Assessing the functionality of over 4,000 genome variants for their role in cancer, with prominence of impact for those related to the immune system and chronic inflammation
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Functional analysis of cancer-associated germline risk variants - Nature Genetics
Analysis of 4,041 single-nucleotide variants (SNVs) linked to 13 cancers performed in primary human cell types identifies 380 potentially regulatory SNVs and their putative target genes. Editing one S...
www.nature.com
February 17, 2025 at 3:47 PM
Assessing the functionality of over 4,000 genome variants for their role in cancer, with prominence of impact for those related to the immune system and chronic inflammation
www.nature.com/articles/s41...
www.nature.com/articles/s41...
🗯️ Festival de BD d'Angoulême: les financeurs publics appellent à renoncer à l'édition 2026
➡️ u.afp.com/Snvs
➡️ u.afp.com/Snvs
November 20, 2025 at 4:00 PM
🗯️ Festival de BD d'Angoulême: les financeurs publics appellent à renoncer à l'édition 2026
➡️ u.afp.com/Snvs
➡️ u.afp.com/Snvs
Man spricht dann von synonymen Mutationen. Synonyme SNVs können aber Einfluss auf die Geschwindigkeit des Übersetzungsprozesses haben.
Nicht-synonyme SNVs verändern die Aminosäure, was Auswirkung auf die Form, Stabilität und Funktion des Eiweißes haben kann.
Eine Sonderform sorgt
3/17
Nicht-synonyme SNVs verändern die Aminosäure, was Auswirkung auf die Form, Stabilität und Funktion des Eiweißes haben kann.
Eine Sonderform sorgt
3/17
January 6, 2025 at 6:40 AM
Man spricht dann von synonymen Mutationen. Synonyme SNVs können aber Einfluss auf die Geschwindigkeit des Übersetzungsprozesses haben.
Nicht-synonyme SNVs verändern die Aminosäure, was Auswirkung auf die Form, Stabilität und Funktion des Eiweißes haben kann.
Eine Sonderform sorgt
3/17
Nicht-synonyme SNVs verändern die Aminosäure, was Auswirkung auf die Form, Stabilität und Funktion des Eiweißes haben kann.
Eine Sonderform sorgt
3/17
Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes:
Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!).
The manuscript was also published this summer in Genome Research!
Links next...
Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!).
The manuscript was also published this summer in Genome Research!
Links next...
September 8, 2026 at 4:17 PM
Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes:
Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!).
The manuscript was also published this summer in Genome Research!
Links next...
Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!).
The manuscript was also published this summer in Genome Research!
Links next...
The use of the phrase “ancestry-specific variant” is increasing, particularly to describe rare Single-nucleotide variants (SNVs). But these alleles are not ancestry-specific. They have not yet been found elsewhere, but they will be. 1/n
February 28, 2024 at 1:44 PM
The use of the phrase “ancestry-specific variant” is increasing, particularly to describe rare Single-nucleotide variants (SNVs). But these alleles are not ancestry-specific. They have not yet been found elsewhere, but they will be. 1/n
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV
Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...
www.biorxiv.org
September 29, 2025 at 7:45 PM
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
What are your favorite papers that linked patients, traced outbreaks, or distinguished epidemiological hypotheses on the careful basis of just a few SNVs? Like ~ <20? Bacterial best, viruses OK too
July 8, 2026 at 9:09 PM
What are your favorite papers that linked patients, traced outbreaks, or distinguished epidemiological hypotheses on the careful basis of just a few SNVs? Like ~ <20? Bacterial best, viruses OK too
SNPs, SNVs, & GWAS studies . . . youtu.be/GvHrH4NrP5M
SNPs, SNVs, and GWAS studies
YouTube video by the bumbling biochemist
youtu.be
August 20, 2026 at 9:48 PM
SNPs, SNVs, & GWAS studies . . . youtu.be/GvHrH4NrP5M
Hereditary cancer NGS workflows are built to detect SNVs and indels. But what about clinically significant CNVs?
Register for our latest free webinar: Beyond SNVs: Why CNVs deserve a closer look in hereditary cancer. hubs.la/Q04y6cpX0
Register for our latest free webinar: Beyond SNVs: Why CNVs deserve a closer look in hereditary cancer. hubs.la/Q04y6cpX0
September 24, 2026 at 3:41 PM
Hereditary cancer NGS workflows are built to detect SNVs and indels. But what about clinically significant CNVs?
Register for our latest free webinar: Beyond SNVs: Why CNVs deserve a closer look in hereditary cancer. hubs.la/Q04y6cpX0
Register for our latest free webinar: Beyond SNVs: Why CNVs deserve a closer look in hereditary cancer. hubs.la/Q04y6cpX0
Hier sind nur einzelne Basenpaare verändert, zB. ein G=C-Paar gegen ein A=T-Paar ausgetauscht. Die Folgen davon können unterschiedlich sein: manche SNVs verändern die Aminosäuresequenz nicht (Aminosäuren sind die Bausteine der Eiweiße, die durch die Gene kodiert sind).
2/17
2/17
January 6, 2025 at 6:40 AM
Hier sind nur einzelne Basenpaare verändert, zB. ein G=C-Paar gegen ein A=T-Paar ausgetauscht. Die Folgen davon können unterschiedlich sein: manche SNVs verändern die Aminosäuresequenz nicht (Aminosäuren sind die Bausteine der Eiweiße, die durch die Gene kodiert sind).
2/17
2/17
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/...
academic.oup.com/gigascience/...
June 21, 2025 at 7:05 PM
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/...
academic.oup.com/gigascience/...
CRISPR-Cas9-based editing clarifies thousands of BRCA2 VUSs by categorizing SNVs in humanized mouse stem cells, enhancing genetic test accuracy! #BRCA2Science PMID:39779848, Nature 2025, @Nature @OTSociety https://doi.org/10.1038/s41586-024-08349-1 🧪
February 23, 2025 at 7:50 AM
CRISPR-Cas9-based editing clarifies thousands of BRCA2 VUSs by categorizing SNVs in humanized mouse stem cells, enhancing genetic test accuracy! #BRCA2Science PMID:39779848, Nature 2025, @Nature @OTSociety https://doi.org/10.1038/s41586-024-08349-1 🧪
We also wondered where these animals came from and investigated that by analyzing their DNA as well for SNVs (individual mutations) that are linked to geographic locations.
This is similar to what 23 and Me does to say you are 10% from wherever.
This is similar to what 23 and Me does to say you are 10% from wherever.
September 19, 2024 at 8:13 PM
We also wondered where these animals came from and investigated that by analyzing their DNA as well for SNVs (individual mutations) that are linked to geographic locations.
This is similar to what 23 and Me does to say you are 10% from wherever.
This is similar to what 23 and Me does to say you are 10% from wherever.
4/ Fig. 2 shows that SNVs more frequent in Quechua tend to be associated with higher AMY1 CN, while some SNVs more frequent in Maya are associated with lower AMY1 CN.
This suggests that elevated AMY1 copy number in Andeans is linked to a distinctive haplotypic background near the amylase locus.
This suggests that elevated AMY1 copy number in Andeans is linked to a distinctive haplotypic background near the amylase locus.
May 5, 2026 at 4:28 PM
4/ Fig. 2 shows that SNVs more frequent in Quechua tend to be associated with higher AMY1 CN, while some SNVs more frequent in Maya are associated with lower AMY1 CN.
This suggests that elevated AMY1 copy number in Andeans is linked to a distinctive haplotypic background near the amylase locus.
This suggests that elevated AMY1 copy number in Andeans is linked to a distinctive haplotypic background near the amylase locus.
BRCA2 mutations are not all the same. Rather, single nucleotide variants (SNVs) confer variable risk for breast, prostate, pancreatic & other cancers. While not definitive, this study of distinct #BRCA variants is a step toward clarifying prognosis @nature.com www.nature.com/articles/s41... #OncSky
January 10, 2025 at 1:55 PM
BRCA2 mutations are not all the same. Rather, single nucleotide variants (SNVs) confer variable risk for breast, prostate, pancreatic & other cancers. While not definitive, this study of distinct #BRCA variants is a step toward clarifying prognosis @nature.com www.nature.com/articles/s41... #OncSky
scSNViz: Visualization and analysis of Cell-Specific expressed SNVs. #SingleCell #scRNAseq #SNVs #DataVisualization #Genomics #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
January 17, 2026 at 8:32 AM
scSNViz: Visualization and analysis of Cell-Specific expressed SNVs. #SingleCell #scRNAseq #SNVs #DataVisualization #Genomics #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Happy to see this work led by @katwalter.bsky.social out! In #TB outbreaks & high transmission settings, we often see many Mtb genomes that are identical or have 1-2 SNVs. Katharine asked whether we could leverage within host diversity & shared minority variants to better link transmission pairs.
New research article in The Lancet Microbe
Signatures of transmission in within-host #Mycobacterium #tuberculosis complex variation: a retrospective genomic epidemiology study
www.thelancet.com/journals/lan...
#IDSky #MicroSky #TB #OpenAccess #OA
Signatures of transmission in within-host #Mycobacterium #tuberculosis complex variation: a retrospective genomic epidemiology study
www.thelancet.com/journals/lan...
#IDSky #MicroSky #TB #OpenAccess #OA
November 29, 2024 at 3:50 PM
Happy to see this work led by @katwalter.bsky.social out! In #TB outbreaks & high transmission settings, we often see many Mtb genomes that are identical or have 1-2 SNVs. Katharine asked whether we could leverage within host diversity & shared minority variants to better link transmission pairs.
Sjoerd is doing a decent job of explaining the VERY basics: traits people show are due to genetics; traits are coded by SNVs (single-nucelotide variants). SNPs (single-nucleotide polymorphism-- abbreviated it sounds like "snips") are of greatest interest in gene association studies.
September 11, 2026 at 4:43 PM
Sjoerd is doing a decent job of explaining the VERY basics: traits people show are due to genetics; traits are coded by SNVs (single-nucelotide variants). SNPs (single-nucleotide polymorphism-- abbreviated it sounds like "snips") are of greatest interest in gene association studies.
Here's the first minute of 'The Civil War.'
What a stunning way to frame your program.
(Ken Burns, 1990) - "Wilmer McLean"
www.youtube.com/watch?v=snvS...
What a stunning way to frame your program.
(Ken Burns, 1990) - "Wilmer McLean"
www.youtube.com/watch?v=snvS...
Wilmur McLean: The Beginning and The End
YouTube video by McKeow Tube (McKeowTube)
www.youtube.com
September 2, 2025 at 5:49 AM
Here's the first minute of 'The Civil War.'
What a stunning way to frame your program.
(Ken Burns, 1990) - "Wilmer McLean"
www.youtube.com/watch?v=snvS...
What a stunning way to frame your program.
(Ken Burns, 1990) - "Wilmer McLean"
www.youtube.com/watch?v=snvS...
The Somatic Mosaicism across Human Tissues Network
#SMaHT
13 tissues (incld #Aorta😆) 7 donors
Short-/Long-/Ultra-long-read sequencing to cover SNVs, indels, structural variants & large chromosomal aberrations
bulk + single-cell WGS
RNAseq
data.smaht.org
#Nature 2025
www.nature.com/articles/s41...
#SMaHT
13 tissues (incld #Aorta😆) 7 donors
Short-/Long-/Ultra-long-read sequencing to cover SNVs, indels, structural variants & large chromosomal aberrations
bulk + single-cell WGS
RNAseq
data.smaht.org
#Nature 2025
www.nature.com/articles/s41...
July 7, 2025 at 12:05 PM
The Somatic Mosaicism across Human Tissues Network
#SMaHT
13 tissues (incld #Aorta😆) 7 donors
Short-/Long-/Ultra-long-read sequencing to cover SNVs, indels, structural variants & large chromosomal aberrations
bulk + single-cell WGS
RNAseq
data.smaht.org
#Nature 2025
www.nature.com/articles/s41...
#SMaHT
13 tissues (incld #Aorta😆) 7 donors
Short-/Long-/Ultra-long-read sequencing to cover SNVs, indels, structural variants & large chromosomal aberrations
bulk + single-cell WGS
RNAseq
data.smaht.org
#Nature 2025
www.nature.com/articles/s41...
A study of 311 Alzheimer’s brains found over 1,000 somatic SNVs in cancer genes, linked to clonal hematopoiesis, driving inflammatory microglial states. PMID:42019491, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00341-7 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
https://www.cell.com/cell/fulltext/S0092-8674(26)00341-7
No description available
www.cell.com
September 1, 2026 at 9:00 PM
V2P (variant-to-phenotype) is live: nature.com/articles/s41...
To our knowledge, first genomewide SNVs+indels model jointly predicting pathogenicity + disease domain (23 HPO groups; e.g. cardiac/immune/metabolic).
Great work by David Stein in collaboration with @schlessingerlab.bsky.social
To our knowledge, first genomewide SNVs+indels model jointly predicting pathogenicity + disease domain (23 HPO groups; e.g. cardiac/immune/metabolic).
Great work by David Stein in collaboration with @schlessingerlab.bsky.social
December 15, 2025 at 6:02 PM
V2P (variant-to-phenotype) is live: nature.com/articles/s41...
To our knowledge, first genomewide SNVs+indels model jointly predicting pathogenicity + disease domain (23 HPO groups; e.g. cardiac/immune/metabolic).
Great work by David Stein in collaboration with @schlessingerlab.bsky.social
To our knowledge, first genomewide SNVs+indels model jointly predicting pathogenicity + disease domain (23 HPO groups; e.g. cardiac/immune/metabolic).
Great work by David Stein in collaboration with @schlessingerlab.bsky.social
Thrilled to share the lab's latest preprint on the phenotypic impact of SNVs and INDELs in human rDNA using UK Biobank data!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Germline sequence variation within the ribosomal DNA is associated with human complex traits
The ribosome is one of the core macromolecules in the cell. The ribosomal RNAs (rRNA), which are essential components of the ribosome, are coded by the multi-copy ribosomal DNA (rDNA). Despite its hig...
www.biorxiv.org
February 8, 2025 at 1:15 PM
Thrilled to share the lab's latest preprint on the phenotypic impact of SNVs and INDELs in human rDNA using UK Biobank data!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
See the bigger picture in cancer with #SigniosBio's @pacbio.bsky.social #HiFi long reads. Detect SNVs, Indels, SVs, full-length RNA isoforms & DNA methylation (#5mC) in one workflow. Explore what's possible: www.signiosbio.com/contact/ #LongReads #CancerGenomics #Epigenetics #Multiomics
April 30, 2025 at 3:11 PM
See the bigger picture in cancer with #SigniosBio's @pacbio.bsky.social #HiFi long reads. Detect SNVs, Indels, SVs, full-length RNA isoforms & DNA methylation (#5mC) in one workflow. Explore what's possible: www.signiosbio.com/contact/ #LongReads #CancerGenomics #Epigenetics #Multiomics
Excited to share our latest preprint! Grateful to @reimand.bsky.social and the entire team for their support!
We show that protein motif-rewiring SNVs (rwSNVs) can reconfigure kinase signaling, linking mutational processes to functional proteomic changes.
www.biorxiv.org/content/10.6...
We show that protein motif-rewiring SNVs (rwSNVs) can reconfigure kinase signaling, linking mutational processes to functional proteomic changes.
www.biorxiv.org/content/10.6...
www.biorxiv.org
March 20, 2026 at 7:11 PM
Excited to share our latest preprint! Grateful to @reimand.bsky.social and the entire team for their support!
We show that protein motif-rewiring SNVs (rwSNVs) can reconfigure kinase signaling, linking mutational processes to functional proteomic changes.
www.biorxiv.org/content/10.6...
We show that protein motif-rewiring SNVs (rwSNVs) can reconfigure kinase signaling, linking mutational processes to functional proteomic changes.
www.biorxiv.org/content/10.6...