Finally, a large group of patients are those with heterozygous COL4A3 and COL4A4 variants who do well long term with only microscopic hematuria. The problem is that you don't know which patients will fall into this bucket and which will fall into the buckets above by genotyping alone. #KidneyWk
November 6, 2025 at 6:39 PM
Finally, a large group of patients are those with heterozygous COL4A3 and COL4A4 variants who do well long term with only microscopic hematuria. The problem is that you don't know which patients will fall into this bucket and which will fall into the buckets above by genotyping alone. #KidneyWk
An amplicon panel for high-throughput and low-cost genotyping of Yesso scallop Mizuhopecten yessoensis https://www.biorxiv.org/content/10.1101/2025.11.05.686843v1
November 7, 2025 at 4:38 AM
An amplicon panel for high-throughput and low-cost genotyping of Yesso scallop Mizuhopecten yessoensis https://www.biorxiv.org/content/10.1101/2025.11.05.686843v1
Pre-phasing long reads improves structural variant genotyping academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/Zilong-Li/SV...
October 27, 2025 at 3:55 PM
Pre-phasing long reads improves structural variant genotyping academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/Zilong-Li/SV...
WHY did none of you tell me that ONE BATTLE AFTER ANOTHER features plot-critical onscreen electrophoresis-based genotyping???!!
October 26, 2025 at 3:30 AM
WHY did none of you tell me that ONE BATTLE AFTER ANOTHER features plot-critical onscreen electrophoresis-based genotyping???!!
Pre-phasing long reads improves structural variant genotyping. #LongReads #Sequencing #ReadsPhasing #StructuralVariants #Genotyping #Genomics #Bioinformatics
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
October 25, 2025 at 7:32 AM
Pre-phasing long reads improves structural variant genotyping. #LongReads #Sequencing #ReadsPhasing #StructuralVariants #Genotyping #Genomics #Bioinformatics
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
The Great Genotyper: a graph-based method for population genotyping of small and structural variants
Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequenc...
pmc.ncbi.nlm.nih.gov
October 7, 2025 at 8:32 PM
A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1
October 2, 2025 at 6:28 AM
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
- there is almost no circumstance where MTHFR genotyping needs to be done because it doesn't change management, and most of the claimed disease associations for it are not supported.
- Folate receptor autoantibodies (FRAAs) ≠ cerebral folate deficiency
(5/7)
- Folate receptor autoantibodies (FRAAs) ≠ cerebral folate deficiency
(5/7)
September 28, 2025 at 8:16 PM
- there is almost no circumstance where MTHFR genotyping needs to be done because it doesn't change management, and most of the claimed disease associations for it are not supported.
- Folate receptor autoantibodies (FRAAs) ≠ cerebral folate deficiency
(5/7)
- Folate receptor autoantibodies (FRAAs) ≠ cerebral folate deficiency
(5/7)
What could you uncover with data from over 3,500 participants with prostate cancer? 🤔💭
🔗 Get inspired by the latest prostate cancer publications using CanPath data: canpath.ca/publications...
#ProstateCancerAwarenessMonth
🔗 Get inspired by the latest prostate cancer publications using CanPath data: canpath.ca/publications...
#ProstateCancerAwarenessMonth
September 26, 2025 at 5:28 PM
What could you uncover with data from over 3,500 participants with prostate cancer? 🤔💭
🔗 Get inspired by the latest prostate cancer publications using CanPath data: canpath.ca/publications...
#ProstateCancerAwarenessMonth
🔗 Get inspired by the latest prostate cancer publications using CanPath data: canpath.ca/publications...
#ProstateCancerAwarenessMonth
(2/6) Probabilistic genotyping, used to analyze complex DNA mixtures, is a growing tool in forensics. But in Sandoval’s case, prosecutors sought to suppress unfavorable results. Why?
December 16, 2024 at 3:03 PM
(2/6) Probabilistic genotyping, used to analyze complex DNA mixtures, is a growing tool in forensics. But in Sandoval’s case, prosecutors sought to suppress unfavorable results. Why?
20 years since Typhi was sequenced, so by now good resources are available. Big collaborations have been established. Metadata standards, genotyping schemes, and an AMR dictionary have been developed.
April 28, 2024 at 7:41 PM
20 years since Typhi was sequenced, so by now good resources are available. Big collaborations have been established. Metadata standards, genotyping schemes, and an AMR dictionary have been developed.
Open Access UCL Research: Phenotyping and genotyping inherited retinal diseases: Molecular genetics, clinical and imaging features, and therapeutics of macular dystrophies, cone and cone-rod dystrophies, rod-cone dystrophies, leber congenital amaurosis, and [...] discovery.ucl.ac.uk/id/eprint/10...
Phenotyping and genotyping inherited retinal diseases: Molecular genetics, clinical and imaging features, and therapeutics of macular dystrophies, cone and cone-rod dystrophies, rod-cone dystr...
UCL Discovery is UCL's open access repository, showcasing and providing access to UCL research outputs from all UCL disciplines.
discovery.ucl.ac.uk
January 27, 2025 at 12:41 PM
Open Access UCL Research: Phenotyping and genotyping inherited retinal diseases: Molecular genetics, clinical and imaging features, and therapeutics of macular dystrophies, cone and cone-rod dystrophies, rod-cone dystrophies, leber congenital amaurosis, and [...] discovery.ucl.ac.uk/id/eprint/10...
New Paper: A high density SNP chip for genotyping great tit (Parus major) populations In; Mol.Ecol. Res. http://hdl.handle.net/20.500.11755/74eeae51-4453-4791-8d45-f2406963540b
A high density SNP chip for genotyping great tit (Parus m...
hdl.handle.net
December 3, 2024 at 11:54 PM
New Paper: A high density SNP chip for genotyping great tit (Parus major) populations In; Mol.Ecol. Res. http://hdl.handle.net/20.500.11755/74eeae51-4453-4791-8d45-f2406963540b
This study developed #microsatellite markers for sequence-based high-throughput #genotyping of the non-model Neotropical tree species Anadenanthera colubrina (#Fabaceae)
➡️ doi.org/10.5091/plec...
➡️ doi.org/10.5091/plec...
January 29, 2025 at 10:41 AM
This study developed #microsatellite markers for sequence-based high-throughput #genotyping of the non-model Neotropical tree species Anadenanthera colubrina (#Fabaceae)
➡️ doi.org/10.5091/plec...
➡️ doi.org/10.5091/plec...
the reported essay started with a prompt from undark’s editors: how has science enabled surveillance? arguably it hasn’t. but one study showed that scientists could ID people by plucking their DNA out of A/C units. that study too involved probabilistic genotyping software doi.org/10.1002/elps...
December 16, 2024 at 1:54 PM
the reported essay started with a prompt from undark’s editors: how has science enabled surveillance? arguably it hasn’t. but one study showed that scientists could ID people by plucking their DNA out of A/C units. that study too involved probabilistic genotyping software doi.org/10.1002/elps...
Learn how to use the Applied Biosystems™ HIV-1 Genotyping Kit with Integrase for drug resistance studies in this comprehensive video series | CoListy
#thermofisher #appliedbiosystemshiv-1genotypingkit #hiv-1genotyping #drugresistancemutations
colisty.netlify.app/courses/appl...
#thermofisher #appliedbiosystemshiv-1genotypingkit #hiv-1genotyping #drugresistancemutations
colisty.netlify.app/courses/appl...
Applied Biosystems™ HIV-1 Genotyping Kit with Integrase
Learn how to use the Applied Biosystems™ HIV-1 Genotyping Kit with Integrase for drug resistance studies in this comprehensive video series | CoListy
colisty.netlify.app
January 16, 2025 at 4:14 PM
Learn how to use the Applied Biosystems™ HIV-1 Genotyping Kit with Integrase for drug resistance studies in this comprehensive video series | CoListy
#thermofisher #appliedbiosystemshiv-1genotypingkit #hiv-1genotyping #drugresistancemutations
colisty.netlify.app/courses/appl...
#thermofisher #appliedbiosystemshiv-1genotypingkit #hiv-1genotyping #drugresistancemutations
colisty.netlify.app/courses/appl...
The first chapter of my dissertation comparing genotyping methods for describing wolverine populations in their northwestern North American range is now published in the Journal of Mammalogy, check it out here!
academic.oup.com/jmammal/arti...
#PopGen
#PopulationGenetics
#PopulationGenomics
academic.oup.com/jmammal/arti...
#PopGen
#PopulationGenetics
#PopulationGenomics
Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada
Increasing the number and density of genetic loci has increased the resolution of population structure analysis in wide-ranging mammal species. This study
academic.oup.com
January 15, 2025 at 8:15 PM
The first chapter of my dissertation comparing genotyping methods for describing wolverine populations in their northwestern North American range is now published in the Journal of Mammalogy, check it out here!
academic.oup.com/jmammal/arti...
#PopGen
#PopulationGenetics
#PopulationGenomics
academic.oup.com/jmammal/arti...
#PopGen
#PopulationGenetics
#PopulationGenomics
and if you should disagree, well, you can pay for both our karyotyping/genotyping and i'll gladly share *my* results :)
March 26, 2025 at 6:51 AM
and if you should disagree, well, you can pay for both our karyotyping/genotyping and i'll gladly share *my* results :)
There's a lot of D1.3 in wild birds and poultry these days
Now we know from CDC that last month's Ohio hospitalization was also D1.3
I think this marks first known U.S. human with D1.3. No concerning genetic changes reported
www.cdc.gov/bird-flu/spo... bsky.app/profile/hlni...
Now we know from CDC that last month's Ohio hospitalization was also D1.3
I think this marks first known U.S. human with D1.3. No concerning genetic changes reported
www.cdc.gov/bird-flu/spo... bsky.app/profile/hlni...
March 19, 2025 at 5:11 PM
There's a lot of D1.3 in wild birds and poultry these days
Now we know from CDC that last month's Ohio hospitalization was also D1.3
I think this marks first known U.S. human with D1.3. No concerning genetic changes reported
www.cdc.gov/bird-flu/spo... bsky.app/profile/hlni...
Now we know from CDC that last month's Ohio hospitalization was also D1.3
I think this marks first known U.S. human with D1.3. No concerning genetic changes reported
www.cdc.gov/bird-flu/spo... bsky.app/profile/hlni...
Had high variance in coverage at the VCF stage AFTER downsampling bams. I'd marked but not removed dups. Found out I had large variance in duplication rates (and high rates period) across samples. Good reason to remove them!
#genomics
#PopGen
#PopulationGenetics
#PopulationGenomics
#genomics
#PopGen
#PopulationGenetics
#PopulationGenomics
March 18, 2025 at 5:47 AM
Had high variance in coverage at the VCF stage AFTER downsampling bams. I'd marked but not removed dups. Found out I had large variance in duplication rates (and high rates period) across samples. Good reason to remove them!
#genomics
#PopGen
#PopulationGenetics
#PopulationGenomics
#genomics
#PopGen
#PopulationGenetics
#PopulationGenomics
At the time phenotyping was far, far cheaper than genotyping, and by genotyping on a subset of places of a genome in a pedigree (family tree) one could make good estimates of the "best" sire/bull (male) or dam/cow (female) to mate for a given trait.
December 27, 2024 at 5:53 PM
At the time phenotyping was far, far cheaper than genotyping, and by genotyping on a subset of places of a genome in a pedigree (family tree) one could make good estimates of the "best" sire/bull (male) or dam/cow (female) to mate for a given trait.
TRGT enables accurate genotyping of tandem repeats (TRs) from PacBio HiFi data, detecting expansions, methylation, and mosaicism across 937,122 TRs.
Learn more: pubmed.ncbi.nlm.nih.gov/38168995/
Learn more: pubmed.ncbi.nlm.nih.gov/38168995/
Characterization and visualization of tandem repeats at genome scale - PubMed
Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate full-length sequences and methylation of T...
pubmed.ncbi.nlm.nih.gov
June 13, 2025 at 3:56 PM
TRGT enables accurate genotyping of tandem repeats (TRs) from PacBio HiFi data, detecting expansions, methylation, and mosaicism across 937,122 TRs.
Learn more: pubmed.ncbi.nlm.nih.gov/38168995/
Learn more: pubmed.ncbi.nlm.nih.gov/38168995/
#Genotyping 101: When should you genotype your mouse, and which strategy should you use? 🐁
In @jacksonlab.bsky.social's free online course, you will learn how to run a JAX protocol to genotype your JAX mice successfully.
Enroll: education.learning.jax.org/genotyping-m...
In @jacksonlab.bsky.social's free online course, you will learn how to run a JAX protocol to genotype your JAX mice successfully.
Enroll: education.learning.jax.org/genotyping-m...
Genotyping Mice
Why is genotyping so important when working with mice in research? When should you genotype your mouse, and which strategy should you use? Learn how to successfully run a JAX protocol to genotype your...
education.learning.jax.org
July 23, 2025 at 1:28 PM
#Genotyping 101: When should you genotype your mouse, and which strategy should you use? 🐁
In @jacksonlab.bsky.social's free online course, you will learn how to run a JAX protocol to genotype your JAX mice successfully.
Enroll: education.learning.jax.org/genotyping-m...
In @jacksonlab.bsky.social's free online course, you will learn how to run a JAX protocol to genotype your JAX mice successfully.
Enroll: education.learning.jax.org/genotyping-m...
🌱 The latest #FORGENIUS update is not just a seedling, it is growing into something quite promising!
🌲🧬👀 Explore the new genotyping tools and genomic data for 23 #forest tree species and their Genetic Conservation Units developed by our researchers ⬇️
doi.org/10.1101/2025...
🌲🧬👀 Explore the new genotyping tools and genomic data for 23 #forest tree species and their Genetic Conservation Units developed by our researchers ⬇️
doi.org/10.1101/2025...
The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units
Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is precisely aimed at increasing the quality and quantity of genetic data t...
doi.org
August 27, 2025 at 9:38 AM
🌱 The latest #FORGENIUS update is not just a seedling, it is growing into something quite promising!
🌲🧬👀 Explore the new genotyping tools and genomic data for 23 #forest tree species and their Genetic Conservation Units developed by our researchers ⬇️
doi.org/10.1101/2025...
🌲🧬👀 Explore the new genotyping tools and genomic data for 23 #forest tree species and their Genetic Conservation Units developed by our researchers ⬇️
doi.org/10.1101/2025...
TLDR: >40x coverage needed, rerio basecalling needed. Miniasm works better than Flye for genomic epi, flye works better for amr genotyping.
February 21, 2024 at 8:09 PM
TLDR: >40x coverage needed, rerio basecalling needed. Miniasm works better than Flye for genomic epi, flye works better for amr genotyping.