Data analytics for better patient genetics
This presentation by Herman Verrelst, CEO, delves into the essential role of data analytics in improving genetic diagnosis for patients with developmental anomalies. It highlights techniques such as band stain karyotyping, genomic DNA microarrays, and whole exome analysis. The session discusses patient case studies, including an 8-year-old girl with severe obesity, showcasing the interpretability of genomic data against a backdrop of tools for variant analysis and phenotype correlations. The focus is on collaborative databases and the importance of integrating knowledge for better diagnosis.
Data analytics for better patient genetics
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Presentation Transcript
Data analytics for better patient genetics Herman Verrelst CEO 26-March-2013
Clinical Cytogenetics • band stain karyotyping • genomic DNA microarrays
Interpretability of Genomic Data Interpretability Complexity # Genetic data Analysis bottleneck Price pbp
Full exome analysis • Patient: • female, 8yr • severe obesity • Whole exome trio • patient, 29183 variants • mother, 35541 variants • father, 34764 variants
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, …
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
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 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
& 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
