Newsletter: CEPH, CEU, and why Utah reference samples have a French name blog.stephenturner.us/p/ceph-ceu-c...
CEPH, CEU, and why Utah reference samples have a French name
CEPH organized the families, Utah supplied most of them, Coriell distributes the materials, and CEU specifically names the HapMap subset.
blog.stephenturner.us
September 13, 2026 at 10:28 AM
Newsletter: CEPH, CEU, and why Utah reference samples have a French name blog.stephenturner.us/p/ceph-ceu-c...
Why are there so many competing answers for where the HGDP Russians were sampled?
- Saint Petersburg: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506643/
- Arkhangelsk (even provides the district!): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591355/
- Vologda (seems most...
- Saint Petersburg: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506643/
- Arkhangelsk (even provides the district!): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591355/
- Vologda (seems most...
HGDP and HapMap Analysis by Ancestry Mapper ...
Knowledge of human origins, migrations, and expansions is...
www.ncbi.nlm.nih.gov
January 21, 2025 at 6:31 PM
Why are there so many competing answers for where the HGDP Russians were sampled?
- Saint Petersburg: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506643/
- Arkhangelsk (even provides the district!): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591355/
- Vologda (seems most...
- Saint Petersburg: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506643/
- Arkhangelsk (even provides the district!): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591355/
- Vologda (seems most...
Community member, community liaison and researcher perspectives on the creation of HapMap and 1000 Genomes Project iPSCs https://www.biorxiv.org/content/10.64898/2026.01.09.698717v1
January 14, 2026 at 3:14 PM
Community member, community liaison and researcher perspectives on the creation of HapMap and 1000 Genomes Project iPSCs https://www.biorxiv.org/content/10.64898/2026.01.09.698717v1
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures https://www.biorxiv.org/content/10.1101/2025.09.29.679336v1
October 1, 2025 at 8:33 PM
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures https://www.biorxiv.org/content/10.1101/2025.09.29.679336v1
This basically... worked out (though more on "worked out" later) in that the HapMap was created, cheap genome-wide SNP assays developed and deployed - the very first on Macular degeneration, but then early on by the Wellcome Trust Case Control Consortium which tackled 8 human diseases
December 27, 2024 at 5:53 PM
This basically... worked out (though more on "worked out" later) in that the HapMap was created, cheap genome-wide SNP assays developed and deployed - the very first on Macular degeneration, but then early on by the Wellcome Trust Case Control Consortium which tackled 8 human diseases
As such, there was a goal to develop a genome-wide genetic marker map at a density such that the majority of causal variants should be captured - the so called "HapMap" (Haplotype Map).
December 27, 2024 at 5:53 PM
As such, there was a goal to develop a genome-wide genetic marker map at a density such that the majority of causal variants should be captured - the so called "HapMap" (Haplotype Map).
Now, he is discussing the 1000 Genomes project circa 2007
Four populations selected basically from the HapMap
"The question was: is this sufficient? Is this representative of variation around the globe? Clearly it's not."
#PSB25
Four populations selected basically from the HapMap
"The question was: is this sufficient? Is this representative of variation around the globe? Clearly it's not."
#PSB25
January 7, 2025 at 7:05 PM
Now, he is discussing the 1000 Genomes project circa 2007
Four populations selected basically from the HapMap
"The question was: is this sufficient? Is this representative of variation around the globe? Clearly it's not."
#PSB25
Four populations selected basically from the HapMap
"The question was: is this sufficient? Is this representative of variation around the globe? Clearly it's not."
#PSB25
One of the great strengths of working on great tits: the ability to put together large-scale projects like this:
The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird https://www.biorxiv.org/content/10.1101/561399v1
The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird https://www.biorxiv.org/content/10.1101/561399v1
The great tit HapMap project: a continental-scale analysi...
A major aim of evolutionary biology is to understand why ...
www.biorxiv.org
November 24, 2024 at 12:56 AM
One of the great strengths of working on great tits: the ability to put together large-scale projects like this:
The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird https://www.biorxiv.org/content/10.1101/561399v1
The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird https://www.biorxiv.org/content/10.1101/561399v1
One of the advantages of working on great tits is that many people work on them. After a rather prolonged incubation, very nice to see this collaborative paper involving analysis of genomic variation across 29 populations with collaborators from 23 nations onlinelibrary.wiley.com/doi/10.1111/...
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird
Molecular Ecology Resources is a broad journal publishing computer programs, statistical & molecular advances & more for studies in evolution, ecology & conservation.
onlinelibrary.wiley.com
May 17, 2024 at 9:29 AM
One of the advantages of working on great tits is that many people work on them. After a rather prolonged incubation, very nice to see this collaborative paper involving analysis of genomic variation across 29 populations with collaborators from 23 nations onlinelibrary.wiley.com/doi/10.1111/...
Unified Multi-caller Ensemble (UME) generates an unbiased maize haplotype map for variable coverage whole genome data https://www.biorxiv.org/content/10.1101/2023.12.07.570552v1
Unified Multi-caller Ensemble (UME) generates an unbiased maize haplotype map for variable coverage whole genome data https://www.biorxiv.org/content/10.1101/2023.12.07.570552v1
We present a novel diversity-focused haplotype map (HapMap) that characterizes over 64.5 million mai
www.biorxiv.org
December 8, 2023 at 10:50 PM
Unified Multi-caller Ensemble (UME) generates an unbiased maize haplotype map for variable coverage whole genome data https://www.biorxiv.org/content/10.1101/2023.12.07.570552v1
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures. #SomaticVariantDetection #VariantCalling #Pangenomics #Genomics #Bioinformatics @biorxiv-genomic.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 21, 2025 at 10:30 AM
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures. #SomaticVariantDetection #VariantCalling #Pangenomics #Genomics #Bioinformatics @biorxiv-genomic.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures.#SomaticVariantDetection #HapMap #Pangenomics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 3, 2025 at 5:05 PM
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures.#SomaticVariantDetection #HapMap #Pangenomics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
At what range is this happening? Is there an obvious pattern?
Local LD changes happen often due to recent recombination events.
Local LD changes happen often due to recent recombination events.
September 12, 2025 at 9:45 PM
At what range is this happening? Is there an obvious pattern?
Local LD changes happen often due to recent recombination events.
Local LD changes happen often due to recent recombination events.
Complex genetic variation in nearly complete human genomes
->Nature | #HumanGenome | More info from EcoSearch
->Nature | #HumanGenome | More info from EcoSearch
Complex genetic variation in nearly complete human genomes
A total of 65 diverse humans were included in the current study. The majority of the individuals (63 of 65) originated from the 1kGP sample set11, one (NA21487) from the International HapMap Project67 and one (NA24385, also called HG002) commonly...
www.nature.com
July 23, 2025 at 6:13 PM
Was argued that this would be the case by @johnhawks.net and others 20 years ago.
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Recent acceleration of human adaptive evolution | PNAS
Genomic surveys in humans identify a large amount of recent positive selection. Using
the 3.9-million HapMap SNP dataset, we found that selection h...
www.pnas.org
April 16, 2026 at 10:07 PM
Was argued that this would be the case by @johnhawks.net and others 20 years ago.
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
IW: defining monomorphic as not in dbSNP, HapMap or 1000G. #hgv2011
November 3, 2024 at 1:38 PM
IW: defining monomorphic as not in dbSNP, HapMap or 1000G. #hgv2011
SQ: Compared results to HapMap data and had ~99% agreement- asserts differences are in the HapMap data. #PAGXX
November 3, 2024 at 1:10 PM
SQ: Compared results to HapMap data and had ~99% agreement- asserts differences are in the HapMap data. #PAGXX
JP: Using the HapMap cell lines: 75 Yoruba lymphoblastoid cell lines. Lots of sequence data (1000G) and fxn data (ENCODE). #gcd12
November 3, 2024 at 12:08 PM
JP: Using the HapMap cell lines: 75 Yoruba lymphoblastoid cell lines. Lots of sequence data (1000G) and fxn data (ENCODE). #gcd12
With very little initial knowledge of genetics, I remember asking my advisor @ericgreen “what the heck is a haplotype??” when discussing the ongoing HapMap Project 🫣. Luckily, I persevered with a supportive community of colleagues and friends at Oxford and NHGRI. 6/10
November 10, 2024 at 5:44 PM
With very little initial knowledge of genetics, I remember asking my advisor @ericgreen “what the heck is a haplotype??” when discussing the ongoing HapMap Project 🫣. Luckily, I persevered with a supportive community of colleagues and friends at Oxford and NHGRI. 6/10
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
doi.org/10.1101/2025...
doi.org/10.1101/2025...
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
Somatic mosaicism is essential in human biology and disease, yet robust benchmarks are scarce. The SMaHT Consortium mixed six HapMap cell lines to create artificial somatic variants spanning 0.25% to ...
doi.org
October 7, 2025 at 4:47 AM
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
doi.org/10.1101/2025...
doi.org/10.1101/2025...
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
doi.org/10.1101/2025...
Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet
doi.org/10.1101/2023...
doi.org/10.1101/2025...
Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet
doi.org/10.1101/2023...
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
Somatic mosaicism is essential in human biology and disease, yet robust benchmarks are scarce. The SMaHT Consortium mixed six HapMap cell lines to create artificial somatic variants spanning 0.25% to ...
doi.org
October 2, 2025 at 4:51 AM
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
doi.org/10.1101/2025...
Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet
doi.org/10.1101/2023...
doi.org/10.1101/2025...
Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet
doi.org/10.1101/2023...
🧪🌾PAPER – How can we better capture the genetic diversity of maize?🧬
Miguel Vallebueno-Estrada and @kellyswarts.bsky.social developed a new approach for detecting genetic variation, improving maize diversity studies 🌽.
Read more in @molecology.bsky.social:
doi.org/10.1111/1755...
Miguel Vallebueno-Estrada and @kellyswarts.bsky.social developed a new approach for detecting genetic variation, improving maize diversity studies 🌽.
Read more in @molecology.bsky.social:
doi.org/10.1111/1755...
Unified Multi‐Caller Ensemble (<fc>UME</fc>) Generates an Unbiased Maize Haplotype Map for Variable Coverage Whole Genome Data
We present a novel diversity-focused haplotype map (HapMap) that characterizes over 64.5 million maize (Zea mays ssp. mays) single nucleotide polymorphisms (SNPs) genotyped across 818 individuals fro...
doi.org
August 13, 2026 at 7:08 AM
🧪🌾PAPER – How can we better capture the genetic diversity of maize?🧬
Miguel Vallebueno-Estrada and @kellyswarts.bsky.social developed a new approach for detecting genetic variation, improving maize diversity studies 🌽.
Read more in @molecology.bsky.social:
doi.org/10.1111/1755...
Miguel Vallebueno-Estrada and @kellyswarts.bsky.social developed a new approach for detecting genetic variation, improving maize diversity studies 🌽.
Read more in @molecology.bsky.social:
doi.org/10.1111/1755...
one of the few SNPedia pages with HapMap graphs scrubbed out, by the site owner no less. how odd
Difference between revisions of "Rs53576" - SNPedia
www.snpedia.com
January 28, 2025 at 10:05 PM
one of the few SNPedia pages with HapMap graphs scrubbed out, by the site owner no less. how odd
First organism outside humans to have a HapMap (which was the prerequisite for GWAS).
www.science.org/doi/10.1126/...
www.nature.com/articles/ng2...
www.science.org/doi/10.1126/...
www.nature.com/articles/ng2...
December 8, 2024 at 4:06 PM
First organism outside humans to have a HapMap (which was the prerequisite for GWAS).
www.science.org/doi/10.1126/...
www.nature.com/articles/ng2...
www.science.org/doi/10.1126/...
www.nature.com/articles/ng2...