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Research: Transcriptional consequences of genomic structural aberrations in breast cancer
- Koichiro Inaki,
- Axel M. Hillmer,
- Leena Ukil,
- Fei Yao,
- Xing Yi Woo,
- Leah A. Vardy,
- Kelson Folkvard Braaten Zawack,
- Charlie Wah Heng Lee,
- Pramila Nuwantha Ariyaratne,
- Yang Sun Chan,
- Kartiki Vasant Desai,
- Jonas Bergh,
- Per Hall,
- Thomas Choudary Putti,
- Wai Loon Ong,
- Atif Shahab,
- Valere Cacheux-Rataboul,
- Radha Krishna Murthy Karuturi,
- Wing-Kin Sung,
- Xiaoan Ruan,
- Guillaume Bourque,
- Yijun Ruan,
- and Edison T. Liu
Genome Res. May 2011 21: 676-687; Published in Advance April 5, 2011, doi:10.1101/gr.113225.110
...Transcriptional consequences of genomic structural aberrations in breast cancer Koichiro Inaki 1 , 10 , Axel M. Hillmer 2 , 10 , Leena Ukil 1 , 10 , Fei Yao 2 , 3 , Xing Yi Woo 4 , Leah A. Vardy 5 , Kelson Folkvard...
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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
...-frame indels. The Combined Annotation Dependent Depletion (CADD) method offers a standardized, -wide scoring system (C-score) by integrating sequence conservation and functional annotations (Kircher et al. 2014). FATHMM-MKL improves predictions of functional consequences for both coding and noncoding variants...
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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
...filtering steps such as gene filtering and pathway selection.View larger version: In this window In a new window Figure 5. Clustering of CTCs obtained from ClearCell FX–Polaris system. (A–I) Visualization, clustering, and cluster purity of ClearCell FX–Polaris in presence of independent breast CTC and WBC...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...specific to the target regions are designed such that they anneal to the template upstream and downstream from the ROI. Once amplified, the target(s) can be barcoded if needed, and/or size-selected via gel, then sequenced on either ONT or PacBio instruments (Fig. 1). Long amplicons are quite beneficial...
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LETTER: Novel patterns of genome rearrangement and their association with survival in breast cancer
- James Hicks,
- Alexander Krasnitz,
- B. Lakshmi,
- Nicholas E. Navin,
- Michael Riggs,
- Evan Leibu,
- Diane Esposito,
- Joan Alexander,
- Jen Troge,
- Vladimir Grubor,
- Seungtai Yoon,
- Michael Wigler,
- Kenny Ye,
- Anne-Lise Børresen-Dale,
- Bjørn Naume,
- Ellen Schlicting,
- Larry Norton,
- Torsten Hägerström,
- Lambert Skoog,
- Gert Auer,
- Susanne Månér,
- Pär Lundin,
- and Anders Zetterberg
Genome Res. December 2006 16: 1465-1479; doi:10.1101/gr.5460106
...hypothesis that copy number profiling might provide information useful in making clinical decisions, especially regarding the use or not of systemic therapies (hormonal therapy, chemotherapy), in the management of operable primary breast cancer with ostensibly good prognosis, for example, small, node...
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Methods: Decoding the fine-scale structure of a breast cancer genome and transcriptome
- Stanislav Volik,
- Benjamin J. Raphael,
- Guiqing Huang,
- Michael R. Stratton,
- Graham Bignel,
- John Murnane,
- John H. Brebner,
- Krystyna Bajsarowicz,
- Pamela L. Paris,
- Quanzhou Tao,
- David Kowbel,
- Anna Lapuk,
- Dmitri A. Shagin,
- Irina A. Shagina,
- Joe W. Gray,
- Jan-Fang Cheng,
- Pieter J. de Jong,
- Pavel Pevzner,
- and Colin Collins
Genome Res. March 2006 16: 394-404; Published in Advance February 3, 2006, doi:10.1101/gr.4247306
...using data from the amplified loci. DNA in amplicons is overrepresented in the BAC library and is consequently sequenced to a proportionately greater depth. Interpreted this way, our data suggest that end sequencing ∼60,000 BAC clones per library is necessary for whole- ESP. The sequencing depth can...
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LETTER: Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA
- Yulia Korshunova,
- Rebecca K. Maloney,
- Nathan Lakey,
- Robert W. Citek,
- Blaire Bacher,
- Arief Budiman,
- Jared M. Ordway,
- W. Richard McCombie,
- Jorge Leon,
- Jeffrey A. Jeddeloh,
- and John D. McPherson
Genome Res. January 2008 18: 19-29; Published in Advance November 21, 2007, doi:10.1101/gr.6883307
...) and provided us with a reference control when sequencing breast tissue-derived molecular libraries. The sole exception was the locus ha1p_39189, where one amplicon was outside of the region used in the previous study ( Fig. 1 ). In large part, this was a consequence of the locally elevated CG...
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Research: Genetic inhibitors of APOBEC3B-induced mutagenesis
- Tony M. Mertz,
- Elizabeth Rice-Reynolds,
- Ly Nguyen,
- Anna Wood,
- Cameron Cordero,
- Nicholas Bray,
- Victoria Harcy,
- Rudri K. Vyas,
- Debra Mitchell,
- Kirill Lobachev,
- and Steven A. Roberts
Genome Res. September 2023 33: 1568-1581; Published in Advance August 2, 2023, doi:10.1101/gr.277430.122
...1/2-deficient breast cancers display three- to fourfold more APOBEC-induced mutations. Mirroring our results in yeast, Rev1-mediated C-to-G substitutions are mainly responsible for increased APOBEC-signature mutations in BRCA1/2-deficient tumors, and these mutations associate with lagging strand...
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LETTER: A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
- Oliver A. Hampton,
- Petra Den Hollander,
- Christopher A. Miller,
- David A. Delgado,
- Jian Li,
- Cristian Coarfa,
- Ronald A. Harris,
- Stephen Richards,
- Steven E. Scherer,
- Donna M. Muzny,
- Richard A. Gibbs,
- Adrian V. Lee,
- and Aleksandar Milosavljevic
Genome Res. February 2009 19: 167-177; Published in Advance December 3, 2008, doi:10.1101/gr.080259.108
.... 2008 ) will provide insights into structural mutability. Recent sequencing of four cancer amplicons ( Bignell et al. 2007 ) derived from the HCC1954 breast cancer cell line and two lung cancer cell lines provided evidence for homologous and nonhomologous repair of double-strand DNA breaks induced...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...Grace Avecilla1,2,5, Pieter Spealman1,2,5, Julia Matthews1,2, Elodie Caudal3, Joseph Schacherer3,4 and David Gresham1,2 1Department of Biology, New York University, New York, New York 10003, USA; 2Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA; 3...
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