Genetics of Schizophrenia

Jon McClellan, MD

University of Washington

Disclosures: Grants from NIH, Stanley Medical Foundation, NARSAD

No Industry Sponsored Research, Speaker’s Boards, or Consultation

Schizophrenia GeneticsUntil recently, most widely quoted model in

Psychiatric Genetics:

“Common Disease – Common Allele” Model

“Polygenic model”

Combined impact of common genetic variants, each with small effect on risk, plus interactions with environmental risk factors, results in the illness

“Common Disease – Rare Variants” Model

Rare large effect mutations are responsible for substantial portion of schizophrenia, autism, and perhaps most

complex illnesses

Individual mutations may be specific to single cases or families

Many different genes involved, each with many different disease-causing mutations

Human disease characterized by enormous genetic heterogeneity

McClellan and King, Cell 2010

How can Rare Mutations Explain a Common Psychiatric Disorder?

The majority of human genes are involved with brain development

New mutations are common

Those that cause illnesses may only persist a few generations because of their negative consequences

Any gene important to an illness may be disrupted by 1000’s of different mutations

Each mutation may be rare, but collectively the gene may be responsible for a substantial portion of cases (BRCA1)

Different mutations in different genes may disrupt related neurobiological pathways, leading to the same disorder

Genetic causes of complex disease must reflect evolutionary forces shaping the human genome

Human Migration

Adapted from Cavalli-Sforza & Feldman, Nature Genetics  33, 266 – 275, 2003

A village of a few hundred families, anywhere.

What % of all human variation is here?

10%

50%

80%

90%

Adapted from: Tishkoff & Verrelli Annu Rev Genomics Hum Genet 2003

Human Genetic Diversity

Human Allelic Heterogeneity

The exponential growth of the human population has resulted in a vast number of new mutations

– All possible mutations have occurred and will occur again

– Each person harbors ~ 175 de novo mutations

– Recent alleles usually rare and specific to one population (or even one family)

– Many are deleterious and do not persist beyond a few generations

Schizophrenia and Autism: Caused by recent rare large effect

mutations?

Illnesses persist with similar prevalence world-wide

Familial Disorder, yet most cases sporadic

Persistence of Illness Despite Impact on Fertility

Environmental Exposures

– Increased Risk associated with Paternal Age

– Maternal Famine for Schizophrenia

1.00

1.50

2.00

2.50

3.00

< 30 30 - 35 - 40 - 45 - 50+

Parent’s age at childbirth

Paternal ageMaternal age

Rel

ativ

e ri

sk o

f S

chiz

oph

ren

ia

Schizophrenia and Parental Age

Malaspina et al., Arch Gen Psychiatry 2001

Reichenberg et al., 2006, Arch Gen Psychiatry

Birth month and year

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

Jan-Jun1944

Jul-Dec1944

Jan-Sep1945

Oct-Dec1945

Jan-Jun1946

Jun-Dec1946

Sch

izop

hre

nia

(%

)

Dutch Hongerwinter 1944-45

Susser et al. Arch Gen Psych 1996

Chinese Famine of 1959-60

St. Clair et al. JAMA 2005

0.00

0.50

1.00

1.50

2.00

2.50

1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966

Sch

izo

ph

ren

ia (

%)

Wuhu region of Anhui Province

Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia

Tom Walsh, Jon M. McClellan, Shane E. McCarthy, Anjené M. Addington, Sarah B. Pierce, Greg M. Cooper, Alex S. Nord, Mary Kusenda, Dheeraj Malhotra,Abhishek Bhandari, Sunday M. Stray, Caitlin F. Rippey, Patricia Roccanova, Vlad Makarov, B. Lakshmi, Robert L. Findling, Linmarie Sikich, Thomas Stromberg, Barry Merriman, Nitin Gogtay, Philip Butler, Kristen Eckstrand, Laila Noory, Peter Gochman, Robert Long, Zugen Chen, Sean Davis, Carl Baker, Evan E. Eichler, Paul S. Meltzer, Stanley F. Nelson, Andrew B. Singleton, Ming K. Lee, Judith L. Rapoport, Mary-Claire King, Jonathan Sebat3

Science, 320:539-43, 2008

“Study Ties Genetic Variations to Schizophrenia”

"You're basically screwing up the way that the regulation of brain growth occurs"

Jon McClellan, MD

“Dad, "screwed up" is not a very professional phrase, it makes you sound kind of stupid”

Tessa McClellan

Hypothesis

Rare copy number mutations affecting genes in neurodevelopmental pathways will be more common among persons with schizophrenia than among controls

Subjects

Cases 150 persons with schizophrenia or schizoaffective disorder

Controls 268 persons age >35 Free of signs of neurological or psychiatric illnessSame distribution of self-reported ethnicities as cases

Copy Number Variants

Deletions

Duplications

Copy Number Variants

• Deletions, duplications and inversions of DNA– Can involve thousands, or even millions, of

basepairs

• Most Copy Number Variants are benign and common

• Copying errors that disrupt normal gene function can lead to disease.

Sebat et al., 2004

Definition of Rare CNVs

Not previously reported in Database of Genomic Variants (DGV)

Data from 1000’s of individualsCNV found either only in cases or only in controlsMutation impacts one or more genes100kb or larger in size

del Chr2:211,792,494-212,191,651 del Chr3:7,177,597-7,314,117 del Chr3:197,224,662-198,573,215

del Chr5:36,190,704-36,693,387 dup Chr7:77,358,702-77,857,149 dup Chr8:142,025,432-142,393,948

dup Chr18:7,070,926-7,565,943 dup Chr19:59,045,962-59,363,706 del Chr22:32,048,581-32,715,286

Subset of Rare structural variants detected using high density array CGH

Rare Structural Variants and Schizophrenia

Individuals with Schizophrenia significantly more likely to have a rare deletion or duplication (≥ 100 kb) impacting a gene

15 % vs 5 % of healthy controls

Rate of rare mutations higher in early onset cases (20%)

Each mutation was different, and impacted different genes

Genes disrupted in Schizophrenia cluster in pathways related to neurodevelopment, including glutamate and neuregulin pathways

Walsh et al., Science, 2008

So…

What about other studies?

Enrichment of Rare Structural Variants replicated by several independent groups

8-fold increased risk of de novo structural mutations in Sporadic Schizophrenia (Xu et al., 2008)

Higher frequency of rare duplications and deletions found in large samples of patients with schizophrenia (Stefansson et al., 2008; International Schizophrenia Consortium, 2008)

Recurrent mutations at genomic “Hotspots” found in multiple cases

Several-fold increased risk for disorder (OR’s > 5)

Genomic “Hotspots”

Nonallelic Homologous Recombination due to Segmental DuplicationGenomic “Hot Spots”

ISC Nature 2008

CasesN=3391

ControlsN=3181

13 0

0

1

9

10

22q11.2

(VCFS)

15q13.3

1q21

Genomic Hotspots (so far…)

• 1q21.1, 3q29, 15q11.2, 15q13.3, 16p11.2, 16p12.1, 16p13.11, 17p12, and 22q11.2

• Duplications in the neuropeptide receptor VIPR2

And with better sequencing tools…

Rare deleterious point mutations and indels detected in genes important to neurodevelopmental pathways:

• e.g., GRM1, MAP1A, GRIN2B, and NLGN

– Critical pathways include glutamate functioning, synapse formation, signaling and brain development

• Both rare De novo and inherited events may cause the disorder

Genomic Analysis of Schizophrenia (GENESIS)

R01MH083989

NIMH series: >5000 cases, family members; >5000 controls

Raquel Gur, MGI, U PennsylvaniaDavid Braff, COGS, UC San Diego

Robert Savage, PAARTNERS, U Alabama Vish Nimgaonkar, GSS, U Pittsburgh

Genomic sequencing and analysis, U Washington, SeattleTom Walsh, Jack McClellan, Ming K Lee,

Anne Thornton, Amanda Watts, Sunday Stray

Genomic Analysis of Schizophrenia (GENESIS)

Identification of de novo events

Trios with sporadic schizophreniaAffected proband and unaffected parents Negative family history of schizophrenia, bipolar disorder, or major depression

Exome sequencing of proband and both parents from blood-based DNA

First 22 trios:

19 validated de novo mutations in 19 different genes

Genomic Analysis of Schizophrenia (GENESIS)

Eventually 300 trios, presently 92 trios in pipeline

Strong Association of De Novo Copy Number Mutations with Autism

Jonathan Sebat, B. Lakshmi, Dheeraj Malhotra, Jennifer Troge, Christa Lese-Martin, Tom Walsh, Boris Yamrom, Seungtai Yoon, Alex Krasnitz, Jude Kendall, Anthony Leotta, Deepa Pai,1 Ray Zhang, Yoon-Ha Lee, James Hicks, Sarah J. Spence, Annette T. Lee, Kaija Puura,6 Terho Lehtimäki, David Ledbetter, Peter K. Gregersen, Joel Bregman, James S. Sutcliffe, Vaidehi Jobanputra, Wendy Chung, Dorothy Warburton, Mary-Claire King, David Skuse, Daniel H. Geschwind, T. Conrad Gilliam, Kenny Ye, Michael Wigler

Science, 316:445-449, 2007

Rare Structural Variants and Autism

10 % of Individuals with Sporadic Autism have de novo duplications and deletions (> 100kb, Sebat et al., 2007)

2 % of multiplex cases

1 % of controls

7 % of cases with Sporadic Autism vs 2 % of multiplex cases have de novo CNVs (Marshall et al., 2008)

Replicated several times by independent groups

Rare Mutations and Autism

Genomic Hotspots

1q21.1, 7q11.23, 15q13.3, 16p11.2, 16p13.11, 17p12, and 22q11.2

16p11.2 may explain ~ 1 % of cases

Rare Mutations and Autism

To date, rare deleterious mutations associated with Autism in > 100 genes and > 40 genomic loci

• Genes disrupted associated with pathways critical for neurodevelopment, including synaptic development, neuronal cell-adhesion and ubiquitin degradation

• Many of the same genes and hotspots are also associated with Schizophrenia

Rare Variants and Psychiatric Disease• Rare CNVs, point mutations and indels also reported

for:

Intellectual Disability

Tourette Disorder

ADHD

Bipolar Disorder

• Some mutations/genes same as those found in Schizophrenia

– Includes Genomic Hotspots

Genomics and Psychiatry

• Autism, Schizophrenia , Intellectual Disability, Bipolar Disorder, ADHD and Tourette Disorder each associated with rare deleterious mutations that disrupt genes related to brain development

– Many disease specific mutations appear to be either de novo, or of recent origin

– Genes implicated involved in neural development

Genomics and Psychiatry

• Most individuals have a different mutation involving different gene(s)

• Genomic Hotspots may account for a higher proportion of cases

• Some individuals are found to have more than one deleterious mutation in different genes/loci:

– “Multi-hit” model explains how some events are inherited from nonaffected persons

– Adds further complexity to heritability of disorders

Same Gene, Different Disorder

Blackwood et al., 2001 AJHG

DISC1

18/29

Different Gene(s), Same Disorder

MacrocephalyDevelopmental DelaysAutism

MicrocephalyDevelopmental DelaysSchizophrenia

1q21.1

15q13.3

Developmental DelaysAutismSchizophreniaEpilepsy

Developmental Delays

16p11.2

Developmental DelaysAutism

Developmental DelaysAutismSchizophreniaBipolar Disorder

22q11.2

Developmental DelaysAutism

Developmental DelaysADHDAutismSchizophreniaBipolar Disorder

Developmental DelaysAutismSchizophreniaEpilepsy

NRXN1CNTNAP2

Developmental DelaysADHDAutismSchizophrenia

Developmental DelaysEpilepsy

16p13.11

Meanwhile….

The search for common risk alleles

Genome-wide Association Studies (GWAS) struggle with:

• Lack of replication

• Small dwindling effect sizes (< 1.5)

• Lack of demonstrated biological relevance for disorder

Neuropsychiatric disorders characterized by marked genetic heterogeneity

Most affected individuals may have a different genetic cause

Multiple different mutations in multiple different genes/genomic loci may ultimately act by disrupting neuronal homeostasis (Ramocki & Zoghbi, 2008)

Phenotypic differences may be due to timing and impact of mutation on development, plus other epistatic, epigenetic and/or environmental factors

So…

Psychiatric diagnoses have clinical marked heterogeneity

and

Marked genetic heterogeneity characterizes most complex illnesses

Vast clinical and genetic heterogeneity likely explains why diagnostic issues are so complex and treatment response so variable across individuals with the same illness

ImplicationsDSM diagnostic categories may be too heterogeneous for

major advances in neurobiological understanding of disorders

Research needs to focus on individuals grouped by disrupted neurobiological pathways/genes rather than by broadly defined syndromes

University of WashingtonMary-Claire KingTom WalshJack McClellanSarah PierceCait RippeyDiane DickelSunday StrayMing K. LeeGreg CooperCarl BakerEvan Eichler

Cold Spring Harbor LaboratoryShane McCarthyAbishek BhandariMary KusendaDheeraj MalhotraJonathan Sebat

NIH - NIMHAnjene AddingtonJudith Rapoport

NIH - NIAAndrew Singleton