Supplementary Information
Consanguinity Testing of Pedigree C702
Within-family relationships were confirmed by examination of the degree of homozygosity across the genome using two related methods, both developed in-house by PH and using data from a previous study (Williams et al. 2003).
First, the probability of homozygosity in the absence of inbreeding was evaluated for each genetic marker analysed as the expected probability of a homozygous genotype being the sum of the squares of the allele frequencies. The allele frequencies were obtained from our original linkage study (Williams et al. 2003). The probabilities were summed to show the expected number of homozygous genotypes for an individual. The number of homozygous genotypes for each C702 test individual is calculated and then a chi square test (1 degree of freedom) performed between observed values and expected values.
The second method takes in to account the frequency of alleles in the test subject(s).
The method involved the calculation of an inbreeding coefficient (F), which is the probability that an individual's two alleles at a given locus are IBD:
The probability (P) of a homozygous genotype (for allele i) is:
P(i/i) = ((F x Pi) + (1 - F)) Pi,
(where Pi is the population frequency of allele i)
Whereas the probability of a heterozygous genotype (alleles i and j) is:
P(i/j) = (1 - F) 2PiPj

The calculation was performed for each locus and the overall likelihood obtained by forming the product of the contributions from each locus. Twice the natural logarithm of the ratio of the likelihood maximised with respect to F to its value when F=0 is the test statistic of the null hypothesis of no inbreeding (i.e. F=0), and has a chi-squared distribution on one degree of freedom when the null hypothesis is true.
Supplementary table ST1 shows the results of two methods of testing for consanguinity of pedigree C702. The table shows the 6 affected siblings of pedigree
C702 (Samples 4, 6, 7, 8, 9 and 10), the number of homozygous and heterozygous genotypes for each sample (372 autosomal microsatellite markers (Williams et al.
2003) and an expected value for the number of homozygous genotypes (assuming no inbreeding)).
The chi square statistic for the two methods of analysis is then shown: CHI1 corresponds to the measure of inbreeding based purely on the expected number of homozygous genotypes assuming no consanguinity (E(HOM)). CHI2 takes into account the frequency of alleles that an individual is homozygous for. A chi square of
2.706 gives a p value of 0.05 and none of the siblings achieve this value indicating that the affected siblings of pedigree C702 are not the result of a consanguineous mating. The power of CHI2 (the more informative and therefore powerful measure) based upon the 372 genome scan markers to detect consanguinity in an individual ranges from a power of 20% to detect a second cousin mating, 87% to detect a first cousin mating and 100% to detect a sibling mating (at p≤.05) when F (the maximised inbreeding coefficient) =0.015 corresponds to second-cousin mating, F=0.0625 to first-cousin mating and F=0.25 to sib mating. The pedigree C702 values for F are

consistent with a measure of parent relatedness that is approximately equal to or less than a second cousin mating.
Association Samples
UK Case-Control Samples
All subjects were unrelated, white, and resident in the British Isles and provided written informed consent to participate in genetic studies. Protocols and procedures were approved by all relevant multi-region (MREC) and Local Ethical Approval
(LREC) panels. Consensus best-estimate diagnoses according to DSMIV were made for all cases based on a semi-structured lifetime psychiatric interview, Schedules for
Clinical Assessment in Neuropsychiatry (SCAN) (Wing et al. 1990) and review of case notes (ie. The same procedure as for for family C702). Formative team reliability meetings took place weekly throughout recruitment.
UK Schizophrenia Cases: A total of 696 cases (473 males and 223 females) that met
DSM-IV criteria for schizophrenia were used in this study. No members of family
C702 were analysed in this or any association sample. Of this total sample, a subset of
476 cases (321 males, 155 females) were analysed as part of a whole-genome association study of schizophrenia (O’Donovan et al, 2008). SNP rs873417 was genotyped in an additional 163 cases (112 males, 51 females), giving a total of 639 cases (433 males, 206 females). In a subset of 661 cases (446 males, 215 females), we genotyped the rare alleles identified in pedigree C702.
UK Bipolar Disorders Cases:

All cases were white UK adults meting DSMIV criteria for bipolar I disorder
(N=1736 cases; 647 males and 1089 females) or schizoaffective disorder, bipolar type
(N=62: 22 males, 40 females). Best-estimate diagnoses were made on the basis of all available information (semi-structured lifetime psychiatric interview and review of case records). 1566 individuals with bipolar I disorder and 62 with schizoaffective disorder, bipolar type were genotyped within the Wellcome Trust Case Control
Consortium (WTCCC) genome-wide association study (Wellcome Trust Case Control
Consortium, 2007) and provided information for the common ; polymorphism, rs873417. A set of 760 cases (710 DSMIV Bipolar I disorder; 263 males, 447 females.
50 DSMIV schizoaffective disorder bipolar type; 21 males, 29 females) were used in the rare variant analysis.
UK Controls : The combined UK control sample used for analysis of the rare alleles identified in pedigree C702 consisted of 2824 Caucasian controls (1421 males, 1403 females) resident in the British Isles. Controls were obtained from four sources: (a)
The British Blood Transfusion Service (N=1406; 735 males and 671 females). The sample was not specifically screened for psychiatric illness but individuals were not taking regular prescribed medications. The UK schizophrenia case sample is groupmatched to a sub-set of this sample for age, sex and ethnicity (N=716, 482 males, 234 females). (b) Family practitioner clinic (N=109). Individuals were recruited from amongst those attending for non-psychiatric reasons. This sample was screened to exclude a personal history of mood disorder or schizophrenia. (c) A control sample
(N=362; 158 males, 204 females) of participants who had originally been recruited to the GENESiS (Genetic and Environmental Nature of Emotional States in Siblings)

study (Sham et al. 2000) via general practices in England and Wales. GENESiS participants were approached to take part in the current study if they fell into the bottom 20% of the distribution on the Sham Composite Index of Liability to
Depression and Anxiety (Sham et al. 2000). Controls had no current serious medical illness or disability and were screened to exclude a personal or family history of psychiatric illness using a semi-structured telephone interview. (d) A sample of control individuals (N=1056. 528 males, 528 females) was obtained from the
Wellcome Trust 1958 British birth cohort, the full sample of which has been described in detail elsewhere (Power and Elliott 2006). This sample overlaps with that analysed as part of the WTCCC study of complex disorders (Wellcome Trust Case
Control Consortium 2007), however samples were only counted once in any analyses.
Irish Case-Control Sample
Ethics Committee approval was obtained from all participating hospitals and centres.
Cases provided written informed consent and were interviewed by a psychiatrist or psychiatric nurse trained to use the Structured Clinical Interview for DSM (SCID-P)
(Spitzer et al. 1990). Diagnosis was made by the consensus lifetime best estimate method with DSM-IV criteria using all available information (interview, family or staff report and chart review). All cases were 18 years old or over, of Irish origin and had been screened to exclude substance induced psychotic disorder or psychosis due to a general medical condition.
Irish schizophrenia and schizoaffective disorder cases : 312 cases met DSM-IV criteria for schizophrenia and consisted of 209 males and 103 females. Of these, 296 were genotyped for the rare variants (201 males and 95 females) and 301 were

genotyped for rs873417 (202 males and 99 females). A total of 89 cases met with
DSM-IV criteria for schizoaffective disorder (45 males and 44 females), of these 76 were genotyped for the rare variants (38 males and 38 females) and 86 were genotyped for rs873417 (43 males and 43 females).
Irish controls: A sample of 806 controls (518 males and 288 females) was collected from the Republic of Ireland health services and used for analysis of the rare variants identified in pedigree C702. A separate sample of 998 controls (295 males, 793 females) was also obtained from Republic of Ireland Health services and used for follow-up analysis of the WGAS common variant results. Controls were not screened for psychiatric illness but were not taking regular prescribed medications as such individuals are excluded from blood donation in Ireland.
Bulgarian Parent-Proband Trios and Case-Control Samples
A case-control sample and an overlapping sample of parent-proband trios were ascertained from Bulgaria. All patients were recruited and interviewed by a psychiatrist trained in the use of the Bulgarian version of the SCAN rating instrument
(Wing et al. 1990). Consensus diagnoses were all made by two, or if disagreement, three independent researchers after reviewing the SCAN data and reading all available discharge summaries. In all regions where subjects were recruited, local Ethics
Committee permission was obtained for participation in genetic association studies.
All participants provided written informed consent. A total of 668 cases with DSM-IV schizophrenia (356 males, 312 females) were used. Of these, 611 were used in the case-control sample (324 males and 287 females) and 431 of these were used as probands in the trios sample (230 males, 201 females). A further 127 cases with

DSM-IV schizoaffective disorder (48 males, 79 females) were used in this study. Of these, 93 were used in the case-control study (35 males and 58 females) and 49 were used as probands in the trios sample (31 males, 18 females). Also, 156 probands with bipolar 1 disorder (93 male probands, 63 female probands) and parents were used in the trios sample only. Parental DNA from all probands used in the trios sample was available. Controls (N=658. 321 males and 337 females) were obtained from the nonpsychiatric clinical lists of General Practitioners, people who came to obtain health certificates, and hospital staff.
German Case Control Sample
All individuals were ascertained from the Munich area in Germany. Diagnosis was made according to DSM-IV criteria following detailed assessment of their medical and psychiatric histories, including a clinical interview using the SCID (Spitzer et al.
1990). All diagnoses were double-rated by a senior researcher. Exclusion criteria included a history of head injuries or neurological diseases. Written informed consent was obtained from all subjects after detailed information about the study, which was approved by the local ethics committee and carried out in accordance to the ethical standards laid down in the Declarations of Helsinki.
German Schizophrenia Cases
758 individuals with schizophrenia (483 males, 275 females) had a DSM-IV diagnosis of schizophrenia.
German Controls

Unrelated Caucasian volunteers were randomly selected and contacted by mail.
Subjects were intensively screened to exclude subjects with any brain disorder, or psychotic disorders, or who had first-degree relatives with psychotic disorders, culminating in a comprehensive interview including the SCID I and SCID II (53, 54) to validate the absence of any lifetime psychotic disorder, a neurological examination to exclude CNS impairment, and the Family History Assessment Module (55) to exclude psychotic disorders among their first-degree relatives. These procedures resulted in 1897 control subjects (920 males and 977 females).
Publicly Available Datasets
This study also has data available for 2938 controls, which have also been used in
GWAS analysis of schizophrenia (O'Donovan et al. 2008) and other disorders
(Wellcome Trust Case Control Consortium 2007) where they were described in detail.
Where studies had overlapping samples, each sample was only included once in any analysis.

Supplementary Tables
Supplementary Table ST1: Results of consanguinity testing using microsatellite marker genotypes and allele frequencies from a previous study (Williams et al. 2003) and algorithms developed and implemented by Peter Holmans. HOM= number of homozygous genotypes. HET = number of heterozygous genotypes. E(HOM) = expected value of HOM assuming no inbreeding. CHI1= chi-square based on HOM,
E(HOM) - i.e. not taking account of frequency of homozygosity for alleles. CHI2 = chi-square based on genotype likelihoods - i.e. taking into account the frequency of homozygous alleles. F = max likelihood estimate of inbreeding coefficient. F-LO, F-
HI: upper and lower 95% confidence interval for F
Supplementary Table ST2: Novel polymorphisms identified in PRKCA by mutation screening of 14 unrelated schizophrenics from the British Isles and a pedigree C702 affected sibling. SNP ID indicates an rs, ss or local identifier. Positions given are as
UCSC March 2006 freeze. The described SNP is identified by brackets, e.g. [C/T].
The site indicates the position of the variant relative to the PRKCA mRNA isoforms screened. If a variant is transcribed then the transcript name is given. Polymorphic bases other than the highlighted one are shown by an “N”.
Supplementary Table ST3: Regions harbouring reported CNVs and the PRKCA region homozygous in pedigree C702 were analysed for evidence of a CNV by oaCGH. Shown is the locus ID (either known CNV from UCSC Genome Browser
May 2004 and March 2006 or the Gene ID for the PRKCA homozygous region) and

position (UCSC March 2006). Also shown are the number of datapoints
(oligonucleotide probes) and the mean log 2 ratio for all datapoints in the region.
Supplementary Table ST4: Association analysis of rs62621676 and the C-HAP haplotype in replication samples (Irish schizophrenia and schizoaffective disorder case-control and Bulgarian schizophrenia, schizoaffective disorder and bipolar 1 disorder trios). Shown for each sample are the allele counts, where 1 is the minor allele (or transmissions/non-transmission for the minor allele) the minor allele frequency in case and controls (or probands and parents respectively) and the corresponding association values (note that p values are one tailed for all odds ratios
>1. For cells with allele counts less than 5, a Fisher’s exact test was performed).
Supplementary Table ST5: Affymetrix 500k GeneChip SNPs nominally associated at
PRKCA . Shown are the details of each associated SNP including the position (UCSC
May 2006), alleles (+ strand), associated allele, case and control genotype counts
(minor allele homozygotes/heterozygotes/major allele homozygotes) and minor allele frequency, p value, odds ratio and empirical p value (10,000 permutations).

Supplementary Figures
Supplementary Figure SF1: A pedigree diagram displaying all microsatellite markers genotyped within family 702. The pedigree is shown as the unaffected father (square), unaffected mother for which DNA was absent (circle) and six affected siblings (black square). Given for each individual are marker names (prefix D17S), position in Mb
(UCSC May 2006) and genotype. Markers genotyped by Williams et al (2003) are indicated by an asterisk. The maximum inherited paternal haplotype shared by the siblings (IBD1 region) and the maximum inherited maternal haplotype shared by the siblings (IBD2 region) are shown in orange and green respectively. The IBD2 region is highlighted by a red rectangle and spans a maximum of 11.7Mb (D17S1160-
D17S2182). A stretch of contiguous marker homozygosity within the IBD2 region spanning a maximum of 3.3Mb is shown by the blue joined lines, flanked by heterozygous genotypes at markers D17S924 and D17S1874.
Supplementary Figure SF2: oaCGH results for the PRKCA region homozygous in pedigree C702 siblings as viewed in SignalMap software (NimbleGen Systems Inc).
Shown (in descending order) is the base position across chromosome 17
(chr17:61200000-62720000) followed by each of the four hybridisation experiments
(two C702 siblings and two unrelated controls) and a map of transcripts across the region (green horizontal bars). For each hybridisation experiment each oligonucleotide probe is represented by a black or red bar along the x-axis (base position). The y-axis shows the log
2
ratio at each probe (-3 to +3) and probes outside of the scale are designated by a red bar. The region highlighted transparent red indicates the homozygous region observed in a pedigree C702 sibling and not in 2328

UK controls and covers the 3’ of all PRKCA isoforms (green bars are isoforms
X52479 and BC053321).
Supplementary Figure SF3: Shown is GWAS data at the PRKCA locus (O'Donovan et al. 2008). Shown above is the pedigree C702 IBD2 linkage region at chromosome 17
(chr17:52,996,269-64,651,294. UCSC March 2006), highlighted in a red box. The below GWAS data plot is data within this region. The x-axis indicates the physical distance across the linkage region and the y-axis is the -log
10
of the allelic chi square association p value. Each red dot represents one of the 1028 SNPs analysed at this locus. Also shown is a blue line indicating the p=0.001 level of significance. Two
SNPs have a p value ≤0.001 and their rs numbers and association p values are given.
Also shown is a schematic or the PRKCA gene and it’s position relative to this association data.

Supplementary Figure SF4: Literature evidence suggests chromosome 17 harbours a disease locus for schizophrenia, bipolar disorders and related illnesses. Shown are regions showing evidence for linkage in each of the studies and the novel C702 linkage region reported in this study. Regions considered as showing evidence for linkage were defined as the markers with the highest LOD score(s) or the LOD-1 region, or a bin region in the Lewis et al (Lewis et al. 2003) meta-analysis, as reported in each study publication. Studies are grouped either as “Schizophrenia” or “Bipolar
Disorder” according to the principal phenotype analysed by the study. The red box indicates a subjective region of linkage common to a large proportion of reports including this study. Note that the some of the studies (Lewis et al. 2003; Williams et al. 2003) have overlapping samples.