igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review. #IGV #InteractiveVisualizationss #GeneticVariants #VariantReview @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

A multi-tissue atlas of genetic regulatory effects in sheep. #SheepGenome #GeneticRegulation #GeneticVariants #Genomics #FarmGTEX #SheepGTEX @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

An optimized variant prioritization process for rare disease diagnostics: recommendations for Exomiser and Genomiser. #Exome #Genome #Sequencing #GeneticVariants #RareDiseases #GeneticDiagnostics #GenomeMedicine 🧪🧬 🖥️
genomemedicine.biomedcentral.com/articles/10....

providing insight into the molecular principles that determine how an organism's genes influence its traits
By understanding how #geneticvariants affect #proteinexpression

The Great Genotyper: a graph-based method for population genotyping of small and structural variants. #GeneticVariants #StructuralVariants #GenomeGraphs #PopulationGenomics #Genotyping @gigascience.bsky.social 🧪 🧬 🖥️
academic.oup.com/gigascience/...

Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information. #Ychromosome #EvolutionaryInformation #GeneticVariants #HumanGenome @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/article/...

Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis. #RareDiseases #GeneticVariants #SequencingStrategies #Genomics #GenomeMedicine
genomemedicine.biomedcentral.com/articles/10....

A Vision of How Low-Coverage Sequence Data Should Contribute to Genetic Evaluation in the Future. #LowCoverageSequencing #WGS #GeneticVariants #Genotyping #JournalOfAnimalScience
academic.oup.com/jas/advance-...

Federated Learning for the pathogenicity annotation of genetic variants in multi-site clinical settings. #GeneticVariants #ClinicalClassification #FederatedLearning #Genomics #Bioinformatics
academic.oup.com/bioinformati...

Pangenome-based identification of cryptic pathogenic variants in undiagnosed rare disease patients. #GeneticVariants #PathogenicVariants #Pangenomes #LongRead #Sequencing @medrxivpreprint.bsky.social 🧬 🖥️
www.medrxiv.org/content/10.1...

Assembly of the complete horse genome reveals variants associated with reproduction and temperamental traits. #HorseGenome #T2T #ChromosomeAssembly #GeneticVariants @biorxivpreprint.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

Genetic variants affecting RNA stability influence complex traits and disease risk. #RNAstability #DiseaseRisks #GeneticVariants #Genomics @natgenet.nature.com
www.nature.com/articles/s41...

The potential of AI models to identify regulatory variants underlying cattle traits. #AI #GeneticVariants #RegulatoryVariants #CattleGenomes #CattleTraits @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...

Summary figure details changes in ether lipid metabolism in obesity as indicated by the lipid ratios, liver micro-array data, and GWAS analysis. Coloured text depicts potential changes in enzymatic activity (green: increase; red: decrease), identified through linear regression analysis, adjusting for age and sex, of 82 lipid ratios and waist circumference in the AusDiab cohort (n = 10,399). Lipid ratios were log2 transformed, mean-centered and scaled to standard deviation. p-values were corrected for multiple comparisons using the false discovery rate method of Benjamini and Hochberg. Scatter plots depict consolidated liver micro-array data of male mice across 74 matched strains (n = 2−3 per strain) after either a high-fat/high-sugar (navy, n = 152) or chow (blue, n = 222) diet for eight weeks.

#Lipidomic profiling has linked plasma #EtherLipids with #obesity. This study analyzes a set of biologically informed lipid ratios to reveal obesity-related alterations in enzymatic activity & #GeneticVariants not apparent in traditional lipidomic analyses @plosbiology.org 🧪 plos.io/41vdrO5

GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants. #GeneticVariants #VariantExploration #DataVisualization #GUI #BMCbioinformatics 🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....

Summary figure details changes in ether lipid metabolism in obesity as indicated by the lipid ratios, liver micro-array data, and GWAS analysis. Coloured text depicts potential changes in enzymatic activity (green: increase; red: decrease), identified through linear regression analysis, adjusting for age and sex, of 82 lipid ratios and waist circumference in the AusDiab cohort (n = 10,399). Lipid ratios were log2 transformed, mean-centered and scaled to standard deviation. p-values were corrected for multiple comparisons using the false discovery rate method of Benjamini and Hochberg. Scatter plots depict consolidated liver micro-array data of male mice across 74 matched strains (n = 2−3 per strain) after either a high-fat/high-sugar (navy, n = 152) or chow (blue, n = 222) diet for eight weeks.

#Lipidomic profiling has linked plasma #EtherLipids with #obesity. This study analyzes a set of biologically informed lipid ratios to reveal obesity-related alterations in enzymatic activity & #GeneticVariants not apparent in traditional lipidomic analyses @plosbiology.org 🧪 plos.io/41vdrO5

Summary figure details changes in ether lipid metabolism in obesity as indicated by the lipid ratios, liver micro-array data, and GWAS analysis. Coloured text depicts potential changes in enzymatic activity (green: increase; red: decrease), identified through linear regression analysis, adjusting for age and sex, of 82 lipid ratios and waist circumference in the AusDiab cohort (n = 10,399). Lipid ratios were log2 transformed, mean-centered and scaled to standard deviation. p-values were corrected for multiple comparisons using the false discovery rate method of Benjamini and Hochberg. Scatter plots depict consolidated liver micro-array data of male mice across 74 matched strains (n = 2−3 per strain) after either a high-fat/high-sugar (navy, n = 152) or chow (blue, n = 222) diet for eight weeks.

#Lipidomic profiling has linked plasma #EtherLipids with #obesity. This study analyzes a set of biologically informed lipid ratios to reveal obesity-related alterations in enzymatic activity & #GeneticVariants not apparent in traditional lipidomic analyses @plosbiology.org 🧪 plos.io/41vdrO5

#Medsky🧪 #IDsky #Immunosky #pedsky #publichealth
More evidences and studies have found that #geneticvariants appear to play a significant role in influencing the distinct metabolic pathways observed in Paediatric #MultisystemInflammatorySyndrome (MIS-C) and severe #COVID.

🐎 Horses produce just one #foal after an eleven-month pregnancy, making #reproductiveefficiency critical. Concerns about inbreeding (which can increase harmful #geneticvariants) led researchers to examine whether it impacts foaling rates in #AustralianThoroughbred #mares.

A founder BRCA1 exonic duplication involving breakpoint in T2T reference genome-specific region results in constitutional fusion transcript. #T2T #ReferenceGenome #GeneticVariants #VariantAssessment #HQreferenceGenomes #NPJgenomicMedicine 🧬 🧪 🖥️
www.nature.com/articles/s41...

Coming up in September!
➡️Christina Kajba @ckajba.bsky.social & Michael Herger @michaelherger.bsky.social — pooled prime editing screens in haploid human cells
➡️Jon Acosta — multiplexed in vivo base editing screens
#GeneticVariants #PrimeEditing
ℹ️https://www.varianteffect.org/seminar-series/

The Platinum Pedigree: a long-read benchmark for genetic variants. #HumanGenome #ReferenceGenome #PlatinumPedigree #LongReads #Benchmarking #GeneticVariants @natmethods.nature.com 🧬 🖥️
www.nature.com/articles/s41...

AdaGenes: A streaming processor for high-throughput annotation and filtering of sequence variant data. #GeneticVariants #VariantFiltering #VariantAnnotation #VCFs #Genomics #Bioinformatics @biorxiv-bioinfo.bsky.social‬ 🧬 🖥️
www.biorxiv.org/content/10.1...

Using large-scale population-based data to improve disease risk assessment of clinical variants. #GeneticVariants #ClinVar #DiseaseRiskVariants #Genomics @natgenet.nature.com‬
www.nature.com/articles/s41...

SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments. #SpatilaTranstriptomics #SNVs #TumorSamples #GeneticVariants #Genomics #Bioinformatics @gigascience.bsky.social‬ 🧬 🖥️
academic.oup.com/gigascience/...

Parity modifies the effect of genetic variants associated with gestational duration and birth weight
Andreassen, O. A., Corfield, E. C. et al.
Paper
Details
#GeneticVariants #GestationalDuration #BirthWeightResearch

Transcriptomic signatures of rare variant impacts across sex and the X-chromosome. #RareVariants #GeneticVariants #Xchromosome #Genomics @hggadvances.bsky.social‬
www.cell.com/hgg-advances...

Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain. #GeneticVariants #DeepVariant #NonHumanSpecies #Bioinformatics @genomeresearch.bsky.social‬ 🧬 🖥️
bsky.app/profile/nano...

Analysis-ready VCF at Biobank scale using Zarr. #VCF #Zarr #GeneticVariants #Genomics #Bioinformatics @gigascience.bsky.social‬ 🧬 🖥️
academic.oup.com/gigascience/...

Onkopus: precise interpretation and prioritization of sequence variants for biomedical research and precision medicine. #GeneticVariants #VariantInterpretation #GeneticAlterations #CancerVariants @narjournal.bsky.social‬ 🧬 🖥️
academic.oup.com/nar/advance-...