DNA methylation episignatures: insight into copy number variation

References

• Cacabelos R , TelladoI , CacabelosP. The epigenetic machinery in the life cycle and pharmacoepigenetics. In: Pharmacoepigenetics.Elsevier, Amsterdam, The Netherlands, 1–100 (2019).
   Google Scholar
• Fahrner JA , BjornssonHT. Mendelian disorders of the epigenetic machinery: tipping the balance of chromatin states. Annu. Rev. Genomics Hum. Genet.15, 269–293 (2014).
   PubMed Web of Science ®Google Scholar
• Lyko F . The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat. Rev. Genet.19(2), 81–92 (2018).
   PubMed Web of Science ®Google Scholar
• Hargreaves DC , CrabtreeGR. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res.21(3), 396–420 (2011).
   PubMed Web of Science ®Google Scholar
• Poh WJ , WeeCPP , GaoZ. DNA methyltransferase activity assays: advances and challenges. Theranostics6(3), 369–391 (2016).
   PubMed Web of Science ®Google Scholar
• Gibson WT , HoodRL , ZhanSHet al. Mutations in EZH2 cause weaver syndrome. Am. J. Hum. Genet.90(1), 110–118 (2012).
   PubMed Web of Science ®Google Scholar
• Bjornsson HT . The Mendelian disorders of the epigenetic machinery. Genome Res.25(10), 1473–1481 (2015).
   PubMed Web of Science ®Google Scholar
• Churchill FB . William Johannsen and the genotype concept. J. Hist. Biol.7(1), 5–30 (1974).
   PubMedGoogle Scholar
• Ahnert SE . Structural properties of genotype–phenotype maps. JR Soc. Interface14(132), 20170275 (2017).
   PubMed Web of Science ®Google Scholar
• Gibney ER , NolanCM. Epigenetics and gene expression. Heredity (Edinb.)105(1), 4–13 (2010).
   PubMed Web of Science ®Google Scholar
• Abel HJ , DuncavageEJ. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet.206(12), 432–440 (2013).
   PubMed Web of Science ®Google Scholar
• Zhang Y , HaraksinghR , GrubertFet al. Child development and structural variation in the human genome. Child Dev.84(1), 34–48 (2013).
   PubMed Web of Science ®Google Scholar
• Rice AM , MclysaghtA. Dosage-sensitive genes in evolution and disease. BMC Biol.15(1), 78 (2017).
   Google Scholar
• Yamasaki M , MakinoT , KhorSSet al. Sensitivity to gene dosage and gene expression affects genes with copy number variants observed among neuropsychiatric diseases. BMC Med. Genomics13(1), 55 (2020).
   PubMed Web of Science ®Google Scholar
• Collins RL , BrandH , KarczewskiKJet al. A structural variation reference for medical and population genetics Aggregation Database Production Team*, Genome Aggregation Database Consortium*. Nature581, 444 doi:10.1038/s41586-020-2287-82020) ( Online).
   PubMed Web of Science ®Google Scholar
• Karczewski KJ , FrancioliLC , TiaoGet al. The mutational constraint spectrum quantified from variation in 141,456 humans, Genome Aggregation Database Consortium. Nature581, 434,doi:10.1038/s41586-020-2308-72020) ( Online).
   PubMed Web of Science ®Google Scholar
• Zarrei M , MacDonaldJR , MericoD , SchererSW. A copy number variation map of the human genome. Nat. Rev. Genet.16(3), 172–183 (2015).
   PubMed Web of Science ®Google Scholar
• Huang N , LeeI , MarcotteEM , HurlesME. Characterising and predicting haploinsufficiency in the human genome. PLOS Genet.6(10), 1–11 (2010).
   Web of Science ®Google Scholar
• Davoli T , XuAW , MengwasserKEet al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell155(4), 948 (2013).
   PubMed Web of Science ®Google Scholar
• Tatton-Brown K , ColeTR , RahmanNet al. Sotos Syndrome. In: Gene Reviews.Seattle, WA (2004).
   Google Scholar
• Zhang H , LuX , BeasleyJet al. Reversed clinical phenotype due to a microduplication of Sotos syndrome region detected by array CGH: microcephaly, developmental delay and delayed bone age. Am. J. Med. Genet. A155(6), 1374–1378 (2011).
   Google Scholar
• Dikow N , MaasB , GasparHet al. The phenotypic spectrum of duplication 5q35.2–q35.3 encompassing NSD1: is it really a reversed sotos syndrome? Am. J. Med. Genet. A 161(9), 2158–2166 (2013).
   Web of Science ®Google Scholar
• Brunetti-Pierri N , BergJS , ScagliaFet al. Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities. Nat. Genet.40(12), 1466–1471 (2008).
   PubMed Web of Science ®Google Scholar
• Lebon S , ChenQ , Martin-BrevetSet al. Defining the effect of the 16p11.2 duplication on cognition, behavior, and medical comorbidities. JAMA Psychiatry73(1), 20–30 (2016). doi:10.1001/jamapsychiatry.2015.2123
   PubMed Web of Science ®Google Scholar
• Jacquemont S , ReymondA , ZuffereyFet al. Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus. Nature478(7367), 97–102 (2011).
   PubMed Web of Science ®Google Scholar
• Leblanc JJ , NelsonCA. Deletion and duplication of 16p11.2 are associated with opposing effects on visual evoked potential amplitude. Mol. Autism7(1), 30 (2016).
   PubMedGoogle Scholar
• Chung WK , RobertsTP , SherrEH , SnyderLAG , SpiroJE. 16p11.2 deletion syndrome. Curr. Opin. Genet. Dev.68, 49–56 (2021).
   PubMed Web of Science ®Google Scholar
• Adamo A , AtashpazS , GermainPLet al. 7q11.23 dosage-dependent dysregulation in human pluripotent stem cells affects transcriptional programs in disease-relevant lineages. Nat. Genet.47(2), 132–141 (2015).
   PubMed Web of Science ®Google Scholar
• Strong E , ButcherDT , SinghaniaRet al. Symmetrical dose-dependent DNA-methylation profiles in children with deletion or duplication of 7q11.23. Am. J. Hum. Genet.97(2), 216–227 (2015).
   PubMed Web of Science ®Google Scholar
• Nussinov R , TsaiCJ , JangH. Protein ensembles link genotype to phenotype. PLOS Comput. Biol.15(6), e1006648 (2019).
   PubMed Web of Science ®Google Scholar
• Smajlagić D , LavrichenkoK , BerlandSet al. Population prevalence and inheritance pattern of recurrent CNVs associated with neurodevelopmental disorders in 12,252 newborns and their parents. Eur. J. Hum. Genet.29(1), 205–215 (2021).
   PubMed Web of Science ®Google Scholar
• Nowakowska B . Clinical interpretation of copy number variants in the human genome. J. Appl. Genet.58(4), 449–457 (2017).
   PubMed Web of Science ®Google Scholar
• Kerkhof J , SqueoGM , McConkeyHet al. DNA methylation episignature testing improves molecular diagnosis of Mendelian chromatinopathies. Genet. Med.24(1), 51–60 (2022).
   PubMed Web of Science ®Google Scholar
• Vidal S , XiolC , Pascual-alonsoA , O’callaghanM , PinedaM , ArmstrongJ. Genetic landscape of Rett syndrome spectrum: improvements and challenges. Int. J. Mol. Sci.20(16), 3925 (2019).
   PubMed Web of Science ®Google Scholar
• Wan TSK , HuiEKC , NgMHL. Chromosome recognition. Methods Mol. Biol.1541, 67–74 (2017).
   PubMedGoogle Scholar
• Imataka G , ArisakaO. Chromosome analysis using spectral karyotyping (SKY). Cell Biochem. Biophys.62(1), 13–17 (2012).
   PubMed Web of Science ®Google Scholar
• Lichtenbelt KD , KnoersNVAM , Schuring-BlomGH. From karyotyping to array-CGH in prenatal diagnosis. Cytogenet. Genome Res.135(3–4), 241–250 (2011).
   PubMed Web of Science ®Google Scholar
• Vance GH . Cytogenetics/cytogenomics. In: Rodak’s Hematology.Elsevier, Amsterdam, The Netherlands, 525–539 (2020).
   Google Scholar
• Miller DT , AdamMP , AradhyaSet al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am. J. Hum. Genet.86(5), 749–764 (2010).
   PubMed Web of Science ®Google Scholar
• Y atsenko SA , ShawCA , OuZet al. Microarray-based comparative genomic hybridization using sex-matched reference DNA provides greater sensitivity for detection of sex chromosome imbalances than array-comparative genomic hybridization with sex-mismatched reference DNA. J. Mol. Diagn.11(3), 226–237 (2009).
   PubMed Web of Science ®Google Scholar
• Cheung SW , BiW. Novel applications of array comparative genomic hybridization in molecular diagnostics. Expert Rev. Mol. Diagn.18(6), 531–542 (2018).
   PubMed Web of Science ®Google Scholar
• Levy B , BurnsideRD. Are all chromosome microarrays the same? What clinicians need to know. Prenat. Diagn.39(3), 157–164 (2019).
   PubMed Web of Science ®Google Scholar
• Carter NP . Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet.39(Suppl. 7), S16–S21 (2007).
   PubMedGoogle Scholar
• Vorstman JAS , JalaliGR , RappaportEF , HackerAM , ScottC , EmanuelBS. MLPA: a rapid, reliable, and sensitive method for detection and analysis of abnormalities of 22q. Hum. Mutat.27(8), 814–821 (2006).
   PubMed Web of Science ®Google Scholar
• Fernández L , LapunzinaP , ArjonaDet al. Comparative study of three diagnostic approaches (FISH, STRs and MLPA) in 30 patients with 22q11.2 deletion syndrome. Clin. Genet.68(4), 373–378 (2005).
   PubMed Web of Science ®Google Scholar
• Sørensen KM , AgergaardP , OlesenCet al. Detecting 22q11.2 deletions by use of multiplex ligation-dependent probe amplification on DNA from neonatal dried blood spot samples. J. Mol. Diagn.12(2), 147–151 (2010).
   PubMed Web of Science ®Google Scholar
• Anwar Iqbal M , BroeckelU , LevyBet al. Multi-site technical performance and concordance of optical genome mapping: constitutional postnatal study for SV, CNV, and repeat array analysis. medRxiv doi:10.1101/2021.12.27.21268432 ( Online) ( Epub ahead of print).
   Google Scholar
• Cope H , BarseghyanH , BhattacharyaSet al. Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Mol. Genet. Genomic Med.9(7), e1665 (2021).
   PubMed Web of Science ®Google Scholar
• Sahajpal NS , BarseghyanH , KolheR , HastieA , ChaubeyA. Optical genome mapping as a next-generation cytogenomic tool for detection of structural and copy number variations for prenatal genomic analyses. Genes (Basel)12(3), 398 (2021).
   PubMed Web of Science ®Google Scholar
• N urk S , KorenS , RhieAet al. The complete sequence of a human genome. Science376(6588), 44–53 (2022).
   PubMed Web of Science ®Google Scholar
• Jelin AC , VoraN. Whole exome sequencing: applications in prenatal genetics. Obstet. Gynecol. Clin. North Am.45(1), 69–81 (2018).
   PubMed Web of Science ®Google Scholar
• Pirooznia M , GoesF , ZandiPP. Whole-genome CNV analysis: advances in computational approaches. Front. Genet.6(APR), 138 (2015).
   PubMedGoogle Scholar
• Garrido-Cardenas JA , Garcia-MarotoF , Alvarez-BermejoJA , Manzano-AgugliaroF. DNA sequencing sensors: an overview. Sensors (Switzerland)17(3), 588 (2017).
   PubMed Web of Science ®Google Scholar
• Majewski J , SchwartzentruberJ , LalondeE , MontpetitA , JabadoN. What can exome sequencing do for you?J. Med. Genet.48(9), 580–589 (2011).
   PubMed Web of Science ®Google Scholar
• Liang WS , StephensonK , AdkinsJet al. Whole exome library construction for next generation sequencing. In: Methods in Molecular Biology.Humana Press Inc., NJ, USA, 163–174 (2018).
   Google Scholar
• Kerkhof J , SchenkelLC , ReillyJet al. Clinical validation of copy number variant detection from targeted next-generation sequencing panels. J. Mol. Diagn.19(6), 905–920 (2017).
   PubMedGoogle Scholar
• M anickam K , McClainMR , DemmerLAet al. Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genet. Med.23(11), 2029–2037 (2021).
   PubMed Web of Science ®Google Scholar
• Brown CG , ClarkeJ. Nanopore development at Oxford Nanopore. Nat. Biotechnol.34(8), 810–811 (2016).
   PubMed Web of Science ®Google Scholar
• Kono N , ArakawaK. Nanopore sequencing: review of potential applications in functional genomics. Dev. Growth Differ.61(5), 316–326 (2019).
   PubMed Web of Science ®Google Scholar
• Xiao T , ZhouW. The third generation sequencing: the advanced approach to genetic diseases. Transl. Pediatr.9(2), 163–173 (2020).
   PubMed Web of Science ®Google Scholar
• Charnaud S , MunroJE , SemenecLet al. PacBio long-read amplicon sequencing enables scalable high-resolution population allele typing of the complex CYP2D6 locus. Commun. Biol.5(1), 168 (2022).
   PubMed Web of Science ®Google Scholar
• L evy MA , McConkeyH , KerkhofJet al. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG Adv.3(1), 100075 (2021).
   PubMedGoogle Scholar
• Sadikovic B , LeviMA , KerkhofJet al. Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet. Med.3(1), 1–10 (2021).
   Google Scholar
• Aref-Eshghi E , KerkhofJ , PedroVPet al. Evaluation of DNA methylation episignatures for diagnosis and phenotype correlations in 42 Mendelian neurodevelopmental disorders. Am. J. Hum. Genet.106(3), 356–370 (2020).
   PubMed Web of Science ®Google Scholar
• Schenkel LC , Aref-EshghiE , RooneyKet al. DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome. Cin. Epigenetics13(1), 1–17 (2021). doi:10.1186/s13148-020-00990-7
   PubMed Web of Science ®Google Scholar
• Aref-Eshghi E , BendEG , ColaiacovoSet al. Diagnostic utility of genome-wide DNA methylation testing in genetically unsolved individuals with suspected hereditary conditions. Am. J. Hum. Genet.104(4), 685–700 doi:10.1016/j.ajhg.2019.03.008 (2019) ( Online).
   PubMed Web of Science ®Google Scholar
• Schenkel LC , Aref-EshghiE , SkinnerCet al. Peripheral blood epi-signature of Claes–Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C. Clin.Epigenetics.10(1), 1–11 (2018).
   PubMedGoogle Scholar
• Hood RL , SchenkelLC , NikkelSMet al. The defining DNA methylation signature of Floating–Harbor Syndrome. Sci. Rep.6, 1–9 (2016) ( Online).
   PubMed Web of Science ®Google Scholar
• S chenkel LC , KernohanKD , McBrideAet al. Identification of epigenetic signature associated with alpha thalassemia/mental retardation X-linked syndrome. Epigenetics Chromatin10(1), 1–11 (2017).
   PubMedGoogle Scholar
• Aref-Eshghi E , SchenkelLC , LinHet al. Clinical validation of a genome-wide DNA methylation assay for molecular diagnosis of imprinting disorders. J. Mol. Diagn.19(6), 848–856 doi:10.1016/j.jmoldx.2017.07.002 (2017). ( Online).
   PubMed Web of Science ®Google Scholar
• Joustra VW , LiYim AYF , de BruynJRet al. Peripheral blood DNA methylation profiles do not predict endoscopic post-operative recurrence in Crohn’s disease patients. Int. J. Mol. Sci.23(18), 10467 (2022).
   PubMed Web of Science ®Google Scholar
• Naue J , HoefslootHCJ , MookORFet al. Chronological age prediction based on DNA methylation: massive parallel sequencing and random forest regression. Forensic Sci. Int. Genet.31, 19–28 (2017).
   PubMed Web of Science ®Google Scholar
• Olson RS , UrbanowiczRJ , AndrewsPC , LavenderNA , KiddLC , MooreJH. Automating biomedical data science through tree-based pipeline optimization. (2016). http://arxiv.org/abs/1601.07925
   Google Scholar
• Rooney K , LevyMA , HaghshenasSet al. Identification of a DNA methylation episignature in the 22q11.2 deletion syndrome. Int. J. Mol. Sci.22(16), 8611 (2021).
   PubMed Web of Science ®Google Scholar
• Rooney K , SadikovicB. DNA methylation episignatures in neurodevelopmental disorders associated with large structural copy number variants: clinical implications. Int. J. Mol. Sci.23(14), 7862 (2022). www.mdpi.com/1422-0067/23/14/7862
   PubMed Web of Science ®Google Scholar
• Zhou J , ZhengY , LiangGet al. Atypical deletion of Williams–Beuren syndrome reveals the mechanism of neurodevelopmental disorders. BMC Med. Genomics15(1), 79 (2022).
   PubMed Web of Science ®Google Scholar
• Xiao A , LiH , ShechterDet al. WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature457(7225), 57–62 (2009).
   PubMed Web of Science ®Google Scholar
• Paternoster V , EdhagerAV , QvistPet al. Inactivation of the schizophrenia-associated BRD1 gene in brain causes failure-to-thrive, seizure susceptibility and abnormal histone H3 acetylation and N-tail clipping. Mol. Neurobiol.58(9), 4495–4505 (2021).
   PubMedGoogle Scholar
• L oviglio MN , LeleuM , MännikKet al. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Mol. Psychiatry22(6), 836–849 (2017).
   PubMed Web of Science ®Google Scholar
• Siu MT , ButcherDT , TurinskyALet al. Functional DNA methylation signatures for autism spectrum disorder genomic risk loci: 16p11.2 deletions and CHD8 variants. Cin. Epigenetics11(1), 1–19 (2019).
   PubMedGoogle Scholar
• Krzyzewska IM , MaasSM , HennemanPet al. A genome-wide DNA methylation signature for SETD1B-related syndrome. Clin. Epigenetics11(1), 156 (2019).
   PubMed Web of Science ®Google Scholar
• Barski A , CuddapahS , CuiKet al. High-resolution profiling of histone methylations in the human genome. Cell129(4), 823–837 (2007).
   PubMed Web of Science ®Google Scholar
• Choufani S , CytrynbaumC , ChungBHYet al. NSD1 mutations generate a genome-wide DNA methylation signature. Nat. Commun.6, 10207 (2015).
   PubMed Web of Science ®Google Scholar
• Brennan K , ZhengH , FahrnerJAet al. NSD1 mutations deregulate transcription and DNA methylation of bivalent developmental genes in Sotos syndrome. Hum. Mol. Genet.31(13), 2164–2184 (2022).
   PubMed Web of Science ®Google Scholar
• Zhang L , SongD , ZhuB , WangX. The role of nuclear matrix protein HNRNPU in maintaining the architecture of 3D genome. Semin. Cell Dev. Biol.90, 161–167 (2019).
   PubMed Web of Science ®Google Scholar
• Depienne C , NavaC , KerenBet al. Genetic and phenotypic dissection of 1q43q44 microdeletion syndrome and neurodevelopmental phenotypes associated with mutations in ZBTB18 and HNRNPU. Hum. Genet.136(4), 463–479 (2017).
   PubMed Web of Science ®Google Scholar
• Zhu X , PetrovskiS , XiePet al. Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. Genet. Med.17(10), 774–781 (2015).
   PubMed Web of Science ®Google Scholar
• Le TN , WilliamsSR , AlaimoJT , ElseaSH. Genotype and phenotype correlation in 103 individuals with 2q37 deletion syndrome reveals incomplete penetrance and supports HDAC4 as the primary genetic contributor. Am. J. Med. Genet. A179(5), 782–791 (2019).
   PubMed Web of Science ®Google Scholar
• Holland P , WildhagenM , IstreM , ReiakvamOM , DahlJA , SøraasA. Cri du chat syndrome patients have DNA methylation changes in genes linked to symptoms of the disease. Clin. Epigenetics14(1), 128 (2022).
   PubMed Web of Science ®Google Scholar
• Goodman SJ , CytrynbaumC , ChungBH-Yet al. EHMT1 pathogenic variants and 9q34.3 microdeletions share altered DNA methylation patterns in patients with Kleefstra syndrome. J.Transl. Genet. Genom.4, 144–158 (2020).
   Google Scholar
• Aref-Eshghi E , BendEG , HoodRLet al. BAFopathies’ DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin–Siris and Nicolaides–Baraitser syndromes. Nat. Commun.9(1), 4885 (2018).
   PubMedGoogle Scholar
• Ronzoni L , TagliaferriF , TucciA , BaccarinM , EspositoS , MilaniD. Interstitial 6q25 microdeletion syndrome: ARID1B is the key gene. Am. J. Med. Genet. A170(5), 1257–1261 (2016).
   Web of Science ®Google Scholar
• Awamleh Z , Chater-DiehlE , ChoufaniSet al. DNA methylation signature associated with Bohring–Opitz syndrome: a new tool for functional classification of variants in ASXL genes. Eur. J. Hum. Genet.30(6), 695–702 (2022).
   PubMed Web of Science ®Google Scholar
• Du Q , dela Morena MT , van OersNSC. The genetics and epigenetics of 22q11.2 deletion syndrome. Front. Genet.10, 1365 (2020).
   PubMed Web of Science ®Google Scholar
• K erkhof J , SqueoGM , McConkeyHet al. DNA methylation episignature testing improves molecular diagnosis of Mendelian chromatinopathies. Genet. Med.24(1), 51–60 (2021).
   PubMed Web of Science ®Google Scholar