Genomic analysis of primordial dwarfism reveals novel disease genes

Genome Research

Volumn 24, Issue 2, 2014, Pages 291-299

  Shaheen, Ranad ^a   Faqeih, Eissa ^a   Ansari, Shinu ^a   Abdel Salam, Ghada ^b   Al Hassnan, Zuhair N ^a   Al Shidi, Tarfa ^a   Alomar, Rana ^a   Sogaty, Sameera ^c   Alkuraya, Fowzan S ^a,d  

^a KING FAISAL SPECIALIST HOSPITAL AND RESEARCH CENTER   (Saudi Arabia)

^b NATIONAL RESEARCH CENTRE   (Egypt)

^c KING FAHAD GENERAL HOSPITAL   (Saudi Arabia)

^d ALFAISAL UNIVERSITY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BONE MARROW; CLINICAL ARTICLE; CONSANGUINEOUS MARRIAGE; CONTROLLED STUDY; DWARFISM; EXOME; FACIES; FEMALE; GENE LOCUS; GENE MUTATION; GENETIC LINKAGE; GENOME ANALYSIS; HEAD CIRCUMFERENCE; HOMOZYGOSITY; HUMAN; HUMAN CELL; HUMAN TISSUE; INTRAUTERINE GROWTH RETARDATION; KNOCKOUT MOUSE; MALE; MOLECULAR DIAGNOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PEDIGREE; PHENOTYPE; POSTNATAL DEVELOPMENT; PRIORITY JOURNAL; SECKEL SYNDROME;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; BONE MARROW; BRCA2 PROTEIN; DNA-BINDING PROTEINS; DWARFISM; FEMALE; GENETIC PREDISPOSITION TO DISEASE; HOMOZYGOTE; HUMANS; MALE; MICROCEPHALY; MUSCLE HYPOTONIA; MUTATION; PEDIGREE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SPINE;

EID: 84893674890     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.160572.113     Document Type: Article

References (47)

1. Ahnesorg P, Smith P, Jackson SP. 2006. XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. Cell 124: 301.
2. Al-Dosari MS, Shaheen R, Colak D, Alkuraya FS. 2010. Novel CENPJ mutation causes Seckel syndrome. J Med Genet 47: 411-414.
3. Al-Dosari MS, Al-Shammari M, Shaheen R, Faqeih E, Alghofely MA, Boukai A, Alkuraya FS. 2012. 3M syndrome: An easily recognizable yet underdiagnosed cause of proportionate short stature. J Pediatr 161: 139-145.e1.
4. Alazami AM, Al-Owain M, Alzahrani F, Shuaib T, Al-Shamrani H, Al-Falki YH, Al-Qahtani SM, Alsheddi T, Colak D, Alkuraya FS. 2012. Loss of function mutation in LARP7, chaperone of 7SK ncRNA, causes a syndrome of facial dysmorphism, intellectual disability, and primordial dwarfism. Hum Mutat 33: 1429-1434.
5. Alkuraya FS. 2012. Discovery of rare homozygous mutations from studies of consanguineous pedigrees, Chapter 6: Unit 6.12. In Current protocols in human genetics (ed. Haines JL, et al). Wiley, Hoboken, NJ.
6. Alter BP, Rosenberg PS, Brody LC. 2007. Clinical and molecular features associated with biallelic mutations in FANCD1/BRCA2. J Med Genet 44: 1-9.
7. Ayyagari R, Gomes XV, Gordenin DA, Burgers PM. 2003. Okazaki fragment maturation in yeast I. Distribution of functions between FEN1 and DNA2. J Biol Chem 278: 1618-1625.
8. Bicknell LS, Bongers EM, Leitch A, Brown S, Schoots J, Harley ME, Aftimos S, Al-Aama JY, Bober M, Brown PA. 2011. Mutations in the pre-replication complex cause Meier-Gorlin syndrome. Nat Genet 43: 356-359.
9. Bonapace G, Concolino D, Formicola S, Strisciuglio P. 2003. A novel mutation in a patientwith insulin-like growth factor 1 (IGF1) deficiency. J Med Genet 40: 913-917.
10. Buck D, Moshous D, de Chasseval R, Ma Y, le Deist F, Cavazzana-Calvo M, Fischer A, Casanova JL, Lieber MR, de Villartay JP. 2006. Severe combined immunodeficiency and microcephaly in siblings with hypomorphic mutations in DNA ligase IV. Eur J Immunol 36: 224-235.
11. Budd ME, Antoshechkin IA, Reis C,Wold BJ, Campbell JL. 2011. Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint. Cell Cycle 10: 1690-1698.
12. Carr IM, Flintoff KJ, Taylor GR, MarkhamAF, Bonthron DT. 2006. Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families. Hum Mutat 27: 1041-1046.
13. Clayton PE, Hanson D, Magee L, Murray PG, Saunders E, Abu-Amero SN, Moore GE, Black GCM. 2012. Exploring the spectrumof 3-M syndrome, a primordial short stature disorder of disrupted ubiquitination. Clin Endocrinol 77: 335-342.
14. Daniel M, Kleis L, Cemeroglu AP. 2008. Etiology of failure to thrive in infants and toddlers referred to a pediatric endocrinology outpatient clinic. Clin Pediatr (Phila) 47: 762-765.
15. Delacôte F, Han M, Stamato TD, Jasin M, Lopez BS. 2002. An xrcc4 defect or Wortmannin stimulates homologous recombination specifically induced by double-strand breaks in mammalian cells. Nucleic Acids Res 30: 3454-3463.
16. Gao Y, Sun Y, Frank KM, Dikkes P, Fujiwara Y, Seidl KJ, Sekiguchi JM, Rathbun GA, Swat W, Wang J. 1998. A critical role for DNA end-joining proteins in both lymphogenesis and neurogenesis. Cell 95: 891-902.
17. Girard PM, Kysela B, Harer CJ, Doherty AJ, Jeggo PA. 2004. Analysis of DNA ligase IV mutations found in LIG4 syndrome patients: The impact of two linked polymorphisms. Hum Mol Genet 13: 2369-2376.
18. Griffith E, Walker S, Martin C-A, Vagnarelli P, Stiff T, Vernay B, Al Sanna N, Saggar A, Hamel B, Earnshaw WC. 2007. Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling. Nat Genet 40: 232-236.
19. He H, Liyanarachchi S, Akagi K, Nagy R, Li J, Dietrich RC, LiW, Sebastian N, Wen B, Xin B. 2011. Mutations in U4atac snRNA, a component of the minor spliceosome, in the developmental disorderMOPD I. Science 332: 238-240.
20. Howlett NG, Taniguchi T, Olson S, Cox B, Waisfisz Q, De Die-Smulders C, Persky N, Grompe M, Joenje H, Pals G, et al. 2002. Biallelic inactivation of BRCA2 in Fanconi anemia. Science 297: 606-609.
21. Jaffe AC. 2011. Failure to thrive: Current clinical concepts. Pediatr Rev 32: 100-108.
22. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12: 996-1006.
23. Klingseisen A, Jackson AP. 2011. Mechanisms and pathways of growth failure in primordial dwarfism. Genes Dev 25: 2011-2024.
24. Kumar S, Burgers PM. 2013. Lagging strand maturation factor Dna2 is a component of the replication checkpoint initiation machinery. Genes Dev 27: 313-321.
25. Kuo AJ, Song J, Cheung P, Ishibe-Murakami S, Yamazoe S, Chen JK, Patel DJ, Gozani O. 2012. The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome. Nature 484: 115-119.
26. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
27. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-2079.
28. Ludwig T, Chapman DL, Papaioannou VE, Efstratiadis A. 1997. Targeted mutations of breast cancer susceptibility gene homologs in mice: Lethal phenotypes of Brca1, Brca2, Brca1/Brca2, Brca1/p53, and Brca2/p53 nullizygous embryos. Genes Dev 11: 1226-1241.
29. Ma Y, Lu H, Tippin B, Goodman MF, Shimazaki N, Koiwai O, Hsieh CL, Schwarz K, Lieber MR. 2004. A biochemically defined system for mammalian nonhomologous DNA end joining. Mol Cell 16: 701-713.
30. Majewski F, Goecke T. 1982. Studies of microcephalic primordial dwarfism I: Approach to a delineation of the Seckel syndrome. Am J Med Genet 12: 7-21.
31. Miller JD, McKusick VA, Malvaux P, Temtamy S, Salinas C. 1975. The 3-M syndrome: A heritable low birthweight dwarfism. Birth Defects Orig Artic Ser 11: 39-47.
32. Mimitou EP, Symington LS. 2009. DNA end resection: Many nucleases make light work. DNA Repair (Amst) 8: 983-995.
33. Netchine I, Rossignol S, Dufourg M-N, Azzi S, Rousseau A, Perin L, Houang M, Steunou V, Esteva B, Thibaud N. 2007. 11p15 imprinting center region 1 loss ofmethylation is a common and specific cause of typical Russell-Silver syndrome: Clinical scoring system and epigenetic-phenotypic correlations. J Clin Endocrinol Metab 92: 3148-3154.
34. O'Driscoll M, Ruiz-Perez VL, Woods CG, Jeggo PA, Goodship JA. 2003. A splicing mutation affecting expression of ataxia-telangiectasia and Rad3-related protein (ATR) results in Seckel syndrome. Nat Genet 33: 497-501.
35. Ogi T,Walker S, Stiff T, Hobson E, Limsirichaikul S, Carpenter G, Prescott K, Suri M, Byrd PJ, Matsuse M. 2012. Identification of the first ATRIPdeficient patient and novel mutations in ATR define a clinical spectrum for ATR-ATRIP Seckel Syndrome. PLoS Genet 8: e1002945.
36. Passafaro M, Sala C, Niethammer M, Sheng M. 1999. Microtubule binding by CRIPT and its potential role in the synaptic clustering of PSD-95. Nat Neurosci 2: 1063-1069.
37. Qvist P, Huertas P, Jimeno S, Nyegaard M, Hassan MJ, Jackson SP, Børglum AD. 2011. CtIP mutations cause Seckel and Jawad syndromes. PLoS Genet 7: e1002310.
38. Ronchi D, Di Fonzo A, Lin W, Bordoni A, Liu C, Fassone E, Pagliarani S, Rizzuti M, Zheng L, Filosto M. 2013. Mutations in DNA2 link progressive myopathy to mitochondrial DNA instability. Am J Hum Genet 92: 293-300.
39. Roy R, Chun J, Powell SN. 2012. BRCA1 and BRCA2: Different roles in a common pathway of genome protection. Nat Rev Cancer 12: 68-78.
40. Seckel HPG. 1960. Bird-headed dwarfs: Studies in developmental anthropology including human proportions. CC Thomas, Springfield, IL.
41. Shaheen R, Faqeih E, Shamseldin HE, Noche RR, Sunker A, Alshammari MJ, Al-Sheddi T, Adly N, Al-Dosari MS, Megason SG, et al. 2012. POC1A truncation mutation causes a ciliopathy in humans characterized by primordial dwarfism. Am J Hum Genet 91: 330-336.
42. Wajnrajch MP, Gertner JM, Huma Z, Popovic J, Lin K, Verlander PC, Batish SD, Giampietro PF, Davis JG, New MI. 2001. Evaluation of growth and hormonal status in patients referred to the International Fanconi Anemia Registry. Pediatrics 107: 744-754.
43. Wang Q, Lin JL-C, Reinking BE, Feng H-Z, Chan F-C, Lin C-I, Jin J-P, Gustafson-Wagner EA, Scholz TD, Yang B. 2010. Essential roles of an intercalated disc protein, mXinß, in postnatal heart growth and survival. Circ Res 106: 1468-1478.
44. Woods KA, Camacho-Hubner C, Savage MO, Clark AJ. 1996. Intrauterine growth retardation and postnatal growth failure associated with deletion of the insulin-like growth factor I gene. N Engl J Med 335: 1363-1367.
45. Wu KS, Tang TK. 2012. CPAP is required for cilia formation in neuronal cells. Biol Open 1: 559-565.
46. Zheng L, Zhou M, Guo Z, Lu H, Qian L, Dai H, Qiu J, Yakubovskaya E, Bogenhagen DF, Demple B, et al. 2008. Human DNA2 is a mitochondrial nuclease/helicase for efficient processing of DNA replication and repair intermediates. Mol Cell 32: 325-336.
47. Zhu Z, Chung W-H, Shim EY, Lee SE, Ira G. 2008. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double strand break ends. Cell 134: 981.