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Research Article

Characterization of Parent-of-Origin Methylation Using the Illumina Infinium Methylationepic Array Platform

, , , , , , , , , , , , , , & show all
Pages 941-954 | Received 20 Dec 2017, Accepted 16 Mar 2018, Published online: 02 Jul 2018

References

  • Arnaud P . Genomic imprinting in germ cells: imprints are under control . Reproduction140 ( 3 ), 411 – 423 ( 2010 ).
  • Soellner L , BegemannM , MackayDJet al. Recent advances in imprinting disorders . Clin. Genet.91 ( 1 ), 3 – 13 ( 2017 ).
  • Sanchez-Delgado M , RiccioA , EggermannTet al. Causes and consequences of multi-locus imprinting disturbances in humans . Trends Genet.32 ( 7 ), 444 – 455 ( 2016 ).
  • Mackay DJ , BoonenSE , Clayton-SmithJet al. A maternal hypomethylation syndrome presenting as transient neonatal diabetes mellitus . Hum. Genet.120 ( 2 ), 262 – 269 ( 2006 ).
  • Mackay DJ , CallawayJL , MarksSMet al. Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57 . Nat. Genet.40 ( 8 ), 949 – 951 ( 2008 ).
  • Nakabayashi K , TrujilloAM , TayamaCet al. Methylation screening of reciprocal genome-wide UPDs identifies novel human-specific imprinted genes . Hum. Mol. Genet.20 ( 16 ), 3188 – 3197 ( 2011 ).
  • Court F , TayamaC , RomanelliVet al. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment . Genome Res.24 ( 4 ), 554 – 569 ( 2014 ).
  • Yamazawa K , NakabayashiK , KagamiMet al. Parthenogenetic chimaerism/mosaicism with a Silver–Russell syndrome-like phenotype . J. Med. Genet.47 ( 11 ), 782 – 785 ( 2010 ).
  • Yamazawa K , NakabayashiK , MatsuokaKet al. Androgenetic/biparental mosaicism in a girl with Beckwith–Wiedemann syndrome-like and upd(14)pat-like phenotypes . J. Hum. Genet.56 ( 1 ), 91 – 33 ( 2011 ).
  • Romanelli V , NevadoJ , FragaMet al. Constitutional mosaic genome-wide uniparental disomy due to diploidisation: an unusual cancer-predisposing mechanism . J. Med. Genet.48 ( 3 ), 212 – 216 ( 2010 ).
  • Pidsley R , ZotenkoE , PetersTJet al. Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling . Genome Biol.17 ( 1 ), 208 ( 2016 ).
  • Moran S , ArribasC , EstellerM . Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences . Epigenomics8 ( 3 ), 389 – 399 ( 2016 ).
  • Martin-Trujillo A , VidalE , Monteagudo-SanchezAet al. Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors . Nat. Commun.8 ( 1 ), 467 ( 2017 ).
  • Sanchez-Delgado M , CourtF , VidalEet al. Human oocyte-derived methylation differences persist in the placenta revealing widespread transient imprinting . PLoS Genet.12 ( 11 ), e1006427 ( 2016 ).
  • Monk D , MoralesJ , den DunnenJTet al. Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains . Epigenetics13 ( 2 ), 117 – 121 ( 2018 ).
  • Krueger F , AndrewsSR . Bismark: a flexible aligner and methylation caller for Bisphite-Seq applications . Bioinformatics27 ( 11 ), 1571 – 1572 ( 2011 ).
  • Li H , HandsakerB , WysokerAet al. The sequence alignment/map format and SAMtools . Bioinformatics25 ( 16 ), 2078 – 2079 ( 2009 ).
  • Kumaki Y , OdaM , OkanoM . QUMA: quantification tool for methylation analysis . Nucleic Acids Res.36 ( Web Server issue ), W170 – W175 ( 2008 ).
  • Kobayashi H , YanagisawaE , SakashitaAet al. Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc . Epigenetics8 ( 6 ), 635 – 645 ( 2013 ).
  • Hannula-Jouppi K , MuurinenM , Lipsanen-NymanMet al. Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7 . Epigenetics9 ( 3 ), 351 – 365 ( 2014 ).
  • Joshi RS , GargP , ZaitlenNet al. DNA methylation profiling of uniparental disomy subjects provides a map of parental epigenetic bias in the human genome . Am. J. Hum. Genet.99 ( 3 ), 555 – 566 ( 2016 ).
  • Grothaus K , KanberD , GellhausAet al. Genome-wide methylation analysis of retrocopy-associated CpG islands and their genomic environment . Epigenetics11 ( 3 ), 216 – 226 ( 2016 ).
  • Matsubara K , KagamiM , NakabayashiKet al. Exploration of hydroxymethylation in Kagami–Ogata syndrome caused by hypermethylation of imprinting control regions . Clin. Epigenetics7 ( 1 ), 90 ( 2015 ).
  • Hernandez Mora JR , Sanchez-DelgadoM , PetazziPet al. Profiling of oxBS-450K 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci . Epigenetics13 ( 2 ), 182 – 191 ( 2018 ).
  • Keller TE , HanP , YiSV . Evolutionary transition of promoter and gene body DNA methylation across invertebrate–vertebrate boundary . Mol. Biol. Evol.33 ( 4 ), 1019 – 1028 ( 2016 ).
  • Chamberlain SJ . RNAs of the human chromsome 15q11-q13 imprinted region . Wiley Interdiscip. Rev. RNA4 ( 2 ), 155 – 166 ( 2013 ).
  • Rezwan FI , DochertyLE , PooleRLet al. A statistical method for single sample analysis of HumanMethylation450 array data: genome-wide methylation analysis of patients with imprinting disorders . Clin. Epigenetics7 , 48 ( 2015 ).
  • Docherty LE , RezwanFI , PooleRLet al. Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes . J. Med. Genet.51 ( 4 ), 229 – 338 ( 2014 ).

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