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A de novo 1p34.2 microdeletion identifies the synaptic vesicle gene RIMS3 as a novel candidate for autism.

Kumar RA, Sudi J, Babatz TD, Brune CW, Oswald D, Yen M, Nowak NJ, Cook EH, Christian SL, Dobyns WB - J. Med. Genet. (2009)

Bottom Line: A child with autism and mild microcephaly was found to have a de novo 3.3 Mb microdeletion on chromosome 1p34.2p34.3.To search for submicroscopic chromosomal rearrangements in the child, array comparative genomic hybridisation (aCGH) was performed using a 19 K whole genome human bacterial artificial chromosome (BAC) array and the Illumina 610-Quad BeadChip microarray.A de novo 3.3 Mb deletion containing approximately 43 genes in chromosome 1p34.2p34.3 was identified and subsequently confirmed using fluorescence in situ hybridization (FISH).

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Chicago,Chicago, Illinois 60637, USA.

ABSTRACT

Background: A child with autism and mild microcephaly was found to have a de novo 3.3 Mb microdeletion on chromosome 1p34.2p34.3. The hypothesis is tested that this microdeletion contains one or more genes that underlie the autism phenotype in this child and in other children with autism spectrum disorders.

Methods: To search for submicroscopic chromosomal rearrangements in the child, array comparative genomic hybridisation (aCGH) was performed using a 19 K whole genome human bacterial artificial chromosome (BAC) array and the Illumina 610-Quad BeadChip microarray. Ingenuity pathway analysis (IPA) was used to construct functional biological networks to identify candidate autism genes. To identify putative functional variants in candidate genes, mutation screening was performed using polymerase chain reaction (PCR) based Sanger sequencing in 512 unrelated autism patients and 462 control subjects.

Results: A de novo 3.3 Mb deletion containing approximately 43 genes in chromosome 1p34.2p34.3 was identified and subsequently confirmed using fluorescence in situ hybridization (FISH). Literature review and bioinformatics analyses identified Regulating Synaptic Membrane Exocytosis 3 (RIMS3) as the most promising autism candidate gene. Mutation screening of this gene in autism patients identified five inherited coding variants, including one (p.E177A) that segregated with the autism phenotype in a sibship, was predicted to be deleterious, and was absent in 1161 controls.

Conclusions: This case report and mutation screening data suggest that RIMS3 is an autism causative or contributory gene. Functional studies of RIMS3 variants such as p.E177A should provide additional insight into the role of synaptic proteins in the pathophysiology of autism.

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Related in: MedlinePlus

(A) Array comparative genome hybridisation (aCGH) using a bacterial artificial chromosome (BAC) microarray demonstrates a deletion in chromosome 1p34.2. The aCGH plot shows the log2 ratio of the patient versus reference DNA on the vertical axis. Each individual BAC is represented as a single blue dot and the horizontal axis shows the position of each BAC along chromosome 1. The deletion of 1p34.2 is indicated by an arrow pointing to a vertical line of dots. Interrogation of the UCSC genome browser for the microdeletion region in this region identifies ∼47 RefSeq genes (shown below aCGH plot). Known copy number variants (CNVs) (orange blocks) and Indels (green blocks) are reported in the Database of Genomic Variants track. (B) Fluorescence in situ hybridisation (FISH) analysis confirms the deletion 1p34.2 aCGH results. The distal breakpoint boundary is indicated where RP11-67o15 (green arrows) shows two normal signals while RP11-120G12 (red arrow) shows a single signal in the interphase nucleus.
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fig2: (A) Array comparative genome hybridisation (aCGH) using a bacterial artificial chromosome (BAC) microarray demonstrates a deletion in chromosome 1p34.2. The aCGH plot shows the log2 ratio of the patient versus reference DNA on the vertical axis. Each individual BAC is represented as a single blue dot and the horizontal axis shows the position of each BAC along chromosome 1. The deletion of 1p34.2 is indicated by an arrow pointing to a vertical line of dots. Interrogation of the UCSC genome browser for the microdeletion region in this region identifies ∼47 RefSeq genes (shown below aCGH plot). Known copy number variants (CNVs) (orange blocks) and Indels (green blocks) are reported in the Database of Genomic Variants track. (B) Fluorescence in situ hybridisation (FISH) analysis confirms the deletion 1p34.2 aCGH results. The distal breakpoint boundary is indicated where RP11-67o15 (green arrows) shows two normal signals while RP11-120G12 (red arrow) shows a single signal in the interphase nucleus.

Mentions: We performed aCGH using a 19-K whole genome tiling path BAC microarray in patient LP99-105, and detected a ∼3.3 Mb deletion in chromosome 1p34.2p34.3 that extended from RP11-769L8 to RP11-483I17 and included ∼47 genes (figure 2A). The microdeletion was not detected in 372 control subjects analysed on the same BAC array platform.7 FISH studies confirmed the deletion in the proband (figure 2B), and microsatellite analysis demonstrated that the deletion was de novo (data not shown). We used the Illumina 610-Quad BeadChip microarray to refine the breakpoints to approximately chr1:39,794,296 and chr1:43,058,974 (UCSC Genome Browser, http://genome.ucsc.edu; Build 36.1; accessed November 2008), reducing the size of the microdeletion by ∼56 kb and identifying ∼43 genes within the deleted region.


A de novo 1p34.2 microdeletion identifies the synaptic vesicle gene RIMS3 as a novel candidate for autism.

Kumar RA, Sudi J, Babatz TD, Brune CW, Oswald D, Yen M, Nowak NJ, Cook EH, Christian SL, Dobyns WB - J. Med. Genet. (2009)

(A) Array comparative genome hybridisation (aCGH) using a bacterial artificial chromosome (BAC) microarray demonstrates a deletion in chromosome 1p34.2. The aCGH plot shows the log2 ratio of the patient versus reference DNA on the vertical axis. Each individual BAC is represented as a single blue dot and the horizontal axis shows the position of each BAC along chromosome 1. The deletion of 1p34.2 is indicated by an arrow pointing to a vertical line of dots. Interrogation of the UCSC genome browser for the microdeletion region in this region identifies ∼47 RefSeq genes (shown below aCGH plot). Known copy number variants (CNVs) (orange blocks) and Indels (green blocks) are reported in the Database of Genomic Variants track. (B) Fluorescence in situ hybridisation (FISH) analysis confirms the deletion 1p34.2 aCGH results. The distal breakpoint boundary is indicated where RP11-67o15 (green arrows) shows two normal signals while RP11-120G12 (red arrow) shows a single signal in the interphase nucleus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2921284&req=5

fig2: (A) Array comparative genome hybridisation (aCGH) using a bacterial artificial chromosome (BAC) microarray demonstrates a deletion in chromosome 1p34.2. The aCGH plot shows the log2 ratio of the patient versus reference DNA on the vertical axis. Each individual BAC is represented as a single blue dot and the horizontal axis shows the position of each BAC along chromosome 1. The deletion of 1p34.2 is indicated by an arrow pointing to a vertical line of dots. Interrogation of the UCSC genome browser for the microdeletion region in this region identifies ∼47 RefSeq genes (shown below aCGH plot). Known copy number variants (CNVs) (orange blocks) and Indels (green blocks) are reported in the Database of Genomic Variants track. (B) Fluorescence in situ hybridisation (FISH) analysis confirms the deletion 1p34.2 aCGH results. The distal breakpoint boundary is indicated where RP11-67o15 (green arrows) shows two normal signals while RP11-120G12 (red arrow) shows a single signal in the interphase nucleus.
Mentions: We performed aCGH using a 19-K whole genome tiling path BAC microarray in patient LP99-105, and detected a ∼3.3 Mb deletion in chromosome 1p34.2p34.3 that extended from RP11-769L8 to RP11-483I17 and included ∼47 genes (figure 2A). The microdeletion was not detected in 372 control subjects analysed on the same BAC array platform.7 FISH studies confirmed the deletion in the proband (figure 2B), and microsatellite analysis demonstrated that the deletion was de novo (data not shown). We used the Illumina 610-Quad BeadChip microarray to refine the breakpoints to approximately chr1:39,794,296 and chr1:43,058,974 (UCSC Genome Browser, http://genome.ucsc.edu; Build 36.1; accessed November 2008), reducing the size of the microdeletion by ∼56 kb and identifying ∼43 genes within the deleted region.

Bottom Line: A child with autism and mild microcephaly was found to have a de novo 3.3 Mb microdeletion on chromosome 1p34.2p34.3.To search for submicroscopic chromosomal rearrangements in the child, array comparative genomic hybridisation (aCGH) was performed using a 19 K whole genome human bacterial artificial chromosome (BAC) array and the Illumina 610-Quad BeadChip microarray.A de novo 3.3 Mb deletion containing approximately 43 genes in chromosome 1p34.2p34.3 was identified and subsequently confirmed using fluorescence in situ hybridization (FISH).

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Chicago,Chicago, Illinois 60637, USA.

ABSTRACT

Background: A child with autism and mild microcephaly was found to have a de novo 3.3 Mb microdeletion on chromosome 1p34.2p34.3. The hypothesis is tested that this microdeletion contains one or more genes that underlie the autism phenotype in this child and in other children with autism spectrum disorders.

Methods: To search for submicroscopic chromosomal rearrangements in the child, array comparative genomic hybridisation (aCGH) was performed using a 19 K whole genome human bacterial artificial chromosome (BAC) array and the Illumina 610-Quad BeadChip microarray. Ingenuity pathway analysis (IPA) was used to construct functional biological networks to identify candidate autism genes. To identify putative functional variants in candidate genes, mutation screening was performed using polymerase chain reaction (PCR) based Sanger sequencing in 512 unrelated autism patients and 462 control subjects.

Results: A de novo 3.3 Mb deletion containing approximately 43 genes in chromosome 1p34.2p34.3 was identified and subsequently confirmed using fluorescence in situ hybridization (FISH). Literature review and bioinformatics analyses identified Regulating Synaptic Membrane Exocytosis 3 (RIMS3) as the most promising autism candidate gene. Mutation screening of this gene in autism patients identified five inherited coding variants, including one (p.E177A) that segregated with the autism phenotype in a sibship, was predicted to be deleterious, and was absent in 1161 controls.

Conclusions: This case report and mutation screening data suggest that RIMS3 is an autism causative or contributory gene. Functional studies of RIMS3 variants such as p.E177A should provide additional insight into the role of synaptic proteins in the pathophysiology of autism.

Show MeSH
Related in: MedlinePlus