[1] |
Akalin, A., Kormaksson, M., Li, S. et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles Genome Biol., 13 (2012),pp. 1-9
|
[2] |
Anders, S., Huber, W. Differential expression analysis for sequence count data Genome Biol., 11 (2010),pp. 1-12
|
[3] |
Baubec, T., Colombo, D.F., Wirbelauer, C. et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation Nature, 520 (2015),pp. 243-247
|
[4] |
Baylin, S.B., Jones, P.A. A decade of exploring the cancer epigenome - biological and translational implications Nat. Rev. Cancer, 11 (2011),pp. 726-734
|
[5] |
Bolger, A.M., Lohse, M., Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data Bioinformatics, 30 (2014),pp. 2114-2120
|
[6] |
Centers for Disease Control and Prevention, American Society for Reproductive Medicine, Society for Assisted Reproductive Technology
|
[7] |
Dahdouh, E.M., Balayla, J., Audibert, F. et al. Technical update: preimplantation genetic diagnosis and screening J. Obstet. Gynaecol. Can., 37 (2015),pp. 451-463
|
[8] |
Evers, J.L. Female subfertility Lancet, 360 (2002),pp. 151-159
|
[9] |
Feber, A., Guilhamon, P., Lechner, M. et al. Using high-density DNA methylation arrays to profile copy number alterations Genome Biol., 15 (2014),pp. 1-13
|
[10] |
Fiorentino, F., Biricik, A., Bono, S. et al. Development and validation of a next-generation sequencing based protocol for 24-chromosome aneuploidy screening of embryos Fertil. Steril., 101 (2014),pp. 1375-1382
|
[11] |
Forman, E.J., Hong, K.H., Ferry, K.M. et al. Fertil. Steril., 100 (2013),pp. 100-107
|
[12] |
Fragouli, E., Alfarawati, S., Daphnis, D.D. et al. Cytogenetic analysis of human blastocysts with the use of FISH, CGH and aCGH: scientific data and technical evaluation Hum. Reprod., 26 (2011),pp. 480-490
|
[13] |
Franasiak, J.M., Forman, E.J., Hong, K.H. et al. Aneuploidy across individual chromosomes at the embryonic level in trophectoderm biopsies: changes with patient age and chromosome structure J. Assist. Reprod. Genet., 31 (2014),pp. 1501-1509
|
[14] |
Franasiak, J.M., Forman, E.J., Hong, K.H. et al. The nature of aneuploidy with increasing age of the female partner: a review of 15,169 consecutive trophectoderm biopsies evaluated with comprehensive chromosomal screening Fertil. Steril., 101 (2014),pp. 656-663
|
[15] |
Gu, T.P., Guo, F., Yang, H. et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes Nature, 477 (2011),pp. 606-610
|
[16] |
Guo, H., Zhu, P., Yan, L. et al. The DNA methylation landscape of human early embryos Nature, 511 (2014),pp. 606-610
|
[17] |
Ha, G., Roth, A., Lai, D. et al. Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer Genome Res., 22 (2012),pp. 1995-2007
|
[18] |
Handyside, A.H., Lesko, J.G., Tarin, J.J. et al. New Engl. J. Med., 327 (1992),pp. 905-909
|
[19] |
Hansen, K.D., Timp, W., Bravo, H.C. et al. Increased methylation variation in epigenetic domains across cancer types Nat. Genet., 43 (2011),pp. 768-775
|
[20] |
Hansen, K.D., Langmead, B., Irizarry, R.A. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions Genome Biol., 13 (2012),pp. 1-10
|
[21] |
Hardarson, T., Van Landuyt, L., Jones, G. The blastocyst Hum. Reprod., 27 (2012),pp. 72-91
|
[22] |
Heitmann, R.J., Hill, M.J., Richter, K.S. et al. The simplified SART embryo scoring system is highly correlated to implantation and live birth in single blastocyst transfers J. Assist. Reprod. Genet., 30 (2013),pp. 563-567
|
[23] |
Hill, M.J., Richter, K.S., Heitmann, R.J. et al. Trophectoderm grade predicts outcomes of single-blastocyst transfers Fertil. Steril., 99 (2013),pp. 1283-1289
|
[24] |
Jiang, L., Zhang, J., Wang, J.-J. et al. Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos Cell, 153 (2013),pp. 773-784
|
[25] |
Jirtle, R.L., Skinner, M.K. Environmental epigenomics and disease susceptibility Nat. Rev. Genet., 8 (2007),pp. 253-262
|
[26] |
, McKnight, S.L. Influence of metabolism on epigenetics and disease Cell, 153 (2013),pp. 56-69
|
[27] |
Krueger, F., Andrews, S.R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications Bioinformatics, 27 (2011),pp. 1571-1572
|
[28] |
Lee, H.J., Lowdon, R.F., Maricque, B. et al. Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos Nat. Commun., 6 (2015),p. 6315
|
[29] |
Lehnen, H., Zechner, U., Haaf, T. Epigenetics of gestational diabetes mellitus and offspring health: the time for action is in early stages of life Mol. Hum. Reprod., 19 (2013),pp. 415-422
|
[30] |
Li, E., Bestor, T.H., Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality Cell, 69 (1992),pp. 915-926
|
[31] |
Li, H., Handsaker, B., Wysoker, A. et al. The sequence alignment/map format and SAMtools Bioinformatics, 25 (2009),pp. 2078-2079
|
[32] |
Macklon, N.S., Geraedts, J.P., Fauser, B.C. Conception to ongoing pregnancy: the 'black box' of early pregnancy loss Hum. Reprod. Update, 8 (2002),pp. 333-343
|
[33] |
National Collaborating Centre for Women's and Children's Health (UK)
|
[34] |
Oda, M., Glass, J.L., Thompson, R.F. et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers Nucleic Acids Res., 37 (2009),pp. 3829-3839
|
[35] |
Okano, M., Bell, D.W., Haber, D.A. et al. Cell, 99 (1999),pp. 247-257
|
[36] |
Pujadas, E., Feinberg, A.P. Regulated noise in the epigenetic landscape of development and disease Cell, 148 (2012),pp. 1123-1131
|
[37] |
Schubeler, D. Function and information content of DNA methylation Nature, 517 (2015),pp. 321-326
|
[38] |
, Upham, K.M., Forman, E.J., Hong, K.H. et al. Fertil. Steril., 100 (2013),pp. 697-703
|
[39] |
Shen, H., Laird, P.W. Interplay between the cancer genome and epigenome Cell, 153 (2013),pp. 38-55
|
[40] |
Smith, Z.D., Chan, M.M., Mikkelsen, T.S. et al. A unique regulatory phase of DNA methylation in the early mammalian embryo Nature, 484 (2012),pp. 339-344
|
[41] |
Smith, Z.D., Chan, M.M., Humm, K.C. et al. DNA methylation dynamics of the human preimplantation embryo Nature, 511 (2014),pp. 611-615
|
[42] |
Snedecor, G.W., Cochran, W.G.
|
[43] |
Tee, L., Lim, D.H.K., Dias, R.P. et al. Epimutation profiling in Beckwith-Wiedemann syndrome: relationship with assisted reproductive technology Clin. Epigenetics, 5 (2013)
|
[44] |
Trapnell, C., Pachter, L., Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq Bioinformatics, 25 (2009),pp. 1105-1111
|
[45] |
Wang, L., Zhang, J., Duan, J. et al. Programming and inheritance of parental DNA methylomes in mammals Cell, 157 (2014),pp. 979-991
|
[46] |
Wells, D., Delhanty, J.D. Preimplantation genetic diagnosis: applications for molecular medicine Trends Mol. Med., 7 (2001),pp. 23-30
|