Genética autismo

Causas y Avances Geneacuteticos en los Trastornos del Espectro Autista

Angel Carracedo Fundacioacuten Puacuteblica Galega de Medicina Xenoacutemica- SERGAS

CEGEN-Universidade de Santiago de Compostela

Bata Vilargaciacutea 2013

iquestQueacute es la Geneacutetica y el Genoma y como estaacuten organizados nuestros genes iquestCuaacuteles son las bases geneacuteticas de los TEA y por queacute es importante entenderlas

El genoma es

bull El conjunto completo de genes de un organismo donde se guarda toda la informacioacuten genetica

3200000000 de pares de

bases (A T C G)

GENOMA HUMANO


bases (A T C G)

Alrededor de 25000

genes

ATACCTGCGTCGGATGCTGCGATTGCTGACCAACATCGTGACAGTTAGACAAACGATTGACTGTTAGGATTGACCACCAATTACGATGACGTTGGhellip

Frederik Sanger

ATCGGCTAGCTGATCGACGATGACCGTAGCGTTGATCGGTAGGCTAGCTGAAACTTAACGGA

ATCTACGGATGGCTGACTGATG



GATA GATA GATA GATA GATA GATA GATA GATA

ATTACTGATCGGTAGCTGAGCCAATGGCAGTGATGGATGGTAGCTGAGTGCTGGACAT

Minisatellites

SNPs

MUTACIONES

CON ESE SOL HAY MAS LUZ

CON ESA SAL HAY MAS LUZ

ONE SES OLH AYM ASL UZ

CNVs- Duplication deletions (15-20)

CNV fragmento de ADN de tamantildeo ge 1 kb y que estaacute presente en nuacutemero de copia variable en relacioacuten a un genoma de referencia

PEacuteRDIDAS (deleciones hemicigotas y genotipos nulos o deleciones homocigotas) GANANCIAS (inserciones duplicaciones y amplificaciones)

Delecioacuten homocigota CN 0

Delecioacuten hemicigota CN 1

Normal CN 2

Copy neutral LOH UPD CN 2

Amplificacioacuten CN 6

El teacutermino CNV no implica datos de frecuencia CNV polimoacuterfica polimorfismo de nuacutemero de copia o CNP si gt 1 CNV rara si lt 1 La mayor parte de los CNVs no tienen implicacioacuten en las patologiacuteas y son solo variacioacuten normal pero perdidas o ganancias de copias pueden ser causa de enfermedad Base de datos de variantes genoacutemicas Data Base of Genomic Variants httpprojectstcagcavariation

Deteccioacuten y caracterizacioacuten de CNVs mediante arrays de SNPs

TEA SINDROacuteMICOS TEA NO SINDROacuteMICOS

Complex (~70)

Chromosomal abnormalities (~5)

Single gene disorders (~5-7)

CNVs Duplication Deletions 20

Currently a genetic cause can be identified in 20-25 of children with autism

Specific teratogenic exposures (~2)

Rubella Cytomegalovirus Alcohol Valproic acid Thalidomide Misoprostol

FISH Hibridacioacuten fluorescente in situ

Cromosopatiacuteas y defectos

estructurales

Arrays de CGH (Hibridacioacuten

genoacutemica comparada)

Microarrays de SNPs y sondas para

CNVs

Cariotipo

PCR

bull Chromosomal Disorders (5) Trisomy 21 Children with Down syndrome have autism more commonly than expected The incidence was at least 7 in one study [Kent et al 1999] 45X Turner syndrome 45X46XY mosaicism 47XYY del7q del22q112 Del22q133 del2q37 del18q delXp223

Williams Deletion Region

New findings about Williams syndrome may

shine light on autism research

Journal of Neuroscience 2010

Maternally derived duplication of the Prader-WilliAngelman syndrome critical region (15q11-q13) is the most commonly observed chromosome abnormality in autism detected in 1-3 of children with autism Most commonly this duplication is the result of a de novo supernumerary isodicentric 15q chromosome and less commonly the result of segregation of a parental chromosome translocation or a maternally derived interstitial 15q duplication

Single gene disorders (5) Fragile X syndrome Whereas 1 to 3 of children ascertained on the basis of an autism diagnosis have fragile X syndrome at least half the children with fragile X syndrome have some autistic behaviors

Single Genetic Disorders (molecular) PTEN germiline mutations Rett syndrome Smith-Lemli-Opitz syndrome Smith-Magenis syndrome Tuberous Sclerosis CHARGE syndrome Sotos syndrome Hypomelanosis of Ito San Filippo syndrome Cornelia de Lange syndrome Williams syndrome Timothy syndrome Joubert syndrome NF1 WAGR Duchenne muscular dystrophy

bull Disorders of purine metabolism bull Disorders of pyrimidine metabolism bull Unknown sulfation defect bull Disorders of GABA metabolism bull Disorders of creatine metabolism

mtDNA


A large-scale survey of the novel 15q24 microdeletion syndrome in autism spectrum disorders identifies an atypical deletion that narrows the critical region McInnes et al Molecular Autism 2010 15 doi1011862040-2392-1-5

16p112 deletion is characterized by developmental delay intellectual disability andor autism spectrum disorder (ASD) Developmental delays are more related to diminished language and cognitive function than motor disability Weiss et al [2008] reported 16p112 deletions or duplications in approximately 1 of individuals with autism and 15 of children with developmental or language delays

Mefford HC et al N Engl J Med 2012366733-743

Affymetrix CytoScan HD Array

Affymetrix CytoScan HD Array SOFTWARE Y VISUALIZACION

DISCAPACIDAD INTELECTUAL SEVERA TEA EJEMPLO DE DI DE HERENCIA LIGADA AL X (MRX60 MIM 300486) AFECTO 8E011 (varoacuten) MADRE 1H240 NO PORTADORA

AFECTO delecioacuten en cromosoma X (varoacuten) Madre SANA no portadora de la delecioacuten DELECIOacuteN de novo en Xq12 afectando a gen OPHN1 (gen que codifica la proteiacutena activadora de GTPasa Rho cuya LOF estaacute asociada con DI ligada al X (Kasri et al 2009))


DISCAPACIDAD INTELECTUAL SEVERA TEA EJEMPLO DE TEA SINDROacuteMICO SINDROME DE WOLF-HIRSCHHORN (MIM 194190) Nombres alternativos Siacutendrome de la delecioacuten 4p163 Siacutendrome de PITT-ROGERS-DANKS PRDS Siacutendrome de PITT

FAMILIA 8B710 y 9H424

AFECTO delecioacuten en hemicigosis Madre SANA no portadora de la delecioacuten DELECIOacuteN en 4p163 afectando a muacuteltiples genes

The empiric aggregate risk to sibs of individuals with autism of unknown cause

varies across studies but is generally considered to range from 5 to 10 for

autism and 10 to 15 for milder symptoms including language social and

psychiatric disorders [Bolton et al 1994 Lauritsen et al 2005 Miles et al 2005

Landa 2008 Selkirk et al 2009] For families with two or more affected children

the recurrence risk approaches 35 [Ritvo et al 1989]

Risk to Family MembersmdashAutism of Unknown Cause


NGS

Clinical Genetic Testing for Patients With Autism Spectrum Disorders excluding single gen disorders

bull Karyotype yielded abnormal results in 3

bull Fragile X testing was abnormal 2

bull CNVs identified deletions or duplications in 20

Affy Cytoscan 300 euro (reagents) 20 Fragil X 200 euro (reagents) (Δ25) Exome analysis 700 euro (reagents) (Δ30-35)


Complex-Unknown (~70)


Single gene disorders (~5)

CNVs Duplication Deletions 15-20



TEA NO TEA

Allele 1 Allele 2

Marker A is associated with

Phenotype

Marker A

Allele 1 =

Allele 2 =

Human Genetic Association Study Design

SNP SINGLE NUCLEOTIDE POLYMORPHISM

ATCGGCGTACCTGATTCCGAATCCGTATCG

ATCGGCGTACCTGAATCCGAATCCGTATCG

33 Gigabases Human Genome gt18 M SNP 1 SNPlt200 bp

1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)

NODE 2 Madrid (CNIO)

Scientific advisory board Board

Management unit

CENTRO NACIONAL DE GENOTIPADO CEGEN-ISCIII

Illumina 1K

Affymetrix 60

AXIOM

Assessing the impact of a combined analysis of four common low-risk genetic variants on autism risk Carayol et al Molecular autism 2010 14

Results In both samples odds ratios (ORs) increased significantly as a function of the number of risk alleles with a genetic score of 8 being associated with an OR of 554 (95 confidence interval [CI] 245 to 1249) The sensitivities and specificities for each genetic score were similar in both analyses and the resultant area under the receiver operating characteristic curves were identical (059) Conclusions These results suggest that the accumulation of multiple risk alleles in a genetic score is a useful strategy for assessing the risk of autism in siblings of affected individuals and may be better than studying single polymorphisms for identifying subgroups of individuals with significantly greater risk

Next-Generation Sequencing Technologies

Technology Sequencing method Ampliifcation method

Read lenght (bp) Throughput (Mbrun)

454 Synthesis (Pyrosequencing) emPCR 400 -1000 50-500-900

Illumina Synthesis Bridge PCR 100+100 1020-600000

SOLiD Ligation emPCR 75+35 100000-180000

HeliScope Synthesis None 35 28000

Ion Torrent Synthesis (H+ detection) emPCR 100 10 -100-1000

PacBio Synthesis None 860-1100

Single DNA Molecule Technologies

Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M

Trends Cogn Sci 2012 Jan16(1)81-91 Epub 2011 Dec 10 Neurocognitive endophenotypes of impulsivity and compulsivity towards dimensional psychiatry Robbins TW Gillan CM Smith DG de Wit S Ersche KD

iquestQueacute es la Geneacutetica y el Genoma y como estaacuten organizados nuestros genes iquestCuaacuteles son las bases geneacuteticas de los TEA y por queacute es importante entenderlas

El genoma es



bases (A T C G)

GENOMA HUMANO


bases (A T C G)

Alrededor de 25000

genes


Frederik Sanger







Minisatellites

SNPs

MUTACIONES









Normal CN 2






Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


El genoma es



bases (A T C G)

GENOMA HUMANO


bases (A T C G)

Alrededor de 25000

genes


Frederik Sanger







Minisatellites

SNPs

MUTACIONES









Normal CN 2






Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


GENOMA HUMANO


bases (A T C G)

Alrededor de 25000

genes


Frederik Sanger







Minisatellites

SNPs

MUTACIONES









Normal CN 2






Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


Frederik Sanger







Minisatellites

SNPs

MUTACIONES









Normal CN 2






Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M








Minisatellites

SNPs

MUTACIONES









Normal CN 2






Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M







Normal CN 2






Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M






Normal CN 2






Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M





Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M



Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


Complex (~70)









estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M




estructurales




CNVs

Cariotipo

PCR










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M











mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M










mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M






mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M





mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M




mtDNA





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M






















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M





















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M



















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M

















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M
















NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M














NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M













NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M










NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M



NGS













TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M














TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M








TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


TEA NO TEA

Allele 1 Allele 2


Phenotype

Marker A

Allele 1 =

Allele 2 =






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M






1M SNPs

1M Tag SNPs

identified

Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


Coordination

NODE 1 Santiago de

Compostela (USC)



Management unit


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


Illumina 1K

Affymetrix 60

AXIOM













Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M














Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M












Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M


Recurrent

protein-altering

mutations were

observed in

two

genesCHD8

and

NTNG1 M



Genética autismo

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