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27 Octubre 2014. Presentación de Pablo Lapunzina, Director del Instituto de Medicina Genética Médica y Molecular (INGEMM), de IDIPAZ y de CEBERER, en la "Jornada Avances en Genética y Tecnología Social. La experiencia de la Fundación Síndrome de Dravet ".
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Avances en Genética. Utilidad de la NGS (Next Generation Sequencing) y la Bioinformática. El ejemplo del S. de Dravet.
Pablo Lapunzina, M.D., Ph.D
On behalf of the Dravet Syndrome Genetic Testing Group and the UBEG group.
Bilbao27 de Octubre, 2014
General concepts of epilepsy
Epilepsy is a common neurological condition defined by recurrent, unprovoked seizures that affects 1% of the population, including 1/200 children
Epilepsy risk: 1% on general population 8-12% on first-degree relatives
Clinical classification of epilepsy: Symptomatic Presumed symptomatic Idiopathic
Epilepsy genetics Mendelian genetics: autosomal dominant inheritance Genes encoding ion channels and neurotransmitter receptors
Complex disease with strong genetic component
General concepts of epilepsy
Poduri, A., et al., Curr. Op. Genet & Dev., 2011
Known genes involved in epilepsy syndromes
Incidence of 1/20,000 births, approximately Rare congenital disease Genetic epilepsy: Autosomal dominant or de novo 25% with familial history of epilepsy or febrile seizures 1st seizure <1y
Fever sensitivity Afebrile seizures
Type of seizures: Generalized/partial Tonic/Clonic Myoclonic
Status epilepticus Intellectual disability, autism, sleep disturbancies Atypical absences, ataxia, SUDEP
Dravet Syndrome clinical features
No known treatment nor cure
Early diagnosis is required
Personalized treatment and prognosis
Clinical diagnosis
Medical history of seizures Seizure type Age of onset
EEG, CT, …
Genetic Diagnosis
Familial history Genotype - Phenotype
+
Genetic diagnosis in DS (I)
Identification of the molecular cause of DS
Genetic counseling
Prenatal diagnosis
Accurate and personalized treatment
Confirmation of clinical diagnosis
Genetic diagnosis in DS (II)
DS is a genetic febrile epilepsy
FS: febrile seizures FS+: febrile seizures plus GEFS+: generalized
epilepsy with febrile seizures plus
SIMFE: severe infantil multifocal epilepsy
SMEB: severe myoclonic epilepsy of infancy borderland
EMRF: epilepsy with mental retardation limited to female
ICE-GTC: intractable childhood epilepsy with generalized tonic clonic seazures
SMEI/DS: severe myoclonic epilepsy of infancy www.ice-epilepsy.org
Genes involved on DS 80% of DS patients have mutations on known genes:
SCN1A, PCDH19, GABRG2, SCN2A y SCN1B SCN8A and SCN9A as modifier genes
20% of DS patients with unknown genetic defect
Depienne, C., et al., J Med. Genet., 2009
Sodium channel (I)
333 DS patients
DS patients with family history of epilepsy: 25% with family history of epilepsy, but 90% with “de novo”
mutations
DS patients within GEFS+ families
DS patients with inherited mutation from asymptomatic or with mild pathological phenotypic parents
Mosaicism: May explain a parental clinical history of seizures
Percentage of mosaicism detected in lymphocytes is not correlated to other tissues
May evaluate recurrence risk
Genetic compensation: Protective changes in one ion channel may compensate the damage
in another ion channel
Modifier genes
Other genomic regions that regulate gene expression
DS is genetically heterogeneous
DS Genetic Test of DSF-INGEMM
Free DS genetic test
Patient has to follow the clinical criteria of DSF
Genetic report of SCN1A in ~80 days
Genetic test of other DS genes when SCN1A screening is negative
Extension to other genes related to genetic epilepsies and phenotype modifier genes in the next future
Prenatal screening and genetic testing of relatives
Application of the new high-throughput genomic technology
OBJECTIVE: 100% of DS patients with genetic diagnosis
DS Genetic Test procedure (I)
Document 1Patient Clinical Info
Document 1Patient Clinical Info
Document 2Informed Consent
Document 2Informed Consent
OK
NeuropediatricianNeuropediatrician
Download documents
www.dravetfoundation.eu
Dra. Eva BarrosoBloque Quirúrgico, pl-2Hospital Universitario La PazPº La Castellana, 26128046 MADRID
Date the patient
Date the patient
Blood or gDNA
[email protected]@dravetfoundation.eu
Fill out data and wait for acceptance
Original signed
Fill out and signed
Genetic report
Genetic report
Results
gDNA amplification: PCR
PCR: Polymerase Chain Reaction
Oligonucleotide designed in intronic regions
Oligonucleotides bind specifically to selected regions of genome to the double chain of gDNA
Exponential and specific amplification
Direct sequencing
Sanger sequencing:
dNTPs + ddNTPs labeled with fluorochromes
Capillary electrophoresis + fluorescence detectorp.L1670fsX9
p.A486G
In silico functional analysis by bioinformatic tools
Mutation tasting: http://www.mutationtaster.org/ Polyphen2: http://genetics.bwh.harvard.edu/pph2/ SNP&GO:
http://snps-and-go.biocomp.unibo.it/snps-and-go/ PANTHER: http://www.pantherdb.org/ MUpro: http://mupro.proteomics.ics.uci.edu/ SIFT Human Coding SNPs:
http://sift.jcvi.org/www/SIFT_chr_coords_submit.html Exome Variant Server:
http://evs.gs.washington.edu/EVS/ Human Splicing Finder: http://www.umd.be/HSF/
Array-CGH (Comparative Genomic Hybridization): Complex genomic rearrangements analysis Roche-Nimblegen or Agilent aCGH platforms Genetic Epilepsy Panel of ~300 genes
High-throughput genomic analysis (II)
Solicitud de asistenciaRecepción del volante
Admisión
Consulta Clínica
Evaluación de resultados
Emisión del informe
Asesoramiento Genético
Estudios de ultrasecuenciación (NGS)
Inversión del proceso
Estudio citogenético
Microarrays CGH
Microarrays CGH
Estudio citogenético
Estudios moleculares específicos
The “Genetic” approachStudying “all at the same time”
Before Now
Gene by gene NGS (exomeapproach sq or panels)
NGS (Next-Generation Sequencing): High-throughput genomic sequencing
Complete sequencing of genome Exome sequencing Sequencing of specific regions accordingly a
pre-designed panel Three different NGS platforms on testing DS Panel Genetic Epilepsy Panel of ~300 genes
Roche Illumina Ion Torrent
High-throughput genomic analysis (I)
NGS
Hospital Universitario La Paz
GENOMICS GENETICS EPIGENETICS
All genetic/genomic or epigenetic diseases with knowncause: ~ # 5000 disorders
8-12% 82-87% 2-3%
5 Kb- ? Mb 1 bp- 200 bp No dosage changes
Unknown or No- responsible genes
Distribution of Human Genetic Diseases
The “Genetic Pool”
~ 24,000 MIM genes
100% Genetics
100% Genomics
100% Epigenetics
50% Genetics + 50% Genomics
50% Genetics + 50% Unknown
known gene but not linked to any disorder
The “Genetic Pool”
Genomas, Exomas y Paneles
100 %
1-2 %0,05 %
3,000 Millones de pares de bases
25
2010: 5K$, 10 days2009: Illumina,
Helicos40-50K$
Sequencing the Human Genome
Year
Log10(price)
201020052000
10
8
6
4
22014: 1000$, 36 hrs- Illumina
2008: ABI SOLiD60K$, 2 weeks
2007: 4541M$, 3 months
2001: Celera100M$, 3 years
2001: Human Genome Project2.7G$, 11 years
2015
Capillary Sequencing (Sanger) vs Next Generation Sequencing (NGS)
Before Now
Aproximately 300 bp/analysis (exons)
Aproximately 75-400 bp per read x millons of reads in one assay.
Antes Ahora
1 Km (1 exon ),conocemos el gen~ 300 coches/Km. Queremos verCual es el coche estropeado.
180,000 Km (exones), varios carriles por Km,No sabemos en que carretera (gen) ni donde está el coche defectuoso. Tenemos muchos coches que parecen defectuosos, pero en realidad NO lo están.
Capillary Sequencing (Sanger) vs Next Generation Sequencing (NGS)
El Proceso Actual Antes Ahora
- Extracción de ADN en cada Lab - Extracción de ADN centralizada
- Amplificación x PCR amplification - NGS experiments (panels or exomes)
- Screening de amplicones - Análisis de Bioinformática Ej..(HRM, etc) o Sanger Seq
- Send to “experts” in the field- Análisis y reporte
- Análisis, validación y reporte.
PlatformsIllumina HiSeq X Ten and NextSeq 500
Ion Proton
El Proceso de Dx Genético
Bioinformática- La UBEG
NGS (Next Generation Sequencing)
www.dravetfoundation.eu/bbdd-mutaciones-geneticas.
Interfaz de inicio
*Mutation_ID
*ID
*Gene
*Variant Pathogenicity
*Exon
*cDNA change
*Protein change
Chr coordinate change (hg19)
dbSNP
ClinVar
*Type of variant
*Mutation effect
*Protein domain affected
*RNA change
Reference
Template
Technique
Lista de variables– Descripción de la mutación
Lista de variables – Descripción del fenotipo clínicoClinical phenotype description Answer
General features
Seizure onset (y) Number
*Patient Phenotype/Epilepsy Classification Description
Seizure type
Generalized tonic clonic seizure Y/N/DK
Myoclonic seizure Y/N/DK
Atypical absence Y/N/DK
Partial seizure Y/N/DK
Hemiconvulsion Y/N/DK
Secondary generalization Y/N/DK
Status epilepticus (N)Y/N/DK (Number)
Number of seizures Number
Seizures provoked Y/N/DK
Afebrile seizures Y/N/DK
Photosensitivity Y/N/DKOther stimulus (e.g. vaccination, heat bath, excitation, period) Description
Neurological abnormalities
Mental retardation Y/N/DK
Motor delay Y/N/DK
Ataxia Y/N/DK
Autism Y/N/DK
Sleep disturbancies Y/N/DK
Others Description
IQ NumberComplementary diagnosis tests
Neurophysiology EEG Description
Neuroimage MRI CT Scan Description
Hattori score Number
Genetic inheritance
*Inheritance Type if known
Family history DescriptionTreatment Current treatment DescriptionEthnic origin Ethnic origin DescriptionRemarks/Other comments Remarks/Other comments Description
Paneles de genes personalizados para epilepsias genéticas.
Exomas (23,000 genes) para investigación.
Aproximación diagnóstica actual
Genes MIM en un solo tubo
• (Casi) todos los genes de relevancia clínica
• Sólo un estudio para todos los genes juntos (más de 300).
• Tiempo de respuesta (aproximadamente 2-3 meses)
Para Encefalopatías epilépticas:
Genes implicados en Epilepsias
La vida en Blanco y Negro de la Genética
La vida en Colores de la Genética
¿Hacia donde vamos?
5 Kb- ? Mb 1 bp- 200 bp No dosage changes
GENOMICS
CGH-arraySNP-aray
KaryotypeFISH
GENETICS
NGS panel screening
Exome seq
Sanger Seq
Exome Seq
EPIGENETICS
MS-arrays
Meth- PCR confirmations
FirstStep
Further
Agradecimientos
Todos los integrantesde la Fund. S. de Dravet
BBK-KutxaBank
Microsoft & Microsoft Azure
INGEMM
H o s p i t a l U n i v e r s i t a r i o L a P a z INGEMM – Instituto de Genética Médica y Molecular
Instituto de Genética Médica y Molecular