Searching journal content for articles similar to Zhang et al. 17 (5): 641.

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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...on long-read whole- sequencing to simultaneously identify variants and investigate the contribution of skew to X-linked diseases in females. We used the Oxford Nanopore Technologies PromethION 24 platform and its adaptive sampling capacity to enrich X Chromosome reads. We sequenced peripheral samples...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...was extracted using the Qiagen RNeasy mini kit (Qiagen 74106). cDNA was synthesized using SuperScriptIV VILO master mix (Invitrogen 11756500). Quantitative PCR was performed for selected targets using PowerTrack SYBR green master mix (Applied Biosystems A46109) and quantified using the QuantStudio 6 flex real...
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Research: Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 gr.281003.125; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...purity. While NMD decreases AEV, it 140 can be retained at a higher level with enriched mutant allele dosage. 141 142 Elevated AEV in somatic truncation indels in TCGA 143 To empirically validate the AEV model, we used 106,157 somatic coding indels on the 144 autosomal chromosomes identified by NCI...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...significance was determined by a paired-sample t-test (Supplemental Table S5).We generated replication timing profiles to identify early- and late-replicating genomic regions on each chromosome. In these profiles, enrichment of Repli-seq reads in the early fraction yields a positive score, just as late...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...and cDNA sequencing, based on patient-derived DNA and RNA, to systematically evaluate deep intronic variation. We identified all variants across the full genomic loci of targeted genes, applied the in silico tools SpliceAI and Pangolin to predict variants of functional consequence, and then carried out...
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Method: QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
- Xiaoyu Song,
- Yuqing Shang,
- Michelle E. Ehrlich,
- Panos Roussos,
- Guo-Cheng Yuan,
- and Pei Wang
Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
..., we uncovered interacting cell types, genes involved in their interactions, and the corresponding distances of these interactions. We showed that our identified ICGs among excitatory neurons were enriched in synapse functions, demonstrating the effectiveness of our method in revealing intricate...
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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...; however, the general trend aligns with a higher or lower copy number compared to H1–H1 s. NPY4R, NPY4R2, SYT15, and SYT15B SUNK estimates do not generally align with expectations. Overall, copy-number data support the polymorphic structural configurations that we identified at Chromosome 10q11.22 region...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
.... Genes that control the characteristic color traits could be genetically mapped on the X and Y Chromosomes (Winge 1922; Khoo et al. 1999; Lindholm and Breden 2002; Tripathi et al. 2009a). A genetic map based on EST- and BAC-derived markers was generated, and LG12 was identified as the sex chromosome...
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Research: Optical genome mapping identifies rare structural variants in neural tube defects
- Nikhil S. Sahajpal,
- Jane Dean,
- Benjamin Hilton,
- Timothy Fee,
- Cindy Skinner,
- Alex Hastie,
- Barbara R. DuPont,
- Alka Chaubey,
- Michael J. Friez,
- and Roger E. Stevenson
Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
...or accompanied by anomalies of other systems. The genetic basis of NTDs remains poorly understood using karyotyping, chromosomal microarray, and short-read sequencing, with only a limited number of pathogenic variants identified. Collectively, these technologies may fail to detect rare structural variants (SVs...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...biological replicates for each sex. Total RNA was extracted from each tissue using a TRIzol kit (Invitrogen). The mRNA fractions were isolated from the total RNA extracts with the MicroPoly(A)Purist kit (Ambion). cDNA libraries were prepared for each tissue with the RNA-seq library kit (Gnomegen) following...

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