PORTFOLIO

The human genome is an enormous text of information for the structure and function of a human being. The function of the majority of the human genome is unknown. Many human disorders are due to pathogenic mutations in individual genomes, and only a minority of the deleterious mutations has been identified. The technological advances for rapid and inexpensive genome sequencing offer an unprecedented opportunity to identify links between the genomes and the various resulting disorders. Consanguineous families offer the possibility of detecting genes due to the higher incidence of Rare genetic disoredrs in them.

We propose to utilize consanguinity to identify the important genomic elements, that cause selected Rare Genetic Disorders in diverse human populations. The disorders include multiple congenital abnormalities with or without mental retardation, dysmorphic features or mental retardation and global developmental delay. The cause of the disease in each family is likely to be rare. We propose to take advantage of i/ the identity-by-decent of deleterious variants in consanguineous samples, and ii/ the advances in the technological platforms that allow the rapid and relatively inexpensive exploration of individual genomes.

The specific aims are:
1. To identify homozygous microdeletions of the genome in cases of disease phenotypes from consanguineous samples
2. To identify the causative mutations in genes of samples from consanguineous families with sufficient number of affected and non-affected individuals.
In both aims the candidate genes identified will be validated by studying a large number of patients from international cohorts.
The deliverables of this project are i/ the identification of a certain number of new genes that cause autosomal recessive disorders, ii/ the generation of numerous new hypotheses for pathogenetic mechanisms, and iii/ the introduction of new diagnostic tests in the families with these rare disorders.

The Gebert Rüf Stiftung is supporting this project because it will identify new genes responsible for rare genetic disorders, and provide a better understanding of the molecular mechanisms of these disorders. This will in turn lead to a more accurate diagnostic and prognostic tests, and open the possibilities for new treatments.

During this project samples from more than 80 families have been collected; the families have prioritized based on their structure and the number of members available for testing in order to maximize the possibility to identify new variants. The analysis pipeline consisted of an arrayCGH of one of the patients, genotyping of all the family members and exome sequencing of one of the affected samples. Using this approach, 50 families have been completely analyzed, and several more are in different stages of analysis. The mean coverage of exome sequencing is 130x, covering 98.2% of the total coding region of RefSeq at least 8x. For every patient we have identified on average about 21,900 variants with a specificity of 99.95%, sensitivity 97.7%, positive predictive value of 99.2% and negative predictive value of 98.6%.

In 18 families (36%) we have identified mutations in known genes, and these findings have been returned to the patients/referring physicians after confirmation. These results show the importance of exome sequencing in diagnosing the molecular basis of rare genetic disorders. In practice, the experience that was gained from this project has been transferred to the Genetic Service of the University Hospitals of Geneva and has already allowed the development of the «Genome Clinic» which actively uses high throughput sequencing for the diagnosis of genetic disorders.

In 27 families (54%) we have identified candidate genes (average: 2.7 per family). For several of them extensive supportive data already exist in the form of known protein function or animal models with similar phenotypes. These genes are currently under investigation aiming to expand our knowledge on the genetic basis of diseases.

Finally in 5 families (10%) no candidate genes have been identified despite the updated filtering and variant prioritization process showing the current limits of genomic diagnosis possibilities.

Makrythanasis et al; Diagnostic exome sequencing to elucidate the genetic basis of likely recessive disorders in consanguineous families; Human Mutation ; In press 2014;
Makrythanasis et al; A novel homozygous mutation in FGFR3 causes tall stature, severe lateral tibial deviation, scoliosis, hearing impairment, camptodactyly and arachnodactyly; Hum Mutation. 2014 May 26. doi: 10.1002/humu.22597;
Hamamy et al; Recessive thrombocytopenia likely due to a homozygous pathogenic variant in the FYB gene; Blood; under review;
Makrythanasis et al; Homozygous missense mutation in KALRN gene and a novel syndrome of intellectual disability with short stature; Genome Medicine; under review.