The Genetics of Developmental Learning Disabilities

1. The Genetics of Developmental Learning Disabilities Minding your ps and qs A tale of alphabets, chromosomes, and alleles Wendy Raskind, M.D., Ph.D. University of Washington IDA 10/29/08

2. Examples of Complex Developmental Disorders • Dyslexia (RD) • Specific language impairment (SLI) • Speech Sound disorder (SSD) • Autism and autistic spectrum disorders (ASD) Disclaimer!!! Too many groups, too many disorders. Therefore, no specific citations.

3. Topics • Evidence for agenetic basis • Population variation • Gene search strategies and current status • “Next gen”approaches

4. Population variation

5. Evidence that a trait is genetic: Clustering Observation Aggregation Twin studies Patterns of transmission Segregation Linkage Genes

6. 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

7. Clustering Observation Hinshelwood:more than one person in family with “congenital word blindness”, 1917 Aggregation Parents and offspring share exactly 50%of alleles Siblings share on average 50% of alleles Unless consanguinous,parents don’t share alleles by descent Twin Studies MZ twins share all alleles;DZ twins share on avg 50% of alleles Can 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

8. Heritability If heritability is high (variation is mostly due to genes) MZ twins will resemble each other in the trait more than DZ twins Heritability of 1 impliesthat the variation is all genetic Heritability of 0 implies it is all environmental A non zero heritability tells nothing about the number of genes Segregation analysis Determinesthe pattern of inheritance of a trait

9. Heritability of dyslexia phenotypesTwin studies and segregation analyses • Composite of word recognition, reading comprehension, and spelling.58 • Wordrecognition(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

10. Molecular Genetics

11. Linkage studies Types of differences used to trace a trait in a family or population Proteinisoform Chromosome/karyotype Short tandem repeat polymorphism (STRP) Single nucleotide polymorphism (SNP) Marker: a polymorphic DNA sequence that varies in the population with known frequency

12. Chromosomes

13. Short tandem repeat polymorphism (STRP) Tetranucleotide …ATTGATTGATTG…ATTG(n) One repeat unit homozygous heterozygous

14. Single nucleotide polymorphism (SNP) electropherogram A and G

15. 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

16. The ps and qs of dyslexia DYX8 DYX3 DYX5 p34-36 p15-16 q22.3 p13-q13 DYX2 DYX7 p21.3-22 p15.5 q13-16.2 DYX4 DYX1 DYX6 q12 q21 p11.2 DYX9 q27.3 UWLDC finding

17. Study 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

18. Candidate genes: 1. DYX1C1 Gene disrupted by t(2;15) in a family with dyslexia is a putative transcription factor Studied SNPs in the gene in subjects and controls Some positive SNP associations: -3GA and 124GT Dyslexia subjects Controls Not confirmed by all Inconsistent risk alleles Dyslexia SNP 1 SNP 2 “Real” risk allele not known = SNP 1 = SNP 2

19. DYX2 locus: 2. KIAA0319 and 3. DCDC2 DCDC2 KIAA0319 Targeted association studies Ann Rev Genomics Human Genet 8:57-79, 2008 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

20. Candidate gene for DYX5: 4. ROBO1 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 However…… 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

21. Functional Studies All four candidate genes are expressed in brain RNAi studies show DYX1C1, KIAA0319 and DCDC2 affect neuronal migration Ann Rev Genomics Human Genet 8:57-79, 2008 ROBO1 affects extension of axons But 50% of genes are expressed in brain No clearly pathogenic mutations yet identified

22. Speech Sound Disorder (SSD): 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

23. SSD confers increased risk for dyslexia Language problems of SSD are shared with other syndromes Targeted linkage analyses of SSD: suggestive but not consistent evidence 15q14 15q21 (DYX1) 6p22 (DYX2) 3p12-q13 (DYX5) 1p36 (DYX8) Prader-Willi Syndrome 15q11-13 Autism 15q11-13

24. Severe vocal dyspraxia 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 Rare mutations found in others with severe vocal dyspraxia but not in “usual” SSD No mutations in dyslexia or autism found

25. Function of FOXP2 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.

26. Specific Language Impairment (SLI) 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 • SLI219q • SLI3 13q21 • No linkage to FOXP2 and no mutations in FOXP2

27. Comorbidity of RD, SLI, SSD: 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

28. Autism • impaired social interaction • speech perseveration • delayed echolalia • social anxiety • gaze aversion • hand flapping and other stereotyped repetitive actions • self injury

29. 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

30. Etiologies 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 Fragile X Syndrome (FRAX, FMR1) • 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”

31. 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

32. 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)

33. Pathways in Autistic Spectrum Disorders Some genes affect synapse function: neuroligins, neurexins, Shank3 Others may interact or have similar function Garber Science 317:190-191, 2007

34. Etiologies of Autism: II. Duplication/Deletion Syndromes Cytogenetic 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

35. Velocardiofacial Syndrome (VCFS) 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

36. Copy 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

37. Complex Disorders: Competing Hypotheses • Common disease/common variant hypothesis (CDCV): much of the genetic variation is due to relativelyfewcommon variants low penetrance, perhaps combination of alleles consider the putative modest effect of DCDC2 and KIAA0319 on dyslexia • Rare disease/rare variant hypothesis: multiple different disorders, each caused by rare alleles genetic heterogeneity, high penetrance

38. 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

39. Next-Generation Sequencing 1953 James Watson and Francis Crick describe double helix 2003 Human Genome Project whole sequence assembly $300,000,000 2007 Resequencing James Watson’s genome $1,000,000 beginning of 2008 $60,000 end of 2008 $10,000 projected for 2012 $100