Article
Biochemistry & Molecular Biology
Robert R. Bowers, Christian M. Jones, Edwin A. Paz, John K. Barrows, Kent E. Armeson, David T. Long, Joe R. Delaney
Summary: Haploinsufficiency drives Darwinian evolution. Aneuploid genetics in cancer result in heterogeneity of monoallelic gene-level copy-number alterations (CNAs). Shifted Weighted Annotation Network (SWAN) analysis identifies drivers and potential vulnerabilities within cancer CNAs, highlighting new targets for solid tumors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Cody Ashby, Eileen M. Boyle, Michael A. Bauer, Aneta Mikulasova, Christopher P. Wardell, Louis Williams, Ariel Siegel, Patrick Blaney, Marc Braunstein, David Kaminetsky, Jonathan Keats, Francesco Maura, Ola Landgren, Brian A. Walker, Faith E. Davies, Gareth J. Morgan
Summary: Deciphering genomic architecture helps identify disease drivers and understand myeloma initiation and progression mechanisms. This study demonstrates that structural variants occur nonrandomly in the genome, and their frequencies vary in different genetic contexts. The study also reveals the heterogeneity of transcriptional dysregulation caused by both canonical and novel structural variants, as well as the impact of complex rearrangements on clinical outcomes. Chromothripsis, in particular, has a significant negative effect on clinical outcome.
BLOOD CANCER JOURNAL
(2022)
Article
Medical Laboratory Technology
L. Y. Lois Choy, Wenlei Peng, Peiyong Jiang, Suk Hang Cheng, Stephanie C. Y. Yu, Huimin Shang, O. Y. Olivia Tse, John Wong, Vincent Wai Sun Wong, Grace L. H. Wong, W. K. Jacky Lam, Stephen L. Chan, Rossa W. K. Chiu, K. C. Allen Chan, Y. M. Dennis Lo
Summary: Background analysis of circulating tumor DNA is crucial for cancer care, but previous studies focused on short DNA fragments. Bisulfite sequencing, a traditional method for methylation analysis, causes DNA degradation. This study overcame these limitations using single-molecule sequencing and discovered a previously unknown long cfDNA population.
CLINICAL CHEMISTRY
(2022)
Article
Medicine, General & Internal
Maren Holand, Kaja C. G. Berg, Ina A. Eilertsen, Bodil Bjerkehagen, Matthias Kolberg, Kjetil Boye, Ole Christian Lingjaerde, Tormod K. Guren, Nils Mandahl, Eva van den Berg, Emanuela Palmerini, Sigbjorn Smeland, Piero Picci, Fredrik Mertens, Anita Sveen, Ragnhild A. Lothe
Summary: MPNSTs were classified into two transcriptomic subtypes: immune active type with sustained immune signals and favorable prognosis, and immune deficient type with aggressive disease course, PRC2 loss, and expression of potential therapeutic targets. Copy number-based proliferative transcriptomic signatures were associated with patient prognosis.
Article
Cell Biology
Miao-Zhen Qiu, Qingjian Chen, Dan-Yang Zheng, Qi Zhao, Qi-Nian Wu, Zhi-Wei Zhou, Li-Qiong Yang, Qiu-Yun Luo, Yu-Ting Sun, Ming-Yu Lai, Sha-Sha Yuan, Feng-Hua Wang, Hui-Yan Luo, Feng Wang, Yu-Hong Li, Hui-Zhong Zhang, Rui-Hua Xu
Summary: Gastric mixed adenoneuroendocrine carcinoma (MANEC) is a heterogeneous tumor composed of adenocarcinoma and neuroendocrine carcinoma. Whole-exome and multi-regional sequencing revealed that MANEC has four significantly mutated genes and shares similarities with chromosomal instability stomach adenocarcinoma. MANEC tumors are of monoclonal origin and the neuroendocrine carcinoma components exhibit more aggressive genomic properties. The phylogenetic trees demonstrate different patterns of tumor divergence, and immunohistochemistry confirms the transition from adenocarcinoma to neuroendocrine carcinoma in MANEC.
Article
Biochemistry & Molecular Biology
Ming-Chin Yu, Tsung-Han Wu, Chao-Wei Lee, Yun-Shien Lee, Jang-Hau Lian, Chia-Lung Tsai, Sen-Yung Hsieh, Chi-Neu Tsai
Summary: The study evaluated the role of chromosomal copy number aberrations in patients with advanced HCC who were treated with sorafenib, finding that higher percentage genome change and amplification of chromosome 7q were associated with sorafenib resistance in advanced HCC.
BIOMEDICAL JOURNAL
(2021)
Article
Oncology
Min Hwan Kim, Gun Min Kim, Jin Mo Ahn, Won-Ji Ryu, Seul-Gi Kim, Jee Hung Kim, Tae Yeong Kim, Hyun Ju Han, Jee Ye Kim, Hyung Seok Park, Seho Park, Byeong Woo Park, Seung Il Kim, Joon Jeong, Jieun Lee, Soonmyung Paik, Sangwoo Kim, Kyung Hae Jung, Eun Hae Cho, Joohyuk Sohn
Summary: This study explored the clinical implication of circulating tumor DNA (ctDNA) copy number aberration (CNA) burden in breast cancer using low-pass whole-genome sequencing (LP-WGS) analysis. The results showed that a high baseline ctDNA CNA burden predicts poor overall survival and progression-free survival of metastatic breast cancer patients. Furthermore, ctDNA CNA burden can be used for molecular profiling and predicting treatment response. These findings emphasize the importance of LP-WGS ctDNA CNA analysis in prognosis prediction and molecular profiling in breast cancer.
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2023)
Article
Oncology
Javier Ganz, Eduardo A. Maury, Basheer Becerra, Sara Bizzotto, Ryan N. Doan, Connor J. Kenny, Taehwan Shin, Junho Kim, Zinan Zhou, Keith L. Ligon, Eunjung Alice Lee, Christopher A. Walsh
Summary: Although oncogenic mutations have been found in non-diseased, proliferative non-neural tissues, their prevalence in the human brain is unknown. This study identified oncogenic somatic single-nucleotide variants (sSNVs) in the brains of individuals without tumor diagnoses, with a higher frequency in subcortical white matter and glial cells, and a lower frequency in older individuals. The study also revealed early events in acquiring oncogenic variants, which can contribute to understanding brain tumor origins and improving diagnostics.
Article
Oncology
Kaja C. G. Berg, Tuva H. Brunsell, Anita Sveen, Sharmini Alagaratnam, Merete Bjornslett, Merete Hektoen, Kristoffer W. Brudvik, Bard I. Rosok, Bjorn Atle Bjornbeth, Arild Nesbakken, Ragnhild A. Lothe
Summary: This study investigated the potential for improved prognostic stratification for patients with colorectal liver metastases undergoing hepatic resection by combined biomarker analysis with DNA copy number aberrations (CNAs). The results showed that RAS/BRAF(V600E) and TP53 co-mutations were associated with a poor patient outcome, and CNAs also had prognostic associations. Combined analysis of RAS/BRAF(V600E)/TP53 mutations and CNAs identified patients with particularly poor outcomes.
MOLECULAR ONCOLOGY
(2021)
Article
Oncology
Hidenari Hirata, Atsushi Niida, Nobuyuki Kakiuchi, Ryutaro Uchi, Keishi Sugimachi, Takaaki Masuda, Tomoko Saito, Shun-Ichiro Kageyama, Yushi Motomura, Shuhei Ito, Tadamasa Yoshitake, Daisuke Tsurumaru, Yusuke Nishimuta, Akira Yokoyama, Takanori Hasegawa, Kenichi Chiba, Yuichi Shiraishi, Junyan Du, Fumihito Miura, Masaru Morita, Yasushi Toh, Masakazu Hirakawa, Yoshiyuki Shioyama, Takashi Ito, Tetsuo Akimoto, Satoru Miyano, Tatsuhiro Shibata, Masaki Mori, Yutaka Suzuki, Seishi Ogawa, Kousei Ishigami, Koshi Mimori
Summary: A study sequencing 52 tumor samples from 33 ESCC patients who received radiotherapy combined with 5-fluorouracil/platinum revealed the impact of chemoradiotherapy on clonal evolution, with MYC gain potentially serving as a marker for therapy resistance. The findings enhance understanding of therapeutic resistance and support the rationale for precision chemoradiotherapy.
Article
Genetics & Heredity
Lisa G. Shaffer, Bradley Hopp, Marek Switonski, Adam Zahand, Blake C. Ballif
Summary: Microarray analysis is an efficient method for identifying cytogenetic imbalances in humans, particularly through the use of SNP arrays. However, this approach is not widely used in clinical practice for canines. The first study utilizing microarray analysis to identify chromosomal anomalies in canines found cases of aneuploidy, indicating potential for uncovering more cases as this technology becomes more routine in canine genetic testing.
Article
Biochemistry & Molecular Biology
Sergio Andonegui-Elguera, Gloria Silva-Roman, Eduardo Pena-Martinez, Keiko Taniguchi-Ponciano, Sandra Vela-Patino, Ilan Remba-Shapiro, Erick Gomez-Apo, Ana-Laura Espinosa-de-los-Monteros, Lesly A. Portocarrero-Ortiz, Gerardo Guinto, Sergio Moreno-Jimenez, Laura Chavez-Macias, Renata Saucedo, Lourdes Basurto-Acevedo, Blas Lopez-Felix, Carolina Gonzalez-Torres, Javier Gaytan-Cervantes, Jorge T. Ayala-Sumuano, Andres Burak-Leipuner, Daniel Marrero-Rodriguez, Moises Mercado
Summary: This study investigated the genomic landscape of ACTH-producing adenomas and identified key gene mutations, including USP8, TP53, AURKA, EGFR, HSD3B1, and CDKN1A.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, Research & Experimental
Xuesong Liu, Ruoxi Hong, Peina Du, Di Yang, Meibo He, Qingnan Wu, Lin Li, Yan Wang, Jie Chen, Qingjie Min, Jinting Li, Weimin Zhang, Qimin Zhan
Summary: The study investigated the metabolic genomic variations in patients with esophageal squamous cell carcinoma (ESCC) and identified genetic alterations associated with metabolic pathways. They identified potential metabolic drivers and validated their role in the malignancy of ESCC. Additionally, they found genetic panels that could stratify patients into different prognostic groups based on metabolic gene alterations.
Article
Genetics & Heredity
Xia Chen, Xue Bai, Huagui Liu, Binbin Zhao, Zhixun Yan, Yali Hou, Qin Chu
Summary: Copy number variation (CNV) plays an important role in chicken domestication and breed shaping, affecting genes related to nervous system, sensory, and follicle development. Comparisons between domestic breeds and wild red jungle fowl (RJF) revealed significant differences in genes associated with nervous, immunity, and reproductive system development. Breed-specific CNVs identified valuable genes related to beard trait, melanin deposition, aggressiveness, and traits like high egg production and fast-growing. These candidate genes provide valuable resources for further studies on phenotypic variation and artificial breeding of chickens.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Meeting Abstract
Oncology
Stephen Huang, Paul Lira, Kai Wang, Cathy Zhang, Amy Jackson-Fisher, Keith Ching, Paul Rejto
Meeting Abstract
Oncology
Kai Wang, Qin Zhang, Danan Li, Keith Ching, Cathy Zhang, Xianxian Zheng, Mark Ozeck, Stephanie Shi, Xiaorong Li, Hui Wang, Paul Rejto, James Christensen, Peter Olson
Article
Oncology
Kai Wang, Qin Zhang, Danan Li, Keith Ching, Cathy Zhang, Xianxian Zheng, Mark Ozeck, Stephanie Shi, Xiaorong Li, Hui Wang, Paul Rejto, James Christensen, Peter Olson
CLINICAL CANCER RESEARCH
(2015)
Meeting Abstract
Oncology
Kai Wang, Suet Yi Leung
CANCER IMMUNOLOGY RESEARCH
(2015)
Meeting Abstract
Oncology
Kai Wang, Hoicheong Siu, Shibing Deng, Jadwiga R. Bienkowska, Suet Yi Leung
Letter
Biochemical Research Methods
Istvan Boerner Horvath, Heather Estrella, Sabine Schefzick, Shibing Deng, Kai Wang, Keith AChing, Ying Ding, Peter Roberts, Paul A. Rejto, Zhengyan Kan
Meeting Abstract
Oncology
Keith A. Ching, Donghui Huang, Kai Wang, Mark Ozeck, Paul Lira, Jingjin Gao, Jadwiga Bienkowska, Paul Rejto, James Hardwick, Thomas O'Brien, Geoffrey Chan
Article
Biotechnology & Applied Microbiology
Tao Xie, Yong Beom Cho, Kai Wang, Donghui Huang, Hye Kyung Hong, Yoon-La Choi, Young Hyeh Ko, Do-Hyun Nam, Juyoun Jin, Heekyoung Yang, Julio Fernandez, Shibing Deng, Paul A. Rejto, Woo Yong Lee, Mao Mao
Article
Biochemistry & Molecular Biology
Manikandan Narayanan, Jimmy L. Huynh, Kai Wang, Xia Yang, Seungyeul Yoo, Joshua McElwee, Bin Zhang, Chunsheng Zhang, John R. Lamb, Tao Xie, Christine Suver, Cliona Molony, Stacey Melquist, Andrew D. Johnson, Guoping Fan, David J. Stone, Eric E. Schadt, Patrizia Casaccia, Valur Emilsson, Jun Zhu
MOLECULAR SYSTEMS BIOLOGY
(2014)
Article
Genetics & Heredity
Kai Wang, Siu Tsan Yuen, Jiangchun Xu, Siu Po Lee, Helen H. N. Yan, Stephanie T. Shi, Hoi Cheong Siu, Shibing Deng, Kent Man Chu, Simon Law, Kok Hoe Chan, Annie S. Y. Chan, Wai Yin Tsui, Siu Lun Ho, Anthony K. W. Chan, Jonathan L. K. Man, Valentina Foglizzo, Man Kin Ng, April S. Chan, Yick Pang Ching, Grace H. W. Cheng, Tao Xie, Julio Fernandez, Vivian S. W. Li, Hans Clevers, Paul A. Rejto, Mao Mao, Suet Yi Leung
Article
Biochemical Research Methods
Shibing Deng, Maruja Lira, Donghui Huang, Kai Wang, Crystal Valdez, Jennifer Kinong, Paul A. Rejto, Jadwiga Bienkowska, James Hardwick, Tao Xie
BMC BIOINFORMATICS
(2018)
Article
Biology
Douglas Arneson, Xia Yang, Kai Wang
COMMUNICATIONS BIOLOGY
(2020)
Article
Biology
Yifeng Xia, Xiaodong Ji, In Sock Jang, Christine Surka, Christy Hsu, Kai Wang, Mark Rolfe, Neil Bence, Gang Lu
Summary: The PRISM platform, combining CRISPR/Cas9 gene editing, cell line DNA barcoding, and next-generation sequencing, allows for genetic and pharmacological assessment of hundreds of cell lines simultaneously. Both compound and CRISPR-knockout PRISM screens showed high consistency with a public database, demonstrating its potential in accelerating anti-cancer drug discovery.
COMMUNICATIONS BIOLOGY
(2021)
Meeting Abstract
Oncology
Maruja E. Lira, Tao Xie, Shibing Deng, Jennifer Kinong, Jingjin Gao, Zhou Zhu, Nathan Lee, Paul Rejto, Jadwiga Bienkowska, James Hardwick, Kai Wang, Stephen Huang
Proceedings Paper
Mathematical & Computational Biology
Keith A. Ching, Kai Wang, Zhengyan Kan, Julio Fernandez, Wenyan Zhong, Jarek Kostrowicki, Tao Xie, Zhou Zhu, Jean-Francois Martini, Maria Koehler, Kim Arndt, Paul Rejto
PACIFIC SYMPOSIUM ON BIOCOMPUTING 2015 (PSB)
(2015)