Affymetrix SNP array data for Pit Bull Terrier
Ontology highlight
ABSTRACT:
ORGANISM(S): Canis lupus familiaris
PROVIDER: GSE53577 | GEO | 2013/12/23
SECONDARY ACCESSION(S): PRJNA232430
REPOSITORIES: GEO
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Project description:The data were used to define the homozygous regions in OCD-risk breeds, together with published Gentrain dataset. Affymetrix SNP arrays were performed according to the manufacturer's directions. Homozygosity analysis was performed.
2013-12-23 | E-GEOD-53577 | biostudies-arrayexpress
Project description:Obsessive-compulsive disorder (OCD), a severe mental disease manifested in time-consuming repetition of behaviors, affects 1-3% of the human population. While highly heritable, complex genetics has hampered attempts to elucidate OCD etiology. Dogs suffer from naturally occurring compulsive disorders that closely model human OCD, manifested as an excessive repetition of normal canine behaviors that only partially responds to drug therapy. The limited diversity within dog breeds makes identifying underlying genetic factors easier. We use genome wide association of 87 Doberman Pinscher cases and 63 controls to identify genomic loci associated with OCD and sequence these regions in 8 affected dogs from high-risk breeds and 8 breed-matched controls. We find 119 variants in evolutionarily conserved sites that are specific to dogs with OCD. These case-only variants are significantly more common in high OCD risk breeds compared to breeds with no known psychiatric problems. Four genes, all with synaptic function, have the most case-only variation: neuronal cadherin (CDH2), catenin alpha2 (CTNNA2), ataxin-1 (ATXN1), and plasma glutamate carboxypeptidase (PGCP). Two different case-only variants targeted the same approximately 500-bp highly conserved regulatory element between the cadherin genes CDH2 and DSC3. We functionally test these variants in a human neuroblastoma cell line and show that they cause significant changes in gene expression, likely due to disrupted transcription factor binding. This work demonstrates how we can use the unique genetics of dog breeds, and mechanistic similarities between human and dog diseases, to find genes and regulatory pathways underlying complex psychiatric disorders.
2013-12-20 | GSE53488 | GEO
Project description:Obsessive-compulsive disorder (OCD), a severe mental disease manifested in time-consuming repetition of behaviors, affects 1-3% of the human population. While highly heritable, complex genetics has hampered attempts to elucidate OCD etiology. Dogs suffer from naturally occurring compulsive disorders that closely model human OCD, manifested as an excessive repetition of normal canine behaviors that only partially responds to drug therapy. The limited diversity within dog breeds makes identifying underlying genetic factors easier. We use genome wide association of 87 Doberman Pinscher cases and 63 controls to identify genomic loci associated with OCD and sequence these regions in 8 affected dogs from high-risk breeds and 8 breed-matched controls. We find 119 variants in evolutionarily conserved sites that are specific to dogs with OCD. These case-only variants are significantly more common in high OCD risk breeds compared to breeds with no known psychiatric problems. Four genes, all with synaptic function, have the most case-only variation: neuronal cadherin (CDH2), catenin alpha2 (CTNNA2), ataxin-1 (ATXN1), and plasma glutamate carboxypeptidase (PGCP). Two different case-only variants targeted the same approximately 500-bp highly conserved regulatory element between the cadherin genes CDH2 and DSC3. We functionally test these variants in a human neuroblastoma cell line and show that they cause significant changes in gene expression, likely due to disrupted transcription factor binding. This work demonstrates how we can use the unique genetics of dog breeds, and mechanistic similarities between human and dog diseases, to find genes and regulatory pathways underlying complex psychiatric disorders. Affymetrix SNP arrays were performed according to the manufacturer's directions. Genome wide association analysis was performed for 87 doberman pinshcers OCD cases and 63 breed-matched controls.
2013-12-20 | E-GEOD-53488 | biostudies-arrayexpress
Project description:The conservation and development of chicken has considerably affected human activities, but the admixture history of chicken breeds has so far been poorly demonstrated especially for Chinese indigenous breeds. Using genotypes from 580961 single nucleotide polymorphism markers scored in 1201 animals, we evaluate the genetic diversity (heterozygosity and proportion of polymorphic markers), Linkage disequilibrium (LD) decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance) and migration events (Treemix and f-statistics) of eight domesticated chicken breeds. All population analytical methods reveal patterns of hybridization which occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture followed by trade have been important forces in shaping modern Chinese chicken genomic variation. Moreover, isolation by distance may play critical role in the shaping genomic variation within Eurasia continent chicken breeds.
2019-10-07 | GSE127968 | GEO
Project description: Not available
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Project description:A consanguineous family segregating anhidrosis (recessive, familial) Shared homozygous regions were identified by comparing SNP genotyping results from four affected family members
2014-09-05 | GSE61122 | GEO
Project description:Ovarian development and maintenance are poorly understood, but diseases affecting them can offer insights into their underlying mechanisms. XX-female gonadal dysgenesis (XX-GD) is a rare, genetically heterogeneous disorder characterized by underdeveloped, dysfunctional ovaries with subsequent lack of spontaneous pubertal development, primary amenorrhea, uterine hypoplasia, and hypergonadotropic hypogonadism. We used SNP arrays to perform homozygosity mapping in order to detect informative genomic regions which are homozygous and shared among affected individuals. This analysis identified genomic regions in which the mutated gene causing the XX-GD phenotype in the affected individuals may reside. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.
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Project description:Relapse is the commonest cause of death in acute myeloid leukaemia (AML), but the mechanisms leading to relapse are unclear. Recently, acquisition of segmental uniparental disomy (UPD) by mitotic recombination (MR) has been reported in 15-20% of AML samples at diagnosis using whole genome single nucleotide polymorphism (SNP) arrays. These cytogenetically invisible abnormalities are associated with homozygous mutations in several types of malignancy. Clonal evolution of heterozygous to homozygous mutations by MR could provide a mechanism for relapse. Keywords: DNA copy number, loss of heterozygosity
2008-05-01 | GSE7210 | GEO
Project description:BackgroundCopy number data are routinely being extracted from genome-wide association study chips using a variety of software. We empirically evaluated and compared four freely-available software packages designed for Affymetrix SNP chips to estimate copy number: Affymetrix Power Tools (APT), Aroma.Affymetrix, PennCNV and CRLMM. Our evaluation used 1,418 GENOA samples that were genotyped on the Affymetrix Genome-Wide Human SNP Array 6.0. We compared bias and variance in the locus-level copy number data, the concordance amongst regions of copy number gains/deletions and the false-positive rate amongst deleted segments.ResultsAPT had median locus-level copy numbers closest to a value of two, whereas PennCNV and Aroma.Affymetrix had the smallest variability associated with the median copy number. Of those evaluated, only PennCNV provides copy number specific quality-control metrics and identified 136 poor CNV samples. Regions of copy number variation (CNV) were detected using the hidden Markov models provided within PennCNV and CRLMM/VanillaIce. PennCNV detected more CNVs than CRLMM/VanillaIce; the median number of CNVs detected per sample was 39 and 30, respectively. PennCNV detected most of the regions that CRLMM/VanillaIce did as well as additional CNV regions. The median concordance between PennCNV and CRLMM/VanillaIce was 47.9% for duplications and 51.5% for deletions. The estimated false-positive rate associated with deletions was similar for PennCNV and CRLMM/VanillaIce.ConclusionsIf the objective is to perform statistical tests on the locus-level copy number data, our empirical results suggest that PennCNV or Aroma.Affymetrix is optimal. If the objective is to perform statistical tests on the summarized segmented data then PennCNV would be preferred over CRLMM/VanillaIce. Specifically, PennCNV allows the analyst to estimate locus-level copy number, perform segmentation and evaluate CNV-specific quality-control metrics within a single software package. PennCNV has relatively small bias, small variability and detects more regions while maintaining a similar estimated false-positive rate as CRLMM/VanillaIce. More generally, we advocate that software developers need to provide guidance with respect to evaluating and choosing optimal settings in order to obtain optimal results for an individual dataset. Until such guidance exists, we recommend trying multiple algorithms, evaluating concordance/discordance and subsequently consider the union of regions for downstream association tests.
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Project description:Abnormalities of chromosome 7q are common in myeloid malignancies but no specific target genes have been identified. Here we describe the finding of homozygous EZH2 mutations in 9 of 12 cases with 7q acquired uniparental disomy. Screening of a total of 614 cases with myeloid disorders revealed 49 monoallelic or biallelic EZH2 mutations in 42 individuals, most commonly myelodysplastic/myeloproliferative neoplasms (27/219; 12%) and myelofibrosis (4/30; 13%). EZH2 encodes the catalytic subunit of the Polycomb repressive complex 2 (PRC2), the highly conserved histone H3 lysine 27 methyltransferase that influences stem cell renewal by epigenetic repression of genes involved in cell fate decisions. EZH2 has oncogenic activity and its overexpression has been causally linked to differentiation blocks in epithelial tumors. Unexpectedly, the mutations we identified resulted in premature chain termination or direct abrogation of histone methyltransferase activity, suggesting that EZH2 acts as a tumor suppressor for myeloid malignancies.
2010-06-30 | GSE21990 | GEO