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Data analytics for better patient genetics

Data analytics for better patient genetics. Herman Verrelst CEO 26-March-2013. Genetic diagnosis of patients with developmental anomalies. Clinical Cytogenetics. band stain karyotyping. genomic DNA microarrays. Medical genetic diagnosis. Technology push. Towards the $ 1,000 genome.

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Data analytics for better patient genetics

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  1. Data analytics for better patient genetics Herman Verrelst CEO 26-March-2013

  2. Genetic diagnosis of patients with developmental anomalies

  3. Clinical Cytogenetics • band stain karyotyping • genomic DNA microarrays

  4. Medical genetic diagnosis

  5. Technology push

  6. Towards the $ 1,000 genome

  7. Interpretability of Genomic Data Interpretability Complexity # Genetic data Analysis bottleneck Price pbp

  8. Full exome analysis • Patient: • female, 8yr • severe obesity • Whole exome trio • patient, 29183 variants • mother, 35541 variants • father, 34764 variants

  9. Information sources to consult… • 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, … • 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, …

  10. 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 / researchgenome variation databases Collaborative Local Community Pooling initiatives Lab - localgenome variant libraries CONFIDENTIEEL

  11. 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

  12. A revolution in the clinic Fertility Prenatal diagnosis Ophthalmology Neonatology Pathology domains & clinical expertise: Oncology Neuro-pediatrics Child psychiatry Gastroenterology Immunology Dental Orthopedics Pneumology Gynecology Pediatrics Obstetrics … ENT Metabolomic diseases Neurology Cardiology

  13. & Molecular variation Cartagenia delivers diagnostic knowledge, systems and servicesto enable genetics labs andcliniciansto perform clinically relevant genetic analysesquickly and efficiently, and offer high quality genetic interpretation and counseling to patients and care providers. Structural variation 100s, 1000s or even millions of variants

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