Data analytics for better patient genetics Herman Verrelst CEO 26-March-2013
Genetic diagnosis of patients with developmental anomalies (c) 2012 Cartagenia - Confidential
Clinical Cytogenetics band stain karyotyping genomic DNA microarrays (c) 2012 Cartagenia - Confidential
Medical genetic diagnosis Cytogenomics Structural Variation CNV´s e.g. Down syndrome Molecular genetics Sequence variation SNP´s e.g. BRCA1, CFTR 4/2/2017
Technology push 4/2/2017
Towards the $ 1,000 genome
Interpretability of Genomic Data Complexity # Genetic data Analysis bottleneck Price pbp
4/2/2017
4/2/2017
Full exome analysis Patient: Whole exome trio female, 8yr severe obesity Whole exome trio patient, 29183 variants mother, 35541 variants father, 34764 variants 4/2/2017
Information sources to consult… Quality information Read depth, PHRED scores, confidence, mapping, … Protein and functional variant annotation ANNOVAR, Mutalyzer, Alamut, MutationTaster, … Disease lists and Gene function OMIM, GeneReviews, PUBMED literature, functional studies, … DECIPHER syndromes, known disease variants, … Variant databases 1000 genomes, exome data sets, dbSNP, LSDBs HGMD, ClinVar, ISCA, DGV, … Splice site prediction tools SpliceSiteFinder, HSF, GeneSPlicer, … Effect prediction tools polyphen, SIFT, … Conservation prediction tools PhastCons, PhyloP, GERP, AGVGD, … Genotype-Phenotype correlations London databases LDDB, Human Phenotype Ontology OMIM links, … Patient registries, GWAS studies, research cohorts, … Internal databases Families, variant lists, excel, access, files, databases, lists, validated findings, … 4/2/2017
Standard of care Need to consult broad / public consensus body of knowledge in routine diagnostics Need to contribute to pool genomic variation and clinical relevance / consequence International / research genome variation databases Collaborative Local Community Pooling initiatives Lab - local genome variant libraries 4/2/2017 CONFIDENTIEEL
Genetic CNV mutation atlas Lab A, Patient 1 Lab B, Patient 2 Lab A, Patient 3 Lab C, patient 4 Lab D, Patient 5 Min. freq. = 1 Min. freq. = 2 Min. freq. = 3 Min. freq. = 4 Min. freq. = 5 Most narrow common region
A revolution in the clinic Pathology domains & clinical expertise: Neonatology Orthopedics Pediatrics Gynecology Dental Immunology Obstetrics Prenatal diagnosis Ophthalmology Cardiology Fertility Child psychiatry Gastroenterology Neuro-pediatrics ENT Neurology Pneumology Oncology Metabolomic diseases …
100s, 1000s or even millions of variants Molecular variation Structural variation & Cartagenia delivers diagnostic knowledge, systems and services to enable genetics labs and clinicians to perform clinically relevant genetic analyses quickly and efficiently, and offer high quality genetic interpretation and counseling to patients and care providers. 100s, 1000s or even millions of variants