Next Generation Sequencing (NGS)

Our institute owns and operates next generation sequencing (NGS) platforms, which are instrumental to perform high throughput DNA sequencing in human samples. We make use of NGS to detect disease-causing mutations in patients and families with monogenic (Mendelian) diseases. These include eye diseases, cardiomyopathies, long QT syndrome, polyneuropathies, familial fever syndromes and others (genetic testing). All of them are characterized by a significant genetic heterogeneity and single gene sequencing is inefficient for comprehensive genetic analysis.

Retinal and Vitreoretinal Diseases
These disorders are characterized by a tremendous genetic heterogeneity and clinical variability. Currently, mutations in more than 250 genes are associated with about 20 retinal and vitreoretinal diseases (for review please refer to: Berger W, Kloeckener-Gruissem B, Neidhardt J, 2010: The molecular basis of human retinal and vitreoretinal diseases. Prog Retin Eye Res 29:335-375; overview). Because of the large number of genes to be screened for mutations, high throughput technologies are required to provide reliable diagnostic testing. The following figures show examples for genetic heterogeneity and clinical variability.

Clinical_variability

Figure: Clinical variability in monogenic retinal and vitreoretinal diseases. The clinical manifestations of mutations in a single gene can be highly variable. The circles represent different clinical diagnoses. Gene symbols in the overlapping areas indicate that mutations may lead to either of the phenotypes, as for example mutations in ABCA4, which can give rise to RP, MD, COD or CORD.
CORD/COD: cone rod dystrophy / cone dystrophy; CVD: colour vision defect; ERVR/EVR: erosive and exudative vitreoretinopathy; LCA: Leber congenital amaurosis; MD: macular degeneration; NB: night blindness; RP: retinitis pigmentos

 

In addition to highly variable clinical manifestations of mutations in several genes, the genetic heterogeneity of retinal and vitreoretinal diseases is particularly challenging for genetic testing of patients and families. One of the most prominent examples for this genetic heterogeneity is retinitis pigmentosa (RP). The figure below shows the large variety of genes involved in RP and other diseases, which predominantly involve the rod photoreceptors.

Rod_diseases

Figure: Genetic heterogeneity of monogenic rod dominated retinal diseases. Rod dominated diseases can be stationary (night blindness) or progressive (retinitis pigmentosa). In syndromic forms, the retinal manifestations are combined with other clinical symptoms as for example deafness in Usher syndrome. The numbers of genes known today (as of September 2015) are given for dominant, recessive and X-linked forms of the diseases. In recessive RP for example, 67 genes were shown to carry disease-causing mutations.

For questions regarding the NGS technology or specific applications please contact Wolfgang Berger or Samuel Koller.

Recent NGS publications from our lab:

  • Gerth-Kahlert C, Tiwari A, Hanson JVM, Batmanabane V, Traboulsi E, Pennesi ME, Al-Qahtani AA, Lam BL, Heckenlively J, Zweifel SA, Vincent A, Fierz F, Barthelmes D, Branham K, Khan N, Bahr A, Baehr L, Magyar I, Koller S, Azzarello-Burri S, Niedrist D, Heon E, Berger W (2017) C2orf71 mutations as a frequent cause of autosomal-recessive retinitis pigmentosa: clinical analysis and presentation of 8 novel mutations. Invest Ophthalmol Vis Sci 58:3840-3850
  • Gerth-Kahlert G, Tiwari A, Hauri M, Hanson JVM, Bahr A, Palmowski-Wolfe A, Güngör T, Berger W (2017) Unusual retinopathy in a child with severe combined immuno deficiency. Ophthalmic Genet (Epub ahead of print)
  • Glöckle N, Kohl S, Mohr J, Scheurenbrand T, Sprecher A, Weisschuh N, Bernd A, Rudolph G, Schubach M, Poloschek C, Zrenner E, Biskup S, Berger W, Wissinger B, Neidhardt J (2014) Panel-based next generation sequencing as a reliable and efficient technique to detect mutations in unselected patients with retinal dystrophies. Eur J Hum Genet 22:99-104
  • Haghighi A, Tiwari A, Piri N, Nurnberg G, Saleh-Gohari N, Haghighi A, Neidhardt J, Nurnberg P, Berger W (2014) Homozygosity mapping and whole exome sequencing reveal a novel homozygous COL18A1 mutation causing Knobloch syndrome. PLoS ONE 9:e112747
  • Medeiros-Domingo A, Saguner AM, Magyar I, Duru F, Bahr A, Akdis D, Brunckhorst C, Berger W (2016) Arrhythmogenic right ventricular cardiomyopathy versus dilated cardiomyopathy: Implications of next generation sequencing in appropriate diagnosis. Europace (Epub ahead of print)
  • Neubauer J, Haas C, Bartsch C, Domingo-Medeiros A, Berger W (2016) Post-mortem whole-exome sequencing (WES) with a focus on cardiac disease-associated genes in five young sudden unexplained death (SUD) cases. Int J Legal Med 130:1011-1021
  • Neubauer J, Lecca MR, Russo G, Bartsch C, Medeiros-Domingo A, Berger W, Haas C (2017) Post-mortem whole exome analysis in a large sudden infant death syndrome cohort with a focus on cardiovascular and metabolic genetic diseases. Eur J Hum Genet (Epub ahead of print)
  • Tiwari A, Bahr, Baehr L, Fleischhauer J, Zinkernagel M, Winkler N, Barthelmes D, Berger L, Gerth-Kahlert C, Neidhardt J, Berger W (2016) Next generation sequencing based identification of disease-associated mutations in Swiss patients with retinal dystrophies. Sci Rep 6:28755
  • Tiwari A., Lemke J, Altmueller J, Thiele H, Glaus E, Fleischhauer J, Nürnberg P, Neidhardt J, Berger W (2016) Identification of novel and recurrent disease-causing mutations in retinal dystrophies using whole exome sequencing (WES): Benefits and limitations. PLoS ONE 11:e0158692