The Annual Israeli CF Society Conference Ein Gedi, 2016

Transcription

1 The Annual Israeli CF Society Conference Ein Gedi, 2016 Nation-wide genetic analysis for molecularly unresolved cystic fibrosis cases in a multi-ethnic society: Implications for preconception screening and post-natal diagnosis Ori Inbar, PhD Father of a 11 years old boy with CF Chairperson, the CF Foundation of Israel Research leader, Evogene (biotech)

2 Nation-wide genetic analysis Ori Inbar 1, Doron M. Behar 2, Moshe Ashkenazi 3, David Shoseyov 4, Michal Shteinberg 5, Huda Mussaffi 6, Fahed Hakim 7, Soliman Alkrinawi 8, Michal Gur 5, Adi Dagan 3, Yifat Sarouk 3, Bat El Bar Aluma 3, Meir Mei-Zahav 6, Patrick Stafler 6, Dario Prais 6, Gidon Akler 9, Concetta A. Bormans 9, Malena Cohen-Cymberknoh 4 ; Joseph Rivlin 5, Elie Picard 2, Micha Aviram 8, Lea Bentur 7, Galit Livnat 5, Hannah Blau 6, Ori Efrati 3, Eitan Kerem 4, Amihood Singer 10 1 The Cystic Fibrosis Foundation of Israel 2 Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel 3 Cystic Fibrosis Center, Sheba Medical Center, Tel Aviv, Israel 4 Cystic Fibrosis Center, Hadassah Medical Centre, Jerusalem, Israel 5 Cystic Fibrosis Center, Carmel Medical Center, Haifa, Israel 6 Cystic Fibrosis Center, Schneider Children's Medical Center, Petach Tikva, Israel 7 Cystic Fibrosis Center, Rambam Medical Center, Haifa, Israel 8 Cystic Fibrosis Center, Soroka Medical Center, Beersheva, Israel 9 Gene By Gene, Genomic Research Center, Houston, TX USA 10 Medical Genetics, Barzilai Medical Center, Ashkelon, Israel

3 Agenda Motivation for the study Study execution and results Implications

4 The motivation of the motivation Bronze Medal, Israel Judo Championship, up to 27 Kg (malnutrition has its benefits)

5 Carrier screening in Israel Like in no other country In Israel significant portion of the population use carriers screens in order to prevent the birth of sick children For the year 2013: 171,000 births 61,000 took the CF carriers screen (which is 36%) But, this screen usually done only before the first pregnancy of the mother On this year 53,000 births are of this category. Hence, the importance of the genetic panel

6 What is the quality of carrier screening genetic panel 5 mutations can identify 95% of the Ashkenazi Jews CF carriers. But, what about the rest of the population? The current genetic panel consist of mutations with the following known coverage of the Israeli ethnic groups: Ashkenazi Jews: 95% Libyan Jews: 91% Turkish Jews: 90% Georgian Jews: 88% Moroccan Jews: 85% Egyptian Jews: 50% Yemenite Jews: 0% Arab Muslim:? Arab Christian:? Druze:? Bedouin:? Iraqi Jews:? Iranian Jews:? Uzbeki Jews:? This is what we call a multi-ethnic society Distributions of immigrants arrived to Israel

7 And if this is not complicated enough Israelis the rate of mix marriages keeps increasing Percent of Israelis whose parents are from different ethnic group at 1995 Age group Okun & Khait-Marelly 2006 So, what is the overall detection rate of the genetic panel?

8 The Israeli genetic panel has only 70% sensitivity Distribution of 502 CF patients following standard genetic testing, the Israeli 2009 registry Number of mutations identified 2 mutations 1 mutation None 2 mutations by sequencing

9 The picture stays the same when looking on recently diagnosed patients Distribution of 94 CF patients diagnosed during when tested with the genetic panel (Stafler at al, 2015) Number of mutations identified 2 mutations 1 mutation None

10 Major Gales We aimed to sequence the 30% of the patients that do not have full genetics in order: To improve the Israeli genetic panel To let every CF patient know if his/her genetics qualify for Kalydeco and coming new personalized drugs

11 Agenda Motivation for the study Study execution and results Implications

12 First, show me the money Expected cost ~$160,000 Jan 2012: April 2012 April 2012 July 2012

13 The Plan Oct, 2013 Start: Nov, 2013 Start: Dec, 2013 Start: Jan, 2014 Start: Apr, 2014 Launch (annual Israeli CF meeting) Samples collection CFTR sequencing and MLPA Genetic Reports to patients Analysis and database generation Partners: The Israeli CF Society (CF physicians) Israeli Society of Medical Geneticists Gene by Gene (Genetic lab) Medison Pharma (Funding) The CF Foundation of Israel (Patient Org.) Identification of patients qualify for Kalydeco Scientific publication Upgrading the Israeli Registry Improving the genetic Israeli panel

14 Action I: Nation wide survey of CF patients (~650) 176 patients identified without full genetics Ethical Issue: Testing both or only one? Of then 24 pairs of siblings 75 (49%) Typical CF & 77 (51%) Atypical CF 152 independent molecular cases

15 Action II: 152 independent molecular cases Medical Records Errors: In 18 cases (10%) the sequencing discovered conflict with the medical record 1. Sanger sequencing of all exons, splice sites & kbC>T 2. NGS of poly GT tracts (for 5T interpretation) 73 cases (48%) with 2 mutations that affect or probably affect function 28 cases (18%) with 1 mutations that affect or probably affect function 51 cases (34%) with NO mutations that affect or probably affect function Molecular workup concluded MLPA large deletions (Multiplex ligation-dependent probe amplification) Molecular workup concluded

16 What constitute a photogenic mutation? Mutation that affects function: 1. Mutations currently defined as CF-causing mutations by CFTR2 Mutation that probably affects function: 1. Mutations currently defined as mutations under evaluation or mutations of varying clinical consequence by CFTR2. 2. Mutations previously reported to be CF-causing mutations in a peer reviewed manuscript including relevant supporting data. 3. Mutations previously reported to be CAVD-causing mutations in a peer reviewed manuscript(s) including relevant supporting data. 4. Novel deletion mutations creating a frame shift change at the protein level. 5. Novel splice site mutations within the obligatory donor or acceptor sites. 6. Novel missense mutations creating an amino acid change at the protein level which is predicted by various algorithms to affect function. 7. The 5T/12TG mutation. Mutation pathogenicity was determined using 10 resources: 1. CFTR2 2. Literature 3. HGMD 4. dbsnp 5. ClinVar 6. LOVD 7. Mutation taster 8. SIFT 9. PolyPhen-2 HumDiv 10. PolyPhen-2 HumVar

17 Action III: MLPA large deletions (a method for identification of heterozygous deletions which are greater than one exon) 5 Cases (which are 18% of the 1 mutation cases) are solved using the MLPA 78 cases (51%) with 2 mutations that affect or probably affect function 60(77%) Typical CF 18(23%) Atypical CF 23 cases (15%) with 1 mutations that affect or probably affect function 7 (30%) Typical CF 16(70%) Atypical CF 51 cases (34%) with NO mutations that affect or probably affect function 8 (16%) Typical CF 43 (84%) Atypical CF Finally, 54 distinct mutations were identified in 152 independent cases Of them, 4 mutations are novel In conclusion, practically all CF patients underwent thorough genetic analysis

18 Agenda Motivation for the study Study execution and results Implications

19 The Plan Oct, 2013 Start: Nov, 2013 Start: Dec, 2013 Start: Jan, 2014 Start: Apr, 2014 Launch (annual Israeli CF meeting) Samples collection CFTR sequencing and MLPA Genetic Reports to patients Analysis and database generation Partners: The Israeli CF Society (CF physicians) Israeli Society of Medical Geneticists Gene by Gene (Genetic lab) Medison Pharma (Funding) The CF Foundation of Israel (Patient Org.) Identification of patients qualify for Kalydeco Scientific publication Upgrading the Israeli Registry Improving the genetic Israeli panel

20 Dec 2014, Kalydeco entered the Israeli health basket (government reimbursement) Today, 12 patients receive Kalydeco Apparently, mapping the genetics of all Israeli CF patients was a requirement of the approval of health basket committee. Moreover, the genetic mapping enabled the introduction of Vertex trials in Israel

21 The plan Oct, 2013 Start: Nov, 2013 Start: Dec, 2013 Start: Jan, 2014 Start: Apr, 2014 Launch (annual Israeli CF meeting) Samples collection CFTR sequencing and MLPA Genetic Reports to patients Analysis and database generation Partners: The Israeli CF Society (CF physicians) Israeli Society of Medical Geneticists Gene by Gene (Genetic lab) Medison Pharma (Funding) The CF Foundation of Israel (Patient Org.) Identification of patients qualify for Kalydeco Scientific publication Upgrading the Israeli Registry Improving the genetic Israeli panel

22 Aims for the near future Carrier screening expand genetic panel Only 16 of 54 mutations discovered are presented at current panel Diagnostic testing expand genetic panel Research molecular analysis for typical CF patient without full genetics

23 Multi-ethnic society with multi-mutations CF community Who is responsible for this genetic mess? At Basel I Founded the Jewish State Theodor Herzl, the first Zionist Congress, 1897 At Basel We Uncovered Another Part of the Israeli Spectrum of CFTR Mutations The Israeli CF Community, ECFS, 2016

24 Thank You! Questions?