Rachel Flomen

Association study of CHRFAM7A copy number and 2bp deletion polymorphisms with schizophrenia and bipolar affective disorder

Schizophrenia and bipolar disorder are major psychiatric diseases that have a strong genetic element. Markers in the vicinity of the CHRNA7 gene at 15q13‐q14 have been linked with an endophenotype of schizophrenia, P50 sensory gating disorder, with schizophrenia itself and with bipolar disorder. We have measured the copy number of the polymorphic partial duplication of CHRNA7 (CHRFAM7A) and genotyped a polymorphic 2bp deletion within exon 6 of CHRFAM7A. In this study, 208 probands with a primary diagnosis of schizophrenia, 217 with a diagnosis of bipolar affective disorder and 28 with schizoaffective or other psychotic disorders were examined together with 197 controls recruited from the same region in Scotland. No significant association was seen for schizophrenia and bipolar disorder by genotype or allele overall for either polymorphism, but a mildly significant association by genotype (P = 0.04) was observed for absence of CHRFAM7A when the sample was analyzed as a single psychosis phenotype.

Detailed analysis of 15q11-q14 sequence corrects errors and gaps in the public access sequence to fully reveal large segmental duplications at breakpoints for Prader-Willi, Angelman, and inv dup(15) syndromes

BackgroundChromosome 15 contains many segmental duplications, including some at 15q11-q13 that appear to be responsible for the deletions that cause Prader-Willi and Angelman syndromes and for other genomic disorders. The current version of the human genome sequence is incomplete, with seven gaps in the proximal region of 15q, some of which are flanked by duplicated sequence. We have investigated this region by conducting a detailed examination of the sequenced genomic clones in the public database, focusing on clones from the RP11 library that originates from one individual.ResultsOur analysis has revealed assembly errors, including contig NT_078094 being in the wrong orientation, and has enabled most of the gaps between contigs to be closed. We have constructed a map in which segmental duplications are no longer interrupted by gaps and which together reveals a complex region. There are two pairs of large direct repeats that are located in regions consistent with the two classes of deletions associated with Prader-Willi and Angelman syndromes. There are also large inverted repeats that account for the formation of the observed supernumerary marker chromosomes containing two copies of the proximal end of 15q and associated with autism spectrum disorders when involving duplications of maternal origin (inv dup[15] syndrome).ConclusionWe have produced a segmental map of 15q11-q14 that reveals several large direct and inverted repeats that are incompletely and inaccurately represented on the current human genome sequence. Some of these repeats are clearly responsible for deletions and duplications in known genomic disorders, whereas some may increase susceptibility to other disorders.

The copy number variant involving part of the alpha 7 nicotinic receptor gene contains a polymorphic inversion

The α7 nicotinic acetylcholine receptor gene (CHRNA7) is located at 15q13–q14 in a region that is strongly linked to the P50 sensory gating deficit, an endophenotype of schizophrenia and bipolar disorder. Part of the gene is a copy number variant, due to a duplication of exons 5–10 and 3′ sequence in CHRFAM7A, which is present in many but not all humans. Maps of this region show that the two genes are in opposite orientation in the individual mainly represented in the public access human DNA sequence database (Build 36), suggesting that an inversion had occurred since the duplication. We have used fluorescent in situ hybridization to investigate this putative inversion. Analysis of interphase chromosomes in 12 individuals confirms the occurrence of an inversion and indicates that CHRFAM7A exists in both orientations with similar frequency. We showed that the 2 bp deletion polymorphism in exon 6 of CHRFAM7A is in strong linkage disequilibrium with the inversion polymorphism (r2=0.82, CI 0.53–1.00, P=0.00003), which can therefore be used as a surrogate marker. Previous associations of endophenotypes of schizophrenia with the 2 bp deletion might therefore be due to the orientation of the duplicon containing CHRFAM7A.

Increased RNA editing in EAAT2 pre-mRNA from amyotrophic lateral sclerosis patients: involvement of a cryptic polyadenylation site.

The astroglial EAAT2 glutamate transporter is essential for clearing glutamate in the central nervous system and protecting against excitotoxicity. It is implicated in amyotrophic lateral sclerosis (ALS, the most common type of motor neurone disease) where less EAAT2 is found, possibly involving aberrant intron 7 retention transcripts. We report adenine/inosine RNA editing at a novel site in intron 7 of EAAT2 pre-mRNA that appears to activate a cryptic alternative polyadenylation site, generating intron 7 retention transcripts. This polyadenylation site includes two overlapping polyadenylation signals opposite the editing site in a strong stem-loop, which is highly conserved in primates. In pre-mRNA, we observed variable editing levels at this site, which were significantly higher in spinal cord (p=0.001) and motor cortex (p=0.005) from ALS patients, but not in cerebellum, demonstrating specificity for clinically relevant regions. By contrast, incomplete mRNA molecules polyadenylated in intron 7 are always completely edited. Cell culture experiments confirm this strong correlation between editing and polyadenylation in intron 7, strongly suggesting activation of the alternative polyadenylation site by editing. Prediction of inosine base-pairing from published data suggests that RNA editing releases the polyadenylation signals from the stem-loop, providing a plausible mechanism. To the best of our knowledge, this is the first report of RNA editing activating an alternative polyadenylation signal.

Common inversion polymorphisms and rare microdeletions at 15q13.3.

Sharp et al1 recently described microdeletions at 15q13.3 associated with mental retardation and seizures. These deletions are between Prader–Willi/Angelman break points BP4 and BP5 and include the nicotinic acetylcholine α7 receptor gene (CHRNA7). The authors also report a common inversion polymorphism in this region, one orientation of which they suggest might predispose to the microdeletions by non-allelic homologous recombination (NAHR).

Association between the 2-bp deletion polymorphism in the duplicated version of the alpha7 nicotinic receptor gene and P50 sensory gating

There is considerable evidence implicating the 15q13.3 region in neuropsychiatric disorders, with the α7 nicotinic receptor gene CHRNA7 the most plausible candidate. This region has multiple duplications and many copy number variants (CNVs). A common CNV involves a partial duplication of CHRNA7 (CHRFAM7A), which occurs in either orientation. We examined the distribution of these alternative genomic arrangements in a large cohort of psychiatric patients, their relatives and controls using the 2-bp deletion polymorphism as a marker for the orientation of CHRFAM7A. We investigated three common alleles for association with psychosis and with the P50 sensory gating deficit, which is strongly associated with psychosis and strongly linked to 15q13.3. We found significant within-family association with P50 (empirical P=0.004), which is robust to population stratification. Most of the effect came from the 2-bp deletion allele, which tags the variant of CHRFAM7A in the same orientation as CHRNA7. This allele is associated with the presence of the P50 sensory gating deficit (empirical P=0.0006). Tests comparing within-family and between-family components of association suggest considerable population stratification in the sample. We found no evidence for association with psychosis, but this may reflect lower power using this phenotype. Four out of six previous association studies found association of different psychiatric phenotypes with the same 2-bp deletion allele.

CHRFAM7A copy number and 2-bp deletion polymorphisms and antisaccade performance

Chromosome 15q13-q14 harbours the gene for the alpha7 nicotinic acetylcholine receptor subunit (CHRNA7) and a related gene (CHRFAM7A) which arises from a partly duplicated portion of CHRNA7. Recent evidence suggests that CHRFAM7A is a locus with a possible role in schizophrenia and cognitive functioning. We studied an antisaccade task as a fronto-parietal measure of executive function that reflects risk for schizophrenia. Association of CHRFAM7A genotype with antisaccade performance was assessed in 103 healthy Caucasian individuals. No significant associations of 2-bp deletion or CHRFAM7A copy number with antisaccade performance parameters were observed. The failure to observe an association between antisaccade performance and polymorphisms in CHRFAM7A gene is consistent with specificity of the gene effects on hippocampal and memory functions as previously demonstrated.