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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...variant at the signal (LD r2 > 0.8) that overlapped a caPeak, which was the driver peak (peak273749). We tested 329 bp DNA elements containing each allele of rs7726117 (Supplemental Table 25) for allelic differences in transcriptional activity using luciferase reporter assays in HepG2 cells (López...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
..., Ye J, Ou H, Jiang T, Guo B, Yang Q, Liang W, et al. 2021. Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function. Mol Psychiatry 26: 6630–6642. doi:10.1038/s41380...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...Chromosome–specific sequences (Lo et al. 1998b) and other paternally inherited sequences (Lo et al. 2010). Fetal-specific paternally inherited alleles include single-nucleotide polymorphisms (SNPs) in which the father is homozygous for a variant (AA) not carried by the mother (BB), and the fetal DNA fraction...
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Resource: A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci
- Kaitlin U. Laverty,
- Jake M. Stout,
- Mitchell J. Sullivan,
- Hardik Shah,
- Navdeep Gill,
- Larry Holbrook,
- Gintaras Deikus,
- Robert Sebra,
- Timothy R. Hughes,
- Jonathan E. Page,
- and Harm van Bakel
Genome Res. January 2019 29: 146-156; Published in Advance November 8, 2018, doi:10.1101/gr.242594.118
...rearrangement and gene duplications at the closely linked THC and CBD acid synthase gene loci.ResultsA combined genetic and physical map reveals that genes and recombination events are concentrated near chromosome endsWe performed PacBio SMRT sequencing of genomic DNA (gDNA) from the female parent PK...
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Method: Detection and characterization of jagged ends of double-stranded DNA in plasma
- Peiyong Jiang,
- Tingting Xie,
- Spencer C. Ding,
- Ze Zhou,
- Suk Hang Cheng,
- Rebecca W.Y. Chan,
- Wing-Shan Lee,
- Wenlei Peng,
- John Wong,
- Vincent W.S. Wong,
- Henry L.Y. Chan,
- Stephen L. Chan,
- Liona C.Y. Poon,
- Tak Y. Leung,
- K.C. Allen Chan,
- Rossa W.K. Chiu,
- and Y.M. Dennis Lo
Genome Res. August 2020 30: 1144-1153; Published in Advance August 14, 2020, doi:10.1101/gr.261396.120
...in the jaggedness between fetal- and maternal-derived plasma DNA molecules, we analyzed the plasma DNA molecules covering informative single nucleotide polymorphism (SNP) loci (Jiang et al. 2017). Informative SNPs refer to SNPs in which the mother was homozygous (i.e., genotype AA) and the fetus was heterozygous (i...
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ARTICLES: Determining relative microsatellite allele frequencies in pooled DNA samples.
- H Khatib,
- A Darvasi,
- Y Plotski,
- and M Soller
Genome Res. August 1994 4: 13-18
.... and Syvanen. A.-C. 1993 . Determination of allele frequencies at loci with length polymorphism by quantitative analysis of DNA amplified from pooled samples. PCR Methods Applic. 2 : 313 – 317 . 10. Khatib, H., Genislav, E. Crittenden, L.B. Bumstead, N. and Soller. M. 1993 . Sequence tagged microsatellite...
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Method: Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis
- Steve Swinnen,
- Kristien Schaerlaekens,
- Thiago Pais,
- Jürgen Claesen,
- Georg Hubmann,
- Yudi Yang,
- Mekonnen Demeke,
- María R. Foulquié-Moreno,
- Annelies Goovaerts,
- Kris Souvereyns,
- Lieven Clement,
- Françoise Dumortier,
- and Johan M. Thevelein
Genome Res. May 2012 22: 975-984; Published in Advance March 7, 2012, doi:10.1101/gr.131698.111
...tolerant to at least 16% ethanol and 31 segregants tolerant to at least 17%. Scoring of SNPs using whole- sequence analysis of DNA from the two pools and parents revealed three major loci and additional minor loci. The latter were more pronounced or only present in the 17% pool compared to the 16% pool...
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METHODS: High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR
- Søren Germer,
- Michael J. Holland,
- and Russell Higuchi
Genome Res. February 1, 2000 10: 258-266; doi:10.1101/gr.10.2.258
...mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17 : 2503 – 2516 . ↵ Pacek P. , Sajantila A. , Syvänen A.-C. ( 1993 ) Determination of allele frequencies at loci with length polymorphism by quantitative analysis of DNA amplified from pooled samples. PCR Methods...
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LETTER: Cis-acting expression quantitative trait loci in mice
- Sudheer Doss,
- Eric E. Schadt,
- Thomas A. Drake,
- and Aldons J. Lusis
Genome Res. May 2005 15: 681-691; Published in Advance April 18, 2005, doi:10.1101/gr.3216905
...to assess on a broad scale whether the cis -acting eQTL detected in any segregating population, including our F 2 cross, are actually likely due to DNA variations in the genes themselves. To assess the fraction of cis -acting eQTL that may be artifacts of probes overlapping DNA polymorphisms, we used...
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Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
- Wilfried M. Guiblet,
- Marzia A. Cremona,
- Monika Cechova,
- Robert S. Harris,
- Iva Kejnovská,
- Eduard Kejnovsky,
- Kristin Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
...loci showed that non-B DNA formation inhibits prokaryotic and eukaryotic DNA polymerases, causing their pausing and stalling of a replication fork (Kang et al. 1995; Samadashwily et al. 1997; Krasilnikova and Mirkin 2004; Voineagu et al. 2008; Eddy et al. 2015). These processes have been postulated...
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