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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...; and neofunctionalization, in which duplicates evolve new functions (Taylor and Raes 2004; Hahn 2009; Kondrashov 2012; Kuzmin et al. 2022). Genome sequencing has supported the view that whole- duplication (WGD) events frequently occur during evolution across all domains of life, with many plant species retaining polyploid...
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Research: Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma
- David H. Gutmann,
- Michael D. McLellan,
- Ibrahim Hussain,
- John W. Wallis,
- Lucinda L. Fulton,
- Robert S. Fulton,
- Vincent Magrini,
- Ryan Demeter,
- Todd Wylie,
- Cyriac Kandoth,
- Jeffrey R. Leonard,
- Abhijit Guha,
- Christopher A. Miller,
- Li Ding,
- and Elaine R. Mardis
Genome Res. March 2013 23: 431-439; Published in Advance December 5, 2012, doi:10.1101/gr.142604.112
...quality than the N50 size. Based on our manual examination of the alignment results, we found that the high-quality assemblies that Gutmann et al. 436 Genome Research www..org contain valid sequence frequently have q > 100 bp. Once assembled, contigs were aligned to their respective local reference...
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Method: Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
- Gavin Ha,
- Andrew Roth,
- Daniel Lai,
- Ali Bashashati,
- Jiarui Ding,
- Rodrigo Goya,
- Ryan Giuliany,
- Jamie Rosner,
- Arusha Oloumi,
- Karey Shumansky,
- Suet-Feung Chin,
- Gulisa Turashvili,
- Martin Hirst,
- Carlos Caldas,
- Marco A. Marra,
- Samuel Aparicio,
- and Sohrab P. Shah
Genome Res. October 2012 22: 1995-2007; Published in Advance May 25, 2012, doi:10.1101/gr.137570.112
...(Fig. 5). Regionswith the highest frequency of amplified LOH were 1q and 17q (Supplemental Fig. S7). The most frequent large-scale event observed in the landscape of zygosity (Fig. 5) was the whole chromosome-level loss of heterozygosity of chromosome 17 in 18 cases (78%). The full list of gene...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...leading to the clonal evolution of cancer cells (Qing et al. 2020; Chakravarty and Solit 2021). Somatic mutations in key genes and their regulatory sequences, especially oncogenes, tumor suppressors, and DNA repair genes, are frequently found in cancers and contribute to tumor progression and therapeutic...
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Research: Human papillomavirus and the landscape of secondary genetic alterations in oral cancers
- Maura L. Gillison,
- Keiko Akagi,
- Weihong Xiao,
- Bo Jiang,
- Robert K.L. Pickard,
- Jingfeng Li,
- Benjamin J. Swanson,
- Amit D. Agrawal,
- Mark Zucker,
- Birgit Stache-Crain,
- Anne-Katrin Emde,
- Heather M. Geiger,
- Nicolas Robine,
- Kevin R. Coombes,
- and David E. Symer
Genome Res. January 2019 29: 1-17; Published in Advance December 18, 2018, doi:10.1101/gr.241141.118
...3CA, BBX, ASAP1, adjusted P < 0.01). Conversely, genes inactivated by somatic variants (e.g., RB1, PTEN, CYLD, EP300, FBXW7, TAF5, IFNGR1, NSD1, and STAT1) were deleted frequently and their expression significantly decreased. In some individual cancers, both somatic variants and CNV coincided...
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Research: Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase
- Ayako Yamanishi,
- Kosuke Yusa,
- Kyoji Horie,
- Masahiro Tokunaga,
- Kohji Kusano,
- Chikara Kokubu,
- and Junji Takeda
Genome Res. September 2013 23: 1462-1473; Published in Advance August 1, 2013, doi:10.1101/gr.152744.112
...in CO frequently associated with gene conversion Among the above 17 non-DEL clones with ISceIo transfection, only clone 73 displayed no CO points within the region (Fig. 2D). PCR amplification and direct sequencing revealed that this clone was a compound heterozygote (Aprtneo/–) at the Aprt locus...
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Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
...-based pseudo-CNV inference allows unbiased characterization of the identified clusters, thereby highlighting the malignant cells.Marker-free capture of CTCsBreast cancer is the most frequent type of cancer and one of the top causes of cancer-related mortality (Kamal et al. 2017). In 2020, breast cancer...
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ARTICLE: Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays
- Rui Mei,
- Patricia C. Galipeau,
- Cynthia Prass,
- Anthony Berno,
- Ghassan Ghandour,
- Nila Patil,
- Roger K. Wolff,
- Mark S. Chee,
- Brian J. Reid,
- and David J. Lockhart
Genome Res. August 1, 2000 10: 1126-1137; doi:10.1101/gr.10.8.1126
...cancer than those with HGD, consistent with data from previous studies ( Barrett et al. 1996 ). Previously published data suggest that premalignant tissues typically contain fewer chromosomal aberrations than cancers and that losses frequently involve regions on chromosomes 9p and 17p, which were...
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Research: Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
- J. Keith Killian,
- Lambert C.J. Dorssers,
- Britton Trabert,
- Ad J.M. Gillis,
- Michael B. Cook,
- Yonghong Wang,
- Joshua J. Waterfall,
- Holly Stevenson,
- William I. Smith, Jr.,
- Natalia Noyes,
- Parvathy Retnakumar,
- J. Hans Stoop,
- J. Wolter Oosterhuis,
- Paul S. Meltzer,
- Katherine A. McGlynn,
- and Leendert H.J. Looijenga
Genome Res. November 2016 26: 1490-1504; Published in Advance October 20, 2016, doi:10.1101/gr.201293.115
...Fig. S5A). Like SEs and sperm, PGCs are demethylated at these genes, while differentiated tissues are methylated (Supplemental Fig. S5B). Thus, hypermethylation of these genes is not specifically malignancy related and is commonly found Figure 1. Somatic copy number aberration (SCNA) profiles in TGCT...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...also discovered 62 tandem duplications present only in the sim-complex s that duplicate one or more protein-coding exons. Such mutations frequently contribute to adaptation, functional innovation, and genetic incompatibilities (Lynch and Force 2000; Long et al. 2003; Ting et al. 2004; Arguello et al...
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