Targeted array CGH as a valuable molecular diagnostic approach: Experience in the diagnosis of mitochondrial and metabolic disorders

Molecular Genetics and Metabolism

Volumn 106, Issue 2, 2012, Pages 221-230

  Wang, Jing ^a   Zhan, Hongli ^a,b   Li, Fang Yuan ^a   Pursley, Amber N ^a   Schmitt, Eric S ^a   Wong, Lee Jun ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b GREENWOOD GENETIC CENTER   (United States)

Author keywords

Gene deletion; Metabolic diseases; Mitochondrial disorders; Molecular diagnosis; Targeted aCGH

Indexed keywords

DNA;

ADULT; ARTICLE; CHILD; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DELETION BREAKPOINT; DISORDERS OF MITOCHONDRIAL FUNCTIONS; FEMALE; GENE DELETION; GENE DOSAGE; GENE SEQUENCE; GENOME; HUMAN; INFANT; MAJOR CLINICAL STUDY; MALE; METABOLIC DISORDER; MITOCHONDRIAL DNA DEPLETION SYNDROME; MITOCHONDRIAL GENOME; MOLECULAR DIAGNOSIS; NEWBORN; NUCLEAR GENOME; OLIGONUCLEOTIDE ARRAY COMPARATIVE GENOMIC HYBRIDIZATION; POLYMERASE CHAIN REACTION; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; SEQUENCE HOMOLOGY; UREA CYCLE; UREA CYCLE DISORDER;

ADOLESCENT; ADULT; BASE SEQUENCE; CHILD; CHILD, PRESCHOOL; CHROMOSOME BREAKAGE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; DNA, MITOCHONDRIAL; FEMALE; GENE DELETION; GENOME, HUMAN; GENOTYPE; HUMANS; INFANT; MALE; METABOLIC DISEASES; MITOCHONDRIAL DISEASES; MOLECULAR SEQUENCE DATA; ORNITHINE CARBAMOYLTRANSFERASE; UREA CYCLE DISORDERS, INBORN; YOUNG ADULT;

EID: 84860916810     PISSN: 10967192     EISSN: 10967206     Source Type: Journal    
DOI: 10.1016/j.ymgme.2012.03.005     Document Type: Article

References (43)

1. Mendell J.R., Buzin C.H., Feng J., Yan J., Serrano C., Sangani D.S., Wall C., Prior T.W., Sommer S.S. Diagnosis of Duchenne dystrophy by enhanced detection of small mutations. Neurology 2001, 57:645-650.
2. Shchelochkov O.A., Li F.Y., Geraghty M.T., Gallagher R.C., Van Hove J.L., Lichter-Konecki U., Fernhoff P.M., Copeland S., Reimschisel T., Cederbaum S., Lee B., Chinault A.C., Wong L.J. High-frequency detection of deletions and variable rearrangements at the ornithine transcarbamylase (OTC) locus by oligonucleotide array CGH. Mol. Genet. Metab. 2009, 96:97-105.
3. Schouten J.P., McElgunn C.J., Waaijer R., Zwijnenburg D., Diepvens F., Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 2002, 30:e57.
4. Monaco A.P., Bertelson C.J., Middlesworth W., Colletti C.A., Aldridge J., Fischbeck K.H., Bartlett R., Pericak-Vance M.A., Roses A.D., Kunkel L.M. Detection of deletions spanning the Duchenne muscular dystrophy locus using a tightly linked DNA segment. Nature 1985, 316:842-845.
5. Bendavid C., Kleta R., Long R., Ouspenskaia M., Muenke M., Haddad B.R., Gahl W.A. FISH diagnosis of the common 57-kb deletion in CTNS causing cystinosis. Hum. Genet. 2004, 115:510-514.
6. Sieber O.M., Lamlum H., Crabtree M.D., Rowan A.J., Barclay E., Lipton L., Hodgson S., Thomas H.J., Neale K., Phillips R.K., Farrington S.M., Dunlop M.G., Mueller H.J., Bisgaard M.L., Bulow S., Fidalgo P., Albuquerque C., Scarano M.I., Bodmer W., Tomlinson I.P., Heinimann K. Whole-gene APC deletions cause classical familial adenomatous polyposis, but not attenuated polyposis or "multiple" colorectal adenomas. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:2954-2958.
7. Schrijver I., Rappahahn K., Pique L., Kharrazi M., Wong L.J. Multiplex ligation-dependent probe amplification identification of whole exon and single nucleotide deletions in the CFTR gene of Hispanic individuals with cystic fibrosis. J. Mol. Diagn. 2008, 10:368-375.
8. Ou Z., Kang S.H., Shaw C.A., Carmack C.E., White L.D., Patel A., Beaudet A.L., Cheung S.W., Chinault A.C. Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses. Genet. Med. 2008, 10:278-289.
9. Boone P.M., Bacino C.A., Shaw C.A., Eng P.A., Hixson P.M., Pursley A.N., Kang S.H., Yang Y., Wiszniewska J., Nowakowska B.A., del Gaudio D., Xia Z., Simpson-Patel G., Immken L.L., Gibson J.B., Tsai A.C., Bowers J.A., Reimschisel T.E., Schaaf C.P., Potocki L., Scaglia F., Gambin T., Sykulski M., Bartnik M., Derwinska K., Wisniowiecka-Kowalnik B., Lalani S.R., Probst F.J., Bi W., Beaudet A.L., Patel A., Lupski J.R., Cheung S.W., Stankiewicz P. Detection of clinically relevant exonic copy-number changes by array CGH. Hum. Mutat. 2010, 31:1326-1342.
10. Dhami P., Coffey A.J., Abbs S., Vermeesch J.R., Dumanski J.P., Woodward K.J., Andrews R.M., Langford C., Vetrie D. Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome. Am. J. Hum. Genet. 2005, 76:750-762.
11. Lu X., Shaw C.A., Patel A., Li J., Cooper M.L., Wells W.R., Sullivan C.M., Sahoo T., Yatsenko S.A., Bacino C.A., Stankiewicz P., Ou Z., Chinault A.C., Beaudet A.L., Lupski J.R., Cheung S.W., Ward P.A. Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS One 2007, 2:e327.
12. Brunetti-Pierri N., Paciorkowski A.R., Ciccone R., Mina E.D., Bonaglia M.C., Borgatti R., Schaaf C.P., Sutton V.R., Xia Z., Jelluma N., Ruivenkamp C., Bertrand M., de Ravel T.J., Jayakar P., Belli S., Rocchetti K., Pantaleoni C., D'Arrigo S., Hughes J., Cheung S.W., Zuffardi O., Stankiewicz P. Duplications of FOXG1 in 14q12 are associated with developmental epilepsy, mental retardation, and severe speech impairment. Eur. J. Hum. Genet. 2010, 19:102-107.
13. Wong L.J., Dimmock D., Geraghty M.T., Quan R., Lichter-Konecki U., Wang J., Brundage E.K., Scaglia F., Chinault A.C. Utility of oligonucleotide array-based comparative genomic hybridization for detection of target gene deletions. Clin. Chem. 2008, 54:1141-1148.
14. Sadikovic B., Wang J., El-Hattab A., Landsverk M., Douglas G., Brundage E.K., Craigen W.J., Schmitt E.S., Wong L.J. Sequence homology at the breakpoint and clinical phenotype of mitochondrial DNA deletion syndromes. PLoS One 2010, 5:e15687.
15. Li F.Y., El-Hattab A.W., Bawle E.V., Boles R.G., Schmitt E.S., Scaglia F., Wong L.J. Molecular spectrum of SLC22A5 (OCTN2) gene mutations detected in 143 subjects evaluated for systemic carnitine deficiency. Hum. Mutat. 2010, 31:E1632-E1651.
16. Zhang S., Li F.Y., Bass H.N., Pursley A., Schmitt E.S., Brown B.L., Brundage E.K., Mardach R., Wong L.J. Application of oligonucleotide array CGH to the simultaneous detection of a deletion in the nuclear TK2 gene and mtDNA depletion. Mol. Genet. Metab. 2010, 99:53-57.
17. Compton A.G., Troedson C., Wilson M., Procopis P.G., Li F.Y., Brundage E.K., Yamazaki T., Thorburn D.R., Wong L.J. Application of oligonucleotide array CGH in the detection of a large intragenic deletion in POLG associated with Alpers Syndrome. Mitochondrion 2010, 11:104-107.
18. Chinault A.C., Shaw C.A., Brundage E.K., Tang L.Y., Wong L.J. Application of dual-genome oligonucleotide array-based comparative genomic hybridization to the molecular diagnosis of mitochondrial DNA deletion and depletion syndromes. Genet. Med. 2009, 11:518-526.
19. Lee N.C., Dimmock D., Hwu W.L., Tang L.Y., Huang W.C., Chinault A.C., Wong L.J. Simultaneous detection of mitochondrial DNA depletion and single-exon deletion in the deoxyguanosine gene using array-based comparative genomic hybridisation. Arch. Dis. Child. 2009, 94:55-58.
20. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29:365-371.
21. Dimmock D., Tang L.Y., Schmitt E.S., Wong L.J. Quantitative evaluation of the mitochondrial DNA depletion syndrome. Clin. Chem. 2010, 56:1119-1127.
22. El-Hattab A.W., Li F.Y., Schmitt E., Zhang S., Craigen W.J., Wong L.J. MPV17-associated hepatocerebral mitochondrial DNA depletion syndrome: new patients and novel mutations. Mol. Genet. Metab. 2010, 99:300-308.
23. Yamaguchi S., Brailey L.L., Morizono H., Bale A.E., Tuchman M. Mutations and polymorphisms in the human ornithine transcarbamylase (OTC) gene. Hum. Mutat. 2006, 27:626-632.
24. Wang J., Shchelochkov O.A., Zhan H., Li F., Chen L.C., Brundage E.K., Pursley A.N., Schmitt E.S., Haberle J., Wong L.J. Molecular characterization of CPS1 deletions by array CGH. Mol. Genet. Metab. 2010, 102:103-106.
25. Wang G.L., Wang J., Douglas G., Browning M., Hahn S., Ganesh J., Cox S., Aleck K., Schmitt E.S., Zhang W., Wong L.J. Expanded molecular features of carnitine acyl-carnitine translocase (CACT) deficiency by comprehensive molecular analysis. Mol. Genet. Metab. 2011, 103:349-357.
26. Shen Y., Irons M., Miller D.T., Cheung S.W., Lip V., Sheng X., Tomaszewicz K., Shao H., Fang H., Tang H.S., Irons M., Walsh C.A., Platt O., Gusella J.F., Wu B.L. Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. Clin. Chem. 2007, 53:2051-2059.
27. Venegas V., Wang J., Dimmock D., Wong L.J. Real-time quantitative PCR analysis of mitochondrial DNA content. Curr. Protoc. Hum. Genet. 2011, 68. (Chapter 19, Unit 19.7.1-19.7.12).
28. Spinazzola A. Mitochondrial DNA mutations and depletion in pediatric medicine. Semin. Fetal Neonatal. Med. 2011, 16:190-196.
29. Spinazzola A., Invernizzi F., Carrara F., Lamantea E., Donati A., Dirocco M., Giordano I., Meznaric-Petrusa M., Baruffini E., Ferrero I., Zeviani M. Clinical and molecular features of mitochondrial DNA depletion syndromes. J. Inherit. Metab. Dis. 2009, 32:143-158.
30. Tang S., Wang J., Lee N.C., Milone M., Halberg M.C., Schmitt E.S., Craigen W.J., Zhang W., Wong L.J. Mitochondrial DNA polymerase gamma mutations: an ever expanding molecular and clinical spectrum. J. Med. Genet. 2011, 48:669-681.
31. Salviati L., Sacconi S., Mancuso M., Otaegui D., Camano P., Marina A., Rabinowitz S., Shiffman R., Thompson K., Wilson C.M., Feigenbaum A., Naini A.B., Hirano M., Bonilla E., DiMauro S., Vu T.H. Mitochondrial DNA depletion and dGK gene mutations. Ann. Neurol. 2002, 52:311-317.
32. Hirano M., Lagier-Tourenne C., Valentino M.L., Marti R., Nishigaki Y. Thymidine phosphorylase mutations cause instability of mitochondrial DNA. Gene 2005, 354:152-156.
33. Spinazzola A., Viscomi C., Fernandez-Vizarra E., Carrara F., D'Adamo P., Calvo S., Marsano R.M., Donnini C., Weiher H., Strisciuglio P., Parini R., Sarzi E., Chan A., DiMauro S., Rotig A., Gasparini P., Ferrero I., Mootha V.K., Tiranti V., Zeviani M. MPV17 encodes an inner mitochondrial membrane protein and is mutated in infantile hepatic mitochondrial DNA depletion. Nat. Genet. 2006, 38:570-575.
34. Bourdon A., Minai L., Serre V., Jais J.P., Sarzi E., Aubert S., Chretien D., de Lonlay P., Paquis-Flucklinger V., Arakawa H., Nakamura Y., Munnich A., Rotig A. Mutation of RRM2B, encoding p53-controlled ribonucleotide reductase (p53R2), causes severe mitochondrial DNA depletion. Nat. Genet. 2007, 39:776-780.
35. Elpeleg O., Miller C., Hershkovitz E., Bitner-Glindzicz M., Bondi-Rubinstein G., Rahman S., Pagnamenta A., Eshhar S., Saada A. Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion. Am. J. Hum. Genet. 2005, 76:1081-1086.
36. Ostergaard E., Christensen E., Kristensen E., Mogensen B., Duno M., Shoubridge E.A., Wibrand F. Deficiency of the alpha subunit of succinate-coenzyme A ligase causes fatal infantile lactic acidosis with mitochondrial DNA depletion. Am. J. Hum. Genet. 2007, 81:383-387.
37. Bai R.K., Wong L.J. Simultaneous detection and quantification of mitochondrial DNA deletion(s), depletion, and over-replication in patients with mitochondrial disease. J. Mol. Diagn. 2005, 7:613-622.
38. Prior T.W., Bridgeman S.J. Experience and strategy for the molecular testing of Duchenne muscular dystrophy. J. Mol. Diagn. 2005, 7:317-326.
39. Hastings P.J., Ira G., Lupski J.R. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 2009, 5:e1000327.
40. Zhang F., Carvalho C.M., Lupski J.R. Complex human chromosomal and genomic rearrangements. Trends Genet. 2009, 25:298-307.
41. Zhang F., Gu W., Hurles M.E., Lupski J.R. Copy number variation in human health, disease, and evolution. Annu. Rev. Genomics Hum. Genet. 2009, 10:451-481.
42. McVey M., Lee S.E. MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. Trends Genet. 2008, 24:529-538.
43. Gu W., Zhang F., Lupski J.R. Mechanisms for human genomic rearrangements. Pathogenetics 2008, 1:4.