Whole-exome sequencing points to considerable genetic heterogeneity of cerebral palsy

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Abstract

Cerebral palsy (CP) is a common, clinically heterogeneous group of disorders affecting movement and posture. Its prevalence has changed little in 50 years and the causes remain largely unknown. The genetic contribution to CP causation has been predicted to be ~2%. We performed whole-exome sequencing of 183 cases with CP including both parents (98 cases) or one parent (67 cases) and 18 singleton cases (no parental DNA). We identified and validated 61 de novo protein-altering variants in 43 out of 98 (44%) case-parent trios. Initial prioritization of variants for causality was by mutation type, whether they were known or predicted to be deleterious and whether they occurred in known disease genes whose clinical spectrum overlaps CP. Further, prioritization used two multidimensional frameworks—the Residual Variation Intolerance Score and the Combined Annotation-dependent Depletion score. Ten de novo mutations in three previously identified disease genes (TUBA1A (n=2), SCN8A (n=1) and KDM5C (n=1)) and in six novel candidate CP genes (AGAP1, JHDM1D, MAST1, NAA35, RFX2 and WIPI2) were predicted to be potentially pathogenic for CP. In addition, we identified four predicted pathogenic, hemizygous variants on chromosome X in two known disease genes, L1CAM and PAK3, and in two novel candidate CP genes, CD99L2 and TENM1. In total, 14% of CP cases, by strict criteria, had a potentially disease-causing gene variant. Half were in novel genes. The genetic heterogeneity highlights the complexity of the genetic contribution to CP. Function and pathway studies are required to establish the causative role of these putative pathogenic CP genes.

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References

  1. 1

    Stanley F, Alberman B . How common are the cerebral palsies? In: Stanley F, Blair E, Alberman B (eds). Cerebral Palsies: Epidemiology and Causal Pathways. Mac Keith Press: London, UK, 2000, pp 22–48.

  2. 2

    Rosenbaum P, Paneth N, Leviton A, Goldstein M, Bax M, Damiano D et al. A report: the definition and classification of cerebral palsy April 2006. Dev Med Child Neurol Suppl 2007; 109: 8–14.

  3. 3

    O'Callaghan ME, MacLennan AH, Gibson C, McMichael G, Haan E, Broadbent J et al. Epidemiologic associations with cerebral palsy. Obstet Gynaecol 2011; 118: 576–582.

  4. 4

    Colver A, Fairhurst C, Pharoah PO . Cerebral palsy. Lancet 2014; 383: 1240–1249.

  5. 5

    Moreno-De-Luca A, Ledbetter DH, Martin CL . Genomic insights into the causes and classification of the cerebral palsies. Lancet Neurol 2012; 11: 283–292.

  6. 6

    Nelson KB, Ellenberg JH . Antecedents of cerebral palsy. Multivariate analysis of risk. N Engl J Med 1986; 315: 81–86.

  7. 7

    Hirata H, Nanda I, van Riesen A, McMichael G, Hu H, Hambrock M et al. ZC4H2 mutations are associated with arthrogryposis multiplex congenita and intellectual disability through impairment of central and peripheral synaptic plasticity. Am J Hum Genet 2013; 92: 681–695.

  8. 8

    Moreno-De-Luca A, Helmers SL, Mao H, Burns TG, Melton AM, Schmidt KR et al. Adaptor protein complex-4 (AP-4) deficiency causes a novel autosomal recessive cerebral palsy syndrome with microcephaly and intellectual disability. J Med Genet 2011; 48: 141–144.

  9. 9

    Tollanes MC, Wilcox AJ, Lie RT, Moster D . Familial risk of cerebral palsy: population based cohort study. BMJ 2014; 349: g4294.

  10. 10

    O'Callaghan ME, MacLennan AH, Gibson CS, McMichael GL, Haan EA, Broadbent JL et al. Fetal and maternal candidate single nucleotide polymorphism associations with cerebral palsy: a case-control study. Pediatrics 2012; 129: e414–e423.

  11. 11

    McMichael G, Girirajan S, Moreno-De-Luca A, Gecz J, Shard C, Nguyen LS et al. Rare copy number variation in cerebral palsy. Eur J Hum Genet 2013; 22: 40–45.

  12. 12

    de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, Kroes T et al. Diagnostic exome sequencing in persons with severe intellectual disability. N Eng J Med 2012; 367: 1921–1929.

  13. 13

    Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 2012; 380: 1674–1682.

  14. 14

    Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 2012; 485: 237–241.

  15. 15

    Xu B, Ionita-Laza I, Roos JL, Boone B, Woodrick S, Sun Y et al. De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nat Genet 2012; 44: 1365–1369.

  16. 16

    Badawi N, Watson L, Petterson B, Blair E, Slee J, Haan E et al. What constitutes cerebral palsy? Dev Med Child Neurol 1998; 40: 520–527.

  17. 17

    Bainbridge MN, Wang M, Wu Y, Newsham I, Muzny DM, Jefferies JL et al. Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol 2011; 12: R68.

  18. 18

    Bainbridge MN, Hu H, Muzny DM, Musante L, Lupski JR, Graham BH et al. De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome. Genome Med 2013; 5: 11.

  19. 19

    Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25: 1754–1760.

  20. 20

    DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet 2011; 43: 491–498.

  21. 21

    MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR et al. Guidelines for investigating causality of sequence variants in human disease. Nature 2014; 508: 469–476.

  22. 22

    Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB . Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet 2013; 9: e1003709.

  23. 23

    Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM., Shendure J . A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genet 2014; 46: 310–315.

  24. 24

    Adzhubei I, Jordan DM, Sunyaev SR . Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet 2013; Chapter 7: Unit7 20.

  25. 25

    Schwarz JM, Rodelsperger C, Schuelke M, Seelow D . MutationTaster evaluates disease-causing potential of sequence alterations. Nature Methods 2010; 7: 575–576.

  26. 26

    Huang N, Lee I, Marcotte EM, Hurles ME . Characterising and predicting haploinsufficiency in the human genome. PLoS Genet 2010; 6: e1001154.

  27. 27

    Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 2012; 485: 242–245.

  28. 28

    O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 2012; 485: 246–250.

  29. 29

    Rujirabanjerd S, Nelson J, Tarpey PS, Hackett A, Edkins S, Raymond FL et al. Identification and characterization of two novel JARID1C mutations: suggestion of an emerging genotype-phenotype correlation. Eur J Hum Genet 2010; 18: 330–335.

  30. 30

    Trudeau MM, Dalton JC, Day JW, Ranum LP, Meisler MH . Heterozygosity for a protein truncation mutation of sodium channel SCN8A in a patient with cerebellar atrophy, ataxia, and mental retardation. J Med Genet 2006; 43: 527–530.

  31. 31

    Poirier K, Saillour Y, Fourniol F, Francis F, Souville I, Valence S et al. Expanding the spectrum of TUBA1A-related cortical dysgenesis to Polymicrogyria. Eur J Hum Genet 2013; 21: 381–385.

  32. 32

    Nie Z, Boehm M, Boja ES, Vass WC, Bonifacino JS, Fales HM et al. Specific regulation of the adaptor protein complex AP-3 by the Arf GAP AGAP1. Dev Cell 2003; 5: 513–521.

  33. 33

    Yamasaki M, Thompson P, Lemmon V . CRASH syndrome: mutations in L1CAM correlate with severity of the disease. Neuropediatrics 1997; 28: 175–178.

  34. 34

    Stum M, Davoine CS, Vicart S, Guillot-Noel L, Topaloglu H, Carod-Artal FJ et al. Spectrum of HSPG2 (Perlecan) mutations in patients with Schwartz-Jampel syndrome. Human Mutat 2006; 27: 1082–1091.

  35. 35

    Rajab A, Yoo SY, Abdulgalil A, Kathiri S, Ahmed R, Mochida GH et al. An autosomal recessive form of spastic cerebral palsy (CP) with microcephaly and mental retardation. Am J Med Genet A 2006; 140: 1504–1510.

  36. 36

    Kruer MC, Jepperson T, Dutta S, Steiner RD, Cottenie E, Sanford L et al. Mutations in gamma adducin are associated with inherited cerebral palsy. Ann Neurol 2013; 74: 805–814.

  37. 37

    Bahi-Buisson N, Poirier K, Fourniol F, Saillour Y, Valence S, Lebrun N et al. The wide spectrum of tubulinopathies: what are the key features for the diagnosis? Brain 2014; 137: 1676–1700.

  38. 38

    Magini P, Pippucci T, Tsai IC, Coppola S, Stellacci E, Bartoletti-Stella A et al. A mutation in PAK3 with a dual molecular effect deregulates the RAS/MAPK pathway and drives an X-linked syndromic phenotype. Hum Mol Genet 2014; 23: 3607–3617.

  39. 39

    Grafodatskaya D, Chung BH, Butcher DT, Turinsky AL, Goodman SJ, Choufani S et al. Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C. BMC Med Genomics 2013; 6: 1.

  40. 40

    Jensen LR, Amende M, Gurok U, Moser B, Gimmel V, Tzschach A et al. Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am J Hum Genet 2005; 76: 227–236.

  41. 41

    Bahi-Buisson N, Poirier K, Boddaert N, Saillour Y, Castelnau L, Philip N et al. Refinement of cortical dysgeneses spectrum associated with TUBA1A mutations. J Med Genet 2008; 45: 647–653.

  42. 42

    Poirier K, Keays DA, Francis F, Saillour Y, Bahi N, Manouvrier S et al. Large spectrum of lissencephaly and pachygyria phenotypes resulting from de novo missense mutations in tubulin alpha 1A (TUBA1A). Human Mutat 2007; 28: 1055–1064.

  43. 43

    Veeramah KR, O'Brien JE, Meisler MH, Cheng X, Dib-Hajj SD, Waxman SG et al. De novo pathogenic SCN8A mutation identified by whole-genome sequencing of a family quartet affected by infantile epileptic encephalopathy and SUDEP. Am J Hum Genet 2012; 90: 502–510.

  44. 44

    Rejeb I, Saillour Y, Castelnau L, Julien C, Bienvenu T, Taga P et al. A novel splice mutation in PAK3 gene underlying mental retardation with neuropsychiatric features. Eur J hum Genet 2008; 16: 1358–1363.

  45. 45

    Klitten LL, Moller RS, Ravn K, Hjalgrim H, Tommerup N . Duplication of MAOA, MAOB, and NDP in a patient with mental retardation and epilepsy. Eur J Hum Genet 2011; 19: 1–2.

  46. 46

    Mochida GH, Walsh CA . Genetic basis of developmental malformations of the cerebral cortex. Arch Neurol 2004; 61: 637–640.

  47. 47

    O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 2012; 338: 1619–1622.

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Acknowledgements

We wish to thank participating CP families, Cerebral Palsy Alliance; Dr James Lupski for critical comments; Dr Jane Valentine and Peta Watts for facilitating blood collections at Princess Margaret Hospital, Western Australia; Dr James Rice and Dr Andrew Tidemann for facilitating blood collections in South Australia; Associate Professor Christopher Barnett for clinical reports; staff of the South Australian Cerebral Palsy Register; Kelly Harper for correlation of neuroimaging reports; Josh Woenig for the technical support; and Dr Kathie Friend and staff at the Department of Genetic Medicine, Women’s and Children’s Hospital, Adelaide and AGRF (Adelaide node) for the support with DNA extractions. DNA/cell lines were established by Genetic Repositories Australia, an Enabling Facility supported by the Australian National Health and Medical Research Council (Grant No. 401184). This work was funded by the Australian National Health and Medical Research Council (Grant No. 1041920 and Grant No. 1019928), JG is supported by NHMRC research fellowship 1041920, The Cerebral Palsy Foundation, The Tenix Foundation, The Robinson Institute, The University of Adelaide, Women’s & Children’s Research Foundation, MC is supported by MS McLeod research fellowship, and the Ter Meulen Fund (stipend to BWMvanB). Supported in part by the National Human Genome Research Institute U54 HG003273 (RAG).

Web Resources

The URLs for data presented herein include:

Cerebral Palsy Research Report; www.cerebralpalsy.org.au/wp-content /uploads /2013/04/ ACPR/

BCM-HGSC protocol; (https://hgsc.bcm.edu/sites/default/files/documents/Illumina _Barcoded _Paired-End _Capture_Library_Preparation.pdf).

Partek; http://www.partek.com/

1000 Genomes; http://browser.1000genomes.org/index.html

dbSNP; http://www.ncbi.nlm.nih.gov/projects/SNP/

Online Mendelian Inheritance in Man (OMIM); http://www.omim.org/

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Correspondence to J Gecz.

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Supplementary Information accompanies the paper on the Molecular Psychiatry website

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