The Genetics of Developmental Learning Disabilities

Wendy Raskind, M.D., Ph.D.University of Washington IDA 10/29/08

Minding your ps and qsMinding your ps and qsA tale of alphabets, chromosomes, and allelesA tale of alphabets, chromosomes, and alleles

Dyslexia (RD)Dyslexia (RD)

Specific language impairment (SLI)Specific language impairment (SLI)

Speech Sound disorder (SSD)Speech Sound disorder (SSD)

Autism and autistic spectrum disorders (ASD)Autism and autistic spectrum disorders (ASD)

Dyslexia (RD)Dyslexia (RD)

Specific language impairment (SLI)Specific language impairment (SLI)

Speech Sound disorder (SSD)Speech Sound disorder (SSD)

Autism and autistic spectrum disorders (ASD)Autism and autistic spectrum disorders (ASD)

Examples of Complex Developmental Examples of Complex Developmental DisordersDisorders

Disclaimer!!! Too many groups, too many disorders. Disclaimer!!! Too many groups, too many disorders. Therefore, no specific citations.Therefore, no specific citations.

Evidence for a genetic basis

Population variation

Gene search strategies and current status

“Next gen” approaches

TopicsTopics

Population variationPopulation variation

Evidence that a trait is genetic:Evidence that a trait is genetic:

Clustering

Genes

Observation

Twin studies

Aggregation

Patterns of transmission

Segregation

Linkage

Dyslexia: Dyslexia: Unexpected difficulty in accuracy and rate of word reading, decoding, text reading, and spelling that is neurobiological in

origin (IDA 2003)

Several lines of evidence that dyslexia has a genetic basis

ClusteringClustering

ObservationHinshelwood: more than one person in family with “congenital word blindness”, 1917

AggregationParents and offspring share exactly 50% of allelesSiblings share on average 50% of allelesUnless consanguinous, parents don’t share alleles by descent

Twin StudiesMZ twins share all alleles; DZ twins share on avg 50% of allelesCan estimate heritability by comparing how similar MZ twins are to how similar DZ twins are

Heritability: proportion of the phenotypic variation in a population that is attributable to genetic variation among individuals

Heritability of 1 implies that the variation is all geneticHeritability of 0 implies it is all environmental

A non zero heritability tells nothing about the number of genes

Segregation analysisSegregation analysisDetermines the pattern of inheritance of a trait

If heritability is high (variation is mostly due to genes) MZ twins will resemble each other in the trait more than DZ twins

HeritabilityHeritability

Heritability of dyslexia phenotypesHeritability of dyslexia phenotypes Twin studies and segregation analyses

•Composite of word recognition, reading comprehension, and spelling .58

•Word recognition ((single word reading) .45

•Phonological decoding (read pronounceable nonwords) .61

•Orthographic coding (choice of real word from homophone) .58

•Phonological awareness (transposition or deletion of phonemes) .56

Molecular GeneticsMolecular Genetics

Linkage studiesLinkage studies

Types of differences used to trace a trait in a Types of differences used to trace a trait in a family or populationfamily or population

Protein isoform

Chromosome/karyotype

Short tandem repeat polymorphism (STRP)

Single nucleotide polymorphism (SNP)

Marker: a polymorphic DNA sequence that varies in the population with known frequency

ChromosomesChromosomes

Short tandem repeat polymorphism Short tandem repeat polymorphism (STRP)(STRP)

Tetranucleotide …ATTGATTGATTG…ATTG(n)

One repeat unit

homozygous

heterozygous

Single nucleotide polymorphism (SNP)Single nucleotide polymorphism (SNP)

A and G

electropherogram

How big is the genome?How big is the genome?

~3 billion base pairs in the haploid genome (3,000,000,000)

~25,000 protein coding genes

~1.5% of the genome codes for protein

So if we differ by 1 base per 1000, there are 3 million

differences in the haploid genome

p15-16

DYX3

DYX6p11.2

DYX5

p13-q13

q13-16.2

DYX4

DYX8p34-36

DYX7p15.5

DYX1

DYX2p21.3-22

q21

DYX9

q27.3

The ps and qs of dyslexiaThe ps and qs of dyslexia

UWLDC finding

q22.3

q12

Study designs varyStudy designs vary

Study populations: single family, sib pairs, multigenerational families

Inclusion criteria: discrepancy vs low performance

Phenotypes: global description, single assessment measures, various combinations of measures

Trait: categorical dichotomous or continuous variable

Candidate genes: 1. Candidate genes: 1. DYX1C1DYX1C1

Gene disrupted by t(2;15) in a family with dyslexia is a putative transcription factor

Some positive SNP associations: -3GA and 124GT

Dyslexia subjects Controls

= SNP 1 = SNP 2

SNP 1

SNP 2

Dyslexia

Studied SNPs in the gene in subjects and controls

Not confirmed by all

Inconsistent risk alleles

“Real” risk allele not known

Ann Rev Genomics Human Genet 8:57-79, 2008

Targeted association studies

DCDC2 KIAA0319

DYX2 locus: 2. DYX2 locus: 2. KIAA0319 KIAA0319 and 3. and 3. DCDC2DCDC2

Associations not corroborated by all studies

Evidence is strongest only for severe phenotypes

Opposite allele association in different studies

Good readers also carry the “risk” SNP haplotype

Nonsynonymous SNP in KIAA0319 - rare allele appears to protect

Candidate gene for DYX5: 4. Candidate gene for DYX5: 4. ROBO1ROBO1

Mapped in a single large Finnish family with AD inheritance

Disrupted by t(3;8)(p12;q11) in a family with dyslexia

Rare SNP haplotype associated with dyslexia and with decreased expression

One person with severe dyslexia in the translocation family did not carry t(3;8)

Expression studies done in lymphocytes

Quite variable effects on expression levels

No mutations in general dyslexia populations

However……

Ann Rev Genomics Human Genet 8:57-79, 2008

RNAi studies show DYX1C1, KIAA0319 and DCDC2 affect neuronal migration

All four candidate genes are expressed in brain

ROBO1 affects extension of axons

But 50% of genes are expressed in brain

No clearly pathogenic mutations yet identified

But 50% of genes are expressed in brain

No clearly pathogenic mutations yet identified

Functional StudiesFunctional Studies

Significant difficulties in acquiring expressive and/or receptive language, despite adequate intelligence and opportunity

Common ~3-5%

More common in males than females

High heritability (familial aggregation but complex segregation patterns)

High comorbidity with dyslexia and specific language impairment

Speech Sound Disorder (SSD): Speech Sound Disorder (SSD):

Prader-Willi Syndrome 15q11-13

Autism 15q11-13

Language problems of SSD are shared with other syndromes

SSD confers increased risk for dyslexia

Targeted linkage analyses of SSD: suggestive but not consistent evidence

15q14

15q21 (DYX1)

6p22 (DYX2)

3p12-q13 (DYX5)

1p36 (DYX8)

Incoordination of muscles used in articulation of speech

Mapped to 7q31 in a single large British family with AD inheritance (SPCH1)

de novo t(5;7)(q22;q31.2) and t(2;7)(p23;q31.3) led to identification of FOXP2

Heterozygous missense mutation in FOXP2 in original family

Severe vocal dyspraxiaSevere vocal dyspraxia

No mutations in dyslexia or autism found

Rare mutations found in others with severe vocal dyspraxia but not in “usual” SSD

Transcription factor: regulates production of RNA from DNA. May initiate, enhance, or inhibit the transcription of a gene.

RNAi knockdown impairs ability of songbirds to imitate songs.

Function of FOXP2Function of FOXP2

Characterized by late onset of expressive language and poor receptive language abilities, poor comprehension relative to reading accuracy, poor understanding of syntax and morphology in the absence of explanatory factors (e.g., low non-verbal IQ, hearing impairment, neurologic damage)

Moderate to high heritability

Male predominance (8% of boys and 6% of girls) Linkage studies: SLI1 16q

SLI2 19q

SLI3 13q21

Specific Language Impairment (SLI) Specific Language Impairment (SLI)

No linkage to FOXP2 and no mutations in FOXP2

Comorbidity of RD, SLI, SSD:Comorbidity of RD, SLI, SSD:

Shared Genetic Influences?Shared Genetic Influences?

All are common disorders with high heritability

Male predominance

Share some clinical features

Only soft evidence for overlap of genomic locations

Can’t really know until the genes are found

Same holds for relationship to ADHD

Autism Autism

impaired social interaction

speech perseveration

delayed echolalia

social anxiety

gaze aversion

hand flapping and other stereotyped repetitive actions

self injury

Autism and autistic spectrum disorders Autism and autistic spectrum disorders

High heritability, > 90%

• MZ twin concordance 70-95%

• DZ twin concordance 0-24%

Does not exhibit Mendelian inheritance pattern

• Risk to sibs is ~5-15%

• Rapid fall off in risk to extended family members

• 4-5:1 male predominance; even more skewed for higher IQ subset

Prevalence rising? Narrow definition 1/500, ASD 1/150

Etiologies of Autism: I. Single Gene DefectsEtiologies of Autism: I. Single Gene Defects

most common inherited form of mental retardation

X-linked inheritance

affects 1/3600 males

mild to moderate intellectual impairment

verbal worse than performance IQ

1/4000 females are carriers of the full mutation; may have executive function impairment

accounts for 4-7% of people with a diagnosis of autism

~33% of people with fragile X have an autism diagnosis

many others have “autistic-like behaviors”

Fragile X Syndrome (FRAX, Fragile X Syndrome (FRAX, FMR1)FMR1)

Rett Syndrome Rett Syndrome

X-linked, ~1/15000 (1/8000 girls)

99.5% sporadic

autistic behaviors onset in 1st 3-4 yrs = repetitive hand wringing, slapping, loss of acquired language

distinct from autism – progressive decline, female predominance, microcephaly

MECP2 gene at Xq28 codes for a protein that is critical for maintenance of methylation status

Loss of function leads to gene reactivation

Developmental arrest of brain and autonomic neurologic system

Additional Genetic Heterogeneity Additional Genetic Heterogeneity

Known genes (e.g., FMR1, MECP2, TS, NF1, PTEN, Shank3, NLGN3, NLGN4)

Linkage studies of multiplex families (e.g., 1p, 2q32, 3p25-26, 5q, 6q21, 7q22, 7q31-22, 13q, 15q11-13, 16p13, 17, 19p)

Translocations (e.g., 2q37, 5p15, 11q25, 16q22.3, 17p11.2, 18q21.1, 18q23, 22q11.2, 22q13.3, Xp22.2-p22.3)

Pathways in Autistic Spectrum DisordersPathways in Autistic Spectrum Disorders

Garber Science 317:190-191, 2007

Some genes affect synapse function: neuroligins, neurexins, Shank3

Others may interact or have similar function

Etiologies of Autism: II. Duplication/Deletion Etiologies of Autism: II. Duplication/Deletion SyndromesSyndromes

Cytogenetic SyndromesCytogenetic Syndromes

Idic(15) is the most frequently identified chromosomal abnormality in autism

Maternal isodisomy or loss of the paternal allele leads to PWS

Paternal isodisomy or loss of the maternal allele leads to AS

Velocardiofacial Syndrome (VCFS)Velocardiofacial Syndrome (VCFS)22q del syndrome 22q del syndrome

broad bulbous nose

square tip of nose

short philtrum

hypertelorism; telecanthus

small head

low set ears

long slender hands and fingers

palatal abnormalities

cardiac abnormalities

immune and autoimmune defects

schizophrenia

autism

learning disabilities

Copy Number Variations (CNVs) and AutismCopy Number Variations (CNVs) and Autism

more common in autism (~10%) than controls (~1%)

some regions overlap with linkage signals

sometimes region contains a strong candidate gene

some regions found by more than one group

some identified regions remain controversial

some are apparently benign population polymorphisms

Common disease/common variant hypothesis (CDCV): much of of the genetic variation is due to relatively few common variants

Rare disease/rare variant hypothesis: multiple different disorders, each caused by rare alleles

genetic heterogeneity, high penetrance

low penetrance, perhaps combination of alleles consider the putative modest effect of DCDC2 and KIAA0319 on dyslexia

Complex Disorders: Competing Hypotheses Complex Disorders: Competing Hypotheses

Genome-Wide Association Studies (GWAS)

Relies on common disease/common variant hypothesis Enabled by HapMap Project

Simultaneous genotyping of thousands of SNPs

Requires large numbers of cases and controls

Rarely finds the functional variant

Usually effect size is very small

May suggest a candidate gene for rare variant search

Next-Generation Sequencing

2003 Human Genome Project whole sequence assembly $300,000,000

1953 James Watson and Francis Crick describe double helix

beginning of 2008 $60,000

end of 2008 $10,000

projected for 2012 $100

2007 Resequencing James Watson’s genome $1,000,000