Open Access

Post-zygotic genomic changes in glutamate and dopamine pathway genes may explain discordance of monozygotic twins for schizophrenia

  • C. A. Castellani1, 3Email author,
  • M. G. Melka1,
  • J. L. Gui1,
  • A. J. Gallo1,
  • R. L. O’Reilly2 and
  • S. M. Singh1, 2
Clinical and Translational Medicine20176:43

https://doi.org/10.1186/s40169-017-0174-1

Received: 10 July 2017

Accepted: 5 November 2017

Published: 28 November 2017

Abstract

Background

Monozygotic twins are valuable in assessing the genetic vs environmental contribution to diseases. In the era of complete genome sequences, they allow identification of mutational mechanisms and specific genes and pathways that offer predisposition to the development of complex diseases including schizophrenia.

Methods

We sequenced the complete genomes of two pairs of monozygotic twins discordant for schizophrenia (MZD), including one representing a family tetrad. The family specific complete sequences have allowed identification of post zygotic mutations between MZD genomes. It allows identification of affected genes including relevant network and pathways that may account for the diseased state in pair specific patient.

Results

We found multiple twin specific sequence differences between co-twins that included small nucleotides [single nucleotide variants (SNV), small indels and block substitutions], copy number variations (CNVs) and structural variations. The genes affected by these changes belonged to a number of canonical pathways, the most prominent ones are implicated in schizophrenia and related disorders. Although these changes were found in both twins, they were more frequent in the affected twin in both pairs. Two specific pathway defects, glutamate receptor signaling and dopamine feedback in cAMP signaling pathways, were uniquely affected in the two patients representing two unrelated families.

Conclusions

We have identified genome-wide post zygotic mutations in two MZD pairs affected with schizophrenia. It has allowed us to use the threshold model and propose the most likely cause of this disease in the two patients studied. The results support the proposition that each schizophrenia patient may be unique and heterogeneous somatic de novo events may contribute to schizophrenia threshold and discordance of the disease in monozygotic twins.

Keywords

SchizophreniaWhole genome sequencingMonozygotic twinsGenome variationSomatic mutationThreshold model

Background

Monozygotic (MZ) twins originate from a single fertilized zygote and have been used to study the relative contribution of nature and nurture on a variety of phenotypes and disorders for well over a century. Schizophrenia, which is among the most devastating of the major mental health disorders, is thought to have both genetic and environmental causes [1]. Results show that although the frequency of schizophrenia is only 1% in the general population, its concordance in MZ twins approximates ~ 50% and not 100% [2]. Interestingly, recent results have shown that MZ twins may differ for de novo events, that include copy number variations (CNVs) [3, 4] and DNA methylation [58]. The timing, rate, extent and impact of such de novo events however, is difficult to ascertain. They may occur anytime during development as a normal aspect of development of an organ [9] and cell type [10]. Also, depending on the developmental stage at which they arise, will determine their presence in all or almost all cells of an individual or represent mosaicism. The random nature of this variation is expected to differ between MZ twins and contribute to twin differences. Although logical and attractive as a potential hypothesis for the cause of disease discordance in MZ twins, the confirmation of this hypothesis faces two challenges. The first is the identification of all or almost all differences between the genomes of discordant MZ twins and the second is establishing the significance of the observed genomic difference in the disease. Although the former is gradually becoming possible through increased resolution of genomic technologies, the latter remains challenging and will demand diligent efforts [11, 12].

The challenge of analysis and interpretation of complete genome sequences is attributed to a variety of factors [13]. First, the sequence coverage is not always 100% and second, the differences between MZ twins are not always easy to confirm due in part to expected mosaicism of unknown frequency and distribution [14], even though it is possible to differentiate between the pre-zygotic or post-zygotic origin of such twin differences using parental sequences. The next challenge is any involvement of observed differences in the development of schizophrenia. This of course is a much more complicated question. Schizophrenia is highly heterogeneous and affects ~ 1% of the world’s population with a heritability estimate of ~ 80% [1, 15]. Extensive research on this disorder has generated a large number of candidate genes. This includes a report involving 150,000 individuals with over 35,000 schizophrenic patients that has implicated over 108 genetic loci [16]. This considerable body of multifactorial and rather trustworthy data provides a standard for assessing the potential role of any new observation. We note that previously identified loci that are considered particularly trustworthy include DRD2, a common anti-psychotic target, as well as a number of glutamate receptors (GRIA1, GRIN2A, GRM3), members of the voltage gated calcium channels (CACNA1C, CACNA1l and CACNB2) and genes involved in synaptic plasticity [16]. As it stands, there are no common variants that account for a substantial portion of the liability to develop this disease [17]. It argues that the disease is highly heterogeneous and that most patients are genetically distinct. Also, any difference, particularly involving previously identified genes between monozygotic twins discordant for the disease, will have a high probability of being involved in the development of the disease. The results will be patient specific and may or may not apply to all or even most patients.

Finally, the results at hand allow us to appraise the threshold model for the development of schizophrenia [18]. It adds that inherited gene mutations [1921] place an individual on a liability scale for the development of this disease. Additional contributors to this scale may include de novo mutations, environment factors and/or epigenetic [22] events, most occurring during ontogenic development [23]. The model predicts that the liability threshold may be met by inherited factors alone or require additional random genetic and epigenetic events including environmental events during development. We propose that this model can be tested using MZ twins discordant for schizophrenia with the assumption that inherited components will be shared between twins. Further, additional de novo mutations (and epimutations) will be acquired during ontogeny in the affected but not in unaffected twin. Given high heterogeneity of the disease, such results across MZD twin pairs may follow similar pattern but differ in the genes affected. Further, the genes affected may belong to a number of common pathways that appear to be invariably affected in this complex disease. Finally, the genes identified in this research are known to be involved in post-synaptic complexes [24] and synaptic strength [25], processes that are known to be defective in several but not all patients with schizophrenia.

Methods

Subjects

This research received ethics approval from the Committee on Research Involving Human Subjects at The University of Western Ontario, London, Ontario, Canada. The methods were carried out in accordance with all approved guidelines and regulations. Two families with monozygotic twins discordant for schizophrenia were selected based on their long term clinical features assessed in-person by Richard O’Reilly (Psychiatrist), using the Structured Clinical Interview for DSM-IV (SCID I and SCID II) and a review of medical records from multiple decades [26, 27]. All participants provided written informed consent. A second senior psychiatrist independently reviewed videotapes of the structured interviews of the twins and confirmed the diagnoses. It has assured a reliable diagnosis and long-term discordance of the two MZ twin pairs used in this study. All six subjects (Fig. 1) provided blood and cheek swab samples that were used to isolate genomic DNA using the PerfectPure DNA blood kit (Blood samples), and the QIAGEN DNA Micro Kit (Buccal samples), following the manufacturer’s protocols. The experimental workflow of the analysis is summarized in Fig. 2.
Fig. 1

Members of the two discordant monozygotic twin pairs and one set of parents included in the study

Fig. 2

Flow chart of methods employed

The twins from family 1 are Afro-American females and contributed DNA samples at age 53. The affected twin (I-2-1) was diagnosed with schizophrenia at age 22. She was admitted to a psychiatric unit on at least 12 occasions and experienced paranoid delusions, auditory hallucinations and occasionally euphoria during her acute episodes of illness. This twin had significant functional decline and lived with her parents throughout her adult life. The diagnosis of schizophrenia was confirmed by the study psychiatrist. I-2-2 did not experience any significant symptoms of mental illness until she developed a brief episode of depression at age 48, which was treated with an antidepressant. Four years later this twin developed an acute episode of mania, which required hospitalization and she was placed on the mood stabilizer divalproex sodium. She was diagnosed as having a bipolar disorder by the study psychiatrist. This twin pair has been previously described in detail [28]. At the time of sample collection, the twins were discordant for schizophrenia for 31 years. The father (I-1-1) of the twins was aged 82 at assessment and had a mild obsessive–compulsive personality disorder but no other psychiatric problems, while the mother (I-1-2) was aged 74 and had never had any psychiatric problems.

At the time of sample collection, the twins from family 2 (Fig. 1) were 43 years of age. The twins are Caucasian females. Twin II-2-1 became ill at age 27. She experienced paranoid delusions and hallucinations, which usually occurred in the context of a euphoric or depressed mood. She lived with her twin sister and had worked intermittently. She was diagnosed with a schizoaffective disorder. The twin sister (II-2-2) sustained skeletal injuries in a motor vehicle accident at age 18 years. A boyfriend died close to the time of this accident and II-2-2 became depressed for a short period around this time. She has had no further episodes of depression or other emotional or psychiatric problems. The twins were considered discordant for 16 years at the time of sample collection.

Genome sequencing

The genome sequence of the six subjects (Fig. 1) was generated at Complete Genomics Inc. (Mountain View, CA) in the form of ~ 2 billion overlapping 70-base nucleotide sequences. They allowed reconstruction of six individual genomes. Duplicates were removed prior to variant calling. The sequences met the criteria of high accuracy (99.999%) and were considered suitable for identification of rare variants including somatic mutations as described by Drmanac et al. [29]. These variants included single nucleotide variants (SNVs), indels and block substitutions as well as larger variants classified as CNVs and SVs that were called in comparison to reference sequence (NCBI Build 37). CNVs were called based on a read depth or depth-of-coverage algorithm provided by Complete Genomics. Sequence coverage was averaged and then GC bias was corrected for over a fixed window (2 kb) and normalized relative to a set of standard (CG 45 genome reference) genomes sequenced by Complete Genomics. A Hidden Markov Model was used to determine the integer copy number state (0–10). Structural variations were detected by identifying discordant mate pair mappings found during the assembly process. Mate pair mappings where each arm maps to the reference genome but with either an unexpected length between them or an anomalous orientation are subjected to local de novo assembly to refine junction breakpoints at single base pair resolution. Complete genomics then generated a high confidence junctions file that reports junctions that are most likely to be accurate. CGAtools junctions2events was then used to convert high confidence junctions to possible SV events using repeat masker 37 data, hg19 reference file and a refseq gene information file. The junctions2events command in CGAtools identifies likely deletion, inversion and translocation events from the list of high confidence junctions delivered by Complete Genomics. SVs were further refined into five categories: deletions, tandem duplications, distal duplications, inter-chromosomal events and inversions. To call small variants in our dataset, Master Variation Files (MasterVar) were generated using CGAtools and hg19 as reference. VCF files were then generated from each MasterVar file using CGAtools command mkvcf. VCF files generated this way were directly inputted into ingenuity variant analysis (Ingenuity Systems, Redwood City, CA). Given the potential for false positives identified in genome sequencing, a stringent read depth of 50 and a call quality of 100 (calculated by complete genomics and based on a phred scale) were chosen as parameters for initial variant filtering. In the analysis of family 1, variants that were present in the affected twin and not present in the unaffected twin or their mother or father were assessed as de novo. Also, in the twin analyses of family 2, without parents, variants that were present in the affected twin and not present in the unaffected twin were labeled as provisional de novo. Variants were annotated with overlapping genes, cytoband, gene region (Exonic, Intronic, Promoter, 5′UTR, 3′UTR, Splice Site), translational impact (if applicable), SIFT function prediction (if applicable), SIFT score (if applicable), dbSNP ID (if applicable) and frequency in the 1000 Genomes as well as frequency in the Complete Genomics Public Genome dataset. The biological context filter in ingenuity variant analysis was applied to downstream data with “Schizophrenia, Neurological Disease and diseases consistent with those two phenotypes” as the filtering criteria. Genes had to have a direct connection to these phenotypes (no hops allowed).

In the case of CNVs and SVs a 50% reciprocal overlap rule [3032] was applied to determine if two variants were the same or different between twins/parents. All CNVs/SVs had to meet the ≥ 50% rule when compared to the other CNV/SV, otherwise, the two were considered unique. Pairwise comparisons were performed for all CNVs and SVs. To increase the efficiency of this, HD-CNV was utilized [33]. Comma delimited files were prepared using a custom python script and the 50% reciprocal overlap rule was applied to determine the CNVs and SVs that were unique to an individual. Interchromosomal and inversion comparisons were analyzed manually due to the limitations of HD-CNV. Inter-chromosomal events were considered the same if the origin and the destination chromosome numbers matched and the junction positions were less than 500 bp apart. Inversions had to share the same direction and 50% or more identity to be classified as shared.

Confirmation of variants

Quantitative PCR using TaqMan® Assays in an Applied Biosystem StepOne were performed on selected CNVs [4] and SVs [6]. CNVs and SVs that were confirmed via Real Time PCR were then assessed in the Buccal DNA from the same individuals to identify if the variant arose before or after the differentiation of the germ layers. RNAseP was used as the reference gene. Predesigned TaqMan assays were ordered from Life Technologies for regions of interest. CopyCaller 2.0 was used to generate the predicted copy numbers. Circos [34] was used for visualization of post-filtering variation data. Unique variants were separated into files to generate relevant tracks in the genome diagram. Structural variants that involved more than one chromosome were visualized using “links” in Circos [34].

Sanger sequencing was used to assess small variants of interest in our dataset [28]. Regions were sequenced at the DNA sequencing center at The London Regional Genomics Centre. Variants that appeared mosaic in nature were further assessed using PASA (PCR amplification of specific alleles).

Pathway analysis

Any unique variant that overlapped a gene was identified and the gene lists were used in Core pathway analysis (Ingenuity Systems, Redwood City, CA) to identify pathways and networks that were overrepresented in the filtered dataset. Only the genes that were identified to overlap high confidence somatic de novo (family 1) or provisional de novo (family 2) variations were included in the pathway analysis. Variants that were found to be unique to unaffected twins were also assessed in a separate pathway analysis. The top 20 canonical pathways found to be overrepresented in each individual were then compared between all members in the study; pathways that were found in affected and unaffected twins were labeled as GP. They were viewed as “shared genetic predisposition” between the two members of the twin pair. Pathways that were unique to affected twins only were labeled as GPD. They were viewed as additional “genetic predisposition that led to disease” in the affected and not the unaffected member of the twin pair.

Results

Defining genetic variation including de novo events

The complete genome sequences of two MZD twin pairs and one set of parents (Fig. 1) were generated with a high call quality above 100 (Additional file 1: Figure S2) and an average read depth of 47–50 fold coverage (Additional file 1: Figure S3) following our workflow (Fig. 2). They represented over 99% of the reference sequence for each genome (Table 1). We compared individual genome sequences with the Genome Reference Consortium Human Genome Build 37 using Complete Genomics Analysis tools (CGAtools) for identification of individual specific variants and their genomic location at single base pair resolution. The results show that each genome harbors 3.3 to 3.9 million single nucleotide variants (SNVs), 370–430 thousand indels (small insertions and deletions), 71–80 thousand block substitutions, 1 thousand structural variations, and 150 copy number variations as well as a transition/transversion ratio of 2.1. The exception to this pattern was the father in family 1 who carried 592 copy number variations and 1110 structural variations, that may be associated with a diagnosis of chronic leukemia unrelated to this study [35]. We further grouped individual variations as small sequence changes, (SSCs—SNVs, indels, block substitutions), copy number variants (CNVs) or structural variants (SVs). An example to structural variation observed in family 1 involving inter-chromosomal translocation is depicted in the Circos plot (Additional file 1: Figure S1).
Table 1

Identity of sequenced genomes

Sample ID

Family

Gender

Age at assessment

Age of onset

Disease status

% of genome called

Normalized average coverage

I-1-1

Family 1

Male

80

N/A

Unaffected

99.037

49.55

I-1-2

Family 1

Female

76

N/A

Unaffected

99.042

47.27

I-2-1

Family 1

Female

43

27

Affected

99.042

48.07

I-2-2

Family 1

Female

43

N/A

Unaffected

99.042

47.41

II-2-1

Family 2

Female

53

22

Affected

99.039

49.71

II-2-2

Family 2

Female

53

N/A

Unaffected

99.037

50.25

Distribution of variants across twins

The frequency of variants across chromosomes that is related to their size is different between parents at each chromosome but rare between the monozygotic twins (Fig. 3). In family 1, some sequence differences between twins were viewed as inherited (present in at least one parent) and others were considered as post zygotic de novo given that they were not present in any of the two parents (Table 2). The de novo variants were further assessed by their presence in exons (Tables 3 and 4). In family 1, two unique CNVs were identified as inherited and five were considered de novo in the affected twin (Table 5). In contrast, in the unaffected twin, five CNVs were identified as inherited and four were labelled as de novo. The CNVs unique to the affected member of twin pair 1 and 2 are given in Tables 6 and 7 respectively. Interestingly, the structural variations followed a pattern similar to small sequence variations (Table 8). Most of these variants are shared between twins, the unshared variants are more common in the affected as compared to their unaffected counterpart and the post-zygotic de novo events are not different between MZD twin in family 1. In the absence of parental sequences for family 2, it was not possible to consider the familial vs somatic de novo nature of the twin differences. For the purpose of this discussion variations that were unique to the affected twin in twin pair 2 were considered as “provisional de novo”. We conclude that most human variations are historical, yet rare variations may be acquired through de novo events during genetic transmission as well as extensive mitosis during development and aging. As expected, the post zygotic de novo variants are often reflected as different degrees of mosaicism, that are not always easy to independently confirm using standard technologies.
Fig. 3

Chromosomal distribution of small sequence variations (SNVs, Indels, block substitutions) in all six samples

Table 2

Shared and de novo small sequence variations (SNVs, substitutions, Indels) as compared to NCBI Build 37

Sample

Total sequence variations before confidence filters applied

High confidence variants unshared with co-twin

Unshared with co-twin

Inherited (present in parent)

De novo (not present in parent)

Family 1 affected (I-2-1)

4,295,920

11,577

7302

4275

Family 1 unaffected (I-2-2)

4,265,089

9345

5776

3569

Family 2 affected (II-2-1)

3,780,127

10,725

N/A

N/A

Family 2 unaffected (II-2-2)

3,789,298

10,351

N/A

N/A

Table 3

Exonic de novo variants in the affected twin in family 1 (I-2-1)

Chr

Position

Ref

Sample

Type

Cytoband

Gene

Translation impact

dbSNP ID

1000 genomes

CG public genomes

1

117142868

CA

TG

Sub

1p13.1

IGSF3

In-frame

   

4

85996

 

C

Ins

4p16.3

ZNF595

Frame shift

   

4

86004

A

G

SNV

4p16.3

ZNF595

Missense

112290390

  

4

86022

CAG

GAC

Sub

4p16.3

ZNF595

In-frame

386670355

  

4

86043

T

C

SNV

4p16.3

ZNF595

Synonymous

377364445

  

7

100549935

T

G

SNV

7q22.1

MUC3A

Missense

73714229

  

7

100549942

T

C

SNV

7q22.1

MUC3A

Missense

73714230

  

7

100552452

T

C

SNV

7q22.1

MUC3A

Synonymous

112050489

  

11

48367133

C

A

SNV

11p11.2

OR4C45

Missense

79453749

  

12

40875389

CCATCAGCTGGAGTGACAGTGACATCCGGA

Del

12q12

MUC19

In-frame

   

12

40880542

C

T

SNV

12q12

MUC19

Missense

370502411

 

14.81

12

40880545

C

G

SNV

12q12

MUC19

Missense

199768257

 

16.66

12

122359397

 

GAGGAGGAGGAGAAA

Ins

12q24.31

WDR66

In-frame

142042908

 

67.59

13

25671607

GA

AG

Sub

13q12.13

PABPC3

In-frame

386769143

  

13

46170723

GATACTCTTCCTCCTCCA

Del

13q14.13

ERICH6B

In-frame

   

17

74288565

TGA

 

Del

17q25.1

QRICH2

In-frame

35035566

46.96

20.37

22

29885594

A

T

SNV

22q12.2

NEFH

Synonymous

79235463

  

22

29885599

AGGAAG

 

Del

22q12.2

NEFH

In-frame

149571560

  

Gene variants in bold are not known to be polymorphic and considered novel and potential pathogenic impact is marked in bolditalic

Table 4

Exonic de novo variants in the affected twin in family 2 (II-2-1)

Chr

Position

Ref

Sample

Type

Cytoband

Gene

Translation impact

dbSNP ID

1000 genomes

CG public genomes

1

1650787

T

C

SNV

1p36.33

CDK11B; CDK11A

Missense

1137003

 

28.7

1

1650797

A

G

SNV

1p36.33

CDK11B; CDK11A

Missense

1059830

 

31.48

1

1650801

T

C

SNV

1p36.33

CDK11B; CDK11A

Synonymous

1137004

 

31.48

1

13183225

T

C

SNV

1p36.21

HNRNPCL1/HNRNPCL2

Synonymous

28634306

  

1

13183228

C

T

SNV

1p36.21

HNRNPCL1/HNRNPCL2

Synonymous

144054379

  

1

13183237

CT

TC

Sub

1p36.21

HNRNPCL1/HNRNPCL2

In-frame

   

1

13183243

T

C

SNV

1p36.21

HNRNPCL1/HNRNPCL2

Synonymous

138897759

  

1

13183248

TC

AA

Sub

1p36.21

HNRNPCL1/HNRNPCL2

In-frame

   

1

17266536

G

C

SNV

1p36.13

CROCC

Missense

9435714

 

10.18

1

62675619

C

T

SNV

1p31.3

L1TD1

Synonymous

4625314

29.85

33.33

1

109007867

G

A

SNV

1p13.3

NBPF4/NBPF6

Missense

  

26.85

1

109007877

T

G

SNV

1p13.3

NBPF4/NBPF6

Synonymous

  

26.85

1

109737063

C

T

SNV

1p13.3

KIAA1324

Synonymous

386565601

71.37

68.51

1

109737090

G

A

SNV

1p13.3

KIAA1324

Synonymous

386565600

71.53

67.59

1

111957583

A

G

SNV

1p13.2

OVGP1

Missense

1126656

 

3.7

1

111957592

A

G

SNV

1p13.2

OVGP1

Missense

56294468

22.32

3.7

1

120539742

G

A

SNV

1p12

NOTCH2

Missense

2258139

  

1

120548025

G

A

SNV

1p12

NOTCH2

Synonymous

140551270

  

1

120548055

T

C

SNV

1p12

NOTCH2

Synonymous

199592384

  

1

144873963

T

 

Del

1q21.1

PDE4DIP

Frame shift

 

28.91

32.4

1

144922523

C

T

SNV

1q21.1

PDE4DIP

Missense

2455994

 

28.7

1

145103928

G

A

SNV

1q21.1

SEC22B

Synonymous

2596251

34.01

35.18

1

201178819

G

A

SNV

1q32.1

IGFN1

Missense

72468019

 

11.11

1

206566904

T

C

SNV

1q32.1

SRGAP2B; SRGAP2D; SRGAP2; SRGAP2C

Synonymous

2919105

49.44

 

1

248813827

T

C

SNV

1q44

OR2T27

Missense

1782241

  

2

132238043

A

C

SNV

2q21.1

TUBA3C/TUBA3D

Synonymous

74625243

 

14.81

3

75786499

CA

TG

Sub

3p12.3

ZNF717

In-frame

  

0.92

3

75786515

GG

AT

Sub

3p12.3

ZNF717

In-frame

 

0.92

 

3

75787265

C

G

SNV

3p12.3

ZNF717

Synonymous

144538707

  

3

75787269

G

T

SNV

3p12.3

ZNF717

Missense

   

3

75788023

C

T

SNV

3p12.3

ZNF717

Missense

76889571

 

50

3

100170634

T

C

SNV

3q12.2

LNP1

Synonymous

9848109

 

24.07

3

195510827

C

T

SNV

3q29

MUC4

Missense

413807

3.53

24.07

3

195511780

G

A

SNV

3q29

MUC4

Missense

391928

  

5

140725160

 

A

Insertion

5q31.3

PCDHGA3; PCDHGA2; PCDHGA1

Frame shift

372306793

  

6

26406255

G

A

SNV

6p22.2

BTN3A1

Synonymous

3857550

 

41.66

6

33037579

AT

TG

Sub

6p21.32

HLA-DPA1

In-frame

386699858

 

37.96

6

33052986

T

C

SNV

6p21.32

HLA-DPB1

Synonymous

 

46.37

37.03

7

100550039

 

CTC

Ins

7q22.1

MUC3A

In-frame

   

7

142460313

T

C

SNV

7q34

PRSS1

Synonymous

6666

39.66

24.07

7

142460335

A

G

SNV

7q34

PRSS1

Missense

201550522

0.16

 

8

10467652

GC

CT

Sub

8p23.1

RP1L1

In-frame

386722180

  

8

103573011

TGCAACCCCTGCAGCCCCTGCAACCCG

Del

8q22.3

ODF1

In-frame

 

31.29

23.14

11

1016776

C

T

SNV

11p15.5

MUC6

Missense

33988517

 

38.88

11

1017110

CGGT

TGCC

Sub

11p15.5

MUC6

In-frame

  

32.4

11

1018069

G

A

SNV

11p15.5

MUC6

Missense

10736904

  

11

1018090

G

 

Del

11p15.5

MUC6

Frame shift

   

11

1018095

G

TA

Sub

11p15.5

MUC6

Frame shift

   

11

1092684

C

T

SNV

11p15.5

MUC2

Synonymous

201269049

  

11

5270686

G

A

SNV

11p15.4

HBG1

Missense

1061234

 

75.92

11

18290866

T

C

SNV

11p15.1

SAA1

Synonymous

1136745

  

11

48346916

G

C

SNV

11p11.2

OR4C3

Missense

77069283

  

11

48346924

T

C

SNV

11p11.2

OR4C3

Synonymous

72911454

  

11

48346932

G

A

SNV

11p11.2

OR4C3

Missense

80285195

0.28

 

11

48347306

G

T

SNV

11p11.2

OR4C3

Missense

73465911

 

33.33

11

48367052

 

AG

Ins

11p11.2

OR4C45

Frame shift

   

11

48367073

A

C

SNV

11p11.2

OR4C45

Missense

7941588

79.55

75

11

56143357

G

A

SNV

11q12.1

OR8U1; OR8U8

Synonymous

76949582

 

36.11

11

56143963

AATCTATAGC

GATTTACAGT

Sub

11q12.1

OR8U1; OR8U8

Synonymous

   

11

56468020

T

C

SNV

11q12.1

OR9G1; OR9G9

Missense

532637

41.21

56.48

11

57982726

G

T

SNV

11q12.1

OR1S1

Synonymous

1993089

52.32

52.77

11

57982763

A

G

SNV

11q12.1

OR1S1

Missense

61763008

 

50.92

11

89703619

G

A

SNV

11q14.3

TRIM64/TRIM64B

Missense

79824618

 

77.77

11

89819403

G

T

SNV

11q14.3

UBTFL1

Missense

   

12

11214857

T

C

SNV

12p13.2

TAS2R46; PRH1

Missense

201891491

  

12

11214870

A

T

SNV

12p13.2

TAS2R46; PRH1

Synonymous

200226376

  

12

11244721

GAA

CAC

Sub

12p13.2

TAS2R43; PRH1

In-frame

  

19.44

12

11244730

AA

GG

Sub

12p13.2

TAS2R43; PRH1

In-frame

  

18.51

12

49522578

T

C

SNV

12q13.12

TUBA1B

Synonymous

1057725

54.49

 

12

49522605

C

T

SNV

12q13.12

TUBA1B

Synonymous

1057548

45.33

 

12

52843610

C

A

SNV

12q13.13

KRT6B

Missense

   

13

46170724

ATACTCTTCCTCCTCCAG

Del

13q14.13

ERICH6B

In-frame

   

13

53216666

G

A

SNV

13q14.3

HNRNPA1L2

Synonymous

113869751

1.08

1.85

13

103399222

G

T

SNV

13q33.1

CCDC168

Stop gain

  

25

18

9887394

C

T

SNV

18p11.22

TXNDC2

Synonymous

2240910

51.84

 

19

4511197

G

A

SNV

19p13.3

PLIN4

Synonymous

199625614

  

19

4511200

C

T

SNV

19p13.3

PLIN4

Synonymous

200718202

0.14

 

19

55286854

A

G

SNV

19q13.42

KIR2DL1/KIR2DL3

Missense

666590

0.08

 

19

55286864

A

C

SNV

19q13.42

KIR2DL1/KIR2DL3

Synonymous

77397437

16.63

 

21

10942923

G

A

SNV

21p11.1

TPTE

Missense

76723236

 

7.4

22

38120180

CTC

 

Del

22q13.1

TRIOBP

In-frame

   

22

39387558

C

T

SNV

22q13.1

APOBEC3A_B; APOBEC3B

Synonymous

1065184

  

Gene variants in bold are not known to be polymorphic and considered de novo and potential pathogenic impact is marked in bolditalic

Table 5

Shared and unshared copy number variants (CNVs) as compared to NCBI Build 37

Sample

Total CNVs

Shared with co-twin

Unshared with co-twin

Shared with co-twin

Unshared with co-twin

Inherited

De novo

Inherited

De novo

Family 1 affected (I-2-1)

152

145

7

131/145

14/145

2/7

5/7

Family 1 unaffected (I-2-2)

154

145

9

131/145

14/145

5/9

4/9

Family 2 affected (II-2-1)

156

151

5

N/A

N/A

N/A

N/A

Family 2 unaffected (II-2-2)

157

151

6

N/A

N/A

N/A

N/A

Table 6

Copy number variants unique to the affected member of family 1 (I-2-1)

Chr

Start

End

Cytoband

Size (bp)

CNV type

Identity

Overlapping genes

5

119380128

119382128

5q23.1

2000

Del

De novo

None

9

6700000

6710000

9p24.1

10,000

Del

De novo

None

10

26998675

27002675

10p12.1

4000

Del

De novo

PDSS1

14

20314000

20328000

14q11.2

14,000

Amp

Inherited

None

15

22422114

22492114

15q11.2

70,000

Amp

De novo

LOC642131

16

34467150

34515150

16p11.2

48,000

Amp

De novo

None

16

55841801

55855801

16q12.2

14,000

Amp

Inherited

CES1

The parental sequences have been used to establish the de novo [absent in parent(s)] or inherited [also present in parent(s)] nature of each CNV. Shared identity is based on a 50% reciprocal overlap rule

Table 7

Copy number variants unique to the affected member of family 2 (II-2-1) as compared to unaffected MZ twin

Chr

Start

End

Cytoband

Size (bp)

CNV Type

Overlapping genes

5

17612657

17620657

5p15.1

8000

Del

None

5

46244657

46246657

5p11

2000

Amp

None

5

135114128

135120128

5q31.1

6000

Del

None

12

114521470

114529470

12q24.21

8000

Amp

None

14

106926000

106930000

14q32.33

4000

Amp

None

Shared identity is based on a 50% reciprocal overlap rule

Table 8

Shared and unshared structural variation (SV) as compared to NCBI Build 37

Sample

Total SVs

Shared with co-twin

Unshared with co-twin

Shared with co-twin

Unshared with co-twin

Inherited

De novo

Inherited

De novo

Family 1 affected (I-2-1)

919

781

138

750

31

97

41

Family 1 unaffected (I-2-2)

893

781

112

750

31

66

46

Family 2 affected (II-2-1)

996

855

141

N/A

N/A

N/A

N/A

Family 2 unaffected (II-2-2)

977

855

122

N/A

N/A

N/A

N/A

Structural variants fell under five categories: deletions, tandem duplications, distal duplications, inter-chromosomal variations and inversions. There were no inversion differences found between twins in either family. They were not included in subsequent analyses

De novo mutational features in twins affected with schizophrenia: SSCs

We classified SNVs, small indels and block substitutions as small sequence changes (SSCs). The identity of de novo (family 1) and provisional de novo (family 2) high confidence variations in affected twins shows that majority of variants are inter-genic SNVs and that each individual harbors approximately equal number of block substitutions, insertions and deletions (Figs. 3 and 4). As expected, the exonic variants are relatively rare. The exonic de novo variations identified were annotated with gene information for the two patients (Tables 3 and 4). Of the exonic variants identified, 13 exonic variants in family 1 and 22 exonic variants in family 2 were related to brain function or previously implicated in schizophrenia and related disorders. The patient in family 1 carries four exonic de novo variants in ZNF595, a zinc finger protein, two of which are predicted to have a functional impact: one frameshift and one missense mutation. Further, two missense mutations in MUC3A (that encode for a transmembrane mucin) and a missense in OR4C45 (that encode for olfactory receptors) may also contribute to pathophysiology. Interestingly, these variations have not been reported in 1000 genomes as well as CG public genomes and may not be polymorphic. In comparison, the patient from family 2 appears to carry a much larger number of variants. However, in the lack of parental sequences this only represents the differences between the discordant twins. Most (51/82) of these variants in this patient have been reported in 1000 genomes and/or CG public genomes and are considered polymorphic. It leaves 31 variants that may be viewed as provisional somatic de novo. The genes affected by missense changes include some that are compatible with the pathophysiology of schizophrenia. These include NOTCH2, OR2T2, ZNF717, MUC4, MUC6, OR4C3, UBTFL1, TAS2R46 and KRT6B (Table 4). However, we note that although these results are appealing, additional validation will be needed to establish a precise role for these genes in the etiology of schizophrenia.
Fig. 4

De novo (family 1) and presumed de novo (family 2) variants identified in the affected twin of family 1 (I-2-1) and the affected twin of family 2 (II-2-1)

De novo mutational features in twins affected with schizophrenia: CNVs

The genome sequences of the six individuals were used to identify individual specific copy number variations as compared to NCBI Build 37. Table 5 shows the distribution of observed CNVs in MZ twins representing the two families. This data allowed classification of CNVs representing inherited (present in at least one parent) and de novo (not present in either parent and also not present in co-twin) for family 1 and unshared between twins in family 2. Of the rare CNVs that were not shared between twins, some represented inherited and others non-inherited and somatic de novo events that must have occurred during independent mitosis following their separation from each other (Tables 6 and 7). In family 1, five of the seven unique CNVs were also not found in either parent. Discordant CNVs between twin pairs were annotated and are presented in Tables 6 and 7, for the affected twin from family 1 and 2, respectively. Three genes overlapped unique CNVs in family 1. The PDSS1, and LOC642131 genes represented somatic de novo events, as they were not present in either parent while CES1 that was present in one parent was viewed as inherited. Although the affected twin of family 2 also carried five CNVs that were not present in her unaffected twin, these regions did not directly overlap any genes.

De novo mutational features in twins affected with schizophrenia: SVs

The complete genome sequences of the six individuals were also used to identify individual specific deletions, tandem duplications, distal duplications, inter-chromosomal variations and inversions in comparison to NCBI Build 37. They were grouped as structural variants (SVs). The SVs ranged from 50 bp to 218 Mb in length. Most of the SVs in family 1 (total 138) and 2 (total 141) represented deletions (78 and 86%), followed by tandem duplications (6 and 10%) and distal duplications (6.5 and 3.5%). Also, we found one inter-chromosomal move involving a translocation of CDC27 from chromosome 2 to 17 in the patient in family 1 (Additional file 1: Figure S1).

Further, we characterized the genomic details of individual SVs that were unique to the affected twins of the two families (Additional file 1: Table S1 and S2). For family 1 where parental sequences are available we were able to eliminate familial events and concentrate on somatic de novo events. We note that these changes have affected two genes (ANKS18 and CLCN5) via deletion, four genes (LOC285768, NTM, SNORD115-29 and GZMM) due to tandem repeats and a 5 Mb tandem duplication on chromosome 1 (825765) affecting 101 genes. Also, it was possible to identify SV differences between twins in family 2, but in the absence of parental sequences they could not be characterized as familial or somatic de novo as in family 1. Consequently, the SV differences between twins in family 2 are viewed as provisional somatic de novo. As in family 1 they affected 47 genes by deletion, seven genes at seven sites by tandem duplication along with a 3 Mb tandem duplication on X (52886720) overlapping 39 genes and 2 genes by distal duplication. Also, the genomes carried rare (two or three) inversions, both twin pairs shared them with their co-twin and all inversions were inherited in family 1. Finally, the sharing of CNVs and SVs between any two individuals is directly correlated with their genetic relatedness; high but not 100% between monozygotic twins, low across unrelated individuals and intermediate between a parent and an offspring, as expected.

Independent confirmation of NGS results

We sought to confirm a random sample of CNVs, SVs and SSCs by independent experiments involving Real Time PCR for confirmation of CNVs and SVs (Table 9) and sanger sequencing for confirmation of SSCs (Fig. 5a, b). They represented 10 randomly chosen structural rearrangements and 30 randomly chosen SSCs, specifically 4 CNVs, 6 SVs and 30 SSCs (two of which failed sanger sequencing). Table 9 outlines the CNVs and SVs that were assessed by Real Time PCR and includes the predicted identity of the variants from sequencing. Each Real Time PCR assay identified the number of copies of each segment of DNA interrogated, which are reported in Table 9. Further, the Real Time PCR for CNVs and SVs using blood DNA confirmed 5/10 variants, three of which were also confirmed on the DNA from buccal swabs from the same individuals. Many of the SSC findings represented shared peaks that may have resulted from expected mosaicism resulting from somatic de novo events during different stages of ontogeny. Given the early differentiation of the germ layers during development, we would expect tissue specific somatic variation to exist, which is compatible with only some of the variation between twins being identified in both blood and buccal tissues in the same individual.
Table 9

Results of real time quantitative PCR analysis on 10 CNV/SV regions predicted by NGS to be unshared between twins

Gene/region

Chr

Start

End

Size (bp)

Family

Type

NGS prediction

Real time result in affected twin

Difference between twins?

Buccal DNA

GABRD

1

825765

5726936

4,901,171

1

SV

Increase

2.62

Yes (2.65)

CLSTN2

3

139670597

139674454

3857

2

SV

Increase

1.16

No (1.64)

OPRM1

6

154446930

154447253

323

2

SV

Decrease

2.15

N/A

STX1A

7

66193913

73382120

7,188,207

1

SV

Decrease

2.75

No (1.98)

12q24.21

12

114521470

114529470

8000

2

CNV

Increase

1.33

Yes (0.82)

ANKS1B

12

99793948

99802771

8823

1

SV

Decrease

1.9

N/A

15q11.2

15

22422114

22492114

70,000

1

CNV

Increase

2.69

Yes (2.58)

CES1

16

55841801

55855801

14,000

1

CNV

Increase

1.56

N/A

16p11.2

16

34467150

34515150

48,000

1

CNV

Increase

1.8

N/A

PLTP

20

44535505

44535941

436

1

SV

Decrease

2.1

N/A

Fig. 5

a Confirmed variant between monozygotic twins in family 1 in the 4th exon of the ZNF595 gene. This variant changes isoleucine to serine. b Confirmed variant between monozygotic twins in family 2 in the 13th exon of the PDE4DIP gene. This variant changes Tryptophan to a premature stop codon

Genetic differences between MZ twins and their discordance for schizophrenia

The results also allow us to assess any involvement of genetic differences between MZ twins in the development of schizophrenia using a threshold model [18]. It assumes that both members of the monozygotic discordant MZD twins will carry family specific genetic predisposition for the disease and rare ontogenetic additional changes in the affected twin will add to the predisposition that will be sufficient for the onset of the disease. This model is testable given near complete coverage of genetic changes in the affected as well as unaffected members of the two MZD twin pairs. It begins with development of a list of all genes that are affected by a variety of mutational mechanisms in four members of the two MZD twin pairs. This list is rather comprehensive and includes all variants, some validated and others not validated. We have used this list to assess the effect of these differences using ingenuity pathway analysis (IPA). It moves the analysis from a focus on affected genes to affected pathways.

Table 10 shows the top 20 individual specific canonical pathways in two affected individuals belonging to the two families. Interestingly, these pathways are not random. Figure 6 incorporates our strategy in assessing the nature of the threshold model in the two patients [36]. Of the top 20 pathways in patient 1 and patient 2, 10 are shared between them (Additional file 1: Figure S4). Also, 8 of the 10 pathways shared by the two patients are present in either of the two unaffected members of the two twin pairs. It leaves two pathways that may be viewed as highly specific to the two patients (Fig. 6). They represent dopamine-DARPP32 feedback in cAMP signaling (Fig. 7a, family 1, p = 2.28E−04; family 2, p = 5.84E−03) and glutamate receptor signaling (Fig. 7b, family 1, p = 1.46E−03; family 2, p = 3.88E−05). We note that 13 and 29 genes of the two pathways respectively are affected in the patient of family 1. The corresponding numbers for the patient in family 2 are 15 and 23 genes for the two pathways, respectively (Table 11). Although few of the mutated genes are patient specific, the two patients share a large number of affected molecules in glutamate receptor signaling as well as dopamine-DARPP32 feedback in cAMP signaling pathways. Further, we note (Table 10) that four of the top five pathways in patient of family 1 and three of the top five canonical pathways in patient of family 2 are relevant to neural functions and have the potential to contribute to the disease in a threshold model discussed in the next section.
Table 10

Top 20 canonical pathways identified by ingenuity pathway analysis (IPA) in the affected twin of each family

Canonical pathways—family 1 affected (1A)

Shared with

p value

1. CREB signaling in neurons

2A, 2U

0.0000041687

2. Neuropathic pain signaling in dorsal horn neurons

2A, 1U, 2U

0.0000083176

3. Axonal guidance signaling

2A, 1U

0.0000630957

4. Cellular effects of sildenafil (Viagra)

2A, 1U

0.0001479108

5. Role of NFAT in cardiac hypertrophy

0.0001513561

6. Dopamine-DARPP32 feedback in cAMP signaling

2A

0.0002290868

7. Synaptic long term depression

2A, 1U, 2U

0.0002398833

8. Wnt/Ca+ pathway

0.0003630781

9. Synaptic long term potentiation

2A, 2U

0.0008511380

10. PPARα/RXRα activation

2U

0.0011748976

11. Gap junction signaling

0.0013803843

12. Glutamate receptor signaling

2A

0.0014791084

13. 14-3-3-mediated signaling

0.0020417379

14. Netrin signaling

2A, 1U, 2U

0.0022908677

15. Leptin signaling in obesity

0.0024547089

16. Nitric oxide signaling in the cardiovascular system

2A, 1U

0.0024547089

17. Hepatic cholestasis

2U

0.0026915348

18. Uracil degradation II (reductive)

2U

0.0029512092

19. Thymine degradation

2U

0.0029512092

20. Melatonin signaling

1U

0.0033113112

Canonical pathways—family 2 affected (2A)

Shared with

p value

1. Sperm motility

1U

0.0000053703

2. Glutamate receptor signaling

1A

0.0000389045

3. Neuropathic pain signaling in dorsal horn neurons

1A, 2U, 1U

0.0000575440

4. Cellular effects of sildenafil (Viagra)

1A, 1U

0.0002238721

5. Nitric oxide signaling in the cardiovascular system

1A, 1U

0.0002884032

6. Synaptic long term depression

1A, 2U, 1U

0.0003235937

7. CREB signaling in neurons

1A, 2U

0.0003630781

8. Synaptic long term potentiation

1A, 2U

0.0005888437

9. Phospholipase C signaling

0.0008709636

10. Netrin signaling

1A, 2U, 1U

0.0010964782

11. G-Protein coupled receptor signaling

2U

0.0012589254

12. α-adrenergic signaling

0.0016595869

13. Protein kinase A signaling

2U, 1U

0.0023442288

14. nNOS signaling in neurons

0.0040738028

15. Huntington’s disease signaling

0.0042657952

16. Dopamine-DARPP32 feedback in cAMP signaling

1A

0.0058884366

17. Cardiac Î2-adrenergic signaling

2U

0.0067608298

18. Calcium signaling

2U

0.0077624712

19. Breast cancer regulation by Stathmin 1

0.0087096359

20. Axonal guidance signaling

1A, 1U

0.0089125094

1A Family 1—affected twin, 1U Family 1—unaffected twin, 2A Family 2—affected twin, 2U Family 2—unaffected twin

Fig. 6

Analysis of ingenuity pathway results

Fig. 7

a Dopamine feedback in cAMP signaling pathway identified using ingenuity pathway analysis (IPA). Genes that were unique to each affected twin were used to generate canonical pathways of interest. This pathway emerged independently in both affected twins. This pathway was also not found to be enriched in unaffected twins in the study. Purple represents genes harboring a unique high confidence variant in each respective patient (family 1, p = 2.28E−04; family 2, p = 5.84E−03). b Glutamate pathway identified using ingenuity pathway analysis (IPA). Genes that were unique to each affected twin were used to generate canonical pathways of interest. This pathway emerged independently in both affected twins. This pathway was also not found to be enriched in unaffected twins in the study. Purple represents genes harboring a unique high confidence variant in each respective patient (family 1, p = 1.46E−03; family 2, p = 3.88E−05)

Table 11

Genes affected in two pathways (glutamate receptor signaling and dopamine feedback in cAMP signaling) unique to the two unrelated schizophrenia patients representing family 1 and family 2

Pathway

Family 1: genes in pathway

Family 2: genes in pathway

Common to both affected twins

Number of genes affected

Identity

Number of genes affected

Identity

Dopamine feedback in cAMP signaling

29

PRKG2, PPP2R1U, GUCY1A3, PRKAG2, ADCY3, PRKCB, PRKAR1B, KCNJ12, ADCY2, PRKCZ, ADCY8, PLCL1, CACNA1D, DRD3, PLCB1, GUCY1A2, EP300, PRKG1, PPP3CA, CACNA1A, GRIN2U, PLCG2, KCNJ3, PRKCA, PLCH2, CACNA1C, PLCL2, PLCZ1, KCNJ10

23

PLCB1, PRKG2, PRKG1, PPM1L, CAMK4, PLCE1, PRKAG2, PPP2R2C, ADCY10, PPP1R14C, GRIN2A, CREB5, PRKCA, CACNA1C, PRKCB, KCNJ12, ITPR1, PRKAR1B, PRKCI, PRKCZ, ADCY8, PRKCG, DRD3

12

(PRKG2, PRKAG2, PRKCB, PRKAR1B, KCNJ12, PRKCZ, ADCY8, DRD3, PLCB1, PRKG1, PRKCA, CACNA1C)

Glutamate receptor signaling

13

GRIA1, GRIK2, GRID1, GNB1, GRIN2U, SLC1A7, GRIK1, GRIK4, GRM7, GRM1, GRM5, GRM8, GRIK3

15

GRID1, GNG7, CAMK4, SLC1A2, HOMER1, SLC1A7, GRIK1, GRIN2A, GRM4, GRIK4, SLC1A1, GRM7, GNG2, GRM5, GRM6

6

(GRID1, SLC1A7, GRIK1, GRIK4, GRM7, GRM5)

Discussion

Individual human genomes contain extensive variability

In general, the nature and distribution of variations observed in this study follow the results on 1000 genomes data and expected distributions based on chromosome size (Figs. 3 and 4). It follows that each individual harbors hundreds of rare variants [37]. The individual genomes have on average, 3.6 million SNVs, 344 thousand indels and 717 large deletions [37] that includes somatic as well as germline de novo variations. However, the rate of somatic de novo mutation appears to vary and may be family specific [38]. Unfortunately, this variability particularly caused by somatic mutations is not always easy to discern. Not surprisingly, almost all de novo mutations reported in the literature are based on germline events. These estimates are much lower than our results that focus on somatic de novo events representing individuals of different ages. Interestingly, our results follow a recent report that found that the rate of de novo somatic mutations in humans and mice is almost two orders of magnitude higher than the germline mutation rate and that both mutation rates are significantly higher in mice than humans [39]. It also adds that somatic de novo mutations are highly variable, may depend on tissue and age of the individual, and could add to predisposition for disease.

Studies of twin sequencing differences in the literature have noted validation rates of variants as low as 1/15 [40]. Often it is attributed to mosaicism resulting from de novo somatic events. In addition, validation rates for data from the 1000 genomes project averaged a validation rate of 1.8%, and similar to our study, large SVs were easier to validate than other types of variation. Our analysis also focused on the use of higher quality variant calls as was done in the 1000 genomes pilot study to evaluate the likelihood of a candidate variant call being a real event [37]. The results show that individual genomes harbor extensive variability and that this variability can be measured both within and between generations.

MZ twins are genomically different

Results included in this report show that the genome sequences of pairs of MZ twins although very similar, are not identical. It follows a number of recent reports on identical twins [4145]. Although likely to be a conservative estimate, Krawczak et al. has predicted that there exists at minimum an average of > 1.3 SNVs discriminating MZ twins in each tissue type [46]. The results of one forensic study found DNA sequence differences between identical twins that appear to reflect mosaicism in that the newly arisen allele was generally only found in a small fraction (approximately 20% of the cells assayed) as estimated by sanger sequencing results [41]. Many reports have now identified genetic and epigenetic differences between identical twins [68]. For example, Bruder et al. [4] reported that all of 19 MZ twins studied differed in CNVs [47] and Forsberg et al. confirmed 10 post-twinning CNV mutations in 159 MZ twin pairs [48]. In addition, many post-twinning single nucleotide mutations have also been reported [4245]. It is likely that older twin pairs will have accumulated more somatic de novo mutations over time [45] and this will be expected to affect the degree of somatic mosaicism across tissues [49]. A recent report that identified somatic mutations at the base-pair level in monozygotic twins found two de novo somatic mutations that appear to have occurred early in embryonic development, suggesting that early development may be enriched for de novo change [12].

De novo changes may add to genetic liability in schizophrenia

Schizophrenia is a multifactorial and highly heterogeneous disorder and may involve both genomic and environmental contributions [50]. Population and family studies have implicated a number of mutational mechanisms (SSCs, CNVs and SVs) and many genes of small effect in the causation of this disease [5153] with no single gene affected in all cases. Conceptually, an accumulation of mutations affecting a number of genes affecting disease specific pathways may establish a genetic liability gradient for schizophrenia where a critical threshold is required for the manifestation of the disease state [54]. Further, the underlying genetic liability is expected to be higher in families with schizophrenia patients. At the individual level, this liability will be much higher in the related family members. In the case of MZ twins where one is affected with the disease, the affected member is expected to have acquired additions to the liability scale via gene mutations and/or environmental factors that contribute to threshold crossing and thus development of disease. It remains an attractive hypothesis but has remained untested, primarily because of the lack of appropriate data. Also, threshold models are often assessed at the level of the population. This study is unique in that it applies this model to cases representing individual patients representing MZD twins along with a genetically matched control.

The current study, with complete genome sequences of pairs of MZD twins is novel and offers a number of advantages. First, it focuses on individual patients and matches the patient with her unaffected monozygotic twin. The consequence is that it drastically reduces genetic heterogeneity between a case and a control. Second, it focuses on the cause of the disease in highly selected and clinically defined individual patients rather than grouping together heterogeneous cases of schizophrenia. Third, the availability of complete genome sequences allows for identification of almost all forms of genetic mutations per individual. Fourth, the identification of all affected genes in a patient allows for further identification of canonical pathways that may be affected by individual specific gene mutations. The threshold model argues that a pathway may be affected by mutations involving different sets of genes in different individuals. More importantly, the two members of a MZD twin pair would share a common genetic liability for the disease with the affected twin acquiring yet additional defects causing it to cross the disease threshold on the liability continuum and develop schizophrenia.

We have assessed the genomic data obtained in our experiments to evaluate the threshold model of schizophrenia (Fig. 6) [36]. This analysis has yielded a set of canonical pathways for four individuals representing two twin pairs. The top 20 pathways identified in four members of the two twin pairs are given in Table 10. We focused on affected pathways that were shared or not shared in the two MZD twins. Within twin pair sharing of pathways was viewed to represent “genetic predisposition” and were considered to not be sufficient to cause the disease; we labeled these predisposing pathways as GP1 in family 1 and GP2 in family 2. Naturally, the composition of GP1 and GP2 (GPN across n pairs of twins) is expected to differ between unrelated pairs. Further, we selected pathways that were unique to the two patients in this study. We argue that these additional defects were needed to cross the threshold and manifest the disease; we labeled these disease-causing pathways GPD. Once again, the composition of GPDs may vary across families and includes all variants, some validated and others not validated. In this analysis, we have identified the same GPDs in both families which involved two pathways; dopamine feedback in cAMP signaling pathway (Fig. 7a) and glutamate receptor signaling (Fig. 7b). Interestingly, a number of pathways identified in the genetic predisposition lists (GP1 and GP2) have been previously implicated in this heterogeneous disease. These include the dopamine feedback in cAMP signaling pathway [5557], glutamate receptor signaling [58, 59], CREB signalling in neurons [60], axonal guidance signalling, Netrin signaling [61] and nNOS signalling in neurons [62]. Independent identification of known schizophrenia related defects from the affected twin supports the argument that the observed differences between MZD twins are not random sequencing artifacts. More important, they offer a logical explanation for the discordance of the two MZ twins with long term discordance for schizophrenia.

Dopamine feedback in cAMP signaling in schizophrenia

The dopamine feedback in cAMP signalling pathway is one of the pathways that has emerged independently in both schizophrenia-affected twins in this study (Fig. 7a). This pathway has been shown to be associated with psychiatric disorders due to the fact that it has critical function in integrating dopaminergic and glutamatergic signalling, and in turn affecting striatal function and plasticity [56, 57]. The leading theory to account for the pathophysiology of schizophrenia involves an excess of the neurotransmitter dopamine, either through excess production or postsynaptic dopamine over-activity possibly mediated by increased receptor density [55]. Recent reports reinforce the importance of dopamine in schizophrenia, including strong associations with DRD2 (a target of many antipsychotic drugs) [16]. The results support the contention that the defects associated with this pathway have the potential to contribute to schizophrenia in the two patients studied.

Glutamate receptor signalling in schizophrenia

A glutamate receptor-signalling pathway is the second pathway that is found in the two patients studied (Fig. 7b). The significance of this pathway in this disease is backed by the underlying neurochemical basis of schizophrenia that includes a hypofunctional glutamate system [63]. Many genes associated with glutamateric neurotransmission have been previously implicated in schizophrenia, including GRM3, GRIN2A, SRR and GRIA1 [16]. Further, morphological alteration of dendrites of glutamatergic neurons in the cerebral cortex of schizophrenia-affected individuals have been reported [64] suggesting a role for glutamate signalling in the etiology of schizophrenia. Interestingly, schizophrenia patients show enriched de novo mutations in genes regulating the postsynaptic density at glutamatergic synapses [58]. Furthermore, small de novo mutations were found to be overrepresented among glutamatergic postsynaptic proteins [59] and genes harbouring detrimental de novo mutations were reported to be enriched in networks affecting protein interactions [65]. In addition, a recent study investigating rare mutations in exonic regions of genes implicated in schizophrenia and autism spectrum disorder revealed that post-synaptic glutamate receptor complexes are key molecular mechanisms associated with schizophrenia and ASD [66]. We propose that the two pathways described above have the potential to at least partially contribute to the disease in these two patients. Also, given that the two pathways were identified from two patients from two unrelated families, they may represent recurring defects in this disease for a subset of patients.

Disease model: somatic de novo mutations interject in the threshold model of schizophrenia

The results included in this report also show that somatic de novo mutations may play a significant role in the development of schizophrenia. These observations are backed by extensive literature that argue for the existence of somatic mutation in our genomes [12, 41, 67, 68]. In this model, MZD twins with the disease are argued to have acquired additional de novo errors onto an already existing background of genetic predisposition and thus contributing to disease liability. These de novo errors must involve somatic mutations during ontogeny [3, 69]. Rare post-zygotic mutations are likely to have been underestimated in the past. Mutations that occur later in development are likely to be seen in very low frequency and simply look like sequencing errors in any analysis [70]. The high-quality results, publicly accessible for further analysis, support the proposition that de novo alterations may play a role in the manifestation of schizophrenia. The mutations identified are predominantly seen in genes already known to be implicated in schizophrenia and related disorders. They help highlight major processes affected in specific patients. They argue for extensive heterogeneity in disease processes. For the two patients studied here, they identify aberrations in dopamine feedback and glutamate receptor signalling pathways.

It has not escaped our mind that this model will account for a variety of results and observations reported in the extensive literature. For example, it is possible to override the liability scale established by small effects of a number of genes with large effects on the disease phenotype [24, 71]. Some of these may result from de novo mutation in MZD or singleton cases [3, 72, 73]. Also, these changes must be present in the brain. In fact, de novo mutations are more likely to occur in schizophrenia patients than unaffected siblings [74] and damaging de novo mutations in schizophrenia patients were found to disrupt genes regulating neurogenesis in the postmortem human brain [21]. Interestingly, de novo mutations are now known to be rather pervasive in the brain [75, 76]. They may represent a unique source of neuronal diversity and individual differences. We also note that by its very nature, the effect of a de novo mutation may or may not be always apparent depending on the organ system affected and the degree of mosaicism. The impact of such mutations on disease causation is being recognized and deserves intensive investigation [77]. Finally, individual specific exceptional comprehensive genome-wide results included in this report provide a promising approach to the understanding of schizophrenia and may apply to other related disorders.

Conclusions

The complete genome sequences of monozygotic twins discordant for schizophrenia have allowed for direct identification of patient specific somatic de novo mutations that may augment the threshold of liability and cause this neurodevelopmental disease. The results also identify variants in the unaffected twin as fragment of genetic predisposition that are not sufficient to manifest the disease. Together they support two propositions. First, somatic de novo mutations, that are pervasive in the brain, may play a role in the development of schizophrenia and second, discordance of monozygotic twins for schizophrenia and related neurodevelopmental diseases in some families may be influenced more heavily by genetic, rather than environmental effects.

Abbreviations

CNV: 

copy number variant

GP: 

genetic predisposition

GPD: 

genetic predisposition leading to disease

IPA: 

ingenuity pathway analysis

MZ: 

monozygotic

MZD: 

monozygotic discordant

SNV: 

single nucleotide variant

SSCs: 

small sequence changes (SNVs, indels, block substitutions)

SV: 

structural variant

Declarations

Authors’ contributions

SMS, RLO and CAC designed the experiment. RLO identified the patients and conducted the clinical assessments. CAC undertook all data analysis under the supervision of SMS. JLG and AJG assisted with data organization and performing of wet lab experiments. CAC and SMS wrote the manuscript. MGM assisted with the writing, organization and review of the manuscript. All authors read and approved the final manuscript.

Acknowledgements

First, we thank the participating twins and their families in this research. This research was conceived and planned by SMS, ROR and CAC and funded by The Schizophrenia Society of Ontario, The Ontario Mental Health Foundation and The Canadian Institutes of Health Research. A number of individuals provided valuable help during the course of investigation. We wish to thank Dr. Jay Rao (Psychiatrist) who provided follow up diagnostic reviews. We are also thankful to Ali Pensamiento for her assistance in the laboratory.

Competing interests

The authors declare that they have no competing interests.

Consent for publication

All subjects provided written informed consent to participate in this study. Further, they have agreed to the sharing of data (genetic and clinical) in any publication.

Data availability statement

Please contact author for data requests.

Ethics approval and consent to participate

All subjects gave informed consent to participate in this study. This research received ethics approval from the Committee on Research Involving Human Subjects at The University of Western Ontario, London, Ontario, Canada.

Funding

This work was funded by The Canadian Institutes of Health Research, The Schizophrenia Society of Ontario and The Ontario Mental Health Foundation. The funders had no role in the design, collection, analysis, interpretation or writing of this manuscript.

Publisher’s Note

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Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors’ Affiliations

(1)
Department of Biology, The University of Western Ontario
(2)
Department of Psychiatry, The University of Western Ontario
(3)
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine

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