Tools for molecular diagnostics laboratorieseuformatics.com/.../08/Euformatics_omnomicsNGS_2016-08.pdf · Tools for molecular diagnostics laboratories ... Support for interpretation

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