INGI variation catalogue
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Homo Sapiens
SUBMITTER: Institute for Maternal and Child Health, IRCCS and Burlo Garofolo
PROVIDER: PRJEB33648 | EVA | 2019-08-02
REPOSITORIES: EVA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERZ1029809_merged.vcf.gz | Vcf | |||
| ERZ1029809_merged.vcf.gz.csi | Vcf | |||
| ERZ1029809_merged.vcf.gz.tbi | Vcf |
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Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers.
2009-12-17 | GSE19440 | GEO
Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers. Twelve C. elegans natural isolate samples were studied. There were no replicates or dye-swap hybridizations.
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Project description:Introduction Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are increasingly isolated, with USA300-0114 being the predominant clone in the USA. Comparative whole genome sequencing of USA300 isolates collected in 2002, 2003 and 2005 showed a limited number of single nucleotide polymorphisms and regions of difference. This suggests that USA300 has undergone rapid clonal expansion without great genomic diversification. However, whole genome comparison of CA-MRSA has been limited to isolates belonging to USA300. The aim of this study was to compare the genetic repertoire of different CA-MRSA clones with that of HA-MRSA from the USA and Europe through comparative genomic hybridization (CGH) to identify genetic clues that may explain the successful and rapid emergence of CA-MRSA. Materials and Methods Hierarchical clustering based on CGH of 48 MRSA isolates from the community and nosocomial infections from Europe and the USA revealed dispersed clustering of the 19 CA-MRSA isolates. This means that these 19 CA-MRSA isolates do not share a unique genetic make-up. Only the PVL genes were commonly present in all CA-MRSA isolates. However, 10 genes were variably present among 14 USA300 isolates. Most of these genes were present on mobile elements. Conclusion The genetic variation present among the 14 USA300 isolates is remarkable considering the fact that the isolates were recovered within one month and originated from a confined geographic area, suggesting continuous evolution of this clone. Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-108 target=_blank>BuG@Sbase</a>
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Project description:The adaptation of fungal pathogens to the host environment via large-scale genomic changes is a poorly characterized phenomenon. We recently discovered clinical strains of Cryptococcus neoformans, the leading cause of fungal meningoencephalitis in HIV/AIDS patients, which are disomic for chromosome 13. In the current study, we examined the relationship between disomy, expression of the virulence factor melanin and virulence in a mouse model of cryptococcosis. We found that melanin production was correlated with monosomy at chromosome 13, and that disomic variants were less melanized and attenuated for virulence in mice. Changes in the copy number of other chromosomes were also detected in strains showing variation in melanin formation after growth in culture and after passage through mice. A survey of environmental and clinical isolates maintained in culture revealed few occurrences of disomic chromosomes. However, an examination of isolates that were freshly collected from the cerebral spinal fluid of AIDS patients and minimally cultured provided evidence for mixed infections and copy number variation. Overall, these results suggest that the genome of C. neoformans exhibits a greater degree of plasticity than previously appreciated. Importantly, genome variation is associated with virulence factor expression and disease severity, and its occurrence in isolates from AIDS patients suggests that it may have clinical relevance.
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Project description:The adaptation of fungal pathogens to the host environment via large-scale genomic changes is a poorly characterized phenomenon. We recently discovered clinical strains of Cryptococcus neoformans, the leading cause of fungal meningoencephalitis in HIV/AIDS patients, which are disomic for chromosome 13. In the current study, we examined the relationship between disomy, expression of the virulence factor melanin and virulence in a mouse model of cryptococcosis. We found that melanin production was correlated with monosomy at chromosome 13, and that disomic variants were less melanized and attenuated for virulence in mice. Changes in the copy number of other chromosomes were also detected in strains showing variation in melanin formation after growth in culture and after passage through mice. A survey of environmental and clinical isolates maintained in culture revealed few occurrences of disomic chromosomes. However, an examination of isolates that were freshly collected from the cerebral spinal fluid of AIDS patients and minimally cultured provided evidence for mixed infections and copy number variation. Overall, these results suggest that the genome of C. neoformans exhibits a greater degree of plasticity than previously appreciated. Importantly, genome variation is associated with virulence factor expression and disease severity, and its occurrence in isolates from AIDS patients suggests that it may have clinical relevance.
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Project description:Here, we analyzed 76 ecologically diverse wild yeast isolates and discovered a wide diversity of replicative lifespan. Phylogenetic analyses pointed to genes and environmental factors that strongly interact to modulate the observed aging patterns. We then identified genetic networks causally associated with natural variation in replicative lifespan across wild yeast isolates, as well as genes, metabolites and pathways, many of which have never been associated with yeast lifespan in laboratory settings. In addition, a combined analysis of lifespan-associated metabolic and transcriptomic changes revealed unique adaptations to interconnected amino acid biosynthesis, glutamate metabolism and mitochondrial function in long-lived strains. Overall, our multi-omic and lifespan analyses across diverse isolates of the same species shows how gene-environment interactions shape cellular processes involved in phenotypic variation such as lifespan.
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