Next generation diagnostics of heritable connective tissue disorders

Matrix Biology

Volumn 33, Issue , 2014, Pages 35-40

  Salam, Amr ^a   Simpson, Michael A ^b   Stone, Kristina L ^b   Takeichi, Takuya ^a,c   Nanda, Arti ^d   Akiyama, Masashi ^c   McGrath, John A ^a  

^a GUY S HOSPITAL   (United Kingdom)

^b KING'S COLLEGE LONDON   (United Kingdom)

^c NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^d AL SABAH HOSPITAL   (Kuwait)

Author keywords

Collagen; Extracellular matrix; Mutation; Whole exome sequencing

Indexed keywords

COLLAGEN; EXTRACELLULAR MATRIX; MUTATION; WHOLE-EXOME SEQUENCING;

BASE SEQUENCE; CONNECTIVE TISSUE DISEASES; DNA MUTATIONAL ANALYSIS; EXOME; GENETIC ASSOCIATION STUDIES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MUTATION;

EID: 84894269506     PISSN: 0945053X     EISSN: 15691802     Source Type: Journal    
DOI: 10.1016/j.matbio.2013.06.004     Document Type: Review

References (30)

1. Adzhubei I.A., Schmidt S., Peshkin L., Ramensky V.E., Gerasimova A., Bork P., Kondrashov A.S., Sunyaev S.R. A method and server for predicting damaging missense mutations. Nat. Methods 2010, 7:248-249.
2. Bamshad M.J., Ng S.B., Bigham A.W., Tabor H.K., Emond M.J., Nickerson D.A., Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 2011, 12:745-755.
3. Bonod-Bidaud C., Roulet M., Hansen U., Elsheikh A., Malbouyres M., Ricard-Blum S., Faye C., Vaganay E., Rousselle P., Ruggiero F. In vivo evidence for a bridging role of a collagen V subtype at the epidermis-dermis interface. J. Invest. Dermatol. 2012, 132:1841-1849.
4. Botstein D., Risch N. Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nat. Genet. 2003, 33:228-237. (Suppl.).
5. Byers P.H., Murray M.L. Ehlers-Danlos syndrome: a showcase of conditions that lead to understanding matrix biology. Matrix Biol. 2014, 33:5-10. (this issue).
6. Choi M., Scholl U.I., Ji W., Liu T., Tikhonova I.R., Zumbo P., Nayir A., Bakkaloglu A., Ozen S., Sanjad S., Nelson-Williams C., Farhi A., Mane S., Lifton R.P. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19096-19101.
7. Cooper G.M., Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 2011, 12:628-640.
8. De Paepe A., Malfait F. The Ehlers-Danlos syndrome, a disorder with many faces. Clin. Genet. 2012, 82:1-11.
9. De Paepe A., Nuytinck L., Hausser I., Anton-Lamprecht I., Naeyaert J.M. Mutations in the COL5A1 gene are causal in the Ehlers-Danlos syndromes I and II. Am. J. Hum. Genet. 1997, 60:547-554.
10. Fine J.D., Johnson L.B., Weiner M., Suchindran C. Cause-specific risks of childhood death in inherited epidermolysis bullosa. J. Pediatr. 2008, 152:276-280.
11. Genomes Project, C., Abecasis G.R., Altshuler D., Auton A., Brooks L.D., Durbin R.M., Gibbs R.A., Hurles M.E., McVean G.A. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
12. Hindorff L.A., Sethupathy P., Junkins H.A., Ramos E.M., Mehta J.P., Collins F.S., Manolio T.A. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:9362-9367.
13. Hoischen A., Gilissen C., Arts P., Wieskamp N., van der Vliet W., Vermeer S., Steehouwer M., de Vries P., Meijer R., Seiqueros J., Knoers N.V., Buckley M.F., Scheffer H., Veltman J.A. Massively parallel sequencing of ataxia genes after array-based enrichment. Hum. Mutat. 2010, 31:494-499.
14. International Human Genome Sequencing, C. Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945.
15. Kimura M. The Neutral Theory Of Molecular Evolution 1983, Cambridge Univ. Press, New York.
16. Ku C.S., Cooper D.N., Polychronakos C., Naidoo N., Wu M., Soong R. Exome sequencing: dual role as a discovery and diagnostic tool. Ann. Neurol. 2012, 71:5-14.
17. MacArthur D.G., Tyler-Smith C. Loss-of-function variants in the genomes of healthy humans. Hum. Mol. Genet. 2010, 19:R125-R130.
18. McGrath J.A., Stone K.L., Begum R., Simpson M.A., Dopping-Hepenstal P.J., Liu L., McMillan J.R., South A.P., Pourreyron C., McLean W.H., Martinez A.E., Mellerio J.E., Parsons M. Germline mutation in EXPH5 implicates the Rab27B effector protein Slac2-b in inherited skin fragility. Am. J. Hum. Genet. 2012, 91:1115-1121.
19. Metzker M.L. Sequencing technologies - the next generation. Nat. Rev. Genet. 2010, 11:31-46.
20. Moore B., Hu H., Singleton M., De La Vega F.M., Reese M.G., Yandell M. Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet. Med. 2011, 13:210-217.
21. Ng P.C., Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001, 11:863-874.
22. Pettersson E., Lundeberg J., Ahmadian A. Generations of sequencing technologies. Genomics 2009, 93:105-111.
23. Ritelli M., Dordoni C., Venturini M., Chiarelli N., Quinzani S., Traversa M., Zoppi N., Vascellaro A., Wischmeijer A., Manfredini E., Garavelli L., Calzavara-Pinton P., Colombi M. Clinical and molecular characterization of 40 patients with classic Ehlers-Danlos syndrome: identification of 18 COL5A1 and 2 COL5A2 novel mutations. Orphanet J. Rare Dis. 2013, 8:58.
24. Schaffer J.V. Molecular diagnostics in genodermatoses. Semin. Cutan. Med. Surg. 2012, 31:211-220.
25. Singleton A.B. Exome sequencing: a transformative technology. Lancet Neurol. 2011, 10:942-946.
26. Smith S.M., Birk D.E. Focus on molecules: collagens V and XI. Exp. Eye Res. 2012, 98:105-106.
27. Stenmark H. Rab GTPases as coordinators of vesicle traffic. Nat. Rev. Mol. Cell Biol. 2009, 10:513-525.
28. Stone E.A., Sidow A. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res. 2005, 15:978-986.
29. Watson J.D., Crick F.H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 1953, 171:737-738.
30. Wenstrup R.J., Langland G.T., Willing M.C., D'Souza V.N., Cole W.G. A splice-junction mutation in the region of COL5A1 that codes for the carboxyl propeptide of pro alpha 1(V) chains results in the gravis form of the Ehlers-Danlos syndrome (type I). Hum. Mol. Genet. 1996, 5:1733-1736.