Diagnostic implications of excessive homozygosity detected by SNP-Based microarrays: Consanguinity, uniparental disomy, and recessive single-gene mutations

Clinics in Laboratory Medicine

Volumn 31, Issue 4, 2011, Pages 595-613

  Kearney, Hutton M ^a   Kearney, Joseph B ^a   Conlin, Laura K ^b  

^a Mission Health System   (United States)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

Author keywords

Autozygosity; Consanguinity; Homozygosity; Microarray; Single nucleotide polymorphism; Uniparental disomy

Indexed keywords

CHROMOSOME ANALYSIS; CLINICAL FEATURE; CONSANGUINITY; CONTROLLED STUDY; COPY NUMBER VARIATION; CYTOGENETICS; GENE FREQUENCY; GENE MAPPING; GENE MUTATION; GENE TRANSLOCATION; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; HETEROZYGOSITY; HOMOLOGOUS RECOMBINATION; HOMOZYGOSITY; MICROARRAY ANALYSIS; MITOSIS; MOSAICISM; NONHUMAN; POPULATION GENETICS; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; UNIPARENTAL DISOMY; ZYGOTE;

CONSANGUINITY; CYTOGENETIC ANALYSIS; FEMALE; GENES, RECESSIVE; HOMOZYGOTE; HUMANS; MALE; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; UNIPARENTAL DISOMY;

EID: 82355181594     PISSN: 02722712     EISSN: 15579832     Source Type: Journal    
DOI: 10.1016/j.cll.2011.08.003     Document Type: Review

References (63)

1. Miller D.T., Adam M.P., Aradhya S., et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010, 86(5):749-764.
2. Manning M., Hudgins L. Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet Med 2010, 12(11):742-745.
3. Conlin L.K., Thiel B.D., Bonnemann C.G., et al. Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum Mol Genet 2010, 19(7):1263-1275.
4. Papenhausen P., Schwartz S., Risheg H., et al. UPD detection using homozygosity profiling with a SNP genotyping microarray. Am J Med Genet A 2011, 155(4):757-768.
5. Nothnagel M., Lu T.T., Kayser M., et al. Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans. Hum Mol Genet 2010, 19(15):2927-2935.
6. Gibson J., Morton N.E., Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet 2006, 15(5):789-795.
7. McQuillan R., Leutenegger A.L., Abdel-Rahman R., et al. Runs of homozygosity in European populations. Am J Hum Genet 2008, 83(3):359-372.
8. Schaaf C.P., Scott D.A., Wiszniewska J., et al. Identification of incestuous parental relationships by SNP-based DNA microarrays. Lancet 2011, 377(9765):555-556.
9. Jinawath N., Zambrano R., Wohler E., et al. Mosaic trisomy 13: understanding origin using SNP array. J Med Genet 2011, 48(5):323-326.
10. Modell B., Darr A. Science and society: genetic counselling and customary consanguineous marriage. Nat Rev Genet 2002, 3(3):225-229.
11. Stoll C., Alembik Y., Dott B., et al. Parental consanguinity as a cause of increased incidence of birth defects in a study of 131,760 consecutive births. Am J Med Genet 1994, 49(1):114-117.
12. Stoltenberg C., Magnus P., Skrondal A., et al. Consanguinity and recurrence risk of birth defects: a population-based study. Am J Med Genet 1999, 82(5):423-428.
13. Bittles A.H., Black M.L. Evolution in health and medicine Sackler colloquium: Consanguinity, human evolution, and complex diseases. Proc Natl Acad Sci U S A 2010, 107(Suppl 1):1779-1786.
14. Leutenegger A.L., Sahbatou M., Gazal S., et al. Consanguinity around the world: what do the genomic data of the HGDP-CEPH diversity panel tell us?. Eur J Hum Genet 2011, 19(5):583-587.
15. Engel E. A new genetic concept: uniparental disomy and its potential effect, isodisomy. Am J Med Genet 1980, 6(2):137-143.
16. Spence J.E., Perciaccante R.G., Greig G.M., et al. Uniparental disomy as a mechanism for human genetic disease. Am J Hum Genet 1988, 42(2):217-226.
17. Kotzot D. Complex and segmental uniparental disomy (UPD): review and lessons from rare chromosomal complements. J Med Genet 2001, 38(8):497-507.
18. Kotzot D. Complex and segmental uniparental disomy updated. J Med Genet 2008, 45(9):545-556.
19. Yamazawa K., Ogata T., Ferguson-Smith A.C. Uniparental disomy and human disease: an overview. Am J Med Genet C Semin Med Genet 2010, 154C(3):329-334.
20. Liehr T. Cytogenetic contribution to uniparental disomy (UPD). Mol Cytogenet 2010, 3:8.
21. Robinson W.P. Mechanisms leading to uniparental disomy and their clinical consequences. Bioessays 2000, 22(5):452-459.
22. Engel E. Uniparental disomy revisited: the first twelve years. Am J Med Genet 1993, 46(6):670-674.
23. Engel E. A fascination with chromosome rescue in uniparental disomy: Mendelian recessive outlaws and imprinting copyrights infringements. Eur J Hum Genet 2006, 14(11):1158-1169.
24. Lapunzina P., Monk D. The consequences of uniparental disomy and copy number neutral loss-of-heterozygosity during human development and cancer. Biol Cell 2011, 103(7):303-317.
25. Liehr T. Cases with uniparental disomy (UPD) Accessed July 8, 2011. http://www.med.uni-jena.de/fish/sSMC/00START-UPD.htm.
26. Morison I. Catalogue of parent of origin effects Accessed July 8, 2011. http://igc.otago.ac.nz/home.html.
27. Robinson W. Chromosomal mosaicism; uniparental disomy Accessed July 8, 2011. http://www.medgen.ubc.ca/wrobinson/mosaic/clinical/prenatal/upd.htm.
28. Jirtle R.L. Geneimprint Accessed July 8, 2011. http://www.geneimprint.com/site/genes-by-species.Homo+sapiens.
29. Nicholls R.D., Knoll J.H., Butler M.G., et al. Genetic imprinting suggested by maternal heterodisomy in nondeletion Prader-Willi syndrome. Nature 1989, 342(6247):281-285.
30. Kotzot D., Utermann G. Uniparental disomy (UPD) other than 15: phenotypes and bibliography updated. Am J Med Genet A 2005, 136(3):287-305.
31. O'Keefe C., McDevitt M.A., Maciejewski J.P. Copy neutral loss of heterozygosity: a novel chromosomal lesion in myeloid malignancies. Blood 2010, 115(14):2731-2739.
32. Moynahan M.E., Jasin M. Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat Rev Mol Cell Biol 2010, 11(3):196-207.
33. Yamazawa K., Nakabayashi K., Kagami M., et al. Parthenogenetic chimaerism/mosaicism with a Silver-Russell syndrome-like phenotype. J Med Genet 2010, 47(11):782-785.
34. Strain L., Warner J.P., Johnston T., et al. A human parthenogenetic chimaera. Nat Genet Oct 1995, 11(2):164-169.
35. Romanelli V., Nevado J., Fraga M., et al. Constitutional mosaic genome-wide uniparental disomy due to diploidisation: an unusual cancer-predisposing mechanism. J Med Genet 2011, 48(3):212-216.
36. Winberg J., Gustavsson P., Lagerstedt-Robinson K., et al. Chimerism resulting from parthenogenetic activation and dispermic fertilization. Am J Med Genet A 2010, 152A(9):2277-2286.
37. Yamazawa K., Nakabayashi K., Matsuoka K., et al. Androgenetic/biparental mosaicism in a girl with Beckwith-Wiedemann syndrome-like and upd(14)pat-like phenotypes. J Hum Genet 2011, 56(1):91-93.
38. Romanelli V., Meneses H.N., Fernandez L., et al. Beckwith-Wiedemann syndrome and uniparental disomy 11p: fine mapping of the recombination breakpoints and evaluation of several techniques. Eur J Hum Genet 2011, 19(4):416-421.
39. Choate K.A., Lu Y., Zhou J., et al. Mitotic recombination in patients with ichthyosis causes reversion of dominant mutations in KRT10. Science 2010, 330(6000):94-97.
40. Morel F., Laudier B., Guerif F., et al. Meiotic segregation analysis in spermatozoa of pericentric inversion carriers using fluorescence in-situ hybridization. Hum Reprod 2007, 22(1):136-141.
41. Carpenter N.J., May K., Roa B., et al. Developmental disabilities. Molecular pathology in clinical practice 2006, 73-86. Springer, New York. 1st edition. D.G.B. Leonard (Ed.).
42. Giardina E., Peconi C., Cascella R., et al. A multiplex molecular assay for the detection of uniparental disomy for human chromosome 15. Electrophoresis 2008, 29(23):4775-4779.
43. Pagon R.A. GeneTests: an online genetic information resource for health care providers. J Med Libr Assoc 2006, 94(3):343-348.
44. Shaffer L.G., Agan N., Goldberg J.D., et al. American College of Medical Genetics statement of diagnostic testing for uniparental disomy. Genet Med 2001, 3(3):206-211.
45. Altug-Teber O., Dufke A., Poths S., et al. A rapid microarray based whole genome analysis for detection of uniparental disomy. Hum Mutat 2005, 26(2):153-159.
46. Bruce S., Leinonen R., Lindgren C.M., et al. Global analysis of uniparental disomy using high density genotyping arrays. J Med Genet 2005, 42(11):847-851.
47. Lander E.S., Botstein D. Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science 1987, 236(4808):1567-1570.
48. Alkuraya F.S. Homozygosity mapping: one more tool in the clinical geneticist's toolbox. Genet Med 2010, 12(4):236-239.
49. Sheffield V.C., Nishimura D.Y., Stone E.M. Novel approaches to linkage mapping. Curr Opin Genet Dev 1995, 5(3):335-341.
50. Alkuraya F.S. Autozygome decoded. Genet Med 2010, 12(12):765-771.
51. Jiang Z., Wierenga K. Genomic oligoarray and SNP array evaluation tool v1.0 Accessed July 8, 2011. http://www.ccs.miami.edu/cgi-bin/ROH/ROH_analysis_tool.cgi.
52. Temple I.K., Mackay D.J.G. Diabetes mellitus, 6q24-related transient neonatal 1993, Accessed July 9, 2011. http://www.ncbi.nlm.nih.gov/pubmed/20301706.
53. Saal H.M. Russell-Silver syndrome 1993, Accessed July 9, 2011. http://www.ncbi.nlm.nih.gov/pubmed/20301499.
54. Shuman C., Beckwith J.B., Smith A.C., et al. Beckwith-Wiedemann syndrome 1993, Accessed July 9, 2011. http://www.ncbi.nlm.nih.gov/pubmed/20301568.
55. Bullman H., Lever M., Robinson D.O., et al. Mosaic maternal uniparental disomy of chromosome 11 in a patient with Silver-Russell syndrome. J Med Genet 2008, 45(6):396-399.
56. Sutton V.R., Shaffer L.G. Search for imprinted regions on chromosome 14: comparison of maternal and paternal UPD cases with cases of chromosome 14 deletion. Am J Med Genet 2000, 93(5):381-387.
57. Murphy S.K., Wylie A.A., Coveler K.J., et al. Epigenetic detection of human chromosome 14 uniparental disomy. Hum Mutat 2003, 22(1):92-97.
58. Kagami M., Sekita Y., Nishimura G., et al. Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes. Nat Genet 2008, 40(2):237-242.
59. Cotter P.D., Kaffe S., McCurdy L.D., et al. Paternal uniparental disomy for chromosome 14: a case report and review. Am J Med Genet 1997, 70(1):74-79.
60. Dagli A.I., Williams C.A. Angelman syndrome 1993, Accessed July 9, 2011. http://www.ncbi.nlm.nih.gov/pubmed/20301323.
61. Cassidy S.B., Schwartz S. Prader-Willi syndrome 1993, July 9, 2011. http://www.ncbi.nlm.nih.gov/pubmed/20301505.
62. Bastepe M., Lane A.H., Juppner H. Paternal uniparental isodisomy of chromosome 20q-and the resulting changes in GNAS1 methylation-as a plausible cause of pseudohypoparathyroidism. Am J Hum Genet 2001, 68(5):1283-1289.
63. Lecumberri B., Fernandez-Rebollo E., Sentchordi L., et al. Coexistence of two different pseudohypoparathyroidism subtypes (Ia and Ib) in the same kindred with independent Gs{alpha} coding mutations and GNAS imprinting defects. J Med Genet 2010, 47(4):276-280.