Jos Jansen

134 Chapter 6 1. Canwe find the pathogenic gene(s) in three families with abnormal glycosylation? In this thesis we used an alternative strategy, yeast homology, for identification of pathogenic variants in exome sequencing data of patients with abnormal Golgi glycosylation. Clustering was possible because of a similar hepatic phenotype of these patients. We identified CCDC115 and TMEM199 as new proteins involved in abnormal Golgi-located N-glycosylation. New strategies for disease gene identification In the introduction I explained different strategies to identify pathogenic variants in exome sequencing data. In chapter 2 and 3 we describe how we used knowledge of the yeast proteome as a tool to find pathogenic variants. Exon 1 of two TMEM199 deficient patients was incompletely covered. This type of technical failure will occur much less in the future as techniques improve. A homozygous variant in CCDC115 was not recognized in the candidate list. With the increased availability of genome sequencing (and with that, the large increase in called variants) new challenges arise. How to deal with exome data of high quality without (or with too much) likely pathogenic candidates? Here I will discuss potential strategies on different cellular levels. Comparative genomics The transfer of knowledge fromone species toanother is a valuable tool indisease gene identification and common practice since the first sequenced genomes. Orthologs are genes derived by a speciation event (in contrast to paralogs, which are derived from a duplication event).(1) The general consensus among comparative genomic researchers is that orthologs have similar function among species.(2) One of the assumptions in comparative genomics is reciprocality, two orthologous genes are more similar to each other than to any other gene. (3) Orthology prediction is one of the cornerstones of comparative genomics and a multitude of models are available to predict orthology.(2) We used an iterative orthology prediction model for yeast proteins based on reciprocality already successfully utilized for mitochondrial proteins (Figure 1).(4)