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Data analytics for better patient genetics

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Presentation on theme: "Data analytics for better patient genetics"— Presentation transcript:

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

2 Genetic diagnosis of patients with developmental anomalies
(c) 2012 Cartagenia - Confidential

3 Clinical Cytogenetics
band stain karyotyping genomic DNA microarrays (c) 2012 Cartagenia - Confidential

4 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

5 Technology push 4/2/2017

6 Towards the $ 1,000 genome

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

8 4/2/2017

9 4/2/2017

10 Full exome analysis Patient: Whole exome trio female, 8yr
severe obesity Whole exome trio patient, variants mother, variants father, variants 4/2/2017

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, … 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

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 4/2/2017 CONFIDENTIEEL

13 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

14 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 …

15 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

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