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ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples.

ABSTRACT: Large reference datasets of annotated genetic variations from genome-scale sequencing are essential for interpreting identified variants, their functional impact, and their possible contribution to diseases and traits. However, to date, no such database of annotated variation from broad cattle populations is publicly available. To overcome this gap and advance bovine NGS-driven variant discovery and interpretation, we obtained and analyzed raw data deposited in the SRA public repository. Short reads from 262 whole-exome sequencing samples of Bos Taurus were mapped to the Bos Taurus ARS-UCD1.2 reference genome. The GATK best practice workflow was applied for variant calling. Comprehensive annotation of all recorded variants was done using the Ensembl Variant Effect Predictor (VEP). An in-depth analysis of the population structure revealed the breeds comprising the database. The Exomes Aggregate of Bovine- ExAgBov is a comprehensively annotated dataset of more than 20 million short variants, of which ~2% are located within open reading frames, splice regions, and UTRs, and more than 60,000 variants are predicted to be deleterious.

SUBMITTER: Raz R

PROVIDER: S-EPMC9345876 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples.

Raz Rotem R Roth Zvi Z Gershoni Moran M

Scientific data 20220802 1

Large reference datasets of annotated genetic variations from genome-scale sequencing are essential for interpreting identified variants, their functional impact, and their possible contribution to diseases and traits. However, to date, no such database of annotated variation from broad cattle populations is publicly available. To overcome this gap and advance bovine NGS-driven variant discovery and interpretation, we obtained and analyzed raw data deposited in the SRA public repository. Short r ...[more]

PMID: 35918364

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Project description:Staphylococci are among the commonly isolated bacteria from intramammary infections in bovines, where Staphylococcus aureus is the most studied species. This species carries a variety of virulence genes, contributing to bacterial survival and spread. Less is known about non-aureus staphylococci (NAS) and their range of virulence genes and mechanisms, but they are the most frequently isolated bacteria from bovine milk. Staphylococci can also carry a range of antimicrobial resistance genes, complicating treatment of the infections they cause. We used Illumina sequencing to whole genome sequence 93 staphylococcal isolates selected from a collection of staphylococcal isolates; 45 S. aureus isolates and 48 NAS isolates from 16 different species, determining their content of antimicrobial resistance genes and virulence genes. Antimicrobial resistance genes were frequently observed in the NAS species as a group compared to S. aureus. However, the lincosamide resistance gene lnuA and penicillin resistance gene blaZ were frequently identified in NAS, as well as a small number of S. aureus. The erm genes conferring macrolide resistance were also identified in several NAS isolates and in a small number of S. aureus isolates. In most S. aureus isolates, no antimicrobial resistance genes were detected, but in five S. aureus isolates three to six resistance genes were identified and all five of these carried the mecA gene. Virulence genes were more frequently identified in S. aureus, which contained on average five times more virulence genes compared to NAS. Among the NAS species there were also differences in content of virulence genes, such as S. chromogenes with a higher average number of virulence genes. By determining the content of a large selection of virulence genes and antimicrobial resistance genes in S. aureus and 16 different NAS species our results contribute with knowledge regarding the genetic basis for virulence and antimicrobial resistance in bovine staphylococci, especially the less studied NAS. The results can create a broader basis for further research into the virulence mechanisms of this important group of bacteria in bovine intramammary infections.

Project description:BackgroundLung adenocarcinomas (LUADs) lead to the majority of deaths attributable to lung cancer. We performed whole-exome sequencing (WES) and immune profiling analyses of a unique set of clinically annotated early-stage LUADs to better understand the pathogenesis of this disease and identify clinically relevant molecular markers.MethodsWe performed WES of 108 paired stage I-III LUADs and normal lung tissues using the Illumina HiSeq 2000 platform. Ten immune markers (PD-L1, PD-1, CD3, CD4, CD8, CD45ro, CD57, CD68, FOXP3 and Granzyme B) were profiled by imaging-based immunohistochemistry (IHC) in a subset of LUADs (n = 92). Associations among mutations, immune markers and clinicopathological variables were analyzed using ANOVA and Fisher's exact test. Cox proportional hazards regression models were used for multivariate analysis of clinical outcome.ResultsLUADs in this cohort exhibited an average of 243 coding mutations. We identified 28 genes with significant enrichment for mutation. SETD2-mutated LUADs exhibited relatively poor recurrence- free survival (RFS) and mutations in STK11 and ATM were associated with poor RFS among KRAS-mutant tumors. EGFR, KEAP1 and PIK3CA mutations were predictive of poor response to adjuvant therapy. Immune marker analysis revealed that LUADs in smokers and with relatively high mutation burdens exhibited increased levels of immune markers. Analysis of immunophenotypes revealed that LUADs with STK11 mutations exhibited relatively low levels of infiltrating CD4+/CD8+ T-cells indicative of a muted immune response. Tumoral PD-L1 was significantly elevated in TP53 mutant LUADs whereas PIK3CA mutant LUADs exhibited markedly down-regulated PD-L1 expression. LUADs with TP53 or KEAP1 mutations displayed relatively increased CD57 and Granzyme B levels indicative of augmented natural killer (NK) cell infiltration.Conclusion(s)Our study highlights molecular and immune phenotypes that warrant further analysis for their roles in clinical outcomes and personalized immune-based therapy of LUAD.

Dataset Information

ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples.

Publications

ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples.

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