Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts

Fertility and Sterility

Volumn 104, Issue 5, 2015, Pages 1276-1285.e1

  Deleye, Lieselot ^a   Dheedene, Annelies ^b   De Coninck, Dieter ^a   Sante, Tom ^b   Christodoulou, Christodoulos ^b   Heindryckx, Björn ^b   Van Den Abbeel, Etienne ^b   De Sutter, Petra ^b   Deforce, Dieter ^a   Menten, Björn ^b   Van Nieuwerburgh, Filip ^a  

^a GHENT UNIVERSITY   (Belgium)

^b GHENT UNIVERSITY HOSPITAL   (Belgium)

Author keywords

blastocyst biopsy; chromosomal rearrangements; Massive parallel sequencing; preimplantation genetic diagnosis; whole genome amplification

Indexed keywords

ADULT; ALGORITHM; ARTICLE; BLASTOCYST; BLASTULA; CHROMOSOME ABERRATION; CHROMOSOME INVERSION; CHROMOSOME REARRANGEMENT; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; ECTODERM; EMBRYO; FEMALE; GENE DELETION; GENE DUPLICATION; GENE SEQUENCE; GENE TRANSLOCATION; GENOME; HETEROZYGOTE; HUMAN; HUMAN CELL; INTRACYTOPLASMIC SPERM INJECTION; MALE; OOCYTE RETRIEVAL; PRENATAL DIAGNOSIS; PRIORITY JOURNAL; RECIPROCAL CHROMOSOME TRANSLOCATION; ROBERTSONIAN CHROMOSOME TRANSLOCATION; BIOPSY; CHROMOSOME DISORDER; COMPARATIVE STUDY; EMBRYO CULTURE; EVALUATION STUDY; GENETIC MARKER; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN CHROMOSOME; PATHOLOGY; PREDICTIVE VALUE; PROCEDURES; UNIVERSITY HOSPITAL;

GENETIC MARKER;

ADULT; BIOPSY; BLASTOCYST; CHROMOSOME DISORDERS; CHROMOSOMES, HUMAN; COMPARATIVE GENOMIC HYBRIDIZATION; EMBRYO CULTURE TECHNIQUES; FEMALE; GENETIC MARKERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOSPITALS, UNIVERSITY; HUMANS; MALE; PREDICTIVE VALUE OF TESTS; PREIMPLANTATION DIAGNOSIS; SPERM INJECTIONS, INTRACYTOPLASMIC; TRANSLOCATION, GENETIC;

EID: 84946483831     PISSN: 00150282     EISSN: 15565653     Source Type: Journal    
DOI: 10.1016/j.fertnstert.2015.07.1144     Document Type: Article

References (35)

1. M. Simopoulou, J.C. Harper, E. Fragouli, A. Mantzouratou, B.E. Speyer, P. Serhal, and et al. Preimplantation genetic diagnosis of chromosome abnormalities: implications from the outcome for couples with chromosomal rearrangements Prenat Diagn 23 2003 652 662
2. E. Fragouli, S. Alfarawati, D.D. Daphnis, N.N. Goodall, A. Mania, T. Griffiths, and et al. Cytogenetic analysis of human blastocysts with the use of FISH, CGH and aCGH: scientific data and technical evaluation Hum Reprod 26 2011 480 490
3. P.N. Scriven, T.L. Kirby, and C.M. Ogilvie FISH for pre-implantation genetic diagnosis J Vis Exp 659 2011 269 282
4. J.C. Harper, and S.B. Sengupta Preimplantation genetic diagnosis: state of the art 2011 Hum Genet 131 2012 175 186
5. E.J. Forman, K.H. Hong, K.M. Ferry, X. Tao, D. Taylor, B. Levy, and et al. In vitro fertilization with single euploid blastocyst transfer: a randomized controlled trial Fertil Steril 100 2013 100 107 e1
6. W.B. Schoolcraft, and M.G. Katz-Jaffe Comprehensive chromosome screening of trophectoderm with vitrification facilitates elective single-embryo transfer for infertile women with advanced maternal age Fertil Steril 100 2013 615 619
7. R.T. Scott Jr., K.M. Upham, E.J. Forman, K.H. Hong, K.L. Scott, D. Taylor, and et al. Blastocyst biopsy with comprehensive chromosome screening and fresh embryo transfer significantly increases in vitro fertilization implantation and delivery rates: a randomized controlled trial Fertil Steril 100 2013 697 703
8. Z. Yang, J. Liu, G.S. Collins, S.A. Salem, X. Liu, S.S. Lyle, and et al. Selection of single blastocysts for fresh transfer via standard morphology assessment alone and with array CGH for good prognosis IVF patients: results from a randomized pilot study Mol Cytogenet 5 2012 24
9. D. Wells, K. Kaur, J. Grifo, M. Glassner, J.C. Taylor, E. Fragouli, and et al. Clinical utilisation of a rapid low-pass whole genome sequencing technique for the diagnosis of aneuploidy in human embryos prior to implantation J Med Genet 51 2014 553 562
10. F. Fiorentino, A. Biricik, S. Bono, L. Spizzichino, E. Cotroneo, G. Cottone, and et al. Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos Fertil Steril 101 2014 1375 1382
11. N.R. Treff, J. Su, X. Tao, B. Levy, and R.T. Scott Jr. Accurate single cell 24 chromosome aneuploidy screening using whole genome amplification and single nucleotide polymorphism microarrays Fertil Steril 94 2010 2017 2021
12. X. Yin, K. Tan, G. Vajta, H. Jiang, Y. Tan, C. Zhang, and et al. Massively parallel sequencing for chromosomal abnormality testing in trophectoderm cells of human blastocysts Biol Reprod 88 2013 69
13. F. Vandekerckhove, J. Gerris, S. Vansteelandt, A. de Baerdemaeker, K. Tilleman, and P. de Sutter Delaying the oocyte maturation trigger by one day leads to a higher metaphase II oocyte yield in IVF/ICSI: a randomised controlled trial Reprod Biol Endocrinol 12 2014 31
14. D.K. Gardner, and W.B. Schoolcraft In-vitro culture of human blastocysts Towards reproductive certainty: fertility and genetics beyond 1999 1999 The Parthenon Publishing Group New York 378 388
15. T. Sante, S. Vergult, P.J. Volders, W.P. Kloosterman, G. Trooskens, K. de Preter, and et al. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation PloS One 9 2014 e113800
16. H. Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM 2013 Oxford University Press New York
17. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, and et al. The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
18. I. Scheinin, D. Sie, H. Bengtsson, M.A. van de Wiel, A.B. Olshen, H.F. van Thuijl, and et al. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly Genome Res 24 2014 2022 2032
19. R Core Team. R: A language and environment for statistical computing. In, Computing RFfS, ed. Vienna, Austria: R Foundation for Statistical Computing; 2013.
20. Consortium EP An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
21. T.J. Pugh, A.D. Delaney, N. Farnoud, S. Flibotte, M. Griffith, H.I. Li, and et al. Impact of whole genome amplification on analysis of copy number variants Nucleic Acids Res 36 2008 e80
22. L. Deleye Whole genome amplification with SurePlex results in better copy number variation detection using sequencing data compared to the MALBAC method Sci Rep 5 2015 11711
23. G.L. Harton, M. de Rycke, F. Fiorentino, C. Moutou, S. SenGupta, J. Traeger-Synodinos, and et al. ESHRE PGD consortium best practice guidelines for amplification-based PGD Hum Reprod 26 2011 33 40
24. S. Seki, and P. Mazur The dominance of warming rate over cooling rate in the survival of mouse oocytes subjected to a vitrification procedure Cryobiology 59 2009 75 82
25. L. Van Landuyt, D. Stoop, G. Verheyen, W. Verpoest, M. Camus, H. van de Velde, and et al. Outcome of closed blastocyst vitrification in relation to blastocyst quality: evaluation of 759 warming cycles in a single-embryo transfer policy Hum Reprod 26 2011 527 534
26. E. Dimitriadou, N. van der Aa, J. Cheng, T. Voet, and J.R. Vermeesch Single cell segmental aneuploidy detection is compromised by S phase Mol Cytogenet 7 2014 46
27. A. De Vos, C. Staessen, M. de Rycke, W. Verpoest, P. Haentjens, P. Devroey, and et al. Impact of cleavage-stage embryo biopsy in view of PGD on human blastocyst implantation: a prospective cohort of single embryo transfers Hum Reprod 24 2009 2988 2996
28. F.J. Los, D. van Opstal, and C. van den Berg The development of cytogenetically normal, abnormal and mosaic embryos: a theoretical model Hum Reprod Update 10 2004 79 94
29. E. Vanneste, T. Voet, C. le Caignec, M. Ampe, P. Konings, C. Melotte, and et al. Chromosome instability is common in human cleavage-stage embryos Nat Med 15 2009 577 583
30. T. Voet, E. Vanneste, and J.R. Vermeesch The human cleavage stage embryo is a cradle of chromosomal rearrangements Cytogenet Genome Res 133 2011 160 168
31. T. Voet, E. Vanneste, N. van der Aa, C. Melotte, S. Jackmaert, T. Vandendael, and et al. Breakage-fusion-bridge cycles leading to inv dup del occur in human cleavage stage embryos Hum Mutat 32 2011 783 793
32. M. Roque, M. Valle, F. Guimaraes, M. Sampaio, and S. Geber Freeze-all policy: fresh vs. frozen-thawed embryo transfer Fertil Steril 103 2015 1190 1193
33. C. Staessen, P. Platteau, E. van Assche, A. Michiels, H. Tournaye, M. Camus, and et al. Comparison of blastocyst transfer with or without preimplantation genetic diagnosis for aneuploidy screening in couples with advanced maternal age: a prospective randomized controlled trial Hum Reprod 19 2004 2849 2858
34. T. Baslan, J. Kendall, L. Rodgers, H. Cox, M. Riggs, A. Stepansky, and et al. Genome-wide copy number analysis of single cells Nat Protoc 7 2012 1024 1041
35. C.A. Miller, O. Hampton, C. Coarfa, and A. Milosavljevic ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads PLoS One 6 2011 e16327