechnology for diagnosis are explained. This review will provide information on dynamic quantification methods for the diagnosis and treatment of AD. The knowledge provided in this review will help develop new integration diagnostic techniques based on FISH and microfluidics.     

单细胞PCR技术的研究进展

快速、准确、敏感和可靠的单细胞PCR技术是开展法医学、古微生物学、种植前遗传学诊断（PGD）等的前提。综述一些常用的单细胞PCR策略,并对这些技术的研究进展作一些介绍。     

Specific Detection of Arcobacter and Campylobacter Strains in Water and Sewage by PCR and Fluorescent In Situ Hybridization

The aim of this study was to evaluate PCR and fluorescent in situ hybridization (FISH) techniques for detecting Arcobacter and Campylobacter strains in river water and wastewater samples. Both 16S and 23S rRNA sequence data were used to design specific primers and oligonucleotide probes for PCR and FISH analyses, respectively. In order to assess the suitability of the methods, the assays were performed on naturally and artificially contaminated samples and compared with the isolation of cells on selective media. The detection range of PCR and FISH assays varied between 1 cell/ml (after enrichment) to 10³ cells/ml (without enrichment). According to our results, both rRNA-based techniques have the potential to be used as quick and sensitive methods for detection of campylobacters in environmental samples.     

Molecular cytogenetic studies towards the full karyotype analysis of human blastocysts and cytotrophoblasts

Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failed to increase the pregnancy rates as expected. We are in the process of developing multi-color FISH-based technologies to score all 24 chromosomes in single cells within a three-day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found to be aneuploid, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate the feasibility of a full karyotype analysis of individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.     

遗传重组微生物的环境监测

遗传重组微生物 (GMM)的环境监测作为生物安全性评价的重要内容之一,正越来越得到广大科研工作者的密切关注。综述了目前遗传工程菌和重组DNA的环境监测的主要方法。一是基于培养的方法,包括利用选择性培养技术,报告基因,基因探针和PCR,免疫监测等;一是基于免培养的方法,包括显微镜观测法,荧光原位杂交技术 (FISH),基于直接提取微生物总DNA的分子生物学方法等。重点介绍了目前常用的几种报告基因和基于直接提取总DNA的DGGE TGGE方法,同时指出我国应加强GMM遗传监控的分子生物学方法的研究及应用。     

A retrospective study of preimplantation embryos diagnosed with monosomy by fluorescence in situ hybridization (FISH)

This report is a retrospective study of preimplantation embryos diagnosed with monosomy for chromosomes 13, 15, 16, 18, 21, 22, X and Y on day 3 to determine the rate of true positives, false positives and/or mosaicism and to assess if these embryos are suitable for in vitro fertilization (IVF) transfer. In a one year period, 80 patients went through preimplantation genetic diagnosis for aneuploidy screening (PGD-AS). Monosomy was diagnosed in 51 embryos. Fluorescence in situ hybridization (FISH) was then performed on the blastomeres at day 5-7 with commercially available probes using the same probe set that initially identified monosomy for chromosomes 13, 16, 21 and 22 or chromosomes 15, 18, X and Y. Based on FISH analysis, the monosomy diagnosed during routine PGD-AS analysis was confirmed in 17 of the 51 embryos. A euploid result for the specific chromosomes tested was observed in 16 of the 51 embryos while mosaicism was found in the remaining 18 embryos. This results in an estimated false positive rate of 3.8% for a diagnosis of monosomy. Reanalysis of these embryos demonstrates that the majority of monosomy diagnoses represents true monosomy or mosaicism and should be excluded for transfer in IVF. Furthermore, improved understanding from recent emerging data regarding the fate of oocytes in women with advanced maternal age undergoing IVF to the development of early embryos may provide a valuable insight into the mechanism of chromosome mosaicism.