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Cambridge, United Kingdom

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Cambridge, United Kingdom
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A method for determining the presence of a copy number imbalance in genomic DNA of a test sample is provided. The method can separately measure hybridization of a single test sample to a first hybridization array and hybridization of a plurality of reference samples to a plurality of other, respective test arrays. A determination of copy number can be based on the best fit reference array, relative to the test array. The best fit can be determined based on the closest or most similar signal-to-noise ratio of the measured signals.

Ramsay N.,University of Cambridge | Ramsay N.,Domantis Ltd. | Jemth A.-S.,University of Cambridge | Jemth A.-S.,University of Stockholm | And 5 more authors.
Journal of the American Chemical Society | Year: 2010

DNA not only transmits genetic information but can also serve as a versatile supramolecular scaffold. Here we describe a strategy for the synthesis and replication of DNA displaying hundreds of substituents using directed evolution of polymerase function by short-patch compartmentalized self-replication (spCSR) and the widely used fluorescent dye labeled deoxinucleotide triphosphates Cy3-dCTP and Cy5-dCTP as substrates. In just two rounds of spCSR selection, we have isolated a polymerase that allows the PCR amplification of double stranded DNA fragments up to 1kb, in which all dC bases are substituted by its fluorescent dye-labeled equivalent Cy3- or Cy5-dC. The resulting "CyDNA" displays hundreds of aromatic heterocycles on the outside of the DNA helix and is brightly colored and highly fluorescent. CyDNA also exhibits significantly altered physicochemical properties compared to standard B-form DNA, including loss of silica and intercalating dye binding, resistance to cleavage by some endonucleases, an up to 40% increased apparent diameter as judged by atomic force microscopy and organic phase partitioning during phenol extraction. CyDNA also displays very bright fluorescence enabling significant signal gains in microarray and microfluidic applications. CyDNA represents a step toward a long-term goal of the encoded synthesis of DNA-based polymers of programmable and evolvable sequence and properties. © 2010 American Chemical Society.

Mamas T.,University College London | Gordon A.,BlueGnome Ltd | Brown A.,BlueGnome Ltd | Harper J.,University College London | And 2 more authors.
Fertility and Sterility | Year: 2012

Objective: To examine the effect of mosaicism in the array comparative genomic hybridization result during preimplantation genetic screening after blastocyst biopsy. Design: Experimental study. Setting: University laboratory. Material(s): Epithelial cell lines. Intervention(s): Mixing of euploid and aneuploid cells to create mosaic trophectoderm and blastocyst models. Main Outcome Measure(s): The level of aneuploidy in samples with different ratios of aneuploid cells was measured after array comparative genomic hybridization. Result(s): 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%. Conclusion(s): 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. © 2012 by American Society for Reproductive Medicine.

Fragouli E.,University of Oxford | Alfarawati S.,University of Oxford | Daphnis D.D.,London Fertility Center | Goodall N.-N.,Reprogenetics LLC | And 4 more authors.
Human Reproduction | Year: 2011

BACKGROUNDRecent studies have suggested that biopsy of several trophectoderm (TE) cells from blastocysts followed by comparative genomic hybridization (CGH) analysis might represent an optimal strategy for aneuploidy detection, but few data on accuracy are available. The main question concerns the rate of mosaicism at the blastocyst stage, and to what extent this might cause misdiagnoses. We assessed blastocyst aneuploidy and mosaicism rates and evaluated the accuracy and efficiency of CGH and microarray-CGH (aCGH) for TE analysis.METHODSA total of 52 blastocysts, from 20 couples, were biopsied and their chromosomes examined by CGH. The remaining cells were spread and tested by fluorescent in situ hybridization (FISH). Of the 52 blastocysts, 20 underwent a second TE biopsy and were tested using aCGH.RESULTSCGH and aCGH produced results for 98 of TE samples. 42.3 of blastocysts were uniformly euploid, 30 were uniformly aneuploid and 32.4 were mosaic. Of the mosaic embryos, 15.4% were found to be composed of a mixture of different aneuploid cell lines, while 17 contained both normal and aneuploid cells. Mosaic diploidaneuploid blastocysts with >30 normal cells accounted for <6 of analysed embryos. CONCLUSIONSComprehensive chromosome screening and follow-up assessment of large numbers of cells provided a unique insight into the cytogenetics of human blastocysts. Meiotic and post-zygotic errors leading to mosaicism were common. However, most mosaic blastocysts contained no normal cells. Hence, CGH or aCGH TE analysis is an accurate aneuploidy detection tool and may assist in identifying viable euploid embryos with higher implantation potential. © 2010 The Author.

Howarth K.D.,University of Cambridge | Pole J.C.M.,University of Cambridge | Pole J.C.M.,BlueGnome Ltd. | Beavis J.C.,University of Cambridge | And 4 more authors.
Genome Research | Year: 2011

Reciprocal chromosome translocations are often not exactly reciprocal. Most familiar are deletions at the breakpoints, up to megabases in extent. We describe here the opposite phenomenon - duplication of tens or hundreds of kilobases at the breakpoint junction, so that the same sequence is present on both products of a translocation. When the products of the translocation are mapped on the genome, they overlap. We report several of these "overlapping-breakpoint" duplications in breast cancer cell lines HCC1187, HCC1806, and DU4475. These lines also had deletions and essentially balanced translocations. In HCC1187 and HCC1806, we identified five cases of duplication ranging between 46 kb and 200 kb, with the partner chromosome showing deletions between 29 bp and 31 Mb. DU4475 had a duplication of at least 200 kb. Breakpoints were mapped using array painting, i.e., hybridization of chromosomes isolated by flow cytometry to custom oligonucleotide microarrays. Duplications were verified by fluorescent in situ hybridization (FISH), PCR on isolated chromosomes, and cloning of breakpoints. We propose that these duplications are the counterpart of deletions and that they are produced at a replication bubble, comprising two replication forks with the duplicated sequence in between. Both copies of the duplicated sequence would go to one daughter cell, on different products of the translocation, while the other daughter cell would show deletion. These duplications may have been overlooked because they may be missed by FISH and array-CGH and may be interpreted as insertions by paired-end sequencing. Such duplications may therefore be quite frequent. © 2011 by Cold Spring Harbor Laboratory Press.

Gray J.C.,University of Cambridge | Hansen M.R.,University of Cambridge | Shaw D.J.,University of Cambridge | Graham K.,University of Cambridge | And 4 more authors.
Plant Journal | Year: 2012

Stromules are highly dynamic stroma-filled tubules that extend from the surface of all plastid types in all multi-cellular plants examined to date. The stromule frequency (percentage of plastids with stromules) has generally been regarded as characteristic of the cell and tissue type. However, the present study shows that various stress treatments, including drought and salt stress, are able to induce stromule formation in the epidermal cells of tobacco hypocotyls and the root hairs of wheat seedlings. Application of abscisic acid (ABA) to tobacco and wheat seedlings induced stromule formation very effectively, and application of abamine, a specific inhibitor of ABA synthesis, prevented stromule induction by mannitol. Stromule induction by ABA was dependent on cytosolic protein synthesis, but not plastid protein synthesis. Stromules were more abundant in dark-grown seedlings than in light-grown seedlings, and the stromule frequency was increased by transfer of light-grown seedlings to the dark and decreased by illumination of dark-grown seedlings. Stromule formation was sensitive to red and far-red light, but not to blue light. Stromules were induced by treatment with ACC (1-aminocyclopropane-1- carboxylic acid), the first committed ethylene precursor, and by treatment with methyl jasmonate, but disappeared upon treatment of seedlings with salicylate. These observations indicate that abiotic, and most probably biotic, stresses are able to induce the formation of stromules in tobacco and wheat seedlings. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Christopikou D.,Center for Human Reproduction | Tsorva E.,Center for Human Reproduction | Economou K.,Center for Human Reproduction | Shelley P.,Bluegnome Ltd. | And 5 more authors.
Human Reproduction | Year: 2013

Study Questio: NHow accurate is array comparative genomic hybridization (array CGH) analysis of the first polar body (PB1) and second polar body (PB2) in predicting aneuploidies of maternal meiotic origin in the cleavage stage embryos of women of advanced maternal age? Summary Answer: Almost all of the aneuploidies detected in cleavage stage embryos were associated with copy number changes in the polar bodies (93%) and all but one (98.5%) were predicted to be aneuploid. A minority of copy number changes (17%), mainly in PB1, did not result in the predicted changes in the embryo, but many of these were small copy number changes, which are likely to be artefacts. What Is Known Already: Chromosome aneuploidy is a major cause of pregnancy failure and loss, abnormal pregnancy and live births. Most aneuploidy is of maternal meiotic origin and increases exponentially in the decade preceding the menopause. A pilot study demonstrated a high rate of concordance between the chromosomal status predicted by polar body analysis and the corresponding zygotes in women of advanced maternal age.STUDY Design: , SIZE AND DURATIONPolar body biopsy and array CGH analysis of mature oocytes, which fertilized normally, to identify segregation errors in meiosis, followed by the analysis of the corresponding cleavage stage embryos (n = 34), in a consecutive series of stimulated and natural IVF cycles in women of advanced maternal age.MATERIALS, SETTING AND METHODSTwenty couples requesting aneuploidy screening (mean ± SD of maternal age 39 ± 3 years) had 16 controlled ovarian hyperstimulation and 7 natural IVF cycles. PB1 and PB2 were biopsied from mature oocytes, prior to intracytoplasmic sperm injection (ICSI) and following confirmation of normal fertilization, respectively. Array CGH was used to detect chromosome copy number changes and to predict aneuploidy in the corresponding embryos. Embryos with normal copy number in both polar bodies were transferred but, 34 cleavage stage embryos, most of which were predicted to have one or more aneuploidies of maternal meiotic origin, were analysed in whole after removal of the zona by array CGH, on Day 3 post-ICSI. Main Results and the Role of Chance: Thirty cleavage stage embryos, predicted to have one or more aneuploidies, were all confirmed to be aneuploid (100% concordant). Seventy four aneuploidies were detected in these embryos. Sixty-nine (93%) aneuploidies were associated with copy number changes in the polar bodies and 68 (98.5%) of these had been predicted to be aneuploid. Also, 19 of 20 (95%) balanced combinations of chromatid gain/loss in PB1/PB2 accurately predicted normal copy number in the corresponding embryos. However, 17 (12%) copy number changes in the polar bodies did not result in the expected outcome, including 12 false positive predictions of aneuploidy. Most of these involved copy number changes that were smaller than would be expected for whole chromosome or chromatid imbalance and occurred significantly more often in PB1 than PB2 (P < 0.0005). Three other embryos with only small copy number changes and one embryo with a partial chromosome loss in PB2, were all confirmed to be euploid. Limitations, Reasons For Cautiona: ccurate false positive and negative rates will require follow-up of both euploid and aneuploid embryos, ideally using molecular genetic markers to detect aneuploidy independently and to identify their origin. Wider Implications of the Findings: Polar body biopsy and array CGH analysis is efficient and accurately predicts most aneuploidies in cleavage stage embryos. However, the size of the ratio shifts, particularly in PB1, should always be compared with the X chromosome shift before it can be concluded that there is a real copy number change. Study Funding/Competing Interest: (S)Study funded by Embryogenesis, Athens. P.S. and A.H.H. are employed full time and part time, respectively, by BlueGnome Ltd, Cambridge, UK. © 2013 The Author.

Fiorentino F.,GENOMA Molecular Genetics Laboratory | Spizzichino L.,GENOMA Molecular Genetics Laboratory | Bono S.,GENOMA Molecular Genetics Laboratory | Biricik A.,GENOMA Molecular Genetics Laboratory | And 6 more authors.
Human Reproduction | Year: 2011

Background: Fluorescence in situ hybridization (FISH) is the most widely used method for detecting unbalanced chromosome rearrangements in preimplantation embryos but it is known to have several technical limitations. We describe the clinical application of a molecular-based assay, array comparative genomic hybridization (array-CGH), to simultaneously screen for unbalanced translocation derivatives and aneuploidy of all 24 chromosomes. Methods: Cell biopsy was carried out on cleavage-stage embryos (Day 3). Single cells were first lysed and DNA amplified by whole-genome amplification (WGA). WGA products were then processed by array-CGH using 24sure arrays, BlueGnome. Balanced/normal euploid embryos were then selected for transfer on Day 5 of the same cycle. Results: Twenty-eight consecutive cycles of preimplantation genetic diagnosis were carried out for 24 couples carrying 18 different balanced translocations. Overall, 187/200 (93.5) embryos were successfully diagnosed. Embryos suitable for transfer were identified in 17 cycles (60.7), with transfer of 22 embryos (mean 1.3 ± 0.5). Twelve couples achieved a clinical pregnancy (70.6 per embryo transfer), with a total of 14 embryos implanted (63.6 per transferred embryo). Three patients delivered three healthy babies, during writing, the other pregnancies (two twins and seven singletons) are ongoing beyond 20 weeks of gestation. Conclusions: The data obtained demonstrate that array-CGH can detect chromosome imbalances in embryos, also providing the added benefit of simultaneous aneuploidy screening of all 24 chromosomes. Array-CGH has the potential to overcome several inherent limitations of FISH-based tests, providing improvements in terms of test performance, automation, sensitivity and reliability. © 2011 The Author.

Bluegnome Ltd | Date: 2014-03-26

The present disclosure relates generally to methods and materials for use in detecting abnormalities of the number of whole chromosomes or chromosome regions (aneuploidy). It has particular utility for assessing the risk of aneuploidy of eggs (i.e., oocytes), fertilised eggs or embryos developed therefrom in the context of in vitro fertilisation.

A method for determining the presence of a copy number imbalance in genomic DNA of a test sample is provided. The method can separately measure hybridization of a single test sample to a first hybridization array and hybridization of a plurality of reference samples to a plurality of other, respective test arrays. A determination of copy number can be based on the best fit reference array, relative to the test array. The best fit can be determined based on the closest or most similar signal-to-noise ratio of the measured signals.

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