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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...methods in estimating accuracy and computational stability. Furthermore, HITSNP offers a new algorithm to predict the number and composition of ancestral populations using a small number of SNPs, and avoiding calculating the number of clusters. Taken together, HITSNP facilitates the research of population...
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Method: Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
- Nadin Rohland,
- Swapan Mallick,
- Matthew Mah,
- Robert Maier,
- Nick Patterson,
- and David Reich
Genome Res. November/December 2022 32: 2068-2078; Published in Advance December 14, 2022, doi:10.1101/gr.276728.122
...history, and tens of thousands of SNPs on the Y Chromosome to allow high-resolution determination of haplotypes. Finally, it enriched for SNPs of phenotypic interest as identified through association studies or scans for signals of natural selection, or through being found within particularly important...
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Resource: A calibrated human Y-chromosomal phylogeny based on resequencing
- Wei Wei,
- Qasim Ayub,
- Yuan Chen,
- Shane McCarthy,
- Yiping Hou,
- Ignazio Carbone,
- Yali Xue,
- and Chris Tyler-Smith
Genome Res. February 2013 23: 388-395; Published in Advance October 4, 2012, doi:10.1101/gr.143198.112
...in the most highly filtered tree, because the relevant SNPs lay outside the region used. The structure recapitulated the known phylogeny of the Y chromosome (Karafet et al. 2008) and identified new splits within the E1b1a8a and I1* branches. In addiFigure 1. Regions of the Y chromosome analyzed...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...frequent haplotypes represented, based on 1000 Genomes EUR reference population) (Supplemental Fig. S1C). SNP selection was based on one of two approaches. First, we utilized our recent QTL analyses (Stolze et al. 2020) to prioritize variants (58% SNPs in the library) using combinations of the following...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...-patient heterogeneity of ESR1 enhancer action. To test this hypothesis, we turned to a known source in variation of breast cancer risk and analyzed our data for a possible overlap with breast cancer risk single-nucleotide polymorphisms (rSNPs) and small indels. Importantly, rSNPs for different cancer types have been...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...nucleotide polymorphism (SNP) diversity between the populations. We find that ancient housekeeping genes are a major source of the overall isoform diversity, and that the generation of alternative first exons plays a major role in generating new isoforms. Given that our data allow us to distinguish between...
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Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...Divya Selvaraju1,2, Filip Wierzbicki1,2 and Robert Kofler1 1Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria; 2Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria Corresponding author: rokofler@gmail.comAbstractTo prevent the spread...
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Research: Reconstructing genetic history of Siberian and Northeastern European populations
- Emily H.M. Wong,
- Andrey Khrunin,
- Larissa Nichols,
- Dmitry Pushkarev,
- Denis Khokhrin,
- Dmitry Verbenko,
- Oleg Evgrafov,
- James Knowles,
- John Novembre,
- Svetlana Limborska,
- and Anton Valouev
Genome Res. January 2017 27: 1-14; Published in Advance December 13, 2016, doi:10.1101/gr.202945.115
...Europeanpopulations also speak languages that are related to Ugric languages spoken by Western Siberians. These populations include Komi, Karelians, Veps, Saami, and Finns, who traditionally occupy areas of Northern and Northeastern Europe. Their languages belong to Permic and Finno-Volgaic language groups...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...at that SNP is evident in the adipose samples and a peak is called (Supplemental Fig. S26). As mesenchymal stem cells are one component of adipose tissue, it is possible that the weak signal in adipose is due to mesenchymal stem cell populations within adipose; this is one area for follow-up when adipose...
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Research: A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize
- Mélisande Blein-Nicolas,
- Sandra Sylvia Negro,
- Thierry Balliau,
- Claude Welcker,
- Llorenç Cabrera-Bosquet,
- Stéphane Dimitri Nicolas,
- Alain Charcosset,
- and Michel Zivy
Genome Res. November 2020 30: 1593-1604; Published in Advance October 15, 2020, doi:10.1101/gr.255224.119
...Montpellier, SupAgro, F34060 Montpellier, France Corresponding authors: michel.zivy@inra.fr, melisande.blein-nicolas@inra.frAbstractThe effect of drought on maize yield is of particular concern in the context of climate change and human population growth. However, the complexity of drought-response mechanisms...

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