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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...to breed characteristic traits. To enhance detection of trait associations, potentially functional variants in constrained genes were analyzed for their association with signatures of breed differentiation.Breed-differentiated regions were defined as 50 kb genomic windows of extreme FST that overlapped 1...
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Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
...). Several inversions also have variable frequencies between continents, although only FST values of HsInv0389 are within the top 5% of the expected distribution (Supplemental Table S6; Giner-Delgado et al. 2019). Finally, the inclusion of longer inversions strengthened the negative correlation between...
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Research: Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals
- Huixin Xu,
- Qi Zhen,
- Mingzhou Bai,
- Lin Fang,
- Yong Zhang,
- Bao Li,
- Huiyao Ge,
- Sunjin Moon,
- Weiwei Chen,
- Wenqing Fu,
- Qiongqiong Xu,
- Yuwen Zhou,
- Yafeng Yu,
- Long Lin,
- Liang Yong,
- Tao Zhang,
- Shirui Chen,
- Siyang Liu,
- Hui Zhang,
- Ruoyan Chen,
- Lu Cao,
- Yuanwei Zhang,
- Ruixue Zhang,
- Huanjie Yang,
- Xia Hu,
- Joshua M. Akey,
- Xin Jin,
- and Liangdan Sun
Genome Res. July 2021 31: 1150-1158; Published in Advance June 21, 2021, doi:10.1101/gr.267963.120
...variants in 9434 cases and 9434 controlsSignatures of selection among PTVsWe calculated FST (Weir and Cockerham 1984; Akey 2002) to identify PTVs that exhibit high variation in allelic frequencies between Chinese (CHN, n = 19,973), non-Finnish Europeans (NFE, n = 33,370), and Africans (AFR, n = 5203...
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Research: Impact of the X Chromosome and sex on regulatory variation
- Kimberly R. Kukurba,
- Princy Parsana,
- Brunilda Balliu,
- Kevin S. Smith,
- Zachary Zappala,
- David A. Knowles,
- Marie-Julie Favé,
- Joe R. Davis,
- Xin Li,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Jianxin Shi,
- Anshul Kundaje,
- Douglas F. Levinson,
- Philip Awadalla,
- Sara Mostafavi,
- Alexis Battle,
- and Stephen B. Montgomery
Genome Res. June 2016 26: 768-777; Published in Advance April 21, 2016, doi:10.1101/gr.197897.115
...expression in the X Chromosome compared to the autosomes, suggesting that we are at least as powered to detect eQTLs in the X Chromosome as we are in the autosomes. We also compared the MAF, FST, and expression levels of detected eQTLs and observed that X Chromosome eQTLs have lower MAFs (0.19 versus 0.23; t...
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Research: Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Xianzhi Lin,
- Tak-Ming Chan,
- Rena Wang,
- and Xinshu Xiao
Genome Res. April 2016 26: 440-450; Published in Advance February 17, 2016, doi:10.1101/gr.193359.115
...(FST) (Weir and Cockerham 1984), and integrated haplotype score (iHS) (Voight et al. 2006). By using data from the 1000 Genomes Project (The 1000 Genomes Project Consortium 2012), we observed that most GMAS SNVs had positive Tajima’s D values that are often statistically greater than controls...
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Method: The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism
- Maximilian P.A. Salm,
- Stuart D. Horswell,
- Claire E. Hutchison,
- Helen E. Speedy,
- Xia Yang,
- Liming Liang,
- Eric E. Schadt,
- William O. Cookson,
- Anthony S. Wierzbicki,
- Rossi P. Naoumova,
- and Carol C. Shoulders
Genome Res. June 2012 22: 1144-1153; Published in Advance March 7, 2012, doi:10.1101/gr.126037.111
...is reflected in a global Fst of 0.213, suggesting greater partitioning of 8p23-inv frequency variance between populations than within populations (Holsinger and Weir 2009). Pairwise Fst values (estimated in the Human Genome Diversity Project [HGDP]) also strongly correlate with the geographic distance between...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...heritable phenotype. Additionally, SPCs improve rare variant association analyses, reducing genomic inflation (e.g., from 7.6 to 1.2 in one analysis), and provide more accurate heritability estimates. Spatial autocorrelation analysis further confirms the ability of SPCs to account for environmental effects...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...window Figure 3. Relationships between genetic differentiation measured from common variants (FST), rare variants (f2), and geography. (A, lower triangle) FST heatmap illustrating genetic divergence between pairs of populations. (Upper triangle) Heatmap of f2 comparisons of doubleton counts between pairs...
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Research: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
- Amanda J. Lea,
- Julie Peng,
- and Julien F. Ayroles
Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
...significant categories are shown). Enrichment map was created with the emapplot function in the R package enrichplot. (D) Distribution of average per-gene FST values for genes that (1) were found to be AA in most (more than two of three) cellular environments or (2) had no effects on ancestry in any cellular...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...-2008, the mobile element ICESpn23FST81, and the cps operon were all detected. The only major locus not detected was the psrP gene. This gene mostly consists of short two to three amino acid serine-containing repeats, and hence, this low complexity repeat sequence that is longer than the split k-mer length cannot...
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