Characterizing the morbid genome of ciliopathies

Background Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge of their morbid genome, pleiotropy, and variable expressivity remains incomplete. Results We applied genomic approaches on a large patient cohort of 371 affected individuals from 265 families, with phenotypes that span the entire ciliopathy spectrum. Likely causal mutations in previously described ciliopathy genes were identified in 85% (225/265) of the families, adding 32 novel alleles. Consistent with a fully penetrant model for these genes, we found no significant difference in their “mutation load” beyond the causal variants between our ciliopathy cohort and a control non-ciliopathy cohort. Genomic analysis of our cohort further identified mutations in a novel morbid gene TXNDC15, encoding a thiol isomerase, based on independent loss of function mutations in individuals with a consistent ciliopathy phenotype (Meckel-Gruber syndrome) and a functional effect of its deficiency on ciliary signaling. Our study also highlighted seven novel candidate genes (TRAPPC3, EXOC3L2, FAM98C, C17orf61, LRRCC1, NEK4, and CELSR2) some of which have established links to ciliogenesis. Finally, we show that the morbid genome of ciliopathies encompasses many founder mutations, the combined carrier frequency of which accounts for a high disease burden in the study population. Conclusions Our study increases our understanding of the morbid genome of ciliopathies. We also provide the strongest evidence, to date, in support of the classical Mendelian inheritance of Bardet-Biedl syndrome and other ciliopathies

Severe Infantile Encephalomyopathy Caused by a Mutation in COX6B1, a Nucleus-Encoded Subunit of Cytochrome C Oxidase

Cytochrome c oxidase (COX) deficiency, one of the most common respiratory-chain defects in humans, has been associated with mutations in either mitochondrial DNA genes or nucleus-encoded proteins that are not part in but promote the biogenesis of COX. Mutations of nucleus-encoded structural subunits were sought for but never found in COX-defective patients, leading to the conjecture that they may be incompatible with extra-uterine survival. We report a disease-associated mutation in one such subunit, COX6B1. Nuclear-encoded COX genes should be reconsidered and included in the diagnostic mutational screening of human disorders related to COX deficiency

Accelerating Novel Candidate Gene Discovery in Neurogenetic Disorders via Whole-Exome Sequencing of Prescreened Multiplex Consanguineous Families

Our knowledge of disease genes in neurological disorders is incomplete. With the aim of closing this gap, we performed whole-exome sequencing on 143 multiplex consanguineous families in whom known disease genes had been excluded by autozygosity mapping and candidate gene analysis. This prescreening step led to the identification of 69 recessive genes not previously associated with disease, of which 33 are here described (SPDL1, TUBA3E, INO80, NID1, TSEN15, DMBX1, CLHC1, C12orf4, WDR93, ST7, MATN4, SEC24D, PCDHB4, PTPN23, TAF6, TBCK, FAM177A1, KIAA1109, MTSS1L, XIRP1, KCTD3, CHAF1B, ARV1, ISCA2, PTRH2, GEMIN4, MYOCD, PDPR, DPH1, NUP107, TMEM92, EPB41L4A, and FAM120AOS). We also encountered instances in which the phenotype departed significantly from the established clinical presentation of a known disease gene. Overall, a likely causal mutation was identified in >73% of our cases. This study contributes to the global effort toward a full compendium of disease genes affecting brain function

Additional file 1: Figure S1. of Characterizing the morbid genome of ciliopathies

Bar graph showing the percentage of the main features for each distinct ciliopathy syndrome. (PPTX 70 kb

Additional file 2: Table S3. of Characterizing the morbid genome of ciliopathies

Clinical and genomic data for all cases in the study. (XLSX 83 kb

Additional file 5: Table S4. of Characterizing the morbid genome of ciliopathies

Identification of TXNDC15 interacting proteins using tandem affinity purification (TAP). The list of 224 unique proteins is significantly enriched in known or predicted ciliary proteins. (XLSX 30 kb

Additional file 6: Table S5. of Characterizing the morbid genome of ciliopathies

Ciliopathy disease burden in the population for each pathogenic variant identified in known ciliopathy genes. (XLSX 19 kb

Additional file 8: Table S1. of Characterizing the morbid genome of ciliopathies

List of diagnostic criteria used to clinically classify each ciliopathy. (XLSX 10 kb

Additional file 7: Table S6. of Characterizing the morbid genome of ciliopathies

List of common variants with MAF of >0.01 that are listed as “disease-causing” variants in HGMD for known ciliopathy genes. (XLSX 12 kb

Additional file 3: of Characterizing the morbid genome of ciliopathies

Supplemental clinical data: clinical details for the affected cases with mutations in novel candidate genes. (DOCX 35 kb