Biobanking – genetic screening - Work package 2

biobanks

Biological samples collected in Pakistan, in the US and in other countries will be genetically screened with next generation sequencing methods, with a focus to identify mutated novel cilia- and centrosome-related genes that represent novel ciliopathy candidates, but have not yet been coupled to a disease. This biological/genetic focus was chosen since the ciliome constitute 1/20 of the human proteome, the number of known ciliopathies are still <100, but involves disorders affecting a variety of organs and dysfunctions; the individual ciliopathy will likely be an orphan disorder, but will frequently have implications for phenotypically overlapping common complex disorders, and the functional studies of the genes/proteins can be systematized.

Aims
The aims of WP2 are to identify novel disease genes/loci, and provide candidate cilia and centrosome genes for WP3 for functional studies, and data and options for the other WPs. The WP2 groups will have the necessary consents from the Danish, Pakistani and US regional/central research ethical committee’s regarding exome and full genome screening, including the local setups for proper counselling of coincidental findings.  

 Specific projects

  • Balanced chromosomal rearrangements (BCR) have been used for decades to identify novel disease genes (Tommerup,1993). By next generation mate-pair sequencing we have shown that BCRs model random mutagenesis (Halgren et al. 2012a;2012b;in preparation). WP2 will exploit this to identify, collect and map numerous novel disease genes, where we estimate that ~1/20 will be cilia/centrosome related. The project includes an ongoing, UCPH-funded Ph.D.-study which is sampling all known Danish BCR carriers. These will be reexamined by established clinical questionnaires (Bache et al., 2006) and by systematic linkage with all Danish Medical Registries. The same questionnaires will be applied in: 1) A US-pilot-project, where BCRs will be sampled from selected genetic diagnostic laboratories. 2) In established and future collaborations with cytogenetic labs from other countries (e.g. Brazil, India, Finland, France, Greece, and other countries).
  • Congenital heart defects (CHD) is one of the most common developmental defects, which we have used as a model to dissect the genetic and environmental factors involved in organ development (Lage et al. 2010;2012). CHDs are often observed in ciliopathies (Koefoed et al. 2013). In order to identify novel ciliary disease genes, DNA from trios (mother, father, affected child) and small families with heterotaxy, isomerisms, and/or arterial malpositions will be screened by exome-sequencing. DNA samples will be selected from our existing CHD biobank, from patients identified via the Danish National Patient Registry, and from collaborators. This will be supplemented with CHD, heterotaxy and ciliopathy/centrosome families from Pakistan, where an extreme degree of consanguineous marriages (75%) results in a 100-1000 fold increase in rare, recessive disorders.
  • The advantage of access to large consanguineous families in Pakistan will also be exploited to search for the almost uncharted cilia-associated lethality genes associated with early embryonic loss, which strikes millions of couples worldwide. In a pilot-project, we will establish a tissue bank from Pakistani spontaneously aborted fetuses with consanguineous parents, for state-of-the-art genomic screening.

Methods
Mate-pair sequencing: For the mapping of BCRs, we presently use the Illumina Nextera mate-pair kit with sequencing on an Illumina HiSeq platform to map BCRs.

Exome-sequencing: We presently use the Illumina Nextera Extended exome  sequencing kit, covering appr. 66 Mb of the genome, including all coding exons, appr. 1500 non-coding RNA genes including microRNAs, and UTR regions, with sequencing on an Illumina HiSeq platform. 

References

  • Bache I, Hjorth M, Bugge M, Holstebroe S, Hilden J, Schmidt L, Brondum-Nielsen K, Bruun-Petersen G, Jensen PK, Lundsteen C, Niebuhr E, Rasmussen K, Tommerup N. (2006). Systematic re-examination of carriers of balanced reciprocal translocations: a strategy to search for candidate regions for common and complex diseases. Eur J Hum Genet 14:410-7.
  • Halgren C, Bache I, Bak M, Myatt MW, Anderson CM, Brøndum-Nielsen K, Tommerup N. (2012a). Haploinsufficiency of CELF4 at 18q12.2 is associated with developmental and behavioral disorders, seizures, eye manifestations, and obesity. Eur J Hum Genet doi: 10.1038/ejhg.2012.92. [Epub ahead of print].
  • Halgren C, Kjaergaard S, Bak M, Hansen C, El-Schich Z, Anderson C, Henriksen K, Hjalgrim H, Kirchhoff M, Bijlsma E, Nielsen M, den Hollander N, Ruivenkamp C, Isidor B, Le Caignec C, Zannolli R, Mucciolo M, Renieri A, Mari F, Anderlid BM, Andrieux J, Dieux A, Tommerup N, Bache I. (2012b). Corpus callosum abnormalities, intellectual disability, speech impairment, and autism in patients with haploinsufficiency of ARID1B. Clin Genet 82(3): 248-255.
  • Koefoed K, Veland IR, Pedersen LB, Larsen LA, Christensen ST. (2013) Cilia and coordination of signaling networks during heart development. Organogenesis Dec 17;10(1). [Epub ahead of print]
  • Lage K, Møllgård K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, Wiese C, Christoffels VM, Roberts AE, Smoot LB, Pu WT, Donahoe PK, Tommerup N, Brunak S, Seidman CE, Seidman JG, Larsen LA. (2010). Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol Syst Biol 6: 381.
  • Lage K, Greenway SC, Rosenfeld JA, Wakimoto H, Gorham JM, Segrè AV, Roberts, AE, Smoot LB, Pu WT, Pereira AC, Mesquita SM, Tommerup N, Brunak S, Ballif BC, Shaffer LG, Donahoe PK, Daly MJ, Seidman JG, Seidman CE, Larsen LA. (2012). Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development. PNAS 109(35): 14035-40.
  • Tommerup N. (1993). Mendelian cytogenetics. Chromosome rearrangements associated with Mendelian inherited disorders. J Med Genet 30: 713-727.