tools for molecular diagnostics...
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Tools for molecular diagnostics laboratoriesVariant interpretation and filtering
Euformatics Oy, Finland
Christophe Roos, CSO, [email protected]
The wider diagnostic context
Interpretation of variant data
● Germ line mutations (Mendelian diseases)● Paired samples, somatic mutations (cancer)● Trio analysis, families (rare diseases)✔ Cohorts (comparison & research)
Researchbioinformaticians
Clinical geneticsbiologists
The bottleneck for realising personalised medicine isThe bottleneck for realising personalised medicine is interpretationinterpretation
Marked medical device
Solution 1: Small and simple
Patient Health serviceprovider
Laboratory diagnosticsmolecular genetics / pathology
Treatment
Seque
nceService
provider
Solution 2: Large and collaborative
Pharma:Trials + drugs
Academia:Research + biomarkers
Hospital:diagnostics + treatment
Speed and consistency in reporting
Observation:A homozygousmutation in thegene F5 at c.1601G>A(pArg534Gln)
Consequence:Factor V Leidenhypercoagulation
Treatmentsuggestion:Anticoagulantmedication canlessen the risk ofdeveloping bloodclots.
@NS500227:25:H7FMMBGXX:1:11101:24240:11381:N:0:20
GGTCACTGTTACTATATTGAGTCCTCATATACAAGAAACTGGGGCCAAGCTTCTC...
+ <AAAAFFAFFFFFAFAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF...
Sequence I n t e r p r e t a t i o n p r o c e s s Understanding
Easy user interface
Filtering: manual or automatic
Filtering and reporting capacities for exomes,can be automated for smaller gene panels.
Nothing left out – all stored
Gene details, sequence, quality, predictions, all is stored in thedatabase and can be accessed upon request or used for filtering
Probands, controls, families, cohorts
Value proposal
● Manages the data➢ Scalable patient variant database➢ Storage of sequenced unclassified variants (UV, VUS) *
● Support for interpretation➢ Reporting when UVs become pathogenic or likely pathogenic *➢ Compare patients or study groups of patients
● Quick & easy to configure for specific use➢ Genetic biomarker tests➢ Virtual gene panels➢ Local variant database for different diseases *➢ Population-specific variants
omnomicsNGS
Value proposalomnomicsNGS
Program family for clinical NGS
Integrated in larger IT systems, or stand-alone
Quality managementValidate, monitor, benchmark
Variant interpretationDecision support, laboratory report