First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

Genova, Francesca; Longeri, M.; Lyons, Leslie A.; Bagnato, A.; Strillacci, M.G.

doi:10.1186/s12864-018-5297-2

Cited by 18 publications

(21 citation statements)

References 57 publications

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“…Besides somatic-CNVs affecting neoplastic cells, normal cells also have variations in the number of copies, representing a source of genomic diversification during evolution 120,121 . Those mutations usually affect smaller genomic regions than somatic-CNVs and some of them-usually referred to as germline-CNVs-are implicated in cancer inheritance 15,16,[122][123][124] .…”

Section: Discussionmentioning

confidence: 99%

“…As far as we know, there is only one publication characterising CNVs in cats according to different breeds (Genova et al 121 ), and none characterising germline-CNVs associated with FMCs predisposition. When comparing our data with those of Genova et al, we observed that none of the animals in that study carried CNGs affecting B4 1-29 Mb and F2 64-82.3 Mb-enriched with cancer-related genes and significantly associated with poor outcome.…”

Section: Discussionmentioning

confidence: 99%

“…As recommended by Genova et al 121 , two different programs were used to call large size aneuploidies by depth of coverage analysis and results were compared to reduce false-positive calls. First, we applied two different programs to generate log2-copy-number-ratios for each cancer sample: 1.…”

Section: Immunohistochemical Examination the Expression Of Er Pr Hmentioning

confidence: 99%

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Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival

Granados-Soler

Bornemann-Kolatzki²,

Beck³

et al. 2020

Sci Rep

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Feline mammary carcinomas (FMCs) are highly malignant. As the disease-free survival (DFS) and overall survival (OS) are short, prognostication is crucial. Copy-number variations (CNVs) analysis by nextgeneration sequencing serves to identify critical cancer-related genomic regions. Thirty-three female cats with FMCs were followed during two years after surgery. Tumours represented tubulopapillary and solid carcinomas encompassing six molecular subtypes. Regardless of the histopathological diagnosis, molecular subtypes showed important differences in survival. Luminal A tumours exhibited the highest DFS (p = 0.002) and cancer-specific OS (p = 0.001), and the lowest amount of CNVs (p = 0.0001). In contrast, basal-like triple-negative FMCs had the worst outcome (DFS, p < 0.0001; and OS, p < 0.00001) and were the most aberrant (p = 0.05). In the multivariate analysis, copy-number losses (CNLs) in chromosome B1 (1-23 Mb) harbouring several tumour-repressors (e.g. CSMD1, MTUS1, MSR1, DBC2, and TUSC3) negatively influenced DFS. Whereas, copy-number gains (CNGs) in B4 (1-29 Mb) and F2 (64-82.3 Mb) comprising epithelial to mesenchymal transition genes and metastasis-promoting transcription factors (e.g. GATA3, VIM, ZEB1, and MYC) negatively influenced DFS and cancer-specific OS. These data evidence an association between specific CNVs in chromosomes B1, B4 and F2, and poor prognosis in FMCs.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival

Granados-Soler

Bornemann-Kolatzki²,

Beck³

et al. 2020

Sci Rep

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“…Use of WGS for CNV detection is highly encouraged, because it overcomes many of the shortcomings of the other CNV detection methods such as the ones using array CGH and SNP data [18][19][20]. Genome-wide studies to discover CNV have already been done in other domesticated species, such as in Sus scrofa [49], Bos taurus [37,50] and Felis catus [38]. Here we provide a first glimpse of the goat genome CNV map at a dense genome coverage, using animals from 34 diverse breeds from the African continent.…”

Section: Discussionmentioning

confidence: 99%

“…Many studies have been carried out to detect CNV using WGS data in various domesticated species: cattle [37], cats [38], chickens [39], dogs [40], etc. So far, there is no report of goat CNV discoveries using WGS data.…”

Section: Introductionmentioning

confidence: 99%

Detection of copy number variants in African goats using whole genome sequence data

Nandolo

Mészáros

Wurzinger

et al. 2020

Preprint

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BackgroundCopy number variations (CNV) are a significant source of variation in the genome, as such they are essential to the genetic characterization of animal breeds. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. ResultsA total of 253,553 CNV (244,876 deletions and 8,677 duplications) were identified, corresponding to an overall average of 1,393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6,231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. ConclusionsThis study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.

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Exploring the genetic factors behind the discrepancy in resistance to bovine tuberculosis between African zebu cattle and European taurine cattle

Lee,

Clémentine,

Kim

2024

Sci Rep

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Caused by the pathogenic agent Mycobacterium bovis, bovine tuberculosis (bTB) is a major concern in cattle breeding due to both its zoonotic potential and economic impact. Greater resistance to this disease has been reported in certain African zebu breeds compared to European taurine breeds. However the genetic basis for the lower susceptibility to bTB infection observed in zebu cattle remains poorly explored. This study was conducted on whole genome sequencing data of three bTB infection-resistant African zebu breeds and two bTB infection-susceptible taurine breeds to decipher the genetic background. A set of four selection signature statistics based on linkage disequilibrium, site frequency spectrum, and population differentiation were used on SNPs whereas between population variance based VST and t-test were used on CNVs. As a complement, genes from previous literature reported as candidate genes for bTB resistance were also inspected to identify genetic variations. Interestingly, the resulting nine candidate genes had deleterious missense variants (SHC3, IFNGR1, TLR2, TLR6, IL1A, LRRK2, EP300 and IRAK4) or a CNV difference (CD48) segregating between the groups. The genes found in the study play a role in immune pathways activated during Mycobacterium infection, contributing to the proliferation of immune cells and the granuloma formation, ultimately modulating the outcome of the infectious event. In particular, a deleterious variant in the LRRK2 gene, whose deficiency has been linked to improved prognosis upon tuberculosis infection, was found in the bTB infection-resistant zebu breeds. Therefore, these genes constitute credible candidates in explaining the discrepancy in Mycobacterium bovis infection susceptibility among different breed.

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First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

Cited by 18 publications

References 57 publications

Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival

Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival

Detection of copy number variants in African goats using whole genome sequence data

Exploring the genetic factors behind the discrepancy in resistance to bovine tuberculosis between African zebu cattle and European taurine cattle

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