Skip to main content

Genetic Databases and Online Ring Chromosome Registry

  • Chapter
  • First Online:
Human Ring Chromosomes
  • 76 Accesses

Abstract

The rapid adaptations of genomic technologies into genetic testing require knowledge-based genetic databases and disease registries in various capacities. General Web resources for clinical and diagnostic genetics include the UCSC (University of California, Santa Cruz) Genome Browser, Online Mendelian Inheritance in Man (OMIM), Clinical Genome Resource (ClinGen), database of chromosomal imbalance and phenotype in humans using ensemble resource (DECIPHER), and Database of Genomic Variants (DGV). Clinical cytogenetics and ring chromosome related web resources include the ChromoSomics database for small supernumerary marker and ring chromosomes (sSMC/sSRC), atlas of genetics and cytogenetics in oncology and hematology (AGCOH), patient advocate organization (PAO) developed supporting and networking groups for specific ring chromosomes, and an online human ring chromosome registry. This registry represents efforts from the international consortium for human ring chromosome (ICHRC) to compile and curate cytogenomic and clinical findings for better diagnostic interpretation and clinical management for patients affected by ring chromosomes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 139.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Almal SH, Padh H (2012) Implications of gene copy-number variation in health and diseases. J Hum Genet 57(1):6–13. https://doi.org/10.1038/jhg.2011.108

    Article  CAS  PubMed  Google Scholar 

  • American College of O, Gynecologists Committee on G (2013) Committee Opinion No. 581: The use of chromosomal microarray analysis in prenatal diagnosis. Obstet Gynecol 122(6):1374–1377. https://doi.org/10.1097/01.AOG.0000438962.16108.d1

  • Bastida-Lertxundi N, Lopez-Lopez E, Pinan MA, Puiggros A, Navajas A, Sole F, Garcia-Orad A (2014) Errors in the interpretation of copy number variations due to the use of public databases as a reference. Canc Genet 207(4):164–167. https://doi.org/10.1016/j.cancergen.2014.03.001

    Article  Google Scholar 

  • Chai H, DiAdamo A, Grommisch B, Xu F, Zhou Q, Wen J, Mahoney M, Bale A, McGrath J, Spencer-Manzon M, Li P, Zhang H (2019) A retrospective analysis of 10-year data assessed the diagnostic accuracy and efficacy of cytogenomic abnormalities in current prenatal and pediatric settings. Front Genet 10:1162. https://doi.org/10.3389/fgene.2019.01162

    Article  PubMed  PubMed Central  Google Scholar 

  • Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloglu A, Ozen S, Sanjad S, Nelson-Williams C, Farhi A, Mane S, Lifton RP (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106(45):19096–19101. https://doi.org/10.1073/pnas.0910672106

    Article  PubMed  PubMed Central  Google Scholar 

  • Corpas M, Bragin E, Clayton S, Bevan P, Firth HV (2012) Interpretation of genomic copy number variants using DECIPHER. Curr Protoc Hum Genet Chapter 8:Unit 8–14. https://doi.org/10.1002/0471142905.hg0814s72

  • Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP (2009) DECIPHER: Database of chromosomal imbalance and phenotype in humans using ensembl resources. Am J Hum Genet 84(4):524–533. https://doi.org/10.1016/j.ajhg.2009.03.010

  • Gordon D, Watson A, Desurkar A, Cowley L, Hiemstra TF (2020) Assessing the role of ketogenic dietary therapy in ring chromosome 20 syndrome: A patient-led approach. Epilepsia Open 5(2):295–300. https://doi.org/10.1002/epi4.12387

  • Hamosh A, Amberger JS, Bocchini C, Scott AF, Rasmussen SA (2021) Online Mendelian Inheritance in Man (OMIM(R)): Victor McKusick’s magnum opus. Am J Med Genet 185A(11):3259–3265. https://doi.org/10.1002/ajmg.a.62407

    Article  PubMed  PubMed Central  Google Scholar 

  • Hao Y, Liu Y, Yang J, Li X, Luo F, Geng Q, Li S, Li P, Wu W, Xie J (2022) Prenatal and postnatal diagnosis of Phelan-McDermid syndrome: A report of 21 cases from a medical center and review of the literature. Front Genet 13:961196. https://doi.org/10.3389/fgene.2022.961196

  • Hu Q, Chai H, Shu W, Li P (2018) Human ring chromosome registry for cases in the Chinese population: Re-emphasizing Cytogenomic and clinical heterogeneity and reviewing diagnostic and treatment strategies. Mol Cytogenet 11(1):19. https://doi.org/10.1186/s13039-018-0367-3

  • Huret JL, Ahmad M, Arsaban M, Bernheim A, Cigna J, Desangles F, Guignard JC, Jacquemot-Perbal MC, Labarussias M, Leberre V, Malo A, Morel-Pair C, Mossafa H, Potier JC, Texier G, Viguie F, Yau Chun Wan-Senon S, Zasadzinski A, Dessen P (2013) Atlas of genetics and cytogenetics in oncology and haematology in 2013. Nucleic Acids Res 41(Database issue):D920–924. https://doi.org/10.1093/nar/gks1082

  • Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C (2004) Detection of large-scale variation in the human genome. Nat Genet 36(9):949–951. https://doi.org/10.1038/ng1416

    Article  CAS  PubMed  Google Scholar 

  • International Standing Committee on Human Cytogenomic Nomenclature, McGowan-Jordan J, Hastings RJ, Moore S (2020) ISCN 2020: An international system for human cytogenomic nomenclature. Hartford, Karger, Basel

    Google Scholar 

  • Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ, University of California Santa C (2003) The UCSC genome browser database. Nucleic Acids Res 31(1):51–54. https://doi.org/10.1093/nar/gkg129

  • Li P, Dupont B, Hu Q, Crimi M, Shen Y, Lebedev I, Liehr T (2022) The past, present, and future for constitutional ring chromosomes: A report of the international consortium for human ring chromosomes. HGG Adv 3(4):100139. https://doi.org/10.1016/j.xhgg.2022.100139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liehr T (2021a) About classical molecular genetics, cytogenetic and molecular cytogenetic data not considered by genome reference consortium and thus not included in genome browsers like UCSC, Ensembl or NCBI. Mol Cytogenet 14(1):20. https://doi.org/10.1186/s13039-021-00540-7

  • Liehr T, Claussen U, Starke H (2004) Small supernumerary marker chromosomes (sSMC) in humans. Cytogenet Genome Res 107(1–2):55–67. https://doi.org/10.1159/000079572

    Article  CAS  PubMed  Google Scholar 

  • Liehr T (2021b) Repetitive elements in humans. Int J Mol Sci 22(4):2072. https://doi.org/10.3390/ijms22042072

  • Lionel AC, Costain G, Monfared N, Walker S, Reuter MS, Hosseini SM, Thiruvahindrapuram B, Merico D, Jobling R, Nalpathamkalam T, Pellecchia G, Sung WWL, Wang Z, Bikangaga P, Boelman C, Carter MT, Cordeiro D, Cytrynbaum C, Dell SD, Dhir P, Dowling JJ, Heon E, Hewson S, Hiraki L, Inbar-Feigenberg M, Klatt R, Kronick J, Laxer RM, Licht C, MacDonald H, Mercimek-Andrews S, Mendoza-Londono R, Piscione T, Schneider R, Schulze A, Silverman E, Siriwardena K, Snead OC, Sondheimer N, Sutherland J, Vincent A, Wasserman JD, Weksberg R, Shuman C, Carew C, Szego MJ, Hayeems RZ, Basran R, Stavropoulos DJ, Ray PN, Bowdin S, Meyn MS, Cohn RD, Scherer SW, Marshall CR (2018) Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test. Genet Med 20(4):435–443. https://doi.org/10.1038/gim.2017.119

    Article  CAS  PubMed  Google Scholar 

  • MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW (2014) The database of genomic variants: A curated collection of structural variation in the human genome. Nucleic Acids Res 42(Database issue):D986–992. https://doi.org/10.1093/nar/gkt958

  • Malvestiti F, De Toffol S, Grimi B, Chinetti S, Marcato L, Agrati C, Di Meco AM, Frascoli G, Trotta A, Malvestiti B, Ruggeri A, Dulcetti F, Maggi F, Simoni G, Grati FR (2014) De novo small supernumerary marker chromosomes detected on 143,000 consecutive prenatal diagnoses: Chromosomal distribution, frequencies, and characterization combining molecular cytogenetics approaches. Prenat Diagn 34(5):460–468. https://doi.org/10.1002/pd.4330

  • Mikhail FM (2014) Copy number variations and human genetic disease. Curr Opin Pediatr 26(6):646–652. https://doi.org/10.1097/MOP.0000000000000142

    Article  CAS  PubMed  Google Scholar 

  • Nassar LR, Barber GP, Benet-Pages A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee BT, Lee CM, Muthuraman P, Nguy B, Pereira T, Nejad P, Perez G, Raney BJ, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kuhn RM, Haeussler M, Kent WJ (2023) The UCSC genome browser database: 2023 update. Nucleic Acids Res 51(D1):D1188–D1195. https://doi.org/10.1093/nar/gkac1072

    Article  CAS  PubMed  Google Scholar 

  • Reddy KS, Aradhya S, Meck J, Tiller G, Abboy S, Bass H (2013) A systematic analysis of small supernumerary marker chromosomes using array CGH exposes unexpected complexity. Genet Med 15(1):3–13. https://doi.org/10.1038/gim.2012.78

    Article  CAS  PubMed  Google Scholar 

  • Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL (2020) Technical standards for the interpretation and reporting of constitutional copy-number variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med 22(2):245–257. https://doi.org/10.1038/s41436-019-0686-8

  • Rinaldi B, Vaisfeld A, Amarri S, Baldo C, Gobbi G, Magini P, Melli E, Neri G, Novara F, Pippucci T, Rizzi R, Soresina A, Zampini L, Zuffardi O, Crimi M (2017) Guideline recommendations for diagnosis and clinical management of Ring14 syndrome-first report of an ad hoc task force. Orphanet J Rare Dis 12(1):69. https://doi.org/10.1186/s13023-017-0606-4

    Article  PubMed  PubMed Central  Google Scholar 

  • Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M (2004) Large-scale copy number polymorphism in the human genome. Science 305(5683):525–528. https://doi.org/10.1126/science.1098918

    Article  CAS  PubMed  Google Scholar 

  • Shaffer LG, Beaudet AL, Brothman AR, Hirsch B, Levy B, Martin CL, Mascarello JT, Rao KW, Working Group of the Laboratory Quality Assurance Committee of the American College of Medical G (2007) Microarray analysis for constitutional cytogenetic abnormalities. Genet Med 9(9):654–662. https://doi.org/10.1097/gim.0b013e31814ce3d9

  • Singh J (2013) The portal for rare diseases and orphan drugs. J Pharmacol Pharmacother 4(2):168–169

    Article  PubMed  PubMed Central  Google Scholar 

  • South ST, Lee C, Lamb AN, Higgins AW, Kearney HM, Working Group for the American College of Medical G, Genomics Laboratory Quality Assurance C (2013) ACMG standards and guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: Revision 2013. Genet Med 15(11):901–909. https://doi.org/10.1038/gim.2013.129

  • Watson A, Watson D, Taylor C (2014) Life with r(20)-Ring chromosome 20 syndrome. Epilepsia 56(3):356–358. https://doi.org/10.1111/epi.12729

  • Xie XL, Chai HY, DiAdamo A, Grommisch B, Wen JD, Zhang H, Li PN (2022) Genotype-phenotype correlations for putative haploin sufficient genes in deletions of 6q26-q27: Report of eight patients and review of literature. Glob Med Genet 9(2):166–174. https://doi.org/10.1055/s-0042-1743568

    Article  Google Scholar 

  • Xu F, Li L, Schulz VP, Gallagher PG, Xiang B, Zhao H, Li P (2014) Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability. Mol Cytogenet 7(1):4. https://doi.org/10.1186/1755-8166-7-4

  • Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res 115(3–4):205–214. https://doi.org/10.1159/000095916

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Qiping Hu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2024 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Hu, Q., Ma, D., Li, P., Liehr, T. (2024). Genetic Databases and Online Ring Chromosome Registry. In: Li, P., Liehr, T. (eds) Human Ring Chromosomes. Springer, Cham. https://doi.org/10.1007/978-3-031-47530-6_3

Download citation

Publish with us

Policies and ethics