Identifying genes for schizophrenia, bipolar disorder and depression in

families and population from Pakistan.

Douglas Blackwood, Professor of Psychiatric Genetics, Division of Psychiatry,
University of Edinburgh. (d.blackwood@ed.ac.uk)
Dr Saqib Mahmood, University of Health Sciences, Lahore, Pakistan.
Muhammad Ayub, Consultant Psychiatrist and Honorary Senior Lecturer University of
Durham (mayub@nhs.net) Associate Professor Queens University Canada.

Recently genome-wide association studies have found substantial overlap of risk

factors between schizophrenia and bipolar disorder and led to a re-evaluation of
models of inheritance. It is proposed that common polygenic variation (OR<1.5)
explains about a third of the genetic contribution to schizophrenia, rare CNVs make
an important additional contribution and a parallel role for rare coding sequence
variants seems likely (ISC 2008). Examples of genes with rare mutations contributing
to schizophrenia, bipolar disorder and depression include DISC1 (Blackwood et al,
2001) and ABCA13 (Knight et al, 2009). Our aim is to identify rare variants causing
schizophrenia, bipolar disorder or depression in large multiply affected families in
Pakistan. We additionally plan to collect case and control samples from the same
population for genome wide association studies, exome or whole genome
sequencing.
Homozygosity mapping (Lander & Botstein 1987) has been a successful strategy to
discover autosomal recessive disease genes in many neurodevelopmental
conditions, for example Muhammad Ayub provided the clinical material from
Pakistani families that recently led to the discovery of novel genes for mental
retardation and ciliopathies and other phenotypes (Mir 2009; Noor et al 2008; Noor et
al 2008, Jacoby 2009).
Homozygosity mapping has also been successfully applied to autism by Morrow et al
(2008) who identified novel recessive autism loci and genes by studying
consanguineous families from the middle-east, Turkey and Pakistan.
Families from Pakistan
In Pakistan over 60% of the population engage in consanguineous marriages of
which 80% are between first cousins (Hussain and Bittles, 1998). In some regions of
Pakistan where the population has been stable for many generations the rate of
consanguineous marriages is even higher leading to a high average co-efficient of
inbreeding (F)=0.028, compared to an out bred European population where
F=0.00005. Families from this population provide a valuable resource for mapping
genes in complex disorders like Psychiatric disorders.
We intend to recruit further families from Pakistan which have multiple members
affected with Psychiatric Disorders.
We will identify and recruit these families through colleagues working in Psychiatric
Services. They will identify and approach the families for informed consent before
recruitment. We will also collect cases and parents patient trios for association
studies (genome wide association, copy number variants and exome or whole
genome sequencing)
Consent
We will use the patient information sheet attached to provide information to the
patients and with their permission to their families about the study. As many patients
are likely to be unable to read we will read and explain the contents of the information
sheet to the patients.
The patients will be clearly informed about their right to decline to participate in the
study. We will make it clear to the patients that not participating in the study will not
affect their right to treatment.

We will allow the patients to have time to think before participating in the study.
We will use the form attached to get written consent. If the patient is unable to sign
their carers will be able to sign on their behalf and this will be witnessed by a third
person.
Procedures
We will gather clinical information to make a diagnosis through an interview with the
patient and with their permission with a carer. With the patients permission we will
seek information about their treatment from their medical records.
We will collect 20-30 ml of blood through a vein. We will also collect a saliva sample.
DNA will be extracted from these samples. The clinical information we gather will be
handled confidentially. Only clinicians will have access to the information which will
be kept locked in a draw and in a locked room. The DNA samples will be given a
code so that nobody outside the research team can identify them.
Depending on the structure of the family we will perform one or more of the following
procedures on the DNA:
1. Genome wide Single Nucleotide Polymorphism or Microsatellite genotyping
and analysis
2. Study of Copy Number Variation
3. Candidate gene sequencing or exome sequencing or whole genome
sequencing
4. Functional Characterisation of the genes identified.
For case control samples and parents/ offspring trios we will perform one or more of
the following procedures and use appropriate method of analysis
1. Genome wide single nucleotide polymorphism or Microsatellite genotyping
2. Candidate gene sequencing or exome sequencing or whole genome
sequencing
International Schizophrenia Consortium (2008) Nature 455:237
Blackwood (2001) American Journal of Human Genetics 69:428-433.
Knight et al, 2009. American Journal of Human Genetics, 85:833.
Lander ES and Botstein D, 1987. Science, 236:1567
Mir A et al, 2009. American Journal of Human Genetics 85:909
Jacoby M et al, 2009. Nature Genetics 41:1027.
Noor et al 2008 American Journal of Human Genetics 84:519
Noor et al 2008 American Journal of Human Genetics 82:1011
Morrow EM et al, 2008. Science 321:218.
Ayub M et al Hum Hered 2008;66:190-198
Knight et al, 2008. European Journal of Human Genetics 16:750