S SenGupta

University College London, Londinium, England, United Kingdom

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Publications (44)139.97 Total impact

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    ABSTRACT: This is a retrospective study aiming to assess telomere length in human embryos 4 days post fertilization and to determine whether it is correlated to chromosomal ploidy, embryo developmental rate and patient age. Embryos were donated from patients undergoing treatment in the assisted conception unit. Seven couples took part, generating 35 embryos consisting of 1130 cells. Quantitative fluorescent in-situ hybridization (FISH) measured the telomere length of every cell using a pan-telomeric probe. Conventional FISH on six chromosomes was used to assess aneuploidy in the same cells. Maternal and paternal age, referral reason, embryo developmental rate and type of chromosomal error were taken into account. Chromosomally abnormal cells were associated with shorter telomeres than normal cells for embryos that were developmentally slow. Cells produced by women of advanced maternal age and those with a history of repeated miscarriage tended to have substantially shorter telomeres. There was no significant difference in telomere length with respect to the rate of embryo development 5 days post fertilization. Telomeres play an important role in cell division and shorter telomeres may affect embryonic ploidy. Reduced telomere length was associated with aneuploid cells and embryos from women of advanced maternal age.
    Reproductive biomedicine online 01/2014; · 2.68 Impact Factor
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    ABSTRACT: Preimplantation genetic diagnosis (PGD) for monogenic disorders currently involves polymerase chain reaction (PCR)-based methods, which must be robust, sensitive and highly accurate, precluding misdiagnosis. Twelve adverse misdiagnoses reported to the ESHRE PGD-Consortium are likely an underestimate. This retrospective study, involving six PGD centres, assessed the validity of PCR-based PGD through reanalysis of untransferred embryos from monogenic-PGD cycles. Data were collected on the genotype concordance at PGD and follow-up from 940 untransferred embryos, including details on the parameters of PGD cycles: category of monogenic disease, embryo morphology, embryo biopsy and genotype assay strategy. To determine the validity of PCR-based PGD, the sensitivity (Se), specificity (Sp) and diagnostic accuracy were calculated. Stratified analyses were also conducted to assess the influence of the parameters above on the validity of PCR-based PGD. The analysis of overall data showed that 93.7% of embryos had been correctly classified at the time of PGD, with Se of 99.2% and Sp of 80.9%. The stratified analyses found that diagnostic accuracy is statistically significantly higher when PGD is performed on two cells versus one cell (P=0.001). Se was significantly higher when multiplex protocols versus singleplex protocols were applied (P=0.005), as well as for PGD applied on cells from good compared with poor morphology embryos (P=0.032). Morphology, however, did not affect diagnostic accuracy. Multiplex PCR-based methods on one cell, are as robust as those on two cells regarding false negative rate, which is the most important criteria for clinical PGD applications. Overall, this study demonstrates the validity, robustness and high diagnostic value of PCR-based PGD.European Journal of Human Genetics advance online publication, 4 December 2013; doi:10.1038/ejhg.2013.277.
    European journal of human genetics: EJHG 12/2013; · 3.56 Impact Factor
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    ABSTRACT: Preimplantation genetic diagnosis (PGD) was first performed over 20 years ago and has become an accepted part of genetic testing and assisted reproduction worldwide. The techniques and protocols necessary to carry out genetic testing at the single-cell level can be difficult to master and have been developed independently by the laboratories worldwide offering preimplantation testing. These factors indicated the need for an external quality assessment (EQA) scheme for monogenic disease PGD. Toward this end, the European Society for Human Reproduction and Embryology came together with United Kingdom National External Quality Assessment Services for Molecular Genetics, to create a pilot EQA scheme followed by practical EQA schemes for all interested parties. Here, we detail the development of the pilot scheme as well as development and findings from the practical (clinical) schemes that have followed. Results were generally acceptable and there was marked improvement in results and laboratory scores for those labs that participated in multiple schemes. Data from the first three schemes indicate that the EQA scheme is working as planned and has helped laboratories improve their techniques and result reporting. The EQA scheme for monogenic PGD will continue to be developed to offer assessment for other monogenic disorders.European Journal of Human Genetics advance online publication, 14 November 2012; doi:10.1038/ejhg.2012.244.
    European journal of human genetics: EJHG 11/2012; · 3.56 Impact Factor
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    ABSTRACT: OBJECTIVE: To compare the oocyte versus the blastocyst transcriptome and provide data on molecular pathways before and after embryonic genome activation. DESIGN: Prospective laboratory research study. SETTING: An IVF clinic and a specialist preimplantation genetics laboratory. PATIENT(S): Couples undergoing or having completed IVF treatment donating surplus oocytes or cryopreserved blastocysts after patient consent. INTERVENTION(S): Sets of pooled metaphase II (MII) oocytes or blastocysts were processed for RNA extraction, RNA amplification, and analysis with the use of the Human Genome Survey Microarrays v2.0 (Applied Biosystems). MAIN OUTCOME MEASURE(S): Association of cell type and gene expression profile. RESULT(S): Totals of 1,909 and 3,122 genes were uniquely expressed in human MII oocytes and human blastocysts respectively, and 4,910 genes were differentially expressed between the two sample types. Expression levels of 560 housekeeping genes, genes involved in the microRNA processing pathway, as well as hormones and hormone receptors were also investigated. CONCLUSION(S): The lists of genes identified may be of use for understanding the processes involved in early embryo development and blastocyst implantation, and for identifying any dysregulation leading to infertility.
    Fertility and sterility 11/2012; · 3.97 Impact Factor
  • Sioban B SenGupta, Joy D A Delhanty
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    ABSTRACT: Over the last 20 years, preimplantation genetic diagnosis (PGD) has changed from being an experimental procedure to one that is carried out in specialized diagnostic centers worldwide. Genetic awareness and the rapid identification of germline mutations or chromosomal abnormalities enable individuals to know their risk of transmitting a genetic disease before they have children. This has created a demand for PGD from couples who wish to avoid terminations of affected pregnancies. Although PGD is expensive because it requires couples to go through IVF, there is a trend for diagnosis to move towards automation, which will reduce cost and the need for specialized expertise. This will allow diagnosis to be carried out in routine molecular diagnostic laboratories.
    Expert Review of Molecular Diagnostics 07/2012; 12(6):585-92. · 4.09 Impact Factor
  • Reproductive biomedicine online 05/2012; 24:S56. · 2.68 Impact Factor
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    ABSTRACT: Since it was established in 1997, the ESHRE PGD Consortium has been collecting data from international preimplantation genetic diagnosis (PGD) centres. Ten papers have been published, including data from January 1997 to December 2007. The data collection originally used a hard-copy format, then an excel database and finally a FileMaker Pro database. The indications are divided into five categories: PGD for chromosome abnormalities, sexing for X-linked disease, PGD for single gene defects, preimplantation genetic screening (PGS) and PGD for social sexing. The main end-points are pregnancy outcome and follow-up of deliveries. In data collection I, 16 centres contributed data, which increased to 57 centres by data X (average of 39 centres per data collection). These centres contributed data on over 27 000 cycles that reached oocyte retrieval. Of these cycles, 61% were for aneuploidy screening, 17% for single gene disorders, 16% for chromosomal abnormalities, 4% for sexing of X-linked disease and 2% for social sexing. Cumulatively, 5187 clinical pregnancies gave rise to 4140 deliveries and 5135 newborns (singletons: 3182, twins: 921, triplets: 37). In this paper, we present an overview of the first 10 years of PGD data, highlighting trends. These include the introduction of laser-assisted biopsy, an increase in polar body and trophectoderm biopsy, new strategies, methodologies and technologies for diagnosis, including recently arrays, and the more frequent use of freezing biopsied embryos. The Consortium data reports represent a valuable resource for information about the practice of PGD.
    Human Reproduction Update 02/2012; 18(3):234-47. · 9.23 Impact Factor
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    ABSTRACT: To examine the effect of mosaicism in the array comparative genomic hybridization result during preimplantation genetic screening after blastocyst biopsy. Experimental study. University laboratory. MATERIAL(S): Epithelial cell lines. Mixing of euploid and aneuploid cells to create mosaic trophectoderm and blastocyst models. The level of aneuploidy in samples with different ratios of aneuploid cells was measured after array comparative genomic hybridization. A shift from normality was present when the level of aneuploid cells in the sample was >25%. Aneuploidy could be confidently called when the level of aneuploid cells was >50%. This study determined that aneuploidy in mosaic samples can be detected by array comparative genomic hybridization and that the result may also indicate the proportion of the aneuploid cells present in the sample.
    Fertility and sterility 01/2012; 97(4):943-7. · 3.97 Impact Factor
  • Sioban B SenGupta, Susan T Vadaparampil, Usha Menon
    Advances in experimental medicine and biology 01/2012; 732:103-13. · 1.83 Impact Factor
  • Joyce C Harper, Sioban B Sengupta
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    ABSTRACT: For the last 20 years, preimplantation genetic diagnosis (PGD) has been mostly performed on cleavage stage embryos after the biopsy of 1-2 cells and PCR and FISH have been used for the diagnosis. The main indications have been single gene disorders and inherited chromosome abnormalities. Preimplantation genetic screening (PGS) for aneuploidy is a technique that has used PGD technology to examine chromosomes in embryos from couples undergoing IVF with the aim of helping select the chromosomally 'best' embryo for transfer. It has been applied to patients of advanced maternal age, repeated implantation failure, repeated miscarriages and severe male factor infertility. Recent randomised controlled trials (RCTs) have shown that PGS performed on cleavage stage embryos for a variety of indications does not improve delivery rates. At the cleavage stage, the cells biopsied from the embryo are often not representative of the rest of the embryo due to chromosomal mosaicism. There has therefore been a move towards blastocyst and polar body biopsy, depending on the indication and regulations in specific countries (in some countries, biopsy of embryos is not allowed). Blastocyst biopsy has an added advantage as vitrification of blastocysts, even post biopsy, has been shown to be a very successful method of cryopreserving embryos. However, mosaicism is also observed in blastocysts. There have been dramatic changes in the method of diagnosing small numbers of cells for PGD. Both array-comparative genomic hybridisation and single nucleotide polymorphism arrays have been introduced clinically for PGD and PGS. For PGD, the use of SNP arrays brings with it ethical concerns as a large amount of genetic information will be available from each embryo. For PGS, RCTs need to be conducted using both array-CGH and SNP arrays to determine if either will result in an increase in delivery rates.
    Human Genetics 07/2011; 131(2):175-86. · 4.63 Impact Factor
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    ABSTRACT: Cleavage-stage embryos often have nuclear abnormalities, one of the most common being binucleate blastomeres, which may contain two diploid or two haploid nuclei. Biopsied cells from preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS) cycles were studied to determine the relative frequency of binucleate cells with two haploid versus two diploid nuclei. The frequency of mononucleate haploid biopsied blastomeres was also recorded. In the chromosomal PGD cycles 45.2% of the biopsied binucleate cells were overall diploid and 38.7% were overall tetraploid, compared with 50.0% and 29.2% for the PGS group, respectively. Placental mesenchymal dysplasia is a rare condition associated with intrauterine growth restriction, prematurity and intrauterine death. Recent work suggests that androgenetic diploid/haploid mosaicism may be a causal mechanism. There are two possible origins of haploid nuclei, either the cell contained only one parental genome initially or they may be derived from the cytokinesis of binucleate cells with two haploid nuclei. Binucleate formation therefore may be a way of doubling up the haploid genome, to produce diploid cells of androgenetic origin as seen in placental mesenchymal dysplasia.
    Reproductive biomedicine online 01/2011; 22(4):362-70. · 2.68 Impact Factor
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    ABSTRACT: 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.
    Human Reproduction 10/2010; 26(1):33-40. · 4.67 Impact Factor
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    ABSTRACT: Accreditation according to an internationally recognized standard is increasingly acknowledged as the single most effective route to comprehensive laboratory quality assurance, and many countries are progressively moving towards compulsory accreditation of medical testing laboratories. The ESHRE PGD Consortium and some regulatory bodies recommend that all PGD laboratories should be accredited or working actively towards accreditation, according to the internationally recognized standard ISO 15189, 'Medical laboratories-Particular requirements for quality and competence'. ISO 15189 requires comprehensive quality assurance. Detailed management and technical requirements are defined in the two major chapters. The management requirements address quality management including the quality policy and manual, document control, non-conformities and corrective actions, continual improvement, auditing, management review, contracts, referrals and resolution of complaints. Technical requirements include personnel competence (both technical and medical), equipment, accommodation and environment, and pre-analytical, analytical and post-analytical processes. Emphasis is placed on the particular requirements of patient care: notably sample identification and traceability, test validation and interpretation and reporting of results. Quality indicators must be developed to monitor contributions to patient care and continual improvement. We discuss the implementation of ISO 15189 with a specific emphasis on the PGD laboratory, highlight elements of particular importance or difficulty and provide suggestions of effective and efficient ways to obtain accreditation. The focus is on the European environment although the principles are globally applicable.
    Human Reproduction 04/2010; 25(4):1051-65. · 4.67 Impact Factor
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    ABSTRACT: Since 2004, there have been 11 randomized controlled trials (RCTs) mainly for advanced maternal age (AMA), which have shown no benefit of performing preimplantation genetic screening (PGS). Ten of the RCTs have been performed at the cleavage stage and one at the blastocyst stage. It is probable that the high levels of chromosomal mosaicism at cleavage stages, which may result in the tested cell not being representative of the embryo, and the inability to examine all of the chromosomes using fluorescence in situ hybridization, have contributed to the lack of positive outcome from the RCTs. We suggest that future RCTs should examine alternative biopsy timing (polar body and/or trophectoderm biopsy), and should apply technologies that allow more comprehensive testing to include all chromosomes (microarray-based testing) to determine if PGS shows an improvement in delivery rate. Currently there is no evidence that routine PGS is beneficial for patients with AMA and conclusive data (RCTs) on repeated miscarriage, implantation failure and severe male factor are missing. To evaluate benefits of PGS, an ESHRE trial has recently been started on patients with AMA using polar body biopsy and array-comparative genomic hybridization, which should bring more information on this patient group in the near future.
    Human Reproduction 04/2010; 25(4):821-3. · 4.67 Impact Factor
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    ABSTRACT: To overcome problems associated with the use of triplet repeat primed polymerase chain reaction (TP-PCR) in preimplantation genetic diagnosis (PGD) of myotonic dystrophy type 1 (DM1). Clinical research study. UCL Centre for PGD and Centre for Reproductive and Genetic Health. Seven couples undergoing PGD for DM1. A modified TP-PCR protocol (mTP-PCR) for the reliable detection of both expanded and nonexpanded alleles in DMPK was optimized using single lymphocytes. Four cycles of PGD were performed with TP-PCR for diagnosis and a further 10 cycles with mTP-PCR. Amplification efficiency, allele dropout, diagnosis rate, and delivery rate. Preliminary testing showed that the TP-PCR amplification efficiency was higher using lymphocytes versus buccal cells. Single lymphocytes gave very high amplification efficiencies for both protocols (99% to 100%). There were no false-positive or false-negative results for 148 single lymphocytes tested with mTP-PCR compared with 9% (5 out of 54) false-positive results with TP-PCR, indicating the improved accuracy of the modified protocol. In embryos, the diagnosis rate was 95.6% with mTP-PCR and 75% with TP-PCR. For PGD of DM1, mTP-PCR is recommended. It may also be applied as a rapid screen for DMPK expansions in individuals with symptoms of DM1, relatives of known mutation carriers, or in prenatal diagnosis.
    Fertility and sterility 02/2010; 94(5):1674-9. · 3.97 Impact Factor
  • Reproductive Biomedicine Online - REPROD BIOMED ONLINE. 01/2010; 20.
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    ABSTRACT: The early preimplantation embryo relies on mRNA and protein from the oocyte to detect DNA damage and activate DNA repair, cell cycle arrest or apoptosis. Expression of some repair genes has been detected in mammalian oocytes and embryos; however, little is known about DNA repair gene expression in human blastocysts. In this study, DNA repair gene expression was investigated in human oocytes and blastocysts to identify the pathways involved at these stages and detect potential differences in repair mechanisms pre- and post-embryonic genome activation. Triplicate sets of pooled metaphase II oocytes or blastocysts were processed for analysis using the Human Genome Survey Microarrays V2.0 (Applied Biosystems). Of 154 DNA repair genes investigated, 109 were detected in blastocysts and 107 in oocytes. Among differentially expressed DNA repair genes, 40/55 (73%) had lower expression levels in blastocysts compared with oocytes (P < 0.05, fold change >3). Despite experimental limitations due to culture or freezing and thawing of samples, large numbers of repair genes were detected indicating that all DNA repair pathways are potentially functional in human oocytes and blastocysts. The higher mRNA level for most repair genes in oocytes compared with blastocysts ensures sufficient availability of template until embryonic genome activation.
    Human Reproduction 06/2009; 24(10):2649-55. · 4.67 Impact Factor
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    ABSTRACT: 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.
    Reproductive biomedicine online 02/2009; 19(1):89-98. · 2.68 Impact Factor
  • Reproductive Biomedicine Online - REPROD BIOMED ONLINE. 01/2009; 18.
  • H Sultan, S SenGupta, R Noble, JC Harper
    Reproductive Biomedicine Online - REPROD BIOMED ONLINE. 01/2009; 18.

Publication Stats

869 Citations
139.97 Total Impact Points

Institutions

  • 2002–2014
    • University College London
      • Institute for Women's Health
      Londinium, England, United Kingdom