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

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Presentation on theme: "Data analytics for better patient genetics Herman Verrelst CEO 26-March-2013."— Presentation transcript:

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

2 Genetic diagnosis of patients with developmental anomalies

3 Clinical Cytogenetics  genomic DNA microarrays  band stain karyotyping

4 Medical genetic diagnosis 6/19/20144 Cytogenomics •Structural Variation •CNV´s •e.g. Down syndrome Molecular genetics •Sequence variation • SNP´s • e.g. BRCA1, CFTR

5 Technology push 6/19/20145

6 Towards the $ 1,000 genome

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

8 6/19/20148

9 9

10 Full exome analysis Patient: female, 8yr severe obesity Whole exome trio patient, 29183 variants mother, 35541 variants father, 34764 variants 6/19/201410

11 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, … 6/19/201411 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, …

12 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 CONFIDENTIEEL 6/19/2014

13 Genetic CNV mutation atlas Min. freq. = 1 Min. freq. = 2 Min. freq. = 3 Min. freq. = 4 Min. freq. = 5 Most narrow common region Lab A, Patient 1 Lab C, patient 4 Lab B, Patient 2 Lab D, Patient 5 Lab A, Patient 3

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

15 100s, 1000s or even millions of variants 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. Molecular variation Structural variation &

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