| OCR Text |
Show Institute of Ophthalmology The 100,000 Genomes Project: Uncovering Pathogenic Variants in Inherited Optic Neuropathies with Whole-Genome Sequencing Neringa Jurkute, MD, FEBO Clinical research associate PhD candidate Moorfields Eye Hospital NHS Foundation Trust, London, UK Institute of Ophthalmology, University College London, London, UK Dr Gavin Arno, Dr Amy Slater, Dr Nikolas Pontikos, Prof Marcela Votruba, Savita Nutan, Prof Andrew R Webster, Dr Patrick YuWai-Man, Genomics England Research Consortium Disclosure I am supported by a Moorfields Eye Charity Research Travel Grant to attend and present research findings at NANOS 2020 I have no other financial disclosers Outline • Inherited optic neuropathy • Genomics England 100,000 Genomes Project • Data interpretation pipeline: Clinical interpretation pipeline Research pipeline • Genomics England 100,000 Genomes Sub-project Spectrum of genotype and phenotype in Inherited Optic Neuropathies • Results • Summary Inherited Optic Neuropathy (ION) s. mitochondrial optic neuropathy, s. inherited optic atrophy - an important cause of blindness in: paediatric adult - estimated prevalence of 1 in 10,000 in the UK Reaching a confirmed molecular diagnosis can be challenging: - Mutations have been identified in both: mitochondrial DNA (mtDNA) nuclear DNA (nDNA) https://kidsbiology.com/wp-content/uploads/1970/01/cell2.jpg - Limited number of genes included in next generation sequencing panels - All inheritance patterns The phenotype: - isolated optic atrophy - accompanied by additional systemic abnormalities (‘plus' phenotype) - pathological hallmark of progressive and irreversible loss of retinal ganglion cells (RGCs), retinal nerve fiber layer (RNFL) Genomics England 100,000 Genomes Project Sequenced 100,000 whole genomes from NHS patients with rare diseases, and their families, as well as patients with common cancers. 13 Genomic Medicine Centres Research: Genomics England Clinical Interpretation Partnership (GeCIP) Researchers and clinicians continually analyse data 2600 researchers in 42 GeCIP research domains (Hearing and Sight GeCIP) The 100,000 Genomes Project funded by: Main: National Institute for Health Research NHS England Additional: The Wellcome Trust, Cancer Research UK and the Medical Research Council Data interpretation pipeline Clinical interpretation pipeline Aim: Clinical diagnostics Research pipeline Aim: enable scientific discovery and accelerate its translation into patient care Research environment - secure workspace with a range of tools to analyse data for approved researchers Data interpretation pipeline Clinical interpretation pipeline Virtual gene panel PanelApp: • Leber hereditary optic neuropathy (3 genes) • Optic neuropathy (48 genes) https://panelapp.genomicsengland.co.uk/ Filtering criteria: E.g. protein altering, familial segregation, MAF (<0.01 for AR and <0.0001 for AD) and etc. Variant tiering Tier 1: Damaging or known pathogenic within the panel. Should be clinically assessed by NHS GMCs Tier 2: Likely damaging within the panel. Should be clinically assessed by NHS GMCs Tier 3: Unknown significance and plausible candidate variants identified in genes outside of known disease gene panel(s). Not expected that NHS GMCs will review all these variants. Data interpretation pipeline Research pipeline Non-coding and structural variants discovery E.g. RTN4IP1 c.307C>T, p.Arg103Cys Large 10kb deletion (involves exon 4) Data interpretation pipeline Research pipeline Non-coding and structural variants discovery Gene discovery E.g. Linkage analysis, homozygosity mapping, analysis of linked regions Data interpretation pipeline Research pipeline Non-coding and structural variants discovery Gene discovery E.g. Linkage analysis, homozygosity mapping, analysis of linked regions Candidate gene panel Different sources and bioinformatics tools were used to create a list of genes, associated or likelyassociated with inherited optic neuropathy Data interpretation pipeline Research pipeline Non-coding and structural variants discovery Gene discovery E.g. Linkage analysis, homozygosity mapping, analysis of linked regions Candidate gene panel Different sources and bioinformatics tools were used to create a list of genes, associated or likelyassociated with inherited optic neuropathy Cohort wide variant analysis in candidate genes Data interpretation pipeline Research pipeline Non-coding and structural variants discovery Gene discovery E.g. Linkage analysis, homozygosity mapping, analysis of linked regions Candidate gene panel Different sources and bioinformatics tools were used to create a list of genes, associated or likelyassociated with inherited optic neuropathy Cohort wide variant analysis in candidate genes In silico analysis E.g. prediction tools, protein modelling, gene ontology, protein expression Data interpretation pipeline Research pipeline Non-coding and structural variants discovery Gene discovery E.g. Linkage analysis, homozygosity mapping, analysis of linked regions Candidate gene panel Different sources and bioinformatics tools were used to create a list of genes, associated or likelyassociated with inherited optic neuropathy Cohort wide variant analysis in candidate genes In silico analysis E.g. prediction tools, protein modelling, gene ontology, protein expression Functional investigation E.g. Segregation, mitochondrial function analysis in patients tissue culture, functional assays, RNA splicing analysis and etc Spectrum of genotype and phenotype in Inherited Optic Neuropathies Genomics England Research Project (Registry ID RR104, 09 January 2019) Lead: Neringa Jurkute Co-leads: Prof Andrew R Webster, Dr Gavin Arno and Dr Patrick Yu-Wai-Man A priori hypothesis: A proportion of these patients will carry novel, non-coding or structural variants in known genes whereas others will be associated with novel optic atrophy genes The aim: To identify associated genetic variants in ION cases The analysis will allow us to: (i) reach a definite molecular diagnosis (ii) unravel novel mechanism of ION (iii) identify novel genotype and phenotype correlations Results Main programme v7-2019-02-28 data release Inherited Optic Neuropathy cohort 141 families Inherited Optic Neuropathy cohort Moorfields Eye Hospital NHS Foundation Trust Moorfields Eye Hospital NHS Foundation Trust 44.2% of total number of families 61 families Other sites 1 - 6 families/site ION cohort Moorfields Eye Hospital foundation Trust ION cohort: Solved cases Using our integrated bioinformatics approach, we have identified likely pathogenic variants in: 36/61 (59.02%) 30/36 (83.33%) known optic atrophy genes 6/36 (16.67%) outside of the gene panel Key findings and discoveries Genes outside the optic atrophy panel: NDUFV1 (11q13.2, OMIM*161015) NDUFAF2 (5q12.1, OMIM*609653) SSBP1 (7q34, OMIM*600439) SLC25A46 (5q22.1, OMIM*610826) A combination of linkage, targeted sequencing and Genomics England 100,000 Genomes Project led to the discovery…. Poster session II Poster no. 216 From 6:30 - 8:30 pm Ann Neurol. 2019 Sep;86(3):368-383. doi: 10.1002/ana.25550. Epub 2019 Jul 31 Cases under investigation 2/25 (8%) 25/61 (40.98%) Candidate novel genes NSUN3 and FASTKD3 5/25 (20%) LHON-like presentation Carries candidate variants in CI subunit genes NSUN3 c.812A>G, p.Glu271Gly (hom.) FASTKD3 c.632G>T, p.Gly211Val (hom.) NSUN3 NOP2/Sun RNA Methyltransferase Family Member 3 2-1 (proband) 2-1 2-3 Phenotype Bilat optic atrophy Mild hearing Bilateral optic atrophy Bilat optic atrophy Mild hearing Age at diagnosis 15-16 years (accidental finding) 18-19 years 25-26 years Visual acuity 6/12 and 6/18 (stable since 2008) 6/18 and 6/18 (stable since 2011) 6/16 and 6/9 (diagnosed in 2019) NSUN3 c.812A>G, p.Glu271Gly (hom.) (rs769633732) PolyPhen-2: probably damaging Mutation taster: disease causing Clinvar: no data GnomAD: 2 alleles (1 homozygous) in South Asian (al.freq.0.000007958) Schematic summary of the mt-tRNAMet formylation pathway and NSUN3 and ABH1 role in mitochondrial translation. Inactivation of NSUN3 (orange), ABH1 (blue) affects f5C34 in mt-tRNAMet or mutations in mtDNA that affect mt-tRNAMet leads to failure of codon recognition, resulting in deficient mitochondrial translation (yellow) (adapted from Lindsey Van Haute et al.). Original case: • Mitochondrial disease at age 3 months • NSUN3 comphet: c.123-615-466+2155del (exon 3 deleted) c.295C>T, p.Arg99* • Findings: NSUN3 protein localised in mitochondria It is required in methylation of mt-tRNAMet Necessary for efficient protein synthesis and respiratory function (studies on pt fibroblasts) Depletion affects mitochondrial translation in human cells To summarise • WGS enabled a molecular diagnosis in over half of all cases investigated. • Identified variants causing ION in genes, which were outside the optic atrophy panel: SLC25A46 (5q22.1, OMIM*610826) SSBP1 (7q34, OMIM*600439) NDUFV1 (11q13.2, OMIM*161015) NDUFAF2 (5q12.1, OMIM*609653) • First report of Mendelian disease caused by mutations in SSBP1 (Check the poster no. 216 !!!) • Novel autosomal dominant optic atrophy phenotype: OA with variable (progressive) retinal degeneration • 25/61 (40.98%%) undiagnosed cases currently undergoing expanded variant discovery analysis, where: 2/25 candidate novel genes were identified 5/25 carries candidate variants in CI subunit genes were identified Acknowledgments Dr Patrick Yu-Wai-Man and Prof Andrew R Webster Dr Gavin Arno Prof Marcela Votruba NIHR at Moorfields Eye Hospital and UCL Institute of Ophthalmology Dr Amy Slater Dr Nikolas Pontikos Supported by a Moorfields Eye Charity Research Travel Grant Savita Nutan |
