Identification of paternal uniparental disomy on chromosome 22 and a de novo deletion on chromosome 18 in individuals with orofacial clefts

Molecular Genetics and Genomic Medicine

Volumn 6, Issue 6, 2018, Pages 924-932

  Oseni, Ganiyu O ^a   Jain, Deepti ^b   Mossey, Peter A ^c   Busch, Tamara D ^d   Gowans, Lord J J ^e   Eshete, Mekonen A ^f   Adeyemo, Wasiu L ^g   Laurie, Cecelia A ^b   Laurie, Cathy C ^b   Owais, Arwa ^h   Olaitan, Peter B ^a   Aregbesola, Babatunde S ⁱ   Oginni, Fadekemi O ⁱ   Bello, Saidu A ^j   Donkor, Peter ^e   Audu, Rosemary ^k   Onwuamah, Chika ^k   Obiri Yeboah, Solomon ^e   Plange Rhule, Gyikua ^e   Ogunlewe, Olugbenga M ^g   James, Olutayo ^g   Halilu, Taiye ^f   Abate, Firke ^f   Abdur Rahman, Lukman O ^l   Oladugba, Abimbola V ^m   Marazita, Mary L ⁿ   Murray, Jeffrey C ^d   Adeyemo, Adebowale A ^o   Butali, Azeez ^h   more..

^a Ladoke Akintola University   (Nigeria)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF DUNDEE   (United Kingdom)

^d UNIVERSITY OF IOWA   (United States)

^e KWAME NKRUMAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Ghana)

^f ADDIS ABABA UNIVERSITY   (Ethiopia)

^g UNIVERSITY OF LAGOS   (Nigeria)

^h UNIVERSITY OF IOWA   (United States)

ⁱ OBAFEMI AWOLOWO UNIVERSITY   (Nigeria)

^j State House Clinic   (Nigeria)

^k NIGERIAN INSTITUTE OF MEDICAL RESEARCH   (Nigeria)

^l UNIVERSITY OF ILORIN   (Nigeria)

^m UNIVERSITY OF NIGERIA   (Nigeria)

ⁿ UNIVERSITY OF PITTSBURGH   (United States)

^o National Human Genomics Research Institute   (United States)

more..

Author keywords

cleft lip and palate; deletions; GWAS; uniparental disomy

Indexed keywords

ADULT; CHILD; CHROMOSOME 18; CHROMOSOME 22; CHROMOSOME DELETION; CHROMOSOME DISORDER; CLEFT LIP; CLEFT PALATE; FEMALE; GENETICS; HUMAN; INFANT; MALE; MIDDLE AGED; MOSAICISM; NEWBORN; PATHOLOGY; TRISOMY; UNIPARENTAL DISOMY;

ADULT; CHILD; CHROMOSOME DELETION; CHROMOSOME DISORDERS; CHROMOSOMES, HUMAN, PAIR 18; CHROMOSOMES, HUMAN, PAIR 22; CLEFT LIP; CLEFT PALATE; FEMALE; HUMANS; INFANT; INFANT, NEWBORN; MALE; MIDDLE AGED; MOSAICISM; TRISOMY; UNIPARENTAL DISOMY;

EID: 85052470057     PISSN: None     EISSN: 23249269     Source Type: Journal    
DOI: 10.1002/mgg3.459     Document Type: Article

References (31)

1. Calzolari, E., Pierini, A., Astolfi, G., Bianchi, F., Neville, A. J., & Rivieri, F. (2007). Associated anomalies in multi-malformed infants with cleft lip and palate: An epidemiologic study of nearly 6 million births in 23 EUROCAT registries. American Journal of Medical Genetics. Part A, 143, 528–537. https://doi.org/10.1002/(ISSN)1552-4833
2. Conlin, L. K., Thiel, B. D., Bonnemann, C. G., Medne, L., Ernst, L. M., Zackai, E. H., … Spinner, N. B. (2010). Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Human Molecular Genetics, 19, 1263–1275. https://doi.org/10.1093/hmg/ddq003
3. Conomos, M. P., & Thornton, T. (2016). GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness. R package version 2.4.0.
4. Dixon, M. J., Marazita, M. L., Beaty, T. H., & Murray, J. C. (2011). Cleft lip and palate: Understanding genetic and environmental influences. Nature Reviews Genetics, 12, 167–178. https://doi.org/10.1038/nrg2933
5. Engel, E. (1980). A new genetic concept: Uniparental disomy and its potential effect, isodisomy. American Journal of Medical Genetics, 6, 137–143. https://doi.org/10.1002/(ISSN)1096-8628
6. Gogarten, S. M., Bhangale, T., Conomos, M. P., Laurie, C. A., McHugh, C. P., Painter, I., … Laurie, C. C. (2012). GWASTools: An R/Bioconductor package for quality control and analysis of genome-wide association studies. Bioinformatics, 28, 3329–3331. https://doi.org/10.1093/bioinformatics/bts610
7. Hahnemann, J. M., Nir, M., Friberg, M., Engel, U., & Bugge, M. (2005). Trisomy 10 mosaicism and maternal uniparental disomy 10 in a liveborn infant with severe congenital malformations. American Journal of Medical Genetics. Part A, 138A, 150–154. https://doi.org/10.1002/(ISSN)1552-4833
8. Harris, P. A., Taylor, R., Thielke Payne, J., Gonzalez, N., & Conde, J. G. (2009). Research electronic data capture (REDCap) – A metadata-driven methodology and workflow process for providing translational research informatics support. Journal of Biomedical Informatics, 42, 377–381. https://doi.org/10.1016/j.jbi.2008.08.010
9. Kallen, B., Harris, J., & Robert, E. (1996). The epidemiology of orofacial clefts. 2. Associated malformations. Journal of Craniofacial Genetics and Developmental Biology, 16, 242–248.
10. Kotzot, D. (2004). Maternal uniparental disomy 14 dissection of the phenotype with respect to rare autosomal recessively inherited traits, trisomy mosaicism, and genomic imprinting. Annales de Genetique, 47, 251–260. https://doi.org/10.1016/j.anngen.2004.03.006
11. Kotzot, D. (2008). Maternal uniparental disomy 7 and Silver-Russell syndrome – clinical update and comparison with other subgroups. European Journal of Medical Genetics, 51, 444–451. https://doi.org/10.1016/j.ejmg.2008.06.001
12. Laurie, C. C., Doheny, K. F., Mirel, D. B., Pugh, E. W., Bierut, L. J., Bhangale, T. … GENEVA Investigators (2010). Quality control and quality assurance in genotypic data for genome-wide association studies. Genetic Epidemiology, 34, 591–602.https://doi.org/10.1002/gepi.20516
13. Laurie, C. C., Laurie, C. A., Rice, K., Doheny, K. F., Zelnick, L. R., McHugh, C. P., … Weir, B. S. (2012). Detectable clonal mosaicism from birth to old age and its relationship to cancer. Nature Genetics, 44, 642–650. https://doi.org/10.1038/ng.2271
14. Leslie, E. J., O'Sullivan, J., Cunningham, M. L., Singh, A., Goudy, S. L., Ababneh, F., … Dixon, M. J. (2015). Expanding the genetic and phenotypic spectrum of popliteal pterygium disorders. American Journal of Medical Genetics. Part A 167A, 545–552. https://doi.org/10.1002/ajmg.a.36896
15. Liehr, T. (2014). Uniparental Disomy (UPD) in Clinical Genetics. A Guide for Clinicians and Patients. Xviii. 192 p. 36 illus. 26 illus. in color. Hardcover ISBN: 978-3-642-55287-8
16. Little, J., Cardy, A., & Munger, R. G. (2004). Tobacco smoking and oral clefts: A meta-analysis. Bulletin of the World Health Organization, 82, 213–218.
17. Maarse, W., Rozendaal, A. M., Pajkrt, E., Vermeij-Keers, C., Mink van der Molen, A. B., & van den Boogaard, M. J. (2012). A systematic review of associated structural and chromosomal defects in oral clefts: When is prenatal genetic analysis indicated? Journal of Medical Genetics, 49, 490–498. https://doi.org/10.1136/jmedgenet-2012-101013
18. Marazita, M. L., Field, L. L., Cooper, M. E., Tobias, R., Maher, B. S., Peanchitlertkajorn, S., & Liu, Y. E. (2002). Nonsyndromic cleft lip with or without cleft palate in China: Assessment of candidate regions. Cleft Palate-Craniofacial Journal, 39, 149–156. https://doi.org/10.1597/1545-1569(2002)039<0149:NCLWOW>2.0.CO;2
19. Nyberg, D. A., Sickler, G. K., Hegge, F. N., Kramer, D. J., & Kropp, R. J. (1995). Fetal cleft lip with and without cleft palate: US classification and correlation with outcome. Radiology, 195, 677–684. https://doi.org/10.1148/radiology.195.3.7753993
20. Peiffer, D. A., Le, J. M., Steemers, F. J., Chang, W., Jenniges, T., Garcia, F., … Gunderson, K. L. (2006). High-rsolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Research, 16, 1136–1148. https://doi.org/10.1101/gr.5402306
21. Perrotin, F., dePoncheville, L. M., Marret, H., Paillet, C., Lansac, J., & Body, G. (2001). Chromosomal defects and associated malformations in fetal cleft lip with or without cleft palate. European Journal of Obstetrics, Gynecology, and Reproductive Biology, 99, 19–24. https://doi.org/10.1016/S0301-2115(01)00347-5
22. Rasmussen, K., Nielsen, J., & Dahl, G. (1982). The prevalence of chromosome abnormalities among mentally retarded persons in a geographically delimited area of Denmark. Clinical Genetics, 22, 244–255.
23. Rittler, M., Cosentino, V., Lopez-Camelo, J. S., Murray, J. C., Wehby, G., & Castilla, E. E. (2011). Associated anomalies among infants with oral clefts at birth and during a 1-year follow-up. American Journal of Medical Genetics. Part A, 155A, 1588–1596. https://doi.org/10.1002/ajmg.a.34046
24. Rittler, M., Lopez-Camelo, J. S., Castilla, E. E., Bermejo, E., Cocchi, G., Correa, A., … Mastroiacovo, P. (2008). Preferential associations between oral clefts and other major congenital anomalies. Cleft Palate-Craniofacial Journal, 45, 525–532. https://doi.org/10.1597/06-250.1
25. Romanelli, V., Meneses, H. N., Fernández, L., Martínez-Glez, V., Gracia-Bouthelier, R., F Fraga, M., … Lapunzina, P. (2011). Beckwith-Wiedemann syndrome and uniparental disomy 11p: Fine mapping of the recombination breakpoints and evaluation of several techniques. European Journal of Human Genetics, 19, 416–421. https://doi.org/10.1038/ejhg.2010.236
26. Salahshourifar, I., Halim, A. S., Sulaiman, W. A., Ariffin, R., Naili Muhamad Nor, N., & Zilfalil, B. A. (2010). Maternal uniparental heterodisomy of chromosome 6 in a boy with an isolated cleft lip and palate. American Journal of Medical Genetics. Part A, 152A, 1818–1821. https://doi.org/10.1002/ajmg.a.33526
27. Tan, T. Y., Amor, D. J., Riley, M., Halliday, J., Kilpatrick, N., Simms, K., & White, S. M. (2009). Registry and clinic-based analyses of birth defects and syndromes associated with cleft lip/palate in Victoria, Australia. Cleft Palate-Craniofacial Journal, 46, 583–587. https://doi.org/10.1597/07-241.1
28. Tsai, A. C., Gibby, T., Beischel, L., McGavran, L., & Johnson, J. P. (2004). A child with Angelman syndrome and trisomy 13 findings due to associated paternal UPD 15 and segmental UPD 13. American Journal of Medical Genetics. Part A, 126A, 208–212. https://doi.org/10.1002/(ISSN)1096-8628
29. Venkatraman, E. S., & Olshen, A. B. (2007). A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 23, 657–663. https://doi.org/10.1093/bioinformatics/btl646
30. Walker, S. J., Ball, R. H., Babcook, C. J., & Feldkamp, M. M. (2001). Prevalence of aneuploidy and additional anatomic abnormalities in fetuses and neonates with cleft lip with or without cleft palate: A population-based study in Utah. Journal of Ultrasound in Medicine, 20, 1175–1180. https://doi.org/10.7863/jum.2001.20.11.1175
31. Zheng, X., Levine, D., Shen, J., Gogarten, S. M., Laurie, C., & Weir, B. S. (2012). A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics, 28, 3326–3328. https://doi.org/10.1093/bioinformatics/bts606