#germline — Public Fediverse posts

Pipeline release! nf-core/sarek v3.9.0 - 3.9.0 - Sarvesjåhkå!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.9.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.9.0 - 3.9.0 - Sarvesjåhkå!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.9.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Fungicide vinclozin causes disease via germline for 20 generations in rats

https://pnas.org/doi/10.1073/pnas.2523071123

#HackerNews #Fungicide #vinclozin #germline #disease #rats #research #health #science #toxicology

Fungicide vinclozin causes disease via germline for 20 generations in rats

https://pnas.org/doi/10.1073/pnas.2523071123

#HackerNews #Fungicide #vinclozin #germline #disease #rats #research #health #science #toxicology

Pipeline release! nf-core/sarek v3.8.1 - 3.8.1 - Laitaure!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.8.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.8.1 - 3.8.1 - Laitaure!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.8.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.8.0 - 3.8.0 - Sitojaure!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.8.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.8.0 - 3.8.0 - Sitojaure!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.8.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.7.1 - 3.7.1 - Buollámtjåhkka!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.7.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.7.1 - 3.7.1 - Buollámtjåhkka!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.7.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.7.0 - 3.7.0 - Saltoluokta!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.7.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.7.0 - 3.7.0 - Saltoluokta!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.7.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.6.1 - Sarek 3.6.1 - Sjnjierák!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.6.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.6.1 - Sarek 3.6.1 - Sjnjierák!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.6.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.6.0 - Sarek 3.6.0 - Kvikkjokk!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.6.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.6.0 - Sarek 3.6.0 - Kvikkjokk!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.6.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Why do old males produce poor quality offspring? Is it the age of their germline, or the age of their sperm? Sanghvi et al. discover some surprising answers!
Read now ahead of print!
https://www.journals.uchicago.edu/doi/10.1086/736479

#male #sperm #germline

Why do old males produce poor quality offspring? Is it the age of their germline, or the age of their sperm? Sanghvi et al. discover some surprising answers!
Read now ahead of print!
https://www.journals.uchicago.edu/doi/10.1086/736479

#male #sperm #germline

Pipeline release! nf-core/sarek v3.5.1 - 3.5.1 - Akkatjåkkå!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.5.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.5.1 - 3.5.1 - Akkatjåkkå!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.5.1

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.5.0 - 3.5.0 - Áhkájiegna!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.5.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.5.0 - 3.5.0 - Áhkájiegna!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.5.0

#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.4.4 - Sarek 3.4.4 - Ruopsokjåkhå!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.4.4

#annotation #cancer #gatk4 #genomics #germline #pre-processing #somatic #target-panels #variant-calling #whole-exome-sequencing #whole-genome-sequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.4.4 - Sarek 3.4.4 - Ruopsokjåkhå!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.4.4

#annotation #cancer #gatk4 #genomics #germline #pre-processing #somatic #target-panels #variant-calling #whole-exome-sequencing #whole-genome-sequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.4.3 - Sarek 3.4.3 - Loametjåhkkå!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.4.3

#annotation #cancer #gatk4 #genomics #germline #pre-processing #somatic #target-panels #variant-calling #whole-exome-sequencing #whole-genome-sequencing #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sarek v3.4.3 - Sarek 3.4.3 - Loametjåhkkå!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.4.3

#annotation #cancer #gatk4 #genomics #germline #pre-processing #somatic #target-panels #variant-calling #whole-exome-sequencing #whole-genome-sequencing #nfcore #openscience #nextflow #bioinformatics

"the strength of the #germline signal regulates the organism’s life span. As a worm ages, the quality of its eggs or sperm declines—what we refer to as biological clock. The decline is also reflected in the germ cells’ changing ability to transmit signals from the brain’s mitochondria. As the worm grows older, its germline transmits the repair signal less effectively, and so its body declines, too."

https://www.quantamagazine.org/cells-across-the-body-talk-to-each-other-about-aging-20240108/

Experiences from a rural hospital in North Carolina show hereditary genetic testing of all breast cancer patients is feasible and can result in changes in care for many patients.

https://sciencebusiness.technewslit.com/?p=45331

#News #Press #Science #Business #BreastCancer #HealthCare #Rural #Hosptial #GeneticTesting #Germline #Inherited #MedicalRecords #OuterBanks

Experiences from a rural hospital in North Carolina show hereditary genetic testing of all breast cancer patients is feasible and can result in changes in care for many patients.

https://sciencebusiness.technewslit.com/?p=45331

#News #Press #Science #Business #BreastCancer #HealthCare #Rural #Hosptial #GeneticTesting #Germline #Inherited #MedicalRecords #OuterBanks

Join Thurs, May 25, at noon CT/1 pm ET as Dr. Kim Nichols of #StJude presents “Hereditary Predisposition to Cancer: At the Tip of the Iceberg.” She’ll discuss the prevalence & spectrum of #cancer predisposing #GermlineVariants in children and young adults, how these variants influence cancer #phenotypes & outcomes, and how #germline info impacts #ClinicalCare—including approaches to #CancerSurveillance & treatment. Register. https://bit.ly/SOCC23-MAS #SOCC23 #ChildhoodCancer #CancerPredisposition

"Mutations in the DREAM complex induce germline-like expression patterns of multiple mechanisms of DNA repair in the soma. Consequently, DREAM mutants confer resistance to a wide range of DNA-damage types during development and aging"

https://www.nature.com/articles/s41594-023-00942-8

#aging #cellular #programming #germline #biology #regulation #DNA #genetics #molecularBiology #cellBiology #geneRegulation #reprogramming #health #senescence #repair #maintenance #damage #replication #informationTheory #data #mutation

Wanted to share this great work on curating #ClonalHematopoiesis (#CHIP) in biobanks just published in #Blood. This work, led by Dr. Caitlyn Vlasschaert, used known CHIP associations with #aging, #germline variants, and #HealthOutcomes to carefully define variant calling criteria in All of Us and UK Biobank studies (N > 500K). The call sets are in the process of being returned to the biobanks so that they may be used by researchers anywhere! Link: https://doi.org/10.1182/blood.2022018825 #medicine #genomics

Wanted to share this great work on curating #ClonalHematopoiesis (#CHIP) in biobanks just published in #Blood. This work, led by Dr. Caitlyn Vlasschaert, used known CHIP associations with #aging, #germline variants, and #HealthOutcomes to carefully define variant calling criteria in All of Us and UK Biobank studies (N > 500K). The call sets are in the process of being returned to the biobanks so that they may be used by researchers anywhere! Link: https://doi.org/10.1182/blood.2022018825 #medicine #genomics

Transcriptional and mutational signatures of the Drosophila ageing germline

#Drosophila #germline #aging

https://www.nature.com/articles/s41559-022-01958-x

Transcriptional and mutational signatures of the Drosophila ageing germline

#Drosophila #germline #aging

https://www.nature.com/articles/s41559-022-01958-x

We were curious about how #TEs would be impacted by #ReproAging, since #TE reactivation is frequent during somatic aging. Because of transgenerational mutagenic potential, dedicated safeguards evolved to keep #TEs in check in the #germline, notably through the #PIWI pathway. 3/n

We were curious about how #TEs would be impacted by #ReproAging, since #TE reactivation is frequent during somatic aging. Because of transgenerational mutagenic potential, dedicated safeguards evolved to keep #TEs in check in the #germline, notably through the #PIWI pathway. 3/n

Hi Mastodon!
I’m a Academic Clinical Lecturer in #genetics at Imperial College London and an MRC Investigator in the #epigenetics section at the London Institute of Medical Sciences studying #germline and #pluripotency. We also have a growing interest in #infertility and developmental disorders #raredisease. Post mainly about #Science #Squash #Scotland #Sport. Also a bit #Sweary - sorry mum. Still on Twitter interested to see what happens here though

Something I find fascinating is how different #germline mutations can affect the risk of acquiring somatic mutations and #cancer. In this recent #hematology paper, the authors found that germline #DDX41 mutations lead to myeloid neoplasia with a different spectrum of somatic mutations. Intriguingly, they also found that DDX41-mutated patients did not have worse survival even with acquired #TP53 mutations (which is normally very bad!): https://ashpublications.org/blood/article/doi/10.1182/blood.2022018221/486974/Germline-DDX41-mutations-define-a-unique-subtype #science #medicine #genomics

My initial #introduction was a bit sparse, so here are more areas where I engage: #health #healthcare #medicine #physicianscientist #MDPhD #DoubleDocs #science #research #academic #biology #humandisease #aging #hematology #haematology #hematopoiesis #blood #stemcells #germline #somaticgenetics #mosaicism #mutation #SNV #mCA #genetics #genomics #populationgenetics #AML #MDS #MPN #myeloid #ClonalHematopoiesis #CHIP #inflammation #bonemarrow #HSC #biobank #molecularbiology #geneediting #CRISPR #NGS

My initial #introduction was a bit sparse, so here are more areas where I engage: #health #healthcare #medicine #physicianscientist #MDPhD #DoubleDocs #science #research #academic #biology #humandisease #aging #hematology #haematology #hematopoiesis #blood #stemcells #germline #somaticgenetics #mosaicism #mutation #SNV #mCA #genetics #genomics #populationgenetics #AML #MDS #MPN #myeloid #ClonalHematopoiesis #CHIP #inflammation #bonemarrow #HSC #biobank #molecularbiology #geneediting #CRISPR #NGS