Genoom-wijde moleculaire technologie toegepast in de genetische
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Genoom-wijde moleculaire technologie toegepast in de genetische diagnostiek Prof Maryse Bonduelle Inleiding Fundamenteel doel van de genetica: ontrafelen van het genotype om het fenotype te verklaren 1977 Sanger sequencing 1 gen per analyse, base per base Combinatie van nieuwe instrumenten, databasen, bioinformatica en robotica exponentiele toename aan de mogelijkheden Next generation sequencing (NGS) of Massive parallel sequencing Enkele miljoenen of biljoenen sequencies in parallel lezen en in één enkele “run” analyseren 2 Genoomwijde Technologie Inleiding 21-5-2014 Drastische toename van capaciteit en snelheid dalen van de kost Introductie van genoomwijde technologie in de dagelijkse diagnostiek Toename toepassingen met diagnostische doeleinden (vb NIPT, gene panels…) Nieuwe vragen en uitdagingen (begrijpen van het functionele genoom van van de variaties) Nieuwe bevindingen ‘incidental findings’ (Informed Consent voor array, NIPT, NGS !) 3 Genoomwijde Technologie Inleiding 21-5-2014 Genoomwijde technologiën in de kliniek Veranderingen in de klinische werking: Voor genoomwijde technologiën: klinische diagnostiek Sanger sequencing 1 gen volgende differentiaal diagnose Sanger sequencing volgend gen Met genoomwijde technologiën: Info over een panel van genen betrokken bij aandoening Info over varianten (polymorphismen) Info over meerdere genen (multicatoriële modellen?) Info over nieuwe genen (nog verder wetenschappelijk te staven via familiestudies en functionele studies) Info over andere niet betrokken genen bij de aandoening = incidental finding ongewenste info, gewenst? 4 … Genoomwijde Technologie Inleiding 21-5-2014 BRIGHT Platform : UZ Brussel-VUB-ULB BRIGHT : BRussels Interuniversity Genomics & High Throughput platform Nieuwe diagnostische en research noden!!! 2012 start zoektocht naar middelen 2013 toekennen middelen voor high troughput platform funding door VUB en UZ Brussel aankoop van high troughput toestellen, scanners Opstart platform deelname ULB in platform samenwerking in IB² bioinformatica platform (VUB-ULB ) 2014 organisatie en uitbreiding platform 5 aankoop nieuwe toestellen Genoomwijde Technologie Inleiding 21-5-2014 Genoom-wijde moleculaire technologie toegepast in de genetische diagnostiek Overzicht van de nieuwe diagnostische tools Array technologie Ingevoerd op de werkvloer ter vervanging van de klassiek karyotypering Toepassingen in de genetische diagnostiek, postnataal, prenataal en preimplantatie NGS technologie 6 Toelichting van verschillende technologieën Toepassing in niet-invasieve diagnostiek (NIPT), mitochondriaal genoom, erfelijke hartritmestoornissen Genoomwijde Technologie Inleiding 21-5-2014 Genoom-wijde moleculaire technologie toegepast in de genetische diagnostiek Algemene introductie en toepassingen in de kliniek Dr M. De Rademaeker & Dr Sci A. Van den Bogaert Array Technologie: Preimplantatie genetische diagnostiek Dr Sci C. Staessen & Prof M. De Rycke Nieuw Genomics platform op de campus UZ Brussel -VUB ir Ben Caljon Niet Invasieve Prenatale Test (NIPT) met genoomwijde analyse Dr Sci S. Van Dooren & Dr K. Van Berkel Mitochondriale genoom sequencing zoekt diagnostische bench. Prof S. Seneca Erfelijke hartritmestoornissen Dr Sci S. Van Dooren & Dr M. Meuwissen 7 Genoomwijde Technologie Inleiding 21-5-2014 Algemene introductie en toepassingen in de kliniek: array technologie Ann Van Den Bogaert Marjan De Rademaeker Array CGH Array gebaseerde vergelijkende genoomhybridisatie (array comparative genomic hybridisation) = array CGH In 1 test: onderzoek van het volledige genoom op kleine (submicroscopische) chromosomale afwijkingen (200-400 kb) 2 Array CGH 22-05-2014 Array CGH DNA 3 array CGH 22-5-2014 Array CGH-Principe Referentie DNA Test DNA Log 2 test/referentie winst 0.3 Labeling 0 Cy 5 Cy 3 -0.3 verlies Mix Chromosomale positie Analyse Hybridisatie Scan 4 array CGH 22-5-2014 Array CGH-in praktijk 4x44K arrays 4 keer 44000 unieke oligonucleotiden (probes/reporters) 60 basen lang over het gehele genoom verspreid Aantal oligo’s per gebied ≠ 5 array CGH 22-5-2014 Procedure Random Prime Labeling Array-CGH hybridisatie Precipitatie Probebereiding Hybridisatie Wassen Scannen Analyse 6 array CGH 22-5-2014 Procedure Random Prime Labeling Array-CGH hybridisatie Precipitatie Probebereiding Hybridisatie Wassen Scannen Analyse 7 array CGH 22-5-2014 Random Prime Labeling-Theorie Binding van korte primersequenties aan gedenatureerd DNA exo-Klenow fragment van DNA polymerase 1: verlenging van de primers Tijdens elongatie: het merken van DNA, resp. met Cy3 en Cy5 ->inbouwen van gemerkte dNTP’s Ongeveer 10 maal geamplificeerd 8 array CGH 22-5-2014 Random Prime Labeling-Theorie Genomisch DNA • Denaturatie van dubbelstrengig DNA naar enkelstrengig DNA •Binding van de random primers • Exo-Klenow fragment bouwt nucleotiden in vanaf de random primers + binding van fluorescente nucleotiden Fluorescent nucleotide Exo-Klenow polymerase Random primer 9 array CGH 22-5-2014 Procedure Random Prime Labeling Array-CGH hybridisatie Precipitatie Probebereiding Hybridisatie Wassen Scannen Analyse 10 array CGH 22-5-2014 Array-CGH hybridisatie-Precipitatie Precipitatie Cy3 gemerkt patiënt DNA + Cy5 gemerkt referentie DNA NaAc 100% EtOH Precipitatie (30 min. bij -80°C) 11 array CGH 22-5-2014 Procedure Random Prime Labeling Array-CGH hybridisatie Precipitatie Probebereiding Hybridisatie Wassen Scannen Analyse 12 array CGH 22-5-2014 Array-CGH hybridisatie-Probebereiding Theorie Stap 1 Random Prime labeling Opzuiveren = verwijderen van niet ingebouwde nucleotiden 13 array CGH 22-5-2014 Array-CGH hybridisatie-Probebereiding Labo 14 array CGH 22-5-2014 Array-CGH hybridisatie-Probebereiding Theorie stap 2 Blokking reagent = blokkeert repetitieve sequenties Niet-specifieke binding : achtergrondsignaal 15 array CGH 22-5-2014 Procedure Random Prime Labeling Array-CGH hybridisatie Precipitatie Probebereiding Hybridisatie Wassen Scannen Analyse 16 array CGH 22-5-2014 Array-CGH hybridisatie-Hybridisatie Theorie Hybridisatie: = de mixen worden aangebracht op de slides Het gelabelde DNA bindt aan de probes die gespot zijn op de slide Vorming dubbelstrengig DNA: binding complementaire sequenties vanop het draagglaasje met het gelabelde DNA (mix patiëntreferentie) 17 array CGH 22-5-2014 Array-CGH hybridisatie-Hybridisatie Theorie Het array glaasje met 4 keer 44000 unieke oligonucleotiden (probes/reporters) Het gelabelde DNA (mix patiënt/referentie) op het oppervlak van het array glaasje + dekglaasje Hybridisatie: competitie tussen verschillend gelabeld patiënt en referentie DNA voor binding met oligonucleotiden op array glaasje 18 array CGH 22-5-2014 Array-CGH hybridisatie-Hybridisatie Labo 65°C, 24 uur 19 array CGH 22-5-2014 Procedure Random Prime Labeling Array-CGH hybridisatie Precipitatie Probebereiding Hybridisatie Wassen Scannen Analyse 20 array CGH 22-5-2014 Array-CGH hybridisatie-Wassen Theorie Wassen Enkel de probes die specifiek gebonden zijn aan het gelabelde DNA kunnen een signaal geven 21 array CGH 22-5-2014 Procedure Random Prime Labeling Array-CGH hybridisatie Precipitatie Probebereiding Hybridisatie Wassen Scannen Analyse 22 array CGH 22-5-2014 Scannen (Agilent microarray scanner) Laser -> excitatie Cy3 en Cy5 23 array CGH 22-5-2014 Scannen (Agilent microarray scanner) Theorie Na het scannen Beelden: Feature Extraction Software Vindt en plaatst microarrayrooster De gemeten intensiteiten~gespot stukje van het genoom (probes) De intensiteit van één spot en de gemiddelde waarden van het achtergrondsignaal rond de spots worden gemeten 24 array CGH 22-5-2014 Feature Extraction Software-Labo Groen signaal 25 array CGH Geel signaal Rood signaal 22-5-2014 Feature Extraction Software-Labo Duplicatie: het gespot DNA op het glaasje bevat meer patiënten DNA (Cy3; groen) dan referentie DNA (Cy5; rood) => Groen signaal in de rooster Deletie: het gespot DNA op het glaasje bevat minder patiënten DNA (Cy3; groen) dan referentie DNA (Cy5; rood) => Rood signaal in de rooster Normaal: het gespot DNA op het glaasje bevat evenveel patiënten DNA (Cy3; groen) dan referentie DNA (Cy5; rood) => Geel signaal in de rooster 26 array CGH 22-5-2014 Procedure Random Prime Labeling Array-CGH hybridisatie Precipitatie Probebereiding Hybridisatie Wassen Scannen Analyse 27 array CGH 22-5-2014 Analyse-Theorie Verwerking en visualisatie: arrayCGHbase (Menten et al., 2005) Ruwe data wordt geconverteerd en gevisualiseerd -> interpretatie Log2-ratio per probe/reporter uitgezet t.o.v. zijn chromosomale positie 28 array CGH 22-5-2014 Analyse in praktijk 29 array CGH 22-5-2014 Analyse array CGH Cartagenia: Labo: array resultaten Artsen: kliniek Labo: koppeling tussen genotype/fenotype Interpretatie onafhankelijk en daarna overleg tussen wetenschappelijke medewerker en arts Verschil postnatale-prenatale arrays 30 array CGH 22-5-2014 Copy Number Variants-theorie CNVs=DNA fragmenten >1Kb Copy Number Variants (CNVs) = de term CNP (Copy Number Polymorphisms) 31 array CGH “Goedaardig/beninge” Normaal 15%-25% van het humane genoom is polymorf Array CGH Effect op ! Genen Genetische aandoeningen/pathogeen 22-5-2014 Copy Number Variants-in praktijk Uitdaging: Het verschil tussen CNVs die wel of niet bijdragen tot de kliniek Publieke databanken CNVs van gezonde personen Databank van genomische varianten (DGV) 32 array CGH 22-5-2014 Array CGH in de kliniek Prenatale diagnose Indicaties/ Interpretatie Casuistiek Postnatale diagnose Indicaties Casuistiek Conclusie 33 array CGH 22-5-2014 Prenatale diagnose Verhoogd risico op chromosomale afwijking (leeftijd, abnormale niet invasieve screening) Verhoogd risico monogene aandoening Echografische afwijkingen Psychosociale redenen 34 array CGH 22-5-2014 Prenatale diagnose België sinds 2013: moleculair karyotype/ array CGH Nationale consensus Centra Medische Genetica België1: Pre en post counseling Interpretatie resultaten Protocoleren resultaten 1Implementation of genomic arrays in prenatal diagnosis: The Belgian approach to meet the challenges, Eur J Med Genet. 2014 Mar;57(4):151-156 35 array CGH 22-5-2014 Prenatale diagnose Benign Pathogeen “Unclassified” Toevallige bevinding Eur J Med Genet. 2014 Mar;57(4):151-156 36 array CGH 22-5-2014 Casus 24 weken Echografische afwijking: duodenale atresie 37 array CGH 22-5-2014 Casus 38 array CGH 22-5-2014 Casus 39 array CGH 22-5-2014 Casus Williams syndroom 40 array CGH 22-5-2014 Casus 25 weken Echografie: cerebellaire atrofie, gedilateerd pyelum, polyhydramnios, normale groei 41 array CGH 22-5-2014 Casus Trisomie 18/ Edwards syndroom Cave: geen laaggradige mozaïcisme! 42 array CGH 22-5-2014 Casus 20 weken Echografie: afwezigheid neusbeentje 43 array CGH 22-5-2014 Casus 2080,2kb duplicatie 1q21.1-q21.2, 33 genen, GJA5 gen 44 array CGH 22-5-2014 Casus 1q21 duplicatie risico factor Macrocefalie Aangeboren afwijkingen Ontwikkelingsstoornissen (autisme, leerstoornissen) Hartafwijkingen (VSD/ASD/PVS/ TOF,..) GJA5 gen 45 array CGH 22-5-2014 Casus 24 weken Echografie: cardiopathie 46 array CGH 22-5-2014 Casus 9,4MB duplicatie16p13.13p12.2 211 genen, 75 proteine coderende genen (NDE1, MYH11, ABCC1, ABCC6,...) 47 array CGH 22-5-2014 Casus 16 p13.11 duplicatie risico factor neurologische problemen (ADHD, autisme,…) Cardiovasculaire problemen (aorta dilatatie,bicuspide aortaklep) MYH11 gen Variabele penetrantie/ expressie Consortium: Ouders: overgëerfd Rapporteren Cardiopathie / grotere duplicatie (meer genen) 48 array CGH 22-5-2014 Casus Zwangerschap 16 weken Indicatie prenatale diagnose: post PGD voor metabole aandoening 49 array CGH 22-5-2014 Casus 339 kb duplicatie van chromosomenband 6q22.3, PLN gen PLN gen puntmutaties of deleties phospholamban associatie met cardiomyopathie duplicatie: slechts 1 casus doch associatie met cardiomyopathie Consortium: Ouders: overgeërfd rapporteren,opvolging mogelijk 50 array CGH 22-5-2014 Postnatale diagnosis Verstandelijke beperking, neuropsychiatrische aandoeningen dysmorfismen, aangeboren afwijkingen Ouders van individu met chromosomale afwijking Abnormaal karyotype verfijnen 51 array CGH 22-5-2014 Casus Jongen Pinealoblastoma 52 array CGH 22-5-2014 Casus Array CGH: 2,4 Mb deletie 22q11 geen deletie van tumorgen SMARCB1 Geen deletie van tumor gen INI1 ► 22q11 deletie syndroom (velocardiofaciaal syndroom), geen verklaring tumor 53 array CGH 22-5-2014 Casus Jongen Microftalmie en hypospadias 54 array CGH 22-5-2014 Casus 1.1 Mb deletion 2q23 ZEB2 gen De novo ZEB2 gen mutaties/ exon deleties/ Mowat Wilson syndroom 55 array CGH 22-5-2014 Casus Meisje, pasgeborene Epileptische encephalopathy 56 array CGH 22-5-2014 Casus Array CGH: 2235,9kb deletion 15q11.2 Overgeërfd van de moeder Risico factor postnataal! Neuropsychiatrische aandoeningen (epilepsie, autisme, gedrags en taalproblemen, verstandelijke beperking) 57 array CGH 22-5-2014 Casus Risico factor → Gekend deletie syndroom 58 array CGH 22-5-2014 Conclusie array CGH Genoomwijd onderzoek van hoge resolutie voor opsporing deleties/duplicaties specifieke postnatale indicaties alle invasieve prenatale diagnoses Cave Beperkte detectie mozaïcisme /geen detectie gebalanceerde afwijkingen Detectie afwijkingen van onduidelijke klinische relevantie 59 array CGH 22-5-2014 Conclusie array CGH Uitdaging Voor elke CNV de relatie tot fenotype bepalen Counseling 60 array CGH 22-5-2014 PGD for chromosomal abnormalities Catherine Staessen, PhD Centre of Medical Genetics The main causes of chromosomal anomalies Highgenetic risk Inheritance of the parental pathology - true inheritance: e.g.parental translocation PGD Low- genetic risk Meiotic nondisjunction 80-85% related to oocytes 10-15% related to spermatozoa Postzygotic mitotic non-disjunction 5-15% of cases of trisomies PGS *Hook EB. Cross PK. Schreinemachers DM. (1983) Mat Age Risk at birth 35 0.5% 38 0.98% 40 1.5% 45 4.8% Carriers of balanced structural chromosomal abnormalities Have a greater chance of being infertile, producing chromosomally abnormal offspring and having multiple spontaneous abortions Incidence 0.2% in neonatal population Higher incidence (Stern et al., 1999) Infertile couples (0.6%) RA couples (9.2%) ICSI population (2 - 3.2%) Analytical methods for chromosomal abnormalities (numerical – structural) FISH-based PGD protocols for chromosomal abnormalities Comparative genome hybridization (aCGH)based PGD for chromosomal abnormalities FISH:principle Multi - color FISH 1 → 3 consecutive FISH procedures Y FISH-based PGD protocols for structural chromosomal abnormalities: pre PGD work-up Determination of meiotic segregation for the specific structural abnormality Karyotype: confirmation chromosomal abnormality Design of probe mixture Lymphocyte FISH work-up: validation of the probe mixture Meiotic segregation reciprocal translocation Alternate: normal/balanced Adjacent 1 Adjacent 2 3:1 segregation 4:0 segregation With/without recombination Anaphase 2 non-disjunction Brandriff et al; AJHG, 38:197-208, 1986. Reciprocal translocation: probe design 46,XX,t(6;11)(q21.1;q22) CEP 6 SA Tel 6q SO CEP 11 SG Tel 11q SO Validation of the probe mixture: metaphase interphase CEP 6 Aqua Der 6 CEP 11 Green Der 11 Tel 11q Orange 6 11 Efficiency of probe mixture: at least 85% Carrier/partner PGD- FISH cycle: day 3 biopsy BIOPSY ROUND 1 ROUND 2 • Sex determination FISH PROCEDURE (x-linked disorder) • Chromosomal aberrations (numerical and structural) FIXATION • Aneuploidy screening PGD-FISH: reciprocal translocation CEP 6 aqua CEP 6 aqua CEP 11 green CEP 11 green Tel 11q orange Tel 11q orange Normal/balanced embryo Unbalanced embryo PGD Round 2 : 16 q11.2 Orange 22 q11.2 Green Round 1 : X p11.1-q11.1 Blue Y p11.1-q11.1 Gold 13 q14 Red 18 p11.1-q11.1 Aqua 21 q22.13-q22.2 Green The causes of misdiagnosis and adverse outcomes in PGD: data collection I - VIII 0.1% misdiagnosis rate Wilton et al., Hum. Reprod., 24(5), 1221-28, 2009 Misdiagnosis: possible reasons Technical: failure FISH signals, overlapping signals, splitted spots Human errors: inadequate probe design Biological: mosaicism Drawback of FISH - based PGD FISH technique related limitations Development of a patient specific protocol = time consuming Fixation of the cell: critical step (possible loss of micronuclei, chromosomes) Subjective analysis of the signals and compromised by weak, splitted or overlapping signals Only chromosomes involved in rearrangement are investigated Development of genome-wide techniques Comparative Genomic hybridization (a-CGH; micro-array) Comparative genome hybridization (aCGH)based PGD for chromosomal abnormalities Procedure: tubing & Whole Genome Amplification (WGA) Tubing of single cell (D3) or multiple cells (D5) WGA Amplification (SurePlex kit BlueGnome) Lysis of the cell(s) Extraction of the DNA Random fragmentation to form a library of DNA Amplification of DNA by PCR Electrophoresis (1.5% agarose) Electrophoresis gel picture after a successfully WGA experiment 1 2 3 4 5 6 7 8 9 Lines 1,2,3,5,6,7 = amplified DNA Line 4 = ladder Line 8 = negative control (PBS) Line 9 = positive control (genomic DNA) Array-CGH cytochip BlueGnome (~ 12-24h) 24 sure (1Mb) 24 sure + (0.5 - 0.25 Mb for telomeric regions) 24 sure cytochip bluegnome 13: 114 Mb; 14: 106 Mb 45,XY, der(13;14)(q10;q10) Result PGD FISH : XX Abnormal (1x LSI 13 Red, 3x LSI 14q32) carrier 46,XX,t(2;5)(p11;q34) PGD-FISH: dup(2)(ptel), del(5)(qtel) 3X tel2p 2X tel2q 88 Mb 2X 5p15.2 1X 5q35 24 sure + cytochip (bluegnome) 12,6 Mb CHR 2 47,XX, dup(2)(ptel-p11.2), del(5)(q34-qtel), +22 CHR 5 Result: succesful WGA – aCGH (D3) Total Number of cycles 24 Embryos biopsied 104 Succesful WGA 99 (95.2%) Result a-CGH 99 (100%) Preliminary: aCGH - genetic result Indication Translocations (8 cycles) PGD enumeration (8 cycles) PGS (8 cycles) Total (24 cycles) N embryos with diagnosis N normal 29 4 (13.8%) 38 2 (5.3%) 32 10 (31.3%) 99 16 (16.2%) Preliminary: aCGH - clinical outcome Indication Translocations (8 cycles) PGD enumeration (8 cycles) PGS (8 cycles) Total (24 cycles) N of ET 3 N of + HCG 2 +1 too early 2 2 5 2 10 6 (60%) Summary PGD a-CGH Total Cycles with pick-up 29 Cycles with biopsy 24 (82.8%) Age 37.6 5.2 COC 9.4 4.6 2PN Biopsied Result WGA Result a-CGH Normal Total N Abnormal 83 5.7 2.7 Detected FISH Not detected with FISH 64 19 104 (4.32.6) n ET 10 99 (95.2%) 99 16 (16.2%) N +HCG N +FHB Outcome Titel van de presentatie | pag. 25 (22.6%) 6 + 1 too early 4 1 delivered rest ongoing aCGH Reliability and feasibility demonstrated for detection of chromosomal imbalances in embryos (Gutiérrez- Mateo et al., 2011; Colls et al., 2012) In comparison with FISH: - Not dependent of critical step of cell fixation - Evaluating multiple loci along the length of each chromosome region - Data analysis performed by computerized analysis of signal intensities (based on a log2 ratio and quality criteria (SD, signal-to-noise ratio)) instead of subjective signal scoring In the future: automated workstations - increase of number of samples - reduces the risk of errors aCGH: Allows screening for all chromosomes in addition to the unbalanced derivatives associated with the specific structural abnormality No development of a patient specific ’probe-mixture’ and preclinical validation - Detection limits: the probability of detecting an unbalanced translocation , and therefore the success of the array-CGH based analysis, is dependent upon the location of the translocation breakpoints in the chromosomes and the size of the unbalanced region(s) Limitations: - aCGH cannot detect haploidy and some triploidies (69,XXX) - cannot differentiate normal versus balanced translocation carrier aCGH represents at this time an expensive option for embryo testing compared to the FISH technology PGD: multidisciplinary team work Center Medical Genetics Accurate genetic diagnosis Fertilisation in vitro Center Reproductive Medicine (IVF or ICSI) OPU – fertilisation in vitro Appropriate genetic counselling Genetic Diagnosis Embryo biopsy Transfer 2 unaffected embryos Preimplantation genetic diagnosis Martine De Rycke [email protected] Preimplantation Genetic Diagnosis an alternative to prenatal diagnosis and TOP involves genetic testing of cells biopsied from in vitro obtained oocytes and/or in vitro fertilised embryos and selective transfer of unaffected embryos for couples at high risk of transmitting a genetic condition to their children 2 titel 20-5-2014 Preimplantation Genetic Screening PGS or aneuploidy screening involves selection of euploid embryos to improve IVF results and reduce miscarriage rates for specific IVF patients groups at low risk (advanced maternal age, recurrent IVF failure or repeated miscarriages) 3 titel 20-5-2014 History of PGD • 1990: Handyside et al.: first PGD for X-linked disease • 1992: Handyside et al.: baby after PGD for Cystic Fibrosis Pregnancies from biopsied human preimplantation embryos sexed by Yspecific DNA amplification A. H. Handyside, E. H. Kontogianni, K. Hardy & R. M. L. Winston Institute of Obstetrics and Gynaecology, Royal Postgraduate Medical School, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK OVER 200 recessive X chromosome-linked diseases, typically affecting only hemizygous males, have been identified. In many of these, prenatal diagnosis is possible by chorion villus sampling (CVS) or amniocentesis, followed by cytogenetic, biochemical or molecular analysis of the cells recovered from the conceptus. In others, the only alternative is to determine the sex of the fetus. If the fetus is affected by the defect or is male, abortion can be offered. Diagnosis of genetic defects in preimplantation embryos would allow those unaffected to be identified and transferred to the uterus1. Here we report the first established pregnancies using this procedure, in two couples known to be at risk of transmitting adrenoleukodystrophy and Xlinked mental retardation. Two female embryos were transferred after in vitro fertilization (IVF), biopsy of a single cell at the six- to eight-cell stage, and sexing by DNA amplification of a Y chromosome-specific repeat sequence. Both women are confirmed as carrying normal female twins. 4 titel 20-5-2014 History of PGD at UZ Brussel 700 600 500 400 300 200 100 0 PGD-PCR 5 titel PGD-FISH PGD-AS 20-5-2014 PGD/PGS: indications for chromosomal aberrations (numerical and structural) PGD-FISH/aCGH sex determination (X-linked disorders) PGD-FISH/aCGH or PGD-PCR (mutation identified) for monogenic diseases (X-linked, autosomal dominant/recessive) and HLA typing PGD-PCR for aneuploidy screening PGS-aCGH 6 titel 20-5-2014 PGD clinical cycle 10 oocytes day 0 ICSI 8 normally fertilised oocytes day 1 6 embryos for biopsy day 3 genetic testing day 3/4 transfer day 5 no diagnosis unaffected affected affected unaffected transfer cryo, if good morphology unaffected bad morphology no transfer PGD clinical cycle amplification embryo biopsy with laser (day 3) FISH 8 titel 20-5-2014 Single cell amplification targeted (2 copies of the region of interest) => single cell multiplex PCR (monogenic diseases) * simultaneous amplification of multiple loci per cell = flanking Short Tandem Repeat markers +/- mutation locus * more accurate: allows diagnosis AND reveals contamination & ADO * fluorescent: allows fragment length detection via capillary electrophoresis on automated sequencers 9 requires extensive optimisation and validation of PCR conditions titel 20-5-2014 Single cell amplification request for mutation/gene/locus 1 => develop single cell PCR 1 request for mutation/gene/locus n => develop single cell PCR n customised protocols: optimisation and validation at the single cell level has to be repeated each time => pre-PGD workup is labour-intensive and time-consuming and yields high costs 10 titel 20-5-2014 Single cell amplification universal single cell Whole Genome Amplification several µg of DNA haplotyping: regular PCR of STR downstream analyses genome-wide tests optimisation and validation of single cell whole genome amplification (WGA): only 1 time! => pre-PGD workup labour, time and costs are reduced 11 titel 20-5-2014 PGD: emerging genetic tests single-cell WGA and SNP arrays - mutation analysis by haplotyping - full chromosomal constitution - Single Nucleotide Polymorphism single-cell WGA and NGS - reveal also point mutations balanced chrom. rearrangements - high cost, still under validation emerging platforms are genome-wide and allow standardisation and automation 12 titel 20-5-2014 SNP bead array preparation 13 titel 20-5-2014 SNP bead array: workflow MDA based 14 titel 20-5-2014 Whole genome amplification: MDA Multiple Displacement Amplification, (MDA) isothermal amplification (30°C) => DNA fragments up to 70 kb, low error rates Dean et al., 2002 15 titel 20-5-2014 SNP array: principle target denaturation and hybridisation on beadChip probe single base extension LaFramboise T , 2009 16 titel 20-5-2014 SNP bead array A = A/T base B = G/C base NC = no call 17 titel 20-5-2014 SNP array: interpretation genotype information 1) identify informative SNPs in region of interest 2) phase SNPs in embryo vs reference aff 18 titel wt aff aff unaff aff 20-5-2014 Genoom-wijde moleculaire technologie toegepast in de genetische diagnostiek Nieuw genomics platform op campus UZ Brussel / VUB 22/5/2014 Infrastructure + applications Ir Ben Caljon Available Sequencers VUB/UZ BRUSSEL CMG ULB Ion Torrent PGM MiSeq GS Junior HiSeq 1500 3 Nieuw genomics platform 22-05-2014 System Comparison Run mode Output range Run time Reads per flowcell Maximum read length Quality 1x400 bp Run mode Output range Run time Reads per flowcell Maximum read length Quality 2x50 bp Quality 2x75 bp Quality 2x100 bp Quality 2x125 bp Quality 2x150 bp Quality 2x250 bp Quality 2x300 bp 4 Roche GS Junior PicoTiterPlate 40 Mb 10h 100 thousand 400 bp (average) >99% > Q20 MiSeq Nano 500 Mb 4-39h 1 million 2x250 bp Ion Torrent PGM 314 chip 30-50 Mb 2,3h 400-550 thousand 1x200 bp (400 bp) Micro 1,2 Gb 4-24h 4 million 2x150 bp 316 chip 300-600 Mb 3,0h 2-3 million 1x200 bp (400 bp) Standard 15 Gb 4-65h 15-25 million 2x300 bp 318 chip 600 Mb-1 Gb 4,4h 4-4,5 million 1x200 bp (400 bp) HiSeq 1500 Rapid Run 5-90 Gb 7-40h 300 million 2x150 bp >85% > Q30 High Output v3 47-300 Gb 2-11 days 1,5 billion 2x100 bp >85% > Q30 High Output v4 64-500 Gb 1-6 days 2 billion 2x125 bp >85% > Q30 >80% > Q30 >80% > Q30 >80% > Q30 >80% > Q30 >85% >Q30 >80% > Q30 >75% > Q30 Nieuw genomics platform >80% > Q30 >75% > Q30 >75% > Q30 22-05-2014 IT infrastructure IT Infrastructure (UZ Brussel) 5 servers installed with Opensuse 12.2 (linux) 5 x (16cpu,192Gb Ram, 1.6 Tb HD) 40 Tb Shared Network drive (backuped) Sever capacity will be doubled in 2014 2x HP Z600 workstation 24 virtual cores (Intel Xeon E5645 2,4 GHz) 2x2Tb (RAID1) 24 Gb RAM 1x Opensuse 12.2 (linux) + 1x Win7 Grid management System: Open Grid Scheduler (ogs/sge) (IB)²: interuniversity bioinformatics unit Collaboration ULB/VUB/UZ Brussel 5 Nieuw genomics platform 22-05-2014 Applications (1) Whole genome sequencing (WGS) Shear DNA (get appropriately sized DNA fragments) Ligate adapters (modify DNA fragments to be compatible with sequencing instruments) Sequence (HiSeq for complex, MiSeq for small genomes) 6 Nieuw genomics platform 22-05-2014 Applications (2) Whole exome sequencing (WES) Shear DNA (get appropriately sized DNA fragments) Ligate adapters (modify DNA fragments to be compatible with sequencing instruments) Enrich targets (capture specific regions/exons with probes) Sequence (HiSeq for complex, MiSeq for small genomes) 7 Nieuw genomics platform 22-05-2014 Applications (3) Non-Invasive Prenatal Testing (NIPT) 1. Phlebotomy 5. Cluster generation 8 Nieuw genomics platform 2. Plasma isolation 6. Sequencing 3. cfDNA extraction 7. Data-analysis 4. Library preparation 8. Reporting 22-05-2014 Applications (4) Bisulphite sequencing Bisulphite treatment + PCR (convert unmethylated C to U) Ligate adapters (modify DNA fragments to be compatible with sequencing instruments) Sequence (HiSeq for complex, MiSeq for small genomes) 9 Nieuw genomics platform 22-05-2014 Applications (5) Mitochondrial resequencing Amplify mtDNA - lrPCR (select for mtDNA copies) Shear lrPCR product (get appropriately sized DNA fragments) Ligate adapters (modify DNA fragments to be compatible with sequencing instruments) Sequence (HiSeq for complex, MiSeq for small genomes) 10 Nieuw genomics platform 22-05-2014 Applications (6) 11 mRNA sequencing Nieuw genomics platform 22-05-2014 Future prospects 12 Small RNA sequencing (miRNA) ChIP sequencing rRNA typing (metagenomics) Molecular Inversion Probe (MIP) assays Nieuw genomics platform 22-05-2014 Questions? 13 Nieuw genomics platform 22-05-2014 Non-invasive prenatal testing 22/05/2014 Dr. Kim van Berkel Dep. Gynaecology– Centre for Medical Genetics Dr. Sci. Sonia Van Dooren – Centre for Medical Genetics What is NIPT ? 1. 2. 3. 4. 5. 6. 7. Definition Introduction NIPT technology Indications, contra-indications and limitations Practical Future Conclusions 2013 Definition NIPT = non-invasive prenatal test Prenatal screening for aneuploidy Risk calculation Introduction Screening for trisomy 21 Ultrasound PAPP-A/combination test (1T) Triple Test (2T) Invasive prenatal diagnosis Chorion villi sampling Amniotic fluid punction Screening for trisomy 21 Ultrasound 1st trimester: nuchal translucency (NT) ductus venosus (DV) tricuspidalis valve (TV) 2nd trimester: soft markers sensitivity max 70% Screening for trisomy 21 NT Screening for trisomy 21 DV Screening for trisomy 21 TV Screening for trisomy 21 PAPP-A/combination test 1st trimester US + biochemical markers in maternal bloed (ßhCG and PAPP-A) Screening for trisomy 21 PAPP-A/combination test 1st trimester echo + biochemical markers in maternal blood (ßhCG and PAPP-A) Combined risk calculation for Down Cutoff 1/250 Sensitivity 80-85% 5% false positive Screening for trisomy 21 TT AFP, ßhCG and oestriol Screenen naar trisomie 21 TT AFP, ßhCG and oestriol Second trimester soft-markers NF, ventriculomegaly Femur, humerus Echogene focus Dense intestines Pyelectasy SUA Screening for trisomy 21 Invasive screening for trisomy 21 Chorionic Villi Sampling (11-13w) Punction of amniotic fluid (>15w) Screening for trisomy 21 Conventional karyotyping Molecular karyotyping Screening for trisomy 21: non-invasive prenatal testing (NIPT) NIPT: cell-free fetal DNA (cffDNA) in maternal plasma shedding of trophoblast cells short half life (2 h clearance) 3% to 20% of total cfDNA reliable detection from 11-12 weeks on Overview NIPT technique 1. Phlebotomy 5. Cluster generation 18 2. Plasma isolation 6. Sequencing NIPT - Non-invasive prenatal testing 3. cfDNA extraction 4. Library preparation 7. Data-analysis 8. Reporting 20-5-2014 NIPT - sampling 19 NIPT - Non-invasive prenatal testing 20-5-2014 NIPT methodologies NIPT cfDNA based cfRNA based Clinical utility SNP based approaches Digital PCR t-MPS qPCR (targeted massive parallel Sequencing) s-MPS (shotgun massive parallel sequencing) (abs quant chr21 vs chr 1) (diff methylated regions) RNA expression (trophoblast vs maternal ) NIPT methodologies NIPT cfDNA based cfRNA based Clinical utility SNP based approaches Digital PCR t-MPS qPCR (targeted massive parallel Sequencing) s-MPS (shotgun massive parallel sequencing) (abs quant chr21 vs chr 1) (diff methylated regions) RNA expression (trophoblast vs maternal ) NIPT – Digital PCR (1) Lo YM, et al. Digital PCR for the molecular detection of fetal chromosomal aneuploidy. Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):13116-21. 22 NIPT - Non-invasive prenatal testing 20-5-2014 NIPT – Digital PCR (2) 23 NIPT - Non-invasive prenatal testing 20-5-2014 NIPT methodologies NIPT cfDNA based cfRNA based Clinical utility SNP based approaches Digital PCR t-MPS qPCR (targeted massive parallel Sequencing) s-MPS (shotgun massive parallel sequencing) (abs quant chr21 vs chr 1) (diff methylated regions) RNA expression (trophoblast vs maternal ) NIPT – DMR: MeDIP PCR or qMSP(1) L. Osherovich, Chromosome triple play, 25 NIPT - Non-invasive prenatal testing 20-5-2014 NIPT – DMR technology (2) Chromosome 21(MeDIP PCR) Papageorgiou et al. Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21. Nat Med. 2011 Apr;17(4):510-3. 26 NIPT - Non-invasive prenatal testing Chromosome 18 (qMSP) Lee et al. Non-Invasive Prenatal Testing of Trisomy 18 by an Epigenetic Marker in First Trimester Maternal Plasma. PLOSOne 2013 Nov; 8(11) 20-5-2014 NIPT methodologies NIPT cfDNA based cfRNA based Clinical utility SNP based approaches Digital PCR t-MPS qPCR (targeted massive parallel Sequencing) s-MPS (shotgun massive parallel sequencing) (abs quant chr21 vs chr 1) (diff methylated regions) RNA expression (trophoblast vs maternal ) NIPT – SNP based approaches 28 NIPT - Non-invasive prenatal testing 20-5-2014 NIPT methodologies NIPT cfDNA based cfRNA based Clinical utility SNP based approaches Digital PCR t-MPS qPCR (targeted massive parallel Sequencing) s-MPS (shotgun massive parallel sequencing) (abs quant chr21 vs chr 1) (diff methylated regions) RNA expression (trophoblast vs maternal ) NIPT – tMPS (1) Sparks AB, et al.. Noninvasive prenatal detection and selective analysis of cell-free DNA obtained from maternal blood: evaluation for trisomy 21 and trisomy 18. Am J Obstet Gynecol. 2012 Apr;206(4):319.e1-9. 30 NIPT - Non-invasive prenatal testing 20-5-2014 NIPT methodologies NIPT cfDNA based cfRNA based Clinical utility SNP based approaches Digital PCR t-MPS qPCR (targeted massive parallel Sequencing) s-MPS (shotgun massive parallel sequencing) (abs quant chr21 vs chr 1) (diff methylated regions) RNA expression (trophoblast vs maternal ) NIPT – sMPS technology 1. Library preparation 2. Cluster generation 3. Sequencing 32 NIPT - Non-invasive prenatal testing 20-5-2014 NIPT – sMPS data analysis Millions 4. Coverage: # of reads/sample 5. Aligning raw data 10 8 6 unmapped reads 4 6. GC correction NIPT23 NIPT21 NIPT19 NIPT17 NIPT15 NIPT13 NIPT11 NIPT9 NIPT7 NIPT5 NIPT3 0 NIPT1 2 mapped reads 7. Data normalisation 8. Counting statistics: Z-score calculation Binning Loess correction 33 # of data NIPT - Non-invasive prenatal testing 20-5-2014 Test performance - targeted NIPT Zimmermann B, et al.. Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci. Prenat Diagn. 2012 Dec;32(13):1233-41. 34 NIPT - Non-invasive prenatal testing 20-5-2014 Test performance - genome-wide NIPT Shaw SW, et al. From Down syndrome screening to noninvasive prenatal testing: 20 years' experience in Taiwan. Taiwan J Obstet Gynecol. 2013 Dec;52(4):470-4. 35 NIPT - Non-invasive prenatal testing 20-5-2014 Claimed accuracy per chromosome Shaw SW, et al. From Down syndrome screening to noninvasive prenatal testing: 20 years' experience in Taiwan. Taiwan J Obstet Gynecol. 2013 Dec;52(4):470-4. Devers PL, Cronister A, Ormond KE, Facio F, Brasington CK, Flodman P. Noninvasive prenatal testing/noninvasive prenatal diagnosis: the position of the National Society of Genetic Counselors. J Genet Couns. 2013 Jun;22(3):291-5 36 NIPT - Non-invasive prenatal testing 20-5-2014 False positive rates and predictive values Bianchi et al. DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med. 2014 Feb 27;370(9):799-808. Indications for NIPT Combination test with higher risk Previous pregnacy with trisomy 21 35 years or older Psycho social Other Contra-indications Dizygotic twin or multiple pregnancy Prior blood transfusion, stem cell therapy, immuno therapy, transplantation Chromosomal abberations Preferably combination test Limitations Mozaicism Small abberations of chromosome 21 Monogenic disorder Obesitas Ultrasound abnormalities Practical 1st trimester US 1112w abnormalities ao abnormalities Counseling options Option1: Option combination 2: NIPT test high risk low risk: US 20w Nl: US 20w higher risk Option3: PND CVS (11-13w) AF (>15w) Future Current reporting : trisomy 21, 18, 13, gender Future reporting: Other chromosomes Small chromosomal abberations Monogenic disorders? Reimbursment Future Conclusion NIPT is an intermediate screening test currently mainly for trisomy 21, 18 and 13 risk calculation: HIGH or EQUAL or LOW high sensitivity and specificity (false pos. rate 1%) Preferentially for high-risk pregnancies Confirmation of abnormal result by invasive test array CGH on chorion villi or amniotic fluid Evolution towards diagnostic test in the future Acknowledgements Medical genetics UZ Brussel Clinic Prof .Dr. Maryse Bonduelle Dr. Kim Van Berkel Dr. Martine Biervliet Dr. Dr. Dr. Dr. Sci. Sci. Sci. Sci. Sonia Van Dooren Catherine Staessen Ann Van de Bogaert Alexander Gheldof NGS platform BRIGHT Ir. Ben Caljon Dr. Sci. Didier Croes Clinic Lab Gynaecology Dr. Anniek Vorsselmans Dr. Kim Van Berkel Scientific partner Clinic Prof. Dr. Eric Legius Lab Dr. Sci. Joris Vermeesch Dr. Sci. Nathalie Brison MT GENOOM SEQUENCING ZOEKT DIAGNOSTISCHE BENCH mtDNA analyze Prof. Sara Seneca mt genoom zoekt diagnostische bench Mitochondriale genoom sekwensing Wat ? Waarom ? 2 mt genoom zoekt diagnostische bench 20/05/2014 overzicht Introductie mt aandoening mtDNA MPS Data analyse & resultaten platform 1 platform2 3 Conclusies mt genoom zoekt diagnostische bench 20/05/2014 mitochondriale aandoeningen 4 zeer heterogene groep aandoeningen multi-systeem ziekte waarbij vele weefsels en organen betrokken (kunnen) zijn incidentie 1/5000 geen genezing, noch therapie vage genotype-fenotype relatie diagnose is complex defect vd ademhalingsketen ( of OXPHOS systeem) mt genoom zoekt diagnostische bench 20/05/2014 illustratie klinisch beeld 5 mt genoom zoekt diagnostische bench 20/05/2014 OXPHOS system energie (ATP) genererend systeem, in mitochondria duale genetische controle voor structurele subeenheden + vele nucleair gecodeerde genproducten direct & indirect defecten van genproducten van OXPHOS systeem mt ziekte Schon 2013 6 mt genoom zoekt diagnostische bench 20/05/2014 mtDNA map 16, 5 kb (1) kleine circulaire dubbel strenige molecule 37 genen 13 protein 22 tRNA 2 rRNA 7 mt genoom zoekt diagnostische bench polymorf 20/05/2014 mtDNA map 16, 5 kb (2) maternele overerving polyploid homoplasmie heteroplasmie range 0-100% drempel effect afhankelijk mutatie afhankelijk weefsel/orgaan afhankelijk leeftijd drempel effect 8 mt genoom zoekt diagnostische bench 20/05/2014 diagnostiek mt aandoening diagnose studies patiënt anamnese klinische onderzoeken familie historiek microscopie, enzymologie, histologie, immunohistochemie, … stamboom genetische test mtDNA nucleair DNA verschillende weefsels (bloed, epitheelcel, fibro’s, spier, lever, …) 9 mt genoom zoekt diagnostische bench 20/05/2014 moleculaire diagnostiek (1) OXPHOS systeem duale genetische controle nucleair DNA mtDNA hier: focus op analyse mtDNA 10 mt genoom zoekt diagnostische bench 20/05/2014 moleculaire diagnostiek (2) mtDNA testing : stapsgewijs proces 11 frekwente punt mutaties PCR gebaseerde screeningstechniek Sanger sekwensing varianten kwantificatie van heteroplasmie deleties : Southern blot of LR-PCR mt genoom zoekt diagnostische bench 20/05/2014 moleculaire diagnostiek (3) hot spot regio’s en hot spot posities melas, merrf, narp, LHON, … verspreid over ganse genoom analyse van volledig mtDNA nodig 12 mt genoom zoekt diagnostische bench 20/05/2014 Massieve Parallel Sekwensing (MPS) 13 mt genoom zoekt diagnostische bench 20/05/2014 MPS van mtDNA 6/32 stalen 3 patiënten + 3 Cs 32 stalen : piloot studie 28 patiënten + 4 Cs LR-PCR library : 3 overlappende of 1 groot amplicon Ion Torrent PGM systeem pH verandering 14 mt genoom zoekt diagnostische bench Illumina MiSeq systeem fluorescentie 20/05/2014 Target enrichment aanrijking van mtDNA NUMTs proove geen amplificatie van nucleaire mt sekwenties ‘PCR based’ methodologie controle van de primerkoppels op amplificatie Long Range-PCR 3 amplicons 1 amplicon 15 mt genoom zoekt diagnostische bench 20/05/2014 Massieve Parallel Sekwensing bepaling van systeem’s detectie drempel onderscheid ts heteroplasmie en systeemfout pUC19 plasmide DNA sekwentie Ion Torrent PGM : ± 0.8% drempel ≥ 5% veelvuldige homopolymeer fouten (gekend probleem) drempel ≥ 5% MiSeq drempel : ± 0.5% drempel ≥ 2 % 16 mt genoom zoekt diagnostische bench 20/05/2014 pUC19 analyse bepaling van detectie drempel systeem foutenmarge : ratio van # niet referentie basen met totaal # basen op eenzelfde specifieke positie wordt bepaald voor elke positie in genoom gemid. systeem fout wordt berekend 17 mt genoom zoekt diagnostische bench 20/05/2014 Massieve Parallel Sekwensing bepaling van systeem’s detectie drempel onderscheid ts heteroplasmie en systeemfout pUC19 plasmide DNA sekwentie Ion Torrent PGM : ± 0.8% drempel ≥ 2% veelvuldige homopolymeer fouten (gekend probleem) drempel ≥ 5% MiSeq drempel : ± 0.5% drempel ≥ 2 % 18 mt genoom zoekt diagnostische bench 20/05/2014 Massieve parallel sekwensing data analyse Ion Torrent PGM versus MiSeq fastq Torrent suite v3.6 VCFfile in-house pipeline (BWA; GATK;…) coverage analysis (samtools) VCFfile Annovar Mitomap rapport varianten + coverage 19 mt genoom zoekt diagnostische bench 20/05/2014 Begrip ‘coverage’ Integrative Genomics Viewer (IGV) beeld 20 mt genoom zoekt diagnostische bench 20/05/2014 MPS resultaten ‘non-deleted’ template ‘single large scale’ deleties 21 mt genoom zoekt diagnostische bench ‘multiple’ deleties 20/05/2014 Coverage profiel (1) relative coverage 3,5 3 2,5 2 1,5 + 1 - 0,5 1 189 377 565 753 941 1129 1317 1505 1693 1881 2069 2257 2445 2633 2821 0 mtDNA position biased 22 mt genoom zoekt diagnostische bench 20/05/2014 Coverage profiel (2) onafhankelijk vh DNA staal onafhankelijk vd primerset in LR-PCR onafhankelijk vd shearing methodologie ook zonder 1ste PCR amplificatie lacZα amp pUC19 ori 23 mt genoom zoekt diagnostische bench 20/05/2014 Coverage profiel (3) Ion Torrent PGM 24 mt genoom zoekt diagnostische bench MiSeq systeem 20/05/2014 Variant calling – stap 1 - deleties ‘non-deleted’ template ‘single large scale’ deleties 25 mt genoom zoekt diagnostische bench ‘multiple’ deleties 20/05/2014 Variant calling – stap 2 - varianten 26 VCF annotatie van varianten mt genoom zoekt diagnostische bench 20/05/2014 Variant calling – stap 3 – Q_filtering detectie limiet Ion Torent PGM : < 5% MiSeq : < 2% 27 mt genoom zoekt diagnostische bench 20/05/2014 Variant calling – stap 3 – Q_filtering detectie limiet Ion Torent PGM : < 5% MiSeq : < 2% 28 QC : heteroplasmie vs gemiddelde systeem fout vgl. mtDNA MPS data set mt genoom zoekt diagnostische bench 20/05/2014 resultaten van de piloot studie Ion Torrent MiSeq 29 mt genoom zoekt diagnostische bench 20/05/2014 Variant calling (1) Sanger sekwensing 34 vals negatieven 30 mt genoom zoekt diagnostische bench MPS sekwensing 828 12 < detectie limiet Sanger sekwensing 20/05/2014 Variant calling (2) Sanger versus Ion Torrent PGM sekwensing piloot studie van 32 DNA stalen # varianten Sanger Ion Torrent PGM 862 828 vals negatieven 34 extra 12 variant m.302-316 31 mt genoom zoekt diagnostische bench # stalen 30 m.16183A>C 3 m.7402delC 1 20/05/2014 Variant calling (3) Sanger sekwensing vs Ion Torrent sekwensing vs MiSeq piloot studie van 6 DNA stalen Sanger sekwensing Ion Torrent PGM MiSeq 214 208 214 vals negatieven 7 0 extra 4 6 # varianten variant 32 mt genoom zoekt diagnostische bench AF m.5609T>C 4.5% m.8207C>T 2% 20/05/2014 Conclusies (1) complete re-sequencing van 28 patiënten stalen nieuwe (pathogene) varianten variant gen weefsel % heteroplasmie m.14721G>A MT-TE spier 48% m.7402delC MT-COI p.(Pro500Hisfs*12) spier 80% m.15453T>C MT-CYB p.(Leu236Pro) bloed 100% 33 mt genoom zoekt diagnostische bench 20/05/2014 Conclusies (2) Sanger stalen/run 1 MiSeq tot 12 tot 145 problematisch uitstekend neen +* +* +** AF>15-20% + AF>5% + AF>2% neen problematisch - coverage deleties punt mutaties Ion Torrent homopolymeren * met bepaling van breekpunten ** 2de techniek nodig voor kwantificatie 34 mt genoom zoekt diagnostische bench 20/05/2014 Met dank aan alle medewerkers REGE VUB CMG UZ Brussel 35 mt genoom zoekt diagnostische bench 20/05/2014 Challenges in cardiogenetics research, diagnostics and prevention Sonia Van Dooren Marije Meuwissen Inherited cardiac arrhythmias LQT SQT Cardiac arrhythmia Primary cardiac arrhythmia BrS electrical disease no structural abnormalities ARVD CPVT Secondary cardiac arrhythmia cardiomyopathy structural abnormalities HCM DCM Brugada syndrome (BrS) Incidence: Lo et al. 2004 0.05 to 0.6 % in adults 0.0006 % in children Congenital primary cardiac arrhythmia autosomal dominant incomplete penetrance & variable expression WF WG 2012 : BrS cardi omic s rese arch 3 20-5-2014 BrS - clinical diagnosis ECG morphology Symptoms: WF WG 2012 :BrS cardi omic s rese arch spontaneous – drug-induced (ajmaline) type: saddle back - coved syncopes palpitations ventricular arrhythmias sudden cardiac death Family history EPS: electrophysiology studies Mizusawa Y , and Wilde A A Circ Arrhythm Electrophysiol 2012;5:606616 20-5-2014 Molecular basis of BrS BrS = Channelopathy Purely electrophysical disease No structural problems Altered function of ion channels in the heart To date NaCN, CaCN & KCN Accessory proteins Imbalance between inward and outward ion currents Rev Esp Cardiol. 2010 May;63(5):620 BrS etiopathogenisis Basic arrhythmogenic mechanisms Principle arrhythmogenic site: RVOT Hypotheses: depolarization hypothesis: slow conduction repolarization hypothesis developmental abnormalities in cardiac neural crest embryonic cells in heart development BrS – genetic diagnosis type gene reference Sodium channel α-subunit SCN5A MAJOR gene Kapplinger, 2010 (compendium) Sodium channel β-subunits SCN1B Watanabe, 2008 SCN3B Hu, 2009 KCND3 Giudicessi, 2011 KCNH2 Verkerk, 2005 KCNE3 Delpón, 2008 KCNE5 Ohno, 2011 KCNJ8 Medeiros-Domingo, 2010 Pacemaker channel HCN4 Ueda, 2009 L-type calcium channels CACNA1C Antzelevitch, 2007 CACNB2B Antzelevitch, 2007 CACNA2D1 Burashnikov, 2010 GPD1-L London, 2007 MOG1 Kattygnarath, 2011 SLMAP Ishikawa, 2012 TRPM4 Liu, 2013 Potassium channels Sodium channel trafficking Diagnostic yield up to 30% +10% 60% remains genetically undiagnosed CMG / UZBrussel experience Clinical diagnostics @ HRMC 400 BrS families 45 new families/year 150 family screenings/year Genetic diagnostics @ CMG SCN5A: ~165 probands SCN1B-4B: ~83 probands targeted resequencing: gene panels whole exome sequencing SCN5A genetic diagnosis & ECG BrS probands ECG SCN5A variant association BrS: 8 (27,6%) 122 BL type 1: 29 (23,8%) +: 10 (34,5%) BL type 2: 27 (22,1%) +: 4 (14,8%) Likely pathogenic: 2 (6,9%) BrS: 2 (7,4%) Disease ass SNP: 2 (7,4%) BrS: 6 (9,1%) Ajm +: 66 (54,1%) +: 9 (7,4%) Arrhythmia: 1 (1,5%) Likely pathogenic: 2 (3,0%) Baseline (BL) type 1: diagnostic yield ~ literature Baseline (BL) type 2 and ajm +: added value Revision of ECGs ECG Baseline ECG after Ajmaline testing proband: BrS + Ajm + ST segment elevation > 2mm family member: conduction abnormality Ajm doubtfull ST segment elevation < 2mm family member: BrS - ? Ajm - widening of QRS complex SCN5A segregation analysis SCN5A+ probands 24 SCN5A+ families 18 14 mutations Segregation 4 variants 12 BrS 2 arrhythmia 4 novel 8 complete 44% 0 complete 1 complete 6% 4 major 22% 2 half 11% 3 incomplete 17% Incomplete segregation of SCN5A mutations and variants Is the identified mutant/variant the MAJOR causal one? Incomplete penetrance and variable expression Recent technological progress Single gene analysis GWAS Sanger sequencing SNP array (Genome-wide association study) Reference: Bezzina et al. 2013 – Nature Genetics NGS (Next Generation Sequencing) Gene panels/whole exome/whole genome NGS approach SCN5A ‘Single gene’ (all exons of a gene) 16 BrS genes ‘Gene panel’ (all exons of a package of genes) all genes ‘Exome’ (all exons of a genome) ± 1 % of the whole human genome ‘All’ coding sequences of a human genome (>180,000 exons), sequenced and analyzed in one experiment Reference: Clark et al. 2011 – Nature Biotechnology - Performance comparison of exome DNA sequencing technologies Genome-wide technologies: impact on BrS ? In general: rare disease diagnostics exome sequencing resolution of cases : ~5% 25% Heterogeneous genetic disorders: more complex Effect on BrS diagnostic yield? Cardiac arrhythmias: next generation sequencing WHOLE EXOME SEQUENCING TARGETED EXON RESEQUENCING 16 BrS + / SCN5A - patients (8 families) Gene panel for primary arrhythmias ( ± 70 genes) Gene panel for structural cardiopathies (± 70 genes) 2 novel variant in known BrS genes 2 novel candidate genes 4 genetically ‘unresolved’ families Functional investigations 15 patients with structural cardiopathies Sequencing extra clinically + or – family members 4 known confirmed variants Validated by Sanger 6 novel variants + genetic diagnosis ? OR functional studies required? Brugada syndrome: Family 1 child wish Known pathogenic SCN5A mutation Complete segregation with phenotype Brugada syndrome: Family 2 SCN5A variant Incomplete segregation Gene panel in progress ? kinderwen s Brugada syndrome: Family 3 SCN5A no mutation Exome sequencing: mutation in candidate gene Complete segregation with phenotype Challenges in cardiogenetics diagnostics Power of Ajmaline testing in clinical diagnosis of BrS Helpful in genetic diagnosis Discordancies Diagnostic criteria too strict? Genotype-phenotype revision needed? Appropriate patient selection for NGS Incomplete segregation Incomplete penetrance and variable expression Every novel and validated variant functional studies? Brugada syndrome monogenic oligogenic polygenic Impact on BrS cardiogenetics prevention Prenatal diagnosis Pre-implantation genetic diagnosis 20 years of experience ~ 500 PGD cycles/year >1600 PGD children born gene # requests # work-ups # cycles for couples (total # of cycles) # pregnancies MYBPC3 6 5 3 (4) 1 MYH7 6 5 3 (5) - TNNT2 1 1 1 1 KCNQ1 6 6 3 (5) 3 SCN5A 5 5 1 BrS (2) 2 BrS + Steinert (10) 1 BrS+ Bartter: (4) 2 1 Cardiomyopathies Primary arrhythmias !!! caution !!! : monogenic ? oligogenic ? complex ? Conclusions In order to improve cardiogenetics prevention invest in genome-wide BrS genetic research & diagnostics Given oligogenic to complex nature large amounts of genome-wide data required extra 5 to 10 to … years of further scientific cardiogenetic progress are needed to resolve questions & current challenges Brugada team + acknowledgements Medical genetics UZ Brussel Clinic Prof .Dr. Maryse Bonduelle Dr. Marije Meuwissen Staff Prof. Dr. Pedro Brugada Prof. Dr. Carlo De Asmundis Dr. Sophie Van Malderen Lab Cardiology UZ Brussel Sonia Van Dooren, Dr Sci Dorien Daneels Uschi Peeters NGS platform BRIGHT Ben Caljon Didier Croes Research nurse Gudrun Pappaert Research partner Prof. Dr. Ramon Brugada Funding Wetenschappelijk fonds Willy Gepts 2010/2012 WOK Prof. P. Brugada Basis financing RGRG cluster IB² (Interuniversity Brussels Bioinformatics Institute) Innoviris (BridgeIris)