Search results for "Copy Number Variation"
showing 10 items of 58 documents
An initial comparative map of copy number variations in the goat (Capra hircus) genome
2010
Abstract Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi,…
A Comparative Analysis of Copy Number Variation of the Sheep and Goat Genomes
2010
Recent studies have shown that copy number variants (CNVs) are important sources of variability of mammalian genomes. We applied a cross species array comparative genome hybridization (aCGH) experiment using as reference the cattle genome to investigate, for the first time, variability in the sheep and goat genomes derived from copy number variation and identified 431 and 358 CNVs, respectively. A comparison of these results to those obtained in other mammals for similar experiments is reported. The identified CNVs could be important in determining phenotypic and production differences between and within breeds. Further studies will be carried out to evaluate the identified CNVs from both f…
Interstitial deletions of chromosome 1p: novel 1p31.3p22.2 microdeletion in a newborn with craniosynostosis, coloboma and cleft palate, and review of…
2022
Abstract Background Rearrangements of unstable DNA sequences may alter the structural integrity or the copy number of dose-sensitive genes, resulting in copy number variations. They may lead more frequently to deletions, in addition to duplications and/or inversions, which are the underlying pathogenic mechanism of a group of conditions known as genomic disorders (or also contiguous gene syndromes). Interstitial deletions of the short arm of chromosome 1 are rare, and only about 30 patients have been reported. Their clinical features are variable, in respect of the extent of the deleted region. They include global developmental delay, central nervous system (CNS) malformations, craniosynost…
Assessing the impact of copy number variants on miRNA genes in autism by Monte Carlo simulation.
2014
Autism Spectrum Disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies have investigated the role of de novo Copy Number Variants (CNVs) and microRNAs as important but distinct etiological factors in ASD. We developed a novel computational procedure to assess the potential pathogenic role of microRNA genes overlapping de novo CNVs in ASD patients. Here we show that for chromosomes # 1, 2 and 22 the actual number of miRNA loci affected by de novo CNVs in patients was found significantly higher than that estimated by Monte Carlo simulation of random CNV events. Out of 24 miRNA genes over-represented in CNVs from these three chromosomes only …
Genomic structural diversity in local goats: Analysis of copy-number variations
2020
Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell&rsquo
Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors.
2009
In goats, classical genetic studies reported a large number of alleles at the Agouti locus with effects on coat color and pattern distribution. From these early studies, the dominant A(Wt) (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat ASIP gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-rich carboxy-terminal domain of the protein (p.Ala96Gly, p.Cys126Gly, and p.Val1…
Isolated bladder exstrophy associated with a de novo 0.9 Mb microduplication on chromosome 19p13.12
2012
BACKGROUND: The exstrophy-epispadias complex (BEEC) is a urogenital birth defect of varying severity. The causes of the BEEC are likely to be heterogeneous, with individual environmental or genetic risk factors still being largely unknown. In this study, we aimed to identify de novo causative copy number variations (CNVs) that contribute to the BEEC. METHODS: Array-based molecular karyotyping was performed to screen 110 individuals with BEEC. Promising CNVs were tested for de novo occurrence by investigating parental DNAs. Genes located in regions of rearrangements were prioritized through expression analysis in mice to be sequenced in the complete cohort, to identify high-penetrance mutati…
A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Braque Français Type Pyrénées Dogs
2019
Simple Summary Copy number variations (CNVs) are important sources of variation in mammalian species. In this study, we used a single nucleotide polymorphisms (SNP) array to detect CNVs in Braque Français, type Pyrénées dogs (BRA). Results overlapped moderately in comparison with previous studies on CNVs in dogs, leading to the identification of 16 novel CNVRs. Several genes were annotated in the CNV regions (CNVRs) detected, some of which related to muscle structure development. This breed is known to be excellent upland game birds dogs. The selection for such hunting behavior could have driven the presence of these genes into the CNVRs. Copy number variations may be of interest to study a…
Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds
2022
Simple Summary The aim of this work is to identify CNVs and perform a CNV-based population genetics analysis in five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs and 365 CNV regions (CNVRs). The different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups. Gene enrichment was described for the 37 CNVRs selected considering the top 10%. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. CNVs represent valuable molecular resources to provide useful information for separating the p…
Mutated tumor alleles are expressed according to their DNA frequency
2014
AbstractThe transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a hig…