- Short paper
- Open Access
Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease
https://doi.org/10.1186/1744-9081-9-9
© Jouan et al; licensee BioMed Central Ltd. 2013
- Received: 22 August 2012
- Accepted: 17 January 2013
- Published: 20 February 2013
Abstract
Background
Schizophrenia is a severe psychiatric disease characterized by a high heritability and a complex genetic architecture. Recent reports based on exome sequencing analyses have highlighted a significant increase of potentially deleterious de novo mutations in different genes in individuals with schizophrenia.
Findings
This report presents the mutation screening results of four candidate genes for which such de novo mutations were previously reported (LRP1, KPNA1, ALS2CL and ZNF480). We have not identified any excess of rare variants in the additional SCZ cases we have screened.
Conclusions
This supports the notion that de novo mutations in these four genes are extremely rare in schizophrenia and further highlights the high degree of genetic heterogeneity of this disease.
Keywords
- Schizophrenia
- De novo mutation
- LRP1
- ALS2CL
- KPNA1
- ZNF480
Schizophrenia (SCZ) is a neurodevelopmental psychiatric disorder that is characterized by severely impaired cognitive processes causing hallucinations, delusions and altered emotional reactivity that disturb social behavior. This disorder is highly prevalent and according to the National Institute of Mental Health affects 1.1% of the U.S. adult population. The genetic factors predisposing to SCZ have not been fully elucidated but twin, adoptee and family studies jointly suggest that genetics is important with a heritability estimated to be up to 80% [1, 2]. Multiple approaches have been used to identify common and rare SCZ-predisposing variants using candidate gene and whole genome-scale studies [3, 4]. However neither large-scale sequencing projects, looking for rare penetrant variants, nor genome wide association studies, looking for common variants, have accounted for a significant fraction of the heritability of SCZ. In light of this limited success, it was hypothesized that deleterious de novo mutations in any of several different genes could explain the high global incidence of SCZ despite a reduced reproductive fitness. Our group first reported the presence of a significant excess of potentially deleterious de novo mutations in 401 synaptic genes using Sanger sequencing in a cohort of SCZ and autism patients [5]. We have later confirmed an excess of exonic de novo mutations and more particularly of nonsense variants in 15 SCZ trios (probands and parents) using exome sequencing. Interestingly, 4:11 ratio of nonsense to missense mutations is significantly higher than the expected 1:20 ratio (P = 0.005467), and according to the Human Gene Mutation Database, the expected ratio of nonsense to missense among all mutations reported to cause Mendelian diseases is 1:4 which in line with what we found (P > 0.05, not significant). This identified four candidate genes (LRP1, KPNA1, ALS2CL and ZNF480) possibly involved in SCZ [6]. The present report describes the mutation screening of these four genes in additional 475 SCZ cases and 189 controls.
Probands were individually interviewed and their diagnosis was based on the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition. Exclusion criteria included patients with psychotic symptoms caused by alcohol, drug abuse or other clinical diagnosis. All samples were collected through informed consent following the approval of their respective institutional ethics review committees. An initial cohort of 189 SCZ patients of European Caucasian ancestry was used in this study. An additional cohort of 285 SCZ subjects, also of European Caucasian ancestry, was used for the screening of ALS2CL and ZNF480 genes. All coding regions and splice site junctions of LRP1, KPNA1, ALS2CL and ZNF480 genes were amplified and then sequenced using Sanger sequencing technology. Variant detection analysis was done using Mutation Surveyor (v. 3.23, Softgenetics) and rare exonic variants were confirmed by re-amplification of the relevant fragment in both probands and parents (when available) using forward and reverse oligos.
Mutations identified in LRP1, ALS2CL, ZNF480 and KPNA1 and occurrence in SCZ and CTR cohorts
Mutation details | Prediction scores | Occurrence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | Genomic Positiona | Nucleotide variantb | AA Change | Typed | dbSNPe | ESVf | 1000 genomesg | Inheritanceh | Pantheri | Siftj | PolyPhenk | SCZ l cohort | CTR cohort |
LRP1 | chr12:57,579,450 | Y2200X c | NS | de novo | |||||||||
LRP1 | chr12:57,538,812 | c.506G > A | G169D | MS | - | A = 2 / G = 10756 | - | N/A | - | 0.01 | 2.337 | 1/189 | - |
LRP1 | chr12:57,539,265 | c.833G > T | S278I | MS | - | - | - | T (mother) | −2.47064 | 0.08 | 1.73 | 1/189 | - |
LRP1 | chr12:57,548,392 | c.1135G > A | R379H | MS | - | - | - | N/A | −2.23136 | 0.07 | 1.571 | 1/189 | - |
LRP1 | chr12:57,574,263 | c.5386 + 1G > A | M1795I | MS | - | - | - | T (mother) | - | 0.06 | 1.968 | 1/189 | - |
LRP1 | chr12:57,577,915 | c.5977C > T | R1993W | MS | rs141826184 | T = 25 / C = 10733 | T = 1 / C = 1093 | N/A | - | 0.05 | 0.037 | 2/189 | - |
LRP1 | chr12:57,578,673 | c.6238G > A | D2080N | MS | rs34577247 | A = 159 / G = 10599 | A = 26 / G = 2162 | N/A | - | 0.45 | 0.375 | >5 | - |
LRP1 | chr12:57,579,328 | c.6478G > A | A2160T | MS | - | A = 1 / G = 10495 | - | N/A | - | 0.60 | 1.147 | 1/189 | - |
LRP1 | chr12:57,587,040 | c.7637G > A | G2546S | MS | rs113379328 | A = 24 / G = 10734 | - | N/A | - | 0.13 | 0.836 | >5 | - |
LRP1 | chr12:57,587,717 | c.7840G > A | R2613Q | MS | rs150340911 | A = 12 / G = 10746 | - | N/A | - | 0.36 | 0.898 | 2/189 | - |
LRP1 | chr12:57,588,275 | c.8057G > A | R2686H | MS | rs148104493 | A = 1 / G = 10755 | - | N/A | - | 0.12 | 0.999 | 1/189 | - |
LRP1 | chr12:57,589,784 | c.8699A > C | Q2900P | MS | rs7397167 | A = 123 / C = 10635 | A = 14 / C = 2174 | N/A | - | 0.53 | - | >5 | - |
LRP1 | chr12:57,590,916 | c.9044G > A | G3015S | MS | rs145303173 | A = 6 / G = 10752 | - | N/A | - | 0.76 | 0.357 | 2/189 | - |
LRP1 | chr12:57,598,513 | c.11175G > A | G3725E | MS | rs151301245 | A = 12 / G = 10746 | - | T (mother) | - | 0.03 | 1.583 | 1/189 | - |
LRP1 | chr12:57,600,508 | c.11843G > A | G3948D | MS | - | - | - | N/A | - | 0.50 | 1.357 | 1/189 | - |
ALS2CL | chr3:46,717,166 | R733X c | NS | de novo | |||||||||
ALS2CL | chr3:46,717,175 | c.2188C > T | G730S | MS | rs142971127 | T = 80 / C = 10678 | T = 12 / C = 2176 | N/A | - | 0.40 | 1.483 | 7/475 | 1/189 |
ALS2CL | chr3:46,718,458 | c.1812G > T | P605T | MS | - | - | - | N/A | −1.70789 | 0.42 | 1.761 | 0/475 | 1/189 |
ALS2CL | chr3:46,718,477 | c.1793C > T | R598H | MS | - | - | - | N/A | −2.73328 | 0.01 | 1.686 | 0/475 | 1/189 |
ALS2CL | chr3:46,719,769 | c.1737G > A | P580S | MS | - | - | - | T (mother) | - | 0.62 | 1.615 | 1/475 | 0/189 |
ALS2CL | chr3:46,719,861 | c.1645T > C | N549S | MS | rs140347863 | C = 9 / T = 10749 | - | T (father). N/A. T (mother). N/A | - | 0.35 | 1.851 | 3/475 | 1/189 |
ALS2CL | chr3:46,722,792 | c.1380G > A | T460M | MS | - | A = 1 / G = 10757 | - | T (father) | −2.00878 | 0.11 | 0.374 | 1/475 | 0/189 |
ALS2CL | chr3:46,725,290 | c.894G > A | A298V | MS | rs141781567 | A = 15 / G = 10757 | - | N/A | −1.6125 | 0.14 | 1.366 | 2/475 | 0/189 |
ALS2CL | chr3:46,725,522 | c.802T > A | T268S | MS | - | - | - | T (mother) | −1.48254 | 0.33 | 1.406 | 1/475 | 0/189 |
ALS2CL | chr3:46,728,477 | c.530A > G | I176T | MS | rs145807890 | G = 8 / A = 10746 | - | N/A | −1.28647 | 0.39 | 1.351 | 0/475 | 1/189 |
ALS2CL | chr3:46,729,700 | c.190C > A | E65X | NS | rs139496961 | A = 20 / C = 10738 | - | N/A. T (father). N/A. N/A | - | - | - | 4/475 | 1/189 |
ALS2CL | chr3:46,729,756 | c.134C > G | E45Q | MS | rs7642448 | G = 4590 / C = 6166 | - | N/A | - | 0.28 | 1.042 | >5 | >5 |
ZNF480 | chr19:52,826,001 | R500X c | NS | de novo | |||||||||
ZNF480 | chr19:52,825,329 | c.826C > T | R276X | NS | - | - | - | N/A | - | - | - | 1/475 | 0/189 |
ZNF480 | chr19:52,825,495 | c.992C > A | A331E | MS | - | - | - | N/A | - | 0.95 | 0.838 | 0/475 | 1/189 |
ZNF480 | chr19:52,826,001 | c.1498C > T | R500X | NS | - | - | - | N/A | - | - | - | 0/475 | 1/189 |
KPNA1 | chr3:122,146,472 | E448X c | NS | de novo | |||||||||
KPNA1 | chr3:122,186,188 | c.218C > T | S73N | MS | rs4678193 | T = 79 / C = 10677 | T = 11 / C = 2177 | N/A | −2.16746 | 0.45 | 0.174 | >5 | - |
While the results of this mutation screening effort did not lead to the identification of additional potentially deleterious de novo mutations in LRP1, KPNA1, ALS2CL and ZNF480 in a larger cohort of SCZ patients, it was a necessary first step to assess their possible contribution to disease. One limitation of this study is that we have focused only on the coding regions. This does not exclude the involvement of disease predisposing variants in non-coding regions, which could affect allelic expression or splicing. Given the known heterogeneity of SCZ and the frequencies of variants reported thus far, the contribution of these particular genes may only emerge after the progressive sequencing of coding and non-coding regions of these genes in much larger cohorts of SCZ cases and control individuals. It’s likely that an additional mechanism (like the polygenic mode) is involved in the genetics of sporadic SCZ. However, we still believe that deleterious de novo mutations play an important role in a proportion of SCZ patients as demonstrated by our group and others [14–16]. It is well known that SCZ is genetically heterogeneous and hundreds and probably thousands of genes are involved. Therefore, to date, very few cases with de novo mutation have been reported to be associated with the same genes. Addressing the complete genetic picture of a polygenic disease such as SCZ is still a major challenge and will require further independent replication studies to clarify the role of these genes.
Websites references
ExonPrimer: http://ihg.gsf.de/ihg/ExonPrimer.html.
Primer3 Plus interface: http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi.
Declarations
Acknowledgements
We thank the families involved in our study. We thank Anne Noreau and Hussein Daoud for scientific advices. We are thankful for the efforts of the members of the Genome Quebec Innovation Centre Sequencing and Bioinformatics groups. Guy A. Rouleau is grateful for the support received through his positions as Canada Research Chair in Genetics of the Nervous System and Jeanne-et-J.-Louis-Levesque Chair for the Genetics of Brain Diseases. We would also like to thank the NHLBI GO Exome Sequencing Project and its ongoing studies which produced and provided exome variant calls for comparison: the Lung GO Sequencing Project (HL-102923), the WHI Sequencing Project (HL-102924), the Broad GO Sequencing Project (HL-102925), the Seattle GO Sequencing Project (HL-102926) and the Heart GO Sequencing Project (HL-103010).
Funding body agreements and policies
This work was supported by a grant from Genome Canada and Génome Québec and was cofunded by Université de Montréal as well as by Era-Net Neuron.
Authors’ Affiliations
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