Proof of principle and first cases using preimplantation genetic haplotyping--a paradigm shift for embryo diagnosis

SNP array-based copy number and genotype analyses for preimplantation genetic diagnosis of human unbalanced translocations

Preimplantation genetic diagnosis (PGD) for chromosomal rearrangements (CR) is mainly based on fluorescence in situ hybridisation (FISH). Application of this technique is limited by the number of available fluorochromes, the extensive preclinical work-up and technical and interpretative artefacts. We aimed to develop a universal, off-the-shelf protocol for PGD by combining single-nucleotide polymorphism (SNP) array-derived copy number (CN) determination and genotyping for detection of unbalanced translocations in cleavage-stage embryos. A total of 36 cleavage-stage embryos that were diagnosed as unbalanced by initial PGD FISH analysis were dissociated (n=146) and amplified by multiple displacement amplification (MDA). SNP CNs and genotypes were determined using SNP array. Epstein-Barr Virus-transformed cell lines with known CR were used for optimising the genomic smoothing (GS) length setting to increase signal to noise ratio. SNP CN analysis showed 23 embryos (64%) that were unbalanced in all blastomeres for the chromosomes involved in the translocation, 5 embryos (14%) that were normal or balanced in all blastomeres and 8 embryos (22%) that were mosaic. SNP genotyping, based on analysis of informative SNP loci with opposing homozygous parental genotypes, confirmed partial monosomies associated with inheritance of unbalanced translocation in surplus embryos. We have developed a universal MDA-SNP array technique for chromosome CN analysis in single blastomeres. SNP genotyping could confirm partial monosomies. This combination of techniques showed improved diagnostic specificity compared with FISH and may provide more reliable PGD analysis associated with higher embryo transfer rate.

Derivation and feeder-free propagation of human embryonic stem cells under xeno-free conditions

BACKGROUND AIMS

Human embryonic stem (hES) cells hold great potential for cell therapy and regenerative medicine because of their pluripotency and capacity for self-renewal. The conditions used to derive and culture hES cells vary between and within laboratories depending on the desired use of the cells. Until recently, stem cell culture has been carried out using feeder cells, and culture media, that contain animal products. Recent advances in technology have opened up the possibility of both xeno-free and feeder-free culture of stem cells, essential conditions for the use of stem cells for clinical purposes. To date, however, there has been limited success in achieving this aim.

METHODS, RESULTS AND CONCLUSIONS

Protocols were developed for the successful derivation of two normal and three specific mutation-carrying (SMC) (Huntington's disease and myotonic dystrophy 1) genomically stable hES cell lines, and their adaptation to feeder-free culture, all under xeno-free conditions.

Whole genome amplification in preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) refers to a procedure for genetically analyzing embryos prior to implantation, improving the chance of conception for patients at high risk of transmitting specific inherited disorders. This method has been widely used for a large number of genetic disorders since the first successful application in the early 1990s. Polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) are the two main methods in PGD, but there are some inevitable shortcomings limiting the scope of genetic diagnosis. Fortunately, different whole genome amplification (WGA) techniques have been developed to overcome these problems. Sufficient DNA can be amplified and multiple tasks which need abundant DNA can be performed. Moreover, WGA products can be analyzed as a template for multi-loci and multi-gene during the subsequent DNA analysis. In this review, we will focus on the currently available WGA techniques and their applications, as well as the new technical trends from WGA products.

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.

PGD for X-linked and gender-dependent disorders using a robust, flexible single-tube PCR protocol

X-linked genetic diseases include a wide range of disorders such as the dystrophinopathies. Additionally in some rare genetic diseases, severity of expression is gender dependent. Prevention of such disorders usually involves prenatal diagnosis and termination of affected pregnancies, while preimplantation genetic diagnosis (PGD) represents a specialized alternative that avoids pregnancy termination. To preclude the rejection of unaffected male embryos that cannot be differentiated from those affected when using fluorescence in-situ hybridization, a flexible protocol based on multiplex fluorescence polymerase chain reaction (PCR) was standardized and validated for gender determination in single cells, which can potentially incorporate any disease-specific locus. The final panel of nine loci included four loci on the Y chromosome, two on the X chromosome plus up to three microsatellite markers to either support the gender diagnosis or to further monitor extraneous contamination. The protocol, standardized on single lymphocytes, established a PCR efficiency of >93% for all loci with maximum allele dropout rates of 4%. Microsatellite analysis excluded external contamination and confirmed biallelic inheritance. Proof of principle for the simplicity and flexibility of the assay was demonstrated through its application to clinical PGD cycles for lipoid congenital adrenal hyperplasia, which presents a more severe clinical course in males, and Duchenne muscular dystrophy.

Preimplantation genetic haplotyping a new application for diagnosis of translocation carrier's embryos- preliminary observations of two robertsonian translocation carrier families

PURPOSE

Preimplantation genetic diagnosis using fluorescence in-situ hybridization (PGD-FISH) is currently the most common reproductive solution for translocation carriers. However, this technique usually does not differentiate between embryos carrying the balanced form of the translocation and those carrying the homologous normal chromosomes. We developed a new application of preimplantation genetic haplotyping (PGH) that can identify and distinguish between all forms of the translocation status in cleavage stage embryos prior to implantation.

METHODS

Polymorphic markers were used to identify and differentiate between the alleles that carry the translocation and those that are the normal homologous chromosomes.

RESULTS

Embryos from two families of robertsonian translocation carriers were successfully analyzed using polymorphic markers haplotyping.

CONCLUSIONS

Our preliminary results indicate that the PGH is capable of distinguishing between normal, balanced and unbalanced translocation carrier embryos. This method will improve PGD and will enable translocation carriers to avoid transmission of the translocation and the associated medical complications to offspring.

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.

Development and successful clinical application of preimplantation genetic haplotyping for Herlitz junctional epidermolysis bullosa

BACKGROUND

Herlitz junctional epidermolysis bullosa (HJEB) is a severe, life-threatening, autosomal recessive blistering skin disease for which no cure is currently available. Prenatal diagnosis for couples at risk is feasible through fetal skin biopsy or analysis of DNA extracted from chorionic villi, but these methods can be applied only after pregnancy has been established. An alternative approach, which involves the analysis of single cells from embryos prior to establishment of pregnancy, is preimplantation genetic diagnosis (PGD). Until now, its clinical uptake has been hindered by lengthy delays in establishing mutation-specific protocols, and by the small amount of template DNA that can be obtained from a single cell. A new method that addresses these problems, preimplantation genetic haplotyping (PGH), relies on whole genome amplification followed by haplotyping of multiple polymorphic markers using standard DNA-based polymerase chain reaction (PCR) assays.

OBJECTIVES

To design and validate a generic PGH assay for HJEB and to transfer this into clinical practice.

MATERIALS AND METHODS

We established a multiplex PCR-based PGH assay involving 16 markers within and flanking the LAMB3 gene (the most frequently mutated gene in HJEB). The assay was then validated in 10 families with at least one previously affected offspring. After licensing by the Human Fertilisation and Embryology Authority (HFEA), the new test was used for PGD in a couple at risk of HJEB.

RESULTS

The chromosome 1 LAMB3 markers within the assay were shown to be of sufficient heterogeneity to have widespread application for preimplantation testing of HJEB. In one couple that were heterozygous carriers of nonsense mutations in LAMB3, we used the new assay to identify unaffected embryos in a series of PGD cycles. Pregnancy was established in the third PGD cycle and a healthy, unaffected child was born. DNA analysis of cord blood confirmed the predicted single-cell mutation status of wild-type LAMB3 alleles.

CONCLUSIONS

PGH represents a major step forward in widening the scope and availability of preimplantation testing for serious mapped single-gene disorders. We have established a generic test that is suitable for the majority of couples at risk of HJEB.

Preimplantation genetic diagnosis for haematologic conditions

PURPOSE OF REVIEW

This review will inform the clinician about the application, success rates and limitations of preimplantation genetic diagnosis (PGD) for haematologic disease to enable clinicians to offer couples with reproductive risk a realistic view of possible treatments. The molecular techniques used to diagnose disease mutations are described, including the newest technologies using whole genome amplification (WGA) and preimplantation genetic haplotyping (PGH) of embryos. The history and ethics involved in performing PGD together with human leukocyte antigen (HLA) testing (PGD-H) to create matched siblings suitable for haematopoietic stem cell transplant (HSCT) are discussed.

RECENT FINDINGS

The greatest diagnostic hurdle in PGD is the paucity of molecular material in the single embryonic cell. WGA allows amplification of the entire genome, which greatly simplifies mutation analysis and increases the possibilities of multiple simultaneous genetic diagnoses. PGH can be applied to the amplified material, and may enable the application of PGD to the less common haematological mutations, and the diagnosis of nonaffected male progeny in cases of X-linked haematologic diseases.

SUMMARY

PGD to exclude embryos carrying serious haematologic disease is a viable alternative to prenatal diagnosis for couples who wish to avoid having affected children and for whom therapeutic termination of affected pregnancies is unacceptable. PGD is not available for all haematologic mutations, is expensive, time consuming and does not guarantee a pregnancy. PGD-H is more diagnostically and ethically challenging, especially when there is the time constraint of urgent provision of HLA-matched stem cells for a sick sibling. To date there is only a handful of reported cases of successful HSCT from siblings created by embryo selection. The evolving technology of PGH following WGA may increase the diagnostic scope and availability of PGD in the future, but certain limitations will remain.

Preimplantation genetic diagnosis for the prevention of sickle cell disease: current trends and barriers to uptake in a London teaching hospital

INTRODUCTION

Sickle cell disease (SCD) is a clinically significant hemoglobinopathy with increasing global incidence. We describe our experience of using pre-implantation genetic diagnosis (PGD) for the prevention of SCD at a tertiary referral centre in London.

METHODS

Between January 2002 and December 2007, of 78 at-risk couples referred for PGD treatment, 12 couples (15%) underwent 16 PGD cycles for the prevention of SCD. RESULTS. The live birth rate was 13% per initiated cycle, 18% per embryo transfer and 17% per couple.

CONCLUSIONS

Although PGD for prevention of the birth of a child affected by SCD is a viable treatment option for couples at risk of having an affected child, potential barriers to uptake of this service need to be fully addressed to ensure its availability to all couples seeking to avoid having a child affected with SCD.

Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24-h protocol

BACKGROUND

Preimplantation genetic screening (PGS) has been used in an attempt to determine embryonic aneuploidy. Techniques that use new molecular methods to determine the karyotype of an embryo are expanding the scope of PGS.

METHODS

We introduce a new method for PGS, termed 'parental support', which leverages microarray measurements from parental DNA to 'clean' single-cell microarray measurements on embryonic cells and explicitly computes confidence in each copy number call. The method distinguishes mitotic and meiotic copy errors and determines parental source of aneuploidy.

RESULTS

Validation with 459 single cells of known karyotype indicated that per-cell false-positive and false-negative rates are roughly equivalent to the 'gold standard' metaphase karyotype. The majority of the cells were run in parallel with a clinical commercial PGS service. Computed confidences were conservative and roughly concordant with accuracy. To examine ploidy in human embryos, the method was then applied to 26 disaggregated, cryopreserved, cleavage-stage embryos for a total of 134 single blastomeres. Only 23.1% of the embryos were euploid, though 46.2% of embryos were mosaic euploid. Mosaicism affected 57.7% of the embryos. Counts of mitotic and meiotic errors were roughly equivalent. Maternal meiotic trisomy predominated over paternal trisomy, and maternal meiotic trisomies were negatively predictive of mosaic euploid embryos.

CONCLUSIONS

We have performed a major preclinical validation of a new method for PGS and found that the technology performs approximately as well as a metaphase karyotype. We also directly measured the mechanism of aneuploidy in cleavage-stage human embryos and found high rates and distinct patterns of mitotic and meiotic aneuploidy.

Preimplantation genetic haplotyping: 127 diagnostic cycles demonstrating a robust, efficient alternative to direct mutation testing on single cells

Preimplantation genetic diagnosis using whole genome amplification and a haplotyping approach (PGH) was first described in 2006 and suggested as an efficient alternative to single-cell PCR for monogenic disorders. DNA from single cells was amplified using multiple displacement amplification; the resulting products were then tested using disease-specific PCR multiplexes applied under standard laboratory conditions to determine the haplotypes in the embryo. This study reports on a total of 127 completed biopsy cycles for 101 couples at risk of: autosomal recessive disease (71 cycles, 53 couples including one germ-line mosaic carrier), autosomal dominant disease (31 cycles, 26 couples including one germ-line mosaic carrier), X-linked recessive disease (18 cycles, 16 couples including one germ-line mosaic carrier), X-linked dominant disease (six cycles, five couples) and a double inheritance of both autosomal and X-linked recessive diseases (one cycle, one couple). Of these, 107 cycles reached embryo transfer. Overall success rates were: fetal heart beat-positive pregnancies (FHB+)/biopsy cycle=28%; FHB+/embryo transfer=34%; FHB+/couple=36%; 26 babies born, 13 ongoing pregnancies. These data demonstrate that PGH provides a robust, efficient and successful alternative to single-cell PCR for monogenic diseases.

Molecular comparison of single cell MDA products derived from different cell types

The quality of DNA obtained from single cells for molecular analysis is primarily dependent on cell type and cell lysis. Multiple displacement amplification (MDA) amplifies the DNA isothermally with the use of Phi29 polymerase and random hexamer primers. The efficiency and accuracy of MDA was assessed on different cell types (buccal cells, lymphocytes, fibroblasts) using two multiplex PCR reactions that have been applied in clinical preimplantation genetic diagnosis cases (DM triplex-DM1, APOC2, Dl9S112 and CF triplex-DF508del, IVS8CA, IVS17TA). These results were compared using the DM triplex with MDA products from single blastomeres. Cells were lysed using a modified protocol excluding dithiothreitol in the alkaline lysis buffer. The MDA amplification efficiency for buccal cells was 82.0% (41/50) compared with 96.0% (48/50) for lymphocytes and 100% (20/20) for fibroblasts. The average allele dropout (ADO) rates were 31.0% for buccal cells, 20.8% for lymphocytes and 20.0% for fibroblasts with high inter-locus variation across all cell types (5.0-45.5%). Overall, MDA on single lymphocytes and fibroblasts lysed using the modified protocol produced DNA of sufficient quantity and quality for subsequent molecular analysis by PCR and gave results comparable with MDA products from blastomeres, in contrast to buccal cells.

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.

Preimplantation genetic diagnosis as a source of human embryonic stem cells for disease research and drug discovery

Embryos surplus to therapeutic requirements following preimplantation genetic diagnosis can be used to derive human embryonic stem cell (hESC) lines carrying mutations significant to human disease. These cells provide a powerful in vitro tool for modelling disease progression in a number of cell types as well as having the potential to revolutionise drug discovery. Robust and reproducible directed differentiation protocols are needed to maximise the potential of these cells. In this review, we explore the current use of hESC and induced pluripotent stem cells in disease-specific research and discuss the use of stem cell technology in drug discovery and toxicity testing.

Management of carriers and babies with haemophilia

Although up to 30% of babies born with haemophilia do not have a family history of the disorder, the remaining 70% are born in families where haemophilia has been diagnosed. It has been estimated that for each male with haemophilia, there are five potential female carriers. Such women will benefit from knowledge of both their genetic (mutation present or not) and phenotype (level of plasma factor activity) status. Genetic counselling services to provide information and testing, together with plasma factor measurement, should be offered where available to all women at risk of being carriers. It is critical that women know their plasma factor measurement as they may have mild haemophilia (factor 5-30%, reference range 50-150%) which requires management at times of medical and surgical procedures and following trauma. Close liaison between adult and paediatric haemophilia centres and obstetric-gynaecology units is important to ensure that clinical carers identify and address carriers' needs. Genetic testing should be performed only after a potential carrier has been counselled and supported to receive such information. There is no coercion to accept such testing. An advantage of genetic testing is to then discuss pre-implantation genetic diagnosis which is an ex-vitro form of prenatal diagnosis. This can assist couples at risk of having a child with haemophilia who wish to reduce their anxieties about reproduction. Approximately 4% of boys with haemophilia, born in countries with good maternal care, will have intracranial haemorrhage in the neonatal period. There are no high-level evidence-based guidelines for the management of delivery or of the newborn with haemophilia. Obstetricians or other birth attendants need to be advised of the possibility of delivery of a boy with haemophilia and seek support from a haemophilia specialist during the pregnancy. The mother can then be monitored and plans for delivery be developed between her medical consultants and discussed with her. It is always preferable for a carrier to know of her genetic and phenotypic status before becoming pregnant so that she is informed as to her options and requirements for safe delivery.

Multiplex rt-PCR expression analysis of developmentally important genes in individual mouse preimplantation embryos and blastomeres

We have developed a microfluidic chip-based qualitative assay for sensitive (10 RNA copies) detection of multiple transcripts in single cells. We determined the expression patterns of 17 developmentally important genes and isoforms in individual mouse preimplantation embryos from superovulated matings and blastomeres. The ubiquitously expressed histone variant H3f3a and the transcription factor Pou5f1 generated mRNA-derived products in all analyzed (1-cell, 2-cell, 4-cell, and morula stage) embryos and in all analyzed blastomeres from 16-cell embryos, indicating a uniform reactivation of pluripotency gene expression during mouse preimplantation development. In contrast, mRNA expression of different methyltransferases for DNA methylation, methylcytosine-binding proteins for chromatin modification, and base excision repair enzymes, which may provide a mechanism for active demethylation, varied considerably between individual cells from the same embryo and even more dramatically between cells from different embryos. We conclude that at a given point in time the transcriptome encoding the reprogramming machinery and, by extrapolation, genome reprogramming differs between blastomeres. By studying the cell-to-cell variability in gene expression, we can distinguish the following two classes: mouse 16-cell embryos in which most cells express the reprogramming machinery and embryos in which most cells do not contain detectable mRNA levels of DNA and chromatin modification genes. Immunolocalization of DNMT3A, MBD3, APEX1, and LIG3 in most or all nuclei of 40-60-cell embryos is a good indicator of functional activity of genes that are activated by the 16-cell stage.

Preimplantation genetic diagnosis of X-linked retinoschisis

The aim of this study was to perform preimplantation genetic diagnosis (PGD) for X-linked retinoschisis using multiple displacement amplification (MDA) for whole genome amplification and linked markers to the RS1 gene. The study evaluates the ability of MDA to amplify the whole genome directly from a single blastomere. MDA products were used for polymerase chain reaction analysis of two polymorphic markers flanking the RS1 gene and a new X/Y marker, X22, to sex embryos in an X-linked retinoschisis PGD programme. Two couples in whom the wives were carriers of the RS1 gene mutation (599G-->A), previously identified in their families, were subjected to two PGD cycles each. The main outcome measure was the ability to analyse single blastomeres for X-linked retinoschisis using MDA. As a result, the development of an MDA-PGD protocol for X-linked retinoschisis allowed for the diagnosis of 20 embryos in the four PGD cycles performed. These were biopsied on day 3 of culture and analysed. Eight embryos were affected males and two embryos were female carriers. In summary, three healthy female and four healthy male embryos, and a female carrier embryo, were transferred 48 h after biopsy. One single pregnancy was achieved. This report shows that the MDA technique is useful for overcoming the problem of insufficient genomic DNA in PGD. It also allows the simultaneous amplification of different targets to perform diagnosis of any known gene defect and sexing test by standard methods and conditions.

An efficient and reliable DNA extraction method for preimplantation genetic diagnosis: a comparison of allele drop out and amplification rates using different single cell lysis methods

OBJECTIVE

To evaluate methods of DNA extraction from single cells for their suitability to amplify and provide a correct diagnosis of target disease genes.

DESIGN

Experimental study.

SETTING

University hospital laboratory.

PATIENT(S)

Two normal adult male and female blood donors.

INTERVENTION(S)

Exon 51 of the dystrophin gene and the ZFX/ZFY gene were amplified from single lymphocytes using nested PCR. Five different methods of DNA extraction were tested (lysis in distilled water with freezing and thawing using liquid nitrogen, lysis in distilled water, alkaline lysis buffer, Proteinase K/sodium dodecyl sulfate (SDS) buffer, and N-lauroylsarcosine salt solution).

MAIN OUTCOME MEASURE(S)

Allele drop out and amplification rate.

RESULT(S)

The amplification efficiency from single unaffected lymphocytes was 89.0% using the liquid nitrogen method, 88.1% with the distilled water lysis method, 97.5% with the alkaline lysis buffer method, 91.5% with the Proteinase K/SDS lysis buffer method, and 84.8% using the N-lauroylsarcosine salt solution method. The mean allele drop out rate was 16.7%, 43.9%, 2.0%, 9.8%, and 18.9%, respectively, for each lysis method using single male lymphocytes as a template.

CONCLUSION(S)

Based on these results, DNA extraction using an alkaline lysis buffer results in more efficient rates of DNA amplification and less allele drop out than the other methods of DNA extraction tested. This method is suitable for the lysis of single cells in clinical preimplantation genetic diagnosis.

Preimplantation genetic diagnosis for Duchenne muscular dystrophy by multiple displacement amplification

OBJECTIVE

To evaluate the use of multiple displacement amplification (MDA) in preimplantation genetic diagnosis (PGD) for female carriers with Duchenne muscular dystrophy (DMD).

DESIGN

MDA was used to amplify a whole genome of single cells. Following the setup on single cells, the test was applied in two clinical cases of PGD. One mutant exon, six short tandem repeats (STR) markers within the dystrophin gene, and amelogenin were incorporated into singleplex polymerase chain reaction (PCR) assays on MDA products of single blastomeres.

SETTING

Center for reproductive medicine in First Affiliated Hospital, Sun Yat-sen University, China.

PATIENT(S)

Two female carriers with a duplication of exons 3-11 and a deletion of exons 47-50, respectively.

INTERVENTION(S)

The MDA of single cells and fluorescent PCR assays for PGD.

MAIN OUTCOME MEASURE(S)

The ability to analyze single blastomeres for DMD using MDA.

RESULT(S)

The protocol setup previously allowed for the accurate diagnosis of each embryo. Two clinical cases resulted in a healthy girl, which was the first successful clinical application of MDA in PGD for DMD.

CONCLUSION(S)

We suggest that this protocol is reliable to increase the accuracy of the PGD for DMD.

Preimplantation genetic diagnosis for autosomal recessive polycystic kidney disease

Autosomal recessive polycystic kidney disease (ARPKD) is one of the most common hereditary renal cystic diseases, and is caused by mutations in the PKHD1 gene. Due to the poor prognosis, there is a strong demand for prenatal diagnosis. Preimplantation genetic diagnosis (PGD) represents an alternative because it avoids the physical and emotional trauma of a pregnancy termination in the case of an affected fetus. A standardized single-cell diagnostic procedure was developed, based on haplotype analysis, enabling PGD to be offered to couples at risk of transmitting ARPKD. Six linked markers within (D6S1714 and D6S243), or in close proximity to (D6S272, D6S436, KIAA0057, D6S1662) the PKHD1 gene were tested by multiplex nested-polymerase chain reaction (PCR), using a Qiagen multiplex PCR kit. PCR analyses were carried out on 50 single lymphocytes. The amplification rate was excellent (100%), with an allele drop-out (ADO) rate ranging from 0 to 8%. Five PGD cycles were performed and 23 embryos were biopsied and analysed using this test. Transferable embryos were obtained in 4 cycles, resulting in two pregnancies and the birth of a healthy boy. This standardized diagnostic procedure allowed the detection of recombination, contamination, and ADO events, providing high assay accuracy with wide applicability.

Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues

BACKGROUND

Whole genome amplification (WGA) and laser assisted micro-dissection represent two recently developed technologies that can greatly advance biological and medical research. WGA allows the analysis of multiple genomic loci from a single genome and has been performed on single cells from cell suspensions and from enzymatically-digested tissues. Laser micro-dissection makes it possible to isolate specific single cells from heterogeneous tissues.

RESULTS

Here we applied for the first time WGA on laser micro-dissected single cells from stained tissue sections, and developed a protocol for sequentially performing the two procedures. The combined procedure allows correlating the cell's genome with its natural morphology and precise anatomical position. From each cell we amplified 122 genomic and mitochondrial loci. In cells obtained from fresh tissue sections, 64.5% of alleles successfully amplified to approximately 700000 copies each, and mitochondrial DNA was amplified successfully in all cells. Multiplex PCR amplification and analysis of cells from pre-stored sections yielded significantly poorer results. Sequencing and capillary electrophoresis of WGA products allowed detection of slippage mutations in microsatellites (MS), and point mutations in P53.

CONCLUSION

Comprehensive genomic analysis of single cells from stained tissue sections opens new research opportunities for cell lineage and depth analyses, genome-wide mutation surveys, and other single cell assays.

Fertility testing and ICSI sperm selection by hyaluronic acid binding: clinical and genetic aspects

The testis-expressed chaperone protein, HspA2 (previously creatine kinase M isoform) was established as a measure of human sperm cellular maturity, function and fertility. The presence of HspA2 in the synaptonemal complex is likely to link low HspA2 expression and increased frequency of chromosomal aneuploidies in arrested-maturity spermatozoa. A relationship also exists between HspA2 expression in elongating spermatids and the associated spermatogenetic events, including plasma membrane remodelling and the formation of zona pellucida and hyaluronic acid (HA) binding sites. The HA receptor of mature spermatozoa, when coupled with HA-coated slides and/or Petri dishes, allows visual observation of sperm-HA binding, providing a basis for sperm maturity testing, a major improvement in semen evaluation, and selection of mature spermatozoa for intracytoplasmic sperm injection (ICSI). Thus, in HA-selected spermatozoa the frequency of chromosomal disomy and diploidy is reduced 4- to 6-fold compared with semen sperm fractions. This reduction is similar to the increase in numerical chromosomal aberrations in ICSI children. Combined studies of sperm shape and chromosome probes demonstrated that sperm morphology does not aid selection of haploid spermatozoa. The HA-mediated sperm selection is a novel and efficient technique that may alleviate potential problems related to ICSI fertilization with visually selected spermatozoa.

Facilitating choice, framing choice: staff views on widening the scope of preimplantation genetic diagnosis in the UK

In the UK, the Human Fertilisation and Embryology Authority (HFEA) is responsible for licensing preimplantation genetic diagnosis (PGD). To date, licenses have been issued for the testing of about 70 genetic conditions, drawing on three key 'ethical principles'. Following a public consultation, the HFEA has recently widened the scope for PGD to include susceptibility to late onset, lower penetrance conditions such as inherited breast cancer. As the numbers and types of conditions which can potentially be tested for rises, the question of how, and indeed what limits should be set is timely. Drawing on qualitative interviews and ethics discussion groups which took place prior to or during the HFEA consultation, this paper explores the views of staff working in or linked to one PGD Unit in the UK, as to how they saw these potential changes. The paper thus provides an opportunity to develop greater understanding of how staff working in a morally contentious, innovative area viewed the potential expansion of their work, prior to that expansion taking place. Key themes include 'drawing lines' on behalf of others, particularly with the current emphasis on individual reproductive autonomy; and balancing the invasiveness and possible risks of PGD treatment against the 'seriousness' of the condition. More broadly, the paper highlights the complexities involved in trying to develop general 'ethical principles' to govern the use of ever evolving reproductive technologies.

Determination of the genetic status of cleavage-stage human embryos by microsatellite marker analysis following multiple displacement amplification

OBJECTIVES

To analyse genotype information from cleavage-stage human embryos and assess the chromosomal status and feasibility of performing aneuploidy screening by microsatellite analysis.

METHODS

DNA from 49 blastomeres from eight cleavage-stage human embryos was amplified using multiple displacement amplification, then tested for panels of 64 polymorphic microsatellite markers on seven different chromosomes, and for two non-polymorphic sequences on the X and Y chromosomes.

RESULTS

There was an overall allele drop out (ADO) rate of 28%. Novel alleles in single cells were seen in 0.3% of amplifications, interpreted as either somatic microsatellite mutation events or 'slippage' of the MDA phi 29 polymerase. Three-allele results for a single marker in a single cell were found in 0.07% of amplifications, interpreted as 'slippage' of the MDA phi 29 polymerase. One apparent segmental duplication was found. Only one embryo with no normal cells was found, probably arising from the chaotic cleavage division following a triploid conception. Six embryos were mosaic, of which four had only one abnormal cell.

CONCLUSIONS

Abnormalities in human embryos may be present in only a single cell, leading to potentially false abnormal results at pre-implantation genetic diagnosis. ADO associated with MDA reduces the efficacy of this approach for detection of aneuploidy. Statistical analysis showed that, for ADO of 28%, seven informative markers would be required to give 95% confidence of detecting trisomic embryos.

Whole genome amplification from a single cell: a new era for preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) is a technique used for determining the genetic status of a single cell biopsied from embryos or oocytes. Genetic analysis from a single cell is both rewarding and challenging, especially in PGD. The starting material is very limited and not replaceable, and the diagnosis has to be made in a very short time. Different whole genome amplification (WGA) techniques have been developed to specifically increase the DNA quantities originating from clinical samples with limited DNA contents. In this review, currently available WGA techniques are introduced and, among them, multiple displacement amplification (MDA) is discussed in detail. MDA generates abundant assay-ready DNA to perform broad panels of genetic assays through its ability to rapidly amplify genomes from single cells. The utilization of MDA for single-cell molecular analysis is expanding at a high rate, and MDA is expected to soon become an integral part of PGD.

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.

Whole-genome multiple displacement amplification from single cells

Multiple displacement amplification (MDA) is a recently described method of whole-genome amplification (WGA) that has proven efficient in the amplification of small amounts of DNA, including DNA from single cells. Compared with PCR-based WGA methods, MDA generates DNA with a higher molecular weight and shows better genome coverage. This protocol was developed for preimplantation genetic diagnosis, and details a method for performing single-cell MDA using the phi29 DNA polymerase. It can also be useful for the amplification of other minute quantities of DNA, such as from forensic material or microdissected tissue. The protocol includes the collection and lysis of single cells, and all materials and steps involved in the MDA reaction. The whole procedure takes 3 h and generates 1-2 microg of DNA from a single cell, which is suitable for multiple downstream applications, such as sequencing, short tandem repeat analysis or array comparative genomic hybridization.