High-sensitive fluorescent DNA sequencing and its application for detection and mass-screening of point mutations

Development of pre-implantation genetic testing protocol for monogenic disorders (PGT-M) of Hb H disease

Hb H disease is the most severe form of α-thalassemia compatible with post-natal life. Compound heterozygous α0-thalassemia- SEA deletion/α+-thalassemia- 3.7kb deletion is the commonest cause of Hb H disease in Thailand. Preimplantation genetics testing for monogenic disorders (PGT-M) is an alternative for couples at risk of the disorder to begin a pregnancy with a healthy baby. This study aims to develop a novel PCR protocol for PGT-M of Hb H disease- SEA/-3.7kb using multiplex fluorescent PCR. A novel set of primers for α+-thalassemia- 3.7kb deletion was developed and tested. The PCR protocol for α0-thalassemia- SEA deletion was combined for Hb H disease- SEA/-3.7kb genotyping. The PCR protocols were applied to genomic DNA extracted from subjects with different thalassemia genotypes and on whole genome amplification (WGA) products from clinical PGT-M cycles of the families at risk of Hb Bart's. The results were compared and discussed. The results showed three PCR products from α+-thalassemia- 3.7kb primer set, and three from α0thalassemiaSEA primer set. The results were consistent with the known thalassemia genotypes. The novel -α3.7 primers protocol was also tested on 37 WGA products from clinical PGT-M cycles giving accurate genotyping results and a satisfying amplification efficiency with the ADO rates of 2.7%, 0%, and 0% for HBA2, HBA1, and internal control fragments, respectively. This novel PCR protocol can precisely distinguish Hb H disease- SEA/-3.7kb from other genotypes. Additionally, this is the first PCR protocol for Hb H disease- SEA/-3.7kb which is optimal for PGT-M.

The Past, Present, and Future of Preimplantation Genetic Testing

Preimplantation genetic testing (PGT) of oocytes and embryos is the earliest form of prenatal testing. PGT requires in vitro fertilization for embryo creation. In the past 25 years, the use of PGT has increased dramatically. The indications of PGT include identification of embryos harboring single-gene disorders, chromosomal structural abnormalities, chromosomal numeric abnormalities, and mitochondrial disorders; gender selection; and identifying unaffected, HLA-matched embryos to permit the creation of a savior sibling. PGT is not without risks, limitations, or ethical controversies. This review discusses the techniques and clinical applications of different forms of PGT and the debate surrounding its associated uncertainty and expanded use.

Preimplantation genetic diagnosis of alpha-thalassemia-SEA using novel multiplex fluorescent PCR

PURPOSE

Preimplantation genetic diagnosis (PGD) is an alternative to prenatal diagnosis (PND) giving couples at risk a chance to start a pregnancy with a disease-free baby. This study aimed to develop a new PGD protocol for alpha-thalassemia(-SEA) mutation, the commonest Mendelian disorder.

PATIENTS AND METHODS

Multiplex fluorescent PCR was employed for mutation, contamination and linkage analysis. A couple experienced termination of pregnancy following positive PND decided to join the project.

RESULTS

Novel primers for alpha-thalassemia(-SEA) mutation amplifying 5 DNA fragments were developed. Two PGD cycles were performed, resulting in an un-affected baby. PND confirmed the heterozygous result. From 24 embryos, 87.5% of affected genotype were of best quality compared to 0% and 18.2% of those with normal and heterozygous, respectively.

CONCLUSIONS

A novel PCR protocol for the common alpha-thalassemia(-SEA) mutation is reported. This test should be widely applicable. Interestingly, a potential effect of alpha-thalassemia(-SEA) mutation on preimplantation embryonic development was noticed.

ESHRE PGD consortium best practice guidelines for amplification-based PGD

In 2005, the European Society for Human Reproduction and Embryology (ESHRE) PGD Consortium published a set of Guidelines for Best Practice PGD to give information, support and guidance to potential, existing and fledgling PGD programmes. The subsequent years have seen the introduction of a number of new technologies as well as the evolution of current techniques. Additionally, in light of recent advice from ESHRE on how practice guidelines should be written and formulated, the Consortium believed it was timely to revise and update the PGD guidelines. Rather than one document that covers all of PGD, as in the original publication, these guidelines are separated into four new documents that apply to different aspects of a PGD programme, i.e. Organization of a PGD centre, fluorescence in situ hybridization-based testing, Amplification-based testing and Polar Body and Embryo Biopsy for PGD/preimplantation genetic screening. Here, we have updated the sections that pertain to amplification-based PGD. Topics covered in this guideline include inclusion/exclusion criteria for amplification-based PGD testing, preclinical validation of tests, amplification-based testing methods, tubing of cells for analysis, set-up of local IVF centre and Transport PGD centres, quality control/quality assurance and diagnostic confirmation of untransferred embryos.

Preimplantation genetic testing: indications and controversies

In the last two decades, the use of preimplantation genetic testing has increased dramatically. This testing is used for identifying singlegene disorders, chromosomal abnormalities, mitochondrial disorders, gender selection in non-mendelian disorders with unequal gender distribution, aneuploidy screening, and other preconceptually identified genetic abnormalities in prospective parents. Genetic testing strategies and diagnostic accuracy continues to improve, but not without risks or controversies. In this review the authors discuss the techniques and clinical application of preimplantation genetic diagnosis, and the debate surrounding its associated uncertainty and expanded use.

PGD for monogenic disorders: aspects of molecular biology

Preimplantation genetic diagnosis (PGD) for monogenic diseases has known a considerable evolution since its first application in the early 1990s. Especially the technical aspects of the genetic diagnosis itself, the single-cell genetic analysis, has constantly evolved to reach levels of accuracy and efficiency nearing those of genetic diagnosis on regular DNA samples. In this review, we will focus on the molecular biological techniques that are currently in use in the most advanced centers for PGD for monogenic disorders, including multiplex polymerase chain reaction (PCR) and post-PCR diagnostic methods, whole genome amplification (WGA) and multiple displacement amplification (MDA). As it becomes more and more clear that when it comes to ethically difficult indications, PGD goes further than prenatal diagnosis (PND), we will also briefly discuss ethical issues.

Molecular genetic testing for prenatal diagnosis

In the past few decades, enormous progress has been made in the field of prenatal molecular genetic testing. Based on the inheritance patterns of the disease and type of mutation, prenatal diagnosis is possible using direct or indirect methods of detection. Although direct mutation analysis is highly accurate, accuracy of indirect mutation analysis depends on the distance of the DNA marker to the disease locus. In the past decade, the discovery of new concepts--such as atypical inheritance patterns due to UPD and imprinting and triplet repeat disorders--have helped to increase understanding of the molecular basis of these unusual genetic disorders. Prenatal diagnosis using a single cell from a blastomere is rapidly becoming routine in clinical practice. Noninvasive procedures to obtain fetal DNA for molecular testing also are progressing very rapidly. With the completion of the genome project, resources now are available for developing new technologies, such as microarrays (DNA chips), for accurate, simultaneous, mutation detection. The next few decades hold the promise of many more advances in genetic testing, drug discovery, and therapy.

Direct comparison of detection systems used for the development of single-cell genetic tests in preimplantation genetic diagnosis

PURPOSE

Single-cell polymerase chain reaction (PCR) requires efficient amplification and accurate detection. We compare the accuracy of heteroduplex, fluorescent-fragment, and fluorescent single-strand conformation polymorphism (F-SSCP) analysis as detection systems for analysis of a PCR assay developed for preimplantation genetic diagnosis.

METHODS

A single-cell, fluorescent multiplex PCR assay was developed for the cystic fibrosis delta F508 mutation and the short tandem repeat, D21S11. Detection systems were compared by analyzing blinded PCR products.

RESULTS

Amplification rates for cystic fibrosis were 89% by heteroduplex and 91% by fragment analysis, while it was 72% for D21S11 by fragment analysis. No difference in allele dropout was detected for cystic fibrosis by any method (2%). Overall accuracy was high, > 97%, although SSCP was the least accurate.

CONCLUSIONS

Heteroduplex and fragment analysis proved equal in the diagnosis of a single amplified locus. We determined that fragment analysis allows maximal accuracy of detection and permits analysis of a second loci, controlling for DNA contamination and allelic dropout.

Diagnosis of Trisomy 21 in Fetal Nucleated Erythrocytes from Maternal Blood by Use of Short Tandem Repeat Sequences

Background: The purpose of this study was to determine whether aneuploid fetal nucleated erythrocytes (NRBCs) could be detected in maternal blood through the use of fluorescent PCR amplification with polymorphic short tandem repeat (STR) markers as an alternative or complementary method to analysis by fluorescent in situ hybridization (FISH).

Methods: Peripheral blood samples were obtained from women who had just undergone termination of pregnancy because of fetal trisomy 21 (three cases, 47,XY,+21; four cases, 47,XX,+21). Candidate fetal cells were isolated by flow-sorting by antibodies to the γ chain of fetal hemoglobin and Hoechst 33342. FISH analysis was performed by the use of chromosome-specific probes for X, Y, and 21. Fetal NRBCs, as defined by the presence of γ staining, characteristic morphology, and three chromosome 21 signals, along with maternal leukocytes, defined as γ negative and two chromosome 21 signals, were micromanipulated separately and subjected to fluorescent PCR amplification of chromosome 21 STR markers (D21S11, D21S1411, and/or D21S1412).

Results: In five of seven cases analyzed, fetal NRBCs were aneuploid, as determined by the presence of triallelic or diallelic peaks of chromosome 21 sequences when compared with sequences from the maternal leukocytes.

Conclusions: Fluorescent PCR amplification of STRs can detect fetal aneuploidy and may be useful in the setting of poor hybridization efficiency with FISH analysis. These results suggest that combined fetal aneuploidy and single-gene diagnoses by the use of DNA microarrays may be feasible in the near future.

4-chloro-o-phenylenediamine induces a dose-related increase in G:C > T:A transversions and one major DNA adduct in the liver of Big Blue mice after 26 weeks in feed treatment

The monocyclic aromatic amine 4-chloro-o-phenylenediamine (4-C-o-PDA), a known mutagen and mouse hepatocarcinogen, was tested for its in vivo mutagenic potential in the Big Blue transgenic mouse assay system. Genomic DNA was isolated from liver tissue of control and treated animals and lacI mutants were recovered. In an initial 2-week study 4-C-o-PDA was administered daily per os to groups of male and female C57BL/6 Big Blue mice at doses of 0 and 200 mg/kg for 2 weeks (on working days) followed by a treatment free expression time of 10 days. Only a weak increase in the mutant frequencies in females was observed. In a 26-week study, where 4-C-o-PDA was given to groups of male and female Big Blue mice in feed at dietary concentrations of 0, 5,000 and 10,000 ppm, 4-C-o-PDA was found to induce a pronounced dose-dependent increase in mutant frequencies in either sex. In the present work, we analyzed the mutation spectrum by automated DNA sequencing of lacI mutants from both studies. Following the 2-week administration of 4-C-oT:A transversions in both sexes. In addition, upon 26-week treatment with 4-C-o-PDA, one major DNA adduct was detected by 33P postlabelling and subsequent multidimensional thin layer chromatography. It is concluded that 4-C-oT:A transversions after 26 weeks in feed treatment. This result indicates that the sensitivity of the Big Blue transgenic assay system, in detecting a unique chemically induced mutation spectrum, is dependent on experimental parameters, such as treatment time. The data suggest that the formation of one major DNA adduct upon 4-C-o-PDA treatment may be critical for its mutagenicity.

Clustering of chi sequence in Escherichia coli genome

An 8-mer DNA sequence called chi (5'-GCTGGTGG) is present on the Escherichia coli chromosome at a high frequency. It is responsible for both the attenuation of RecBCD exonuclease activity and the promotion of RecABCD-mediated homologous recombination. chi was first identified as a site that increased plaque size of bacteriophage lambda. lambda containing chi makes very small plaques on a recC* (recC1004) mutant because chi is poorly recognized by the RecBC*D mutant enzyme. We cloned E. coli chromosomal fragments in lambda that allowed lambda to form larger plaques on this recC* mutant as well as on the rec+ parent. One identified fragment contained a cluster of two copies of chi and several chi-like sequences with the same orientation. It increased recombination in the rec+ strain more than a fragment with one chi did. This fragment was within the rep gene, whose helicase product is known to be required for growth in the absence of functional RecBCD enzyme. The possibility that RecBCD enzyme might interact both with the rep gene and its product is discussed. Many of the other chi clusters identified in the E. coli genome database lie within genes for membrane proteins. The possible significance of these findings is discussed.

Comparison of FISH PRINS, and conventional and fluorescent PCR for single-cell sexing: suitability for preimplantation genetic diagnosis

PURPOSE

Although conventional polymerase chain reaction (PCR) was the first method used for sexing in preimplantation genetic diagnosis, fluorescent in situ hybridization (FISH) has become the method of choice. Recently two new techniques, primed in situ synthesis (PRINS) and fluorescent PCR, have been developed. This study compares the reliability and accuracy of these four techniques in single cells.

RESULTS

In buccal cells, fluorescent PCR and FISH had similar reliability (94 and 93%) and accuracy (97 and 96%) rates. The reliability and accuracy of PRINS (91 and 25%) and conventional PCR (79 and 89%) were lower. In human blastomeres, FISH and fluorescent PCR had similar reliability (100%, 717; 95%, 190/201) rates. Accuracy rates were 71% (517) and 99% (188/190) for FISH and fluorescent PCR, respectively, however, too few blastomeres were analyzed by FISH for meaningful comparison. However, when these data are compared with published data, the method of choice for blastomere sexing appears to be fluorescent PCR.

CONCLUSIONS

Flouroscent PCR has major implications for PGD.

Rapid trisomy diagnosis (21, 18, and 13) using fluorescent PCR and short tandem repeats: applications for prenatal diagnosis and preimplantation genetic diagnosis

PURPOSE AND METHODS

Prenatal diagnosis of fetal trisomies is usually performed by cytogenetic analysis from amniotic fluid. This requires lengthy laboratory procedures and high costs and is unsuitable for large-scale screening of pregnant women. An alternative method, which is rapid and inexpensive and may potentially be suitable for diagnosing trisomies even from single fetal cells, is the fluorescent polymerase chain reaction (F-PCR) using polymorphic small tandem repeats (STRs).

RESULTS

In this paper we present data demonstrating that fluorescent PCR amplification of STRs can be used for rapid diagnosis of trisomy 21, trisomy 18, and trisomy 13 and can be successfully applied to both prenatal diagnosis and diagnosis of single cells. This study also reports significant numbers of prenatal diagnoses using quantitative fluorescent PCR.

CONCLUSIONS

We believe that further studies of greater numbers of samples will determine the absolute reliability of this technique. These results also provide a model for trisomy diagnosis from single cells using multiple STR markers for either preimplantation genetic diagnosis or, potentially, diagnosis from fetal cells isolated from maternal blood.

Applied molecular genetic techniques for prenatal diagnosis

Molecular laboratory techniques are increasingly important in the evaluation of fetuses at risk for a single gene disorder or chromosomal abnormality and for the detection of genetic or other conditions that can lead to an adverse fetal or maternal outcome. The localization and identification of novel disease genes allows for mutation analysis or linkage studies on fetuses at risk for these disorders. New assays or techniques for mutation detection in single gene disorders such as amplification refractory mutation system polymerase chain reaction, fluorescent polymerase chain reaction, heteroduplex analysis and the protein truncation test are now applied in prenatal diagnosis. Recent advances in molecular cytogenetics, such as comparative genomic hybridization, the primed in-situ labeling technique, the development of new telomeric probes and spectral karyotyping, are being evaluated for their role in the prenatal diagnosis of chromosomal abnormalities. These methods may greatly improve the accuracy and applicability of preimplantation genetic diagnosis or diagnosis on fetal cells isolated from maternal blood.

Rapid determination of trisomy 18 parental origin using fluorescent PCR and small tandem repeat markers: case reports

Trisomy 18 is the second most common genetic defect after trisomy 21, almost 90% of which are due to additional chromosome from the mother. The parental origin of the additional chromosome can, if required, be determined by two methods: karyotyping, which takes several weeks; or, more recently, by polymerase chain reaction (PCR) which is often problematic. Fluorescent PCR of small tandem repeats (STRs) can determine the parental origin in the majority of cases within 5 h. Although the incidence of paternal origin is known for both trisomy 21 and trisomy 18, this technique can rapidly determine the parental origin in cases where there is insufficient samples to perform conventional tests. Determining parental origin by these methods may also have clinical significance in the diagnosis of chromosomal translocations or in the diagnosis of genetic disease using linkage analysis.

Fluorescent PCR: a new technique for PGD of sex and single-gene defects

BACKGROUND

For single-cell diagnosis, particularly preimplantation genetic diagnosis to be successful four main criteria must be achieved: sensitivity, reliability, accuracy, and identification/elimination of contamination.

METHODS AND RESULTS

Fluorescent PCR achieves all four necessary criteria and, in addition, currently allows genes on up to nine chromosomes to be simultaneously investigated. Fluorescent PCR has high sensitivity (approximately 1000 x conventional analysis systems), high reliability (97%), and high accuracy (97%) rates for both sex and CF diagnosis in single somatic cells. The low detection threshold allows allelic dropout (one of the main causes of misdiagnosis) to be easily distinguished from PCR phenomena such as preferential amplification. High reliability (90%) and accuracy (97-100%) have been achieved in sex and CF diagnosis in human blastomeres. Fluorescent PCR can also be used to DNA fingerprint (STR profiling) single cells to identify the source/origin of the cell and determine if contamination has occurred.

CONCLUSIONS

Fluorescent PCR is therefore a suitable method for PGD.

Genes and psychosis: old wine in new bottles?

Despite initial setbacks, linkage studies with DNA markers continue to occupy center stage in psychiatric research. Advances in molecular and statistical techniques have revived the search for disease genes, leading to a new harvest of findings. Most interest in recent years has focused on potential linkages between schizophrenia and chromosomes X-Y (the pseudoautosomal region) and 22q12-13.1, and between bipolar affective disorder and chromosomes 18 (pericentromeric region) and 21q22.3. This article provides a critical evaluation of theses studies, with implications for future research. Concerns over earlier linkage trials make this scrutiny current and topical.

Structural analyses of DNA fragments integrated by illegitimate recombination in Schizosaccharomyces pombe

In order to elucidate the mechanisms of illegitimate recombination in eukaryotes, we have studied the structure of DNA fragments integrated by illegitimate recombination into the genome of fission yeast. Nonhomologous recombination was rarely identified when a long region of homology with the chromosomal leu1+ gene was present in the introduced leu1::ura4+ DNA fragment; but a decrease in length of homology leads to an increase in the ratio of non-homologous to homologous recombination events. The introduced DNA fragments were integrated into different sites in the chromosomes by nonhomologous recombination. The results suggested that there are multiple modes of integration; most events simply involve both ends of the fragments, while in other cases, fragments were integrated in a more complicated manner, probably via circularization or multimerization. To analyze the mechanism of the major type of integration, DNA fragments containing the recombination junctions of three recombinants were amplified by inverted polymerase chain reaction (IPCR) and their nucleotide sequences were determined. There was no obvious homology between introduced DNA and chromosomal DNA at these recombination sites. Furthermore it was found that each terminal region of the introduced DNA was deleted, but that there were no or very small deletions in the target sites of chromosomal DNA. Two models are proposed to explain the mechanism of nonhomologous integration.

The complete primary structure of the long form of mouse alpha 1(IX) collagen chain and its expression during limb development

Type IX collagen is a newly discovered collagen molecule that is associated with Type II-containing collagen fibrils in cartilage, vitreous and embryonic cornea. It consists of three distinct chains: alpha 1(IX), alpha 2(IX) and alpha 3(IX). The alpha 1(IX) chain has been to be synthesized in two different forms, which are generated by alternative transcription and splicing. In this manuscript we describe the isolation and sequencing of a cDNA coding for the entire coding region of the long form of mouse alpha 1(IX) chain. Nucleotide sequence analysis of this cDNA determined for the first time the primary structure of the entire long form of the mouse alpha 1(IX) chain. RT-PCR was used to examine collagen gene expression during limb development from day 10 to 18 in mouse embryos. Collagen I and II mRNA levels gradually increased all through the developmental stages. Collagen X expression increased further after day 16 in limb development, whereas the alpha 1(IX)mRNA level dropped at this time. This could be due to active bone formation relative to cartilage synthesis in the embryonic limb bud around day 16 in mouse development.

Mutational analysis of candidate genes in psychiatric disorders

A genetic hypothesis for a disease presupposes the existence of variation in the DNA sequences of affected individuals. A series of techniques known together as "mutational analysis" can be applied towards identifying new sequence variations in selected genes. These techniques can screen a large series of individuals for mutations efficiently, so it is not necessary to determine the nucleotide sequence in every DNA sample. DNA samples suspected of harboring sequence variants are then sequenced. Denaturing gradient gel electrophoresis techniques, single stranded conformation polymorphism paradigms, and chemical cleavage of mismatches are 3 procedures widely used for the molecular screening of mutations today. We discuss each of these techniques for mutation screening.

The rapid detection of unknown mutations in nucleic acids

The task of identifying mutations in nucleic acid sequences is a vital component of research in mammalian genetics. With the advent of the polymerase chain reaction, several useful mutation detection techniques have evolved in recent years. The different methods have complementing strengths and a suitable procedure for virtually any experimental situation is now available.