Jose R Hernandez Mora1, Chiharu Tayama2, Marta Sánchez-Delgado1, Ana Monteagudo-Sánchez1, Kenichiro Hata2, Tsutomu Ogata3, Jose Medrano4, Maria E Poo-Llanillo5, Carlos Simón5,6,7, Sebastian Moran8, Manel Esteller8,9,10, Jair Tenorio11, Pablo Lapunzina11,12, Masayo Kagami13, David Monk1, Kazuhiko Nakabayashi2. 1. Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain. 2. Department of Maternal-Fetal Biology, National Research Institute for Child Health & Development, Tokyo, Japan. 3. Department of Pediatrics, Hamamatsu University School of Medicine, Shizuoka, Japan. 4. Fundación IVI-Instituto Universitario IVI- INCLIVA, Valencia, Spain. 5. Igenomix SL, Valencia, Spain. 6. Department of Obs/Gyn, Valencia University, Valencia, Spain. 7. Department of Obs/Gyn, Stanford University, Palo Alto, CA 94305, USA. 8. Cancer Epigenetics group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain. 9. Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain. 10. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain. 11. Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. 12. CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. 13. Department of Molecular Endocrinology, National Research Institute for Child Health & Development, Tokyo, Japan.
Abstract
AIM: This study aimed to establish a catalog of probes corresponding to imprinted differentially methylated regions (DMRs) on the Infinium HumanMethylationEPIC BeadChip. MATERIALS & METHODS: Reciprocal uniparental diploidies with low normal biparental mosaic contribution, together with normal diploid controls, were subjected to EPIC BeadChip hybridization. The methylation profiles were assessed for imprinted differential methylation. Top candidates were validated using locus-specific PCR-based assays. RESULTS: Seven hundred and eighty-nine CpG probes coincided with 50 known imprinted DMRs and 467 CpG probes corresponding to 124 novel imprinted DMR candidates were identified. Validation led to identification of several subtle DMRs within known imprinted domains as well as novel maternally methylated regions associated with PTCHD3 and JAKMIP1. CONCLUSION: Our comprehensive list of bona fide-imprinted DMR probes will simplify and facilitate methylation profiling of individuals with imprinting disorders and is applicable to other diseases in which aberrant imprinting has been implicated, such as cancer and fetal growth.
AIM: This study aimed to establish a catalog of probes corresponding to imprinted differentially methylated regions (DMRs) on the Infinium HumanMethylationEPIC BeadChip. MATERIALS & METHODS: Reciprocal uniparental diploidies with low normal biparental mosaic contribution, together with normal diploid controls, were subjected to EPIC BeadChip hybridization. The methylation profiles were assessed for imprinted differential methylation. Top candidates were validated using locus-specific PCR-based assays. RESULTS: Seven hundred and eighty-nine CpG probes coincided with 50 known imprinted DMRs and 467 CpG probes corresponding to 124 novel imprinted DMR candidates were identified. Validation led to identification of several subtle DMRs within known imprinted domains as well as novel maternally methylated regions associated with PTCHD3 and JAKMIP1. CONCLUSION: Our comprehensive list of bona fide-imprinted DMR probes will simplify and facilitate methylation profiling of individuals with imprinting disorders and is applicable to other diseases in which aberrant imprinting has been implicated, such as cancer and fetal growth.
Entities:
Keywords:
DNA methylation; imprinting; uniparental diploidy
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