Prof. Milan Macek MD. (with kind permission of Patrick R. Sosnay M.D. on behalf of the CFTR2 project working party)

Transcription

1 Lessons learned from postnatal diagnostics: phenotype-driven penetrance analysis in the assignement of disease liability of genetic variants (CF as model) Prof. Milan Macek MD. (with kind permission of Patrick R. Sosnay M.D. on behalf of the CFTR2 project working party)

2 Milan Macek Prof. M.D., DSc Lessons learned from postnatal diagnostics: phenotype-driven penetrance analysis in the assignement of disease liability of genetic variants. Disclosure information: Vertex Pharmaceuticals unrestricted institutional grant for the genotyping of cystic fibrosis patients in less favored regions of Europe and the Middle East ( ;

3

4 Technology development & Interpretation Gap FORGE Canada C_AR AD n1 -FH Phenotype PMID: PMID:

5 The challenge Over 4700 Mendelian phenotypes with known causative gene (OMIM.org, Orpha.net) Allelic heterogeneity is the rule Many genes have >100 pathogenic variants (mutations) Disease implications Known (usually) for common mutations Variably known for low frequency mutations (<5%) Unknown (usually) for rare mutations (<1%) Clinical diagnostic (NGS) DNA sequencing identifies all 3 types of mutation

6 Over 25 years of CF research We need to be humble

7 Need for accurate assessment of disease-liability of mutations Diagnosis of clinical cases Newborn screening Carrier screening Pregnancy decisions (PGT, PND) Mutation-specific therapy

8 Mutations in the CFTR gene are responsible for cystic fibrosis Milder mutation determines the phenotype 7 7 CFTR CFTR

9

10 Preconception carrier screening - USA

11 Clinical genome testing

12 TrueSightOne Mendeliome CFTR carriership found in hereditary cardiomopathies

13 Cystic Fibrosis Newborn Screening USA (CA)

14 CF Newborn Screening CZ (Prague)- CFSPID

15 DOI: /humu

16

17 CFTR Variant predictions often inconclusive

18 L997F gnomad ( Can use public data to calculate a genotype frequency?

19

20

21 Nonsense mutation S1455X in the Middle East

22 Penetrance proportion of individuals carrying a particular variant (or allele) of a gene (the genotype) that also express an associated trait (the phenotype) As sequencing technology is used for more in clinical applications, variant annotation and defining penetrance will be the most important hurdle to making genetic testing worthwhile. PMID:

23 Collection of clinical / mutation data Clinic Laboratory > 2000 mutations 88,664 patients

24

25 How did we determine which mutations cause CF and which ones don t? A 3-pronged approach for assigning disease liability Clinically consistent mutation Average sweat [Cl-] 60 meq/l Functionally consistent mutation < 10% of WT CFTR function Genetically inconsistent mutation Mutation found not on seen non-transmitted in healthy healthy CFTR CFTR gene gene in father in father of CF of patient CF patient Non-disease CF-causing mutation causing

26 Improved clinical care: CFTR2.org

27

28

29 Correlating CFTR dysfunction with CF traits Lung disease - Airflow measurement Sweat gland Pancreatic exocrine - Sufficiency vs Insufficiency - Sweat [Cl - ]

30 The relationship between log 10 CFTR function and sweat chloride is linear

31 The relationship between log 10 CFTR function and cross-sectional lung function is linear

32 CFTR folding (as % of WT) G551D R334W* S549N G970R R352Q G178R R347H* S1251N* S997F* D110H D1152H F1052V WT Mutations cluster by theratype T338I L927P G1244E S341P 100 # S549R* R347P I336K R1066H P205S R117C G85E L206W R1070W* P67L A455E Channel defect D579G S945L D614G R117H* Folding and channel defect Folding defect Log CFTR chloride current (as % of WT) Mutations in red are potentiated by (ivacaftor) Mutation in blue responds to corrector (lumacaftor)

33 doi: /s

34 Hereditary Brest and Ovarian Cancer enigmaconsortium.org brcaexchange.org/

35 Acknowledgements CFTR2 Contributors and Advisors 43 countries Nearly 89,000 patients, 70,000 living CFTR2 Cell Core: Neeraj Sharma, Arianna Franca, Ted Han, Laura Gottschalk, Allison McCague, Matthew Pellicore, Taylor Evans, Emily Davis CFF, ECFS, Canadian CF Society for their ongoing support of the project

36 Thank you very much! 1657

37

38 Unknown genotype remains a challenge 22093/88664 patients in CFTR2 have 1 or both mutations listed as unknown Several thousand are patients no longer living, but at least half are currently alive and entered in registry as that MAP (and other equivalent programs) are addressing, able to reconcile many An additional 20% are still negative after MAP Vertex sponsored genotyping scheme

39 New CFTR2 Goal: Define theratype CFTR function Inhibt CFTR G551D + VX770 The functional testing done to assess disease liability can be used to: Classify RNA, protein quantity Localize protein Assess channel activity Test therapeutics Activate CFTR Potentiator Caveats: heterologous cell system, expression vs primary cells should be analyzed. Can use this and other work (primary cells regrown, other heterologous, organoids) to determine what drug for what Work: CFTR2 variant Cell Core; Slide c/o S.T.Han

40 findbase.org/

41

42

43 CFTR2 Team Julian Zielenski Ruslan Dorfman

44 Assignment of pathogenicity 159 mutations 0.01% frequency in CFTR2 127 mutations meet clinical AND functional criteria Clinical & functional analysis 19 mutations meet clinical OR functional criteria 13 mutations meet neither criteria 14 6 Penetrance analysis Mutations are CF-causing 20 mutations are indeterminate 12 mutations are non CF-causing