Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Rongrong Ding, Zhanwei Zhuang, Yibin Qiu, Xingwang Wang, Jie Wu, Shenping Zhou, Donglin Ruan, Cineng Xu, Linjun Hong, Ting Gu, Enqin Zheng, Gengyuan Cai, Wen Huang, Zhenfang Wu, Jie Yang
Summary: This study integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to identify genetic variations and genes associated with loin muscle area, loin muscle depth, and lean meat percentage in Duroc pigs. By determining the CNV detection accuracy and constructing a genomic CNV map, valuable genetic variation resources for pig genome research were provided. The utilization of a composite genetic strategy for complex traits in pigs will contribute to elucidating the genetic architecture influenced by multiple forms of variations.
Article
Clinical Neurology
Elif Irem Sarihan, Eduardo Perez-Palma, Lisa-Marie Niestroj, Douglas Loesch, Miguel Inca-Martinez, Andrea R. V. R. Horimoto, Mario Cornejo-Olivas, Luis Torres, Pilar Mazzetti, Carlos Cosentino, Elison Sarapura-Castro, Andrea Rivera-Valdivia, Elena Dieguez, Victor Raggio, Andres Lescano, Vitor Tumas, Vanderci Borges, Henrique B. Ferraz, Carlos R. Rieder, Artur F. Schumacher-Schuh, Bruno L. Santos-Lobato, Carlos Velez-Pardo, Marlene Jimenez-Del-Rio, Francisco Lopera, Sonia Moreno, Pedro Chana-Cuevas, William Fernandez, Gonzalo Arboleda, Humberto Arboleda, Carlos E. Arboleda-Bustos, Dora Yearout, Cyrus P. Zabetian, Timothy A. Thornton, Timothy D. O'Connor, Dennis Lal, Ignacio F. Mata
Summary: Parkinson's disease patients from Latino descent show enrichment of copy number variants affecting known Parkinson's disease genes, with PRKN showing the strongest association. Additionally, 5.6% of early-onset patients carried a copy number variant on PRKN. This study provides insights into the genetic complexity of Parkinson's disease in this understudied population.
MOVEMENT DISORDERS
(2021)
Article
Biochemical Research Methods
Ziyu Tao, Shixiang Wang, Chenxu Wu, Tao Wu, Xiangyu Zhao, Wei Ning, Guangshuai Wang, Jinyu Wang, Jing Chen, Kaixuan Diao, Fuxiang Chen, Xue-Song Liu
Summary: This study developed a mechanism-agnostic method to categorize CNAs based on various fragment properties and revealed novel patterns of CNA. The activities of some CNA signatures consistently predicted cancer patients' prognosis. This study provides important insights into the role of CNA in cancer and its potential implications for cancer prognosis, evolution, and etiology.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Zhipeng Wang, Yuanyuan Guo, Shengwei Liu, Qingli Meng
Summary: Copy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Identification of CNVs from different genetic backgrounds can achieve reliable CNVs mapping. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and protein-coding genes (CNV genes) or miRNAs (CNV-miRNAs) can reveal the potential mechanisms of their regulation.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Linyong Hu, Liangzhi Zhang, Qi Li, Hongjin Liu, Tianwei Xu, Na Zhao, Xueping Han, Shixiao Xu, Xinquan Zhao, Cunfang Zhang
Summary: This study characterized copy number variations (CNVs) in Tibetan sheep using resequencing data and found a large number of CNVs that are associated with genetic structure, dosage regulation, and expression in the sheep genome. The shared CNV regions (CNVRs) were found to be significantly enriched in various pathways and GO terms related to transporters, sensory perception, and oxygen transport. Several CNVRs were also found to overlap with quantitative trait loci (QTLs) related to growth, body weight, and other traits. Vst analysis revealed significant divergence of certain genes between different ecotypic populations of Tibetan sheep. These findings provide valuable genetic variation resources for further elucidating the genetic basis of distinct phenotypic traits and local adaptation in Tibetan sheep.
FRONTIERS IN GENETICS
(2022)
Article
Veterinary Sciences
Xinmiao He, Ming Tian, Wentao Wang, Yanzhong Feng, Zhongqiu Li, Jiahui Wang, Yan Song, Jinfeng Zhang, Di Liu
Summary: Min pigs from northeast China have good meat quality, strong disease- and cold-resistance characters, and unique villi hair traits. The study of villi hair traits is significant for understanding cold resistance and animal welfare. In this study, a population of Large White x Min pigs was used to investigate the association between copy number variations (CNVs) and villi hair appearance. Important villi hair-related genes were identified, providing a reference for the breeding of cold-resistant pigs.
VETERINARY SCIENCES
(2023)
Article
Plant Sciences
Robin Nicole Bosman, Jessica Anne-Marie Vervalle, Danielle Lisa November, Phyllis Burger, Justin Graham Lashbrooke
Summary: Volatile organic compounds, such as terpenes, play a vital role in influencing the quality parameters of grapevine through their contribution to the flavor and aroma profile of grapes. The biosynthesis of these compounds is complex and controlled by multiple genes, many of which are unidentified. By analyzing volatile metabolic data from a grapevine mapping population, researchers identified several significant genomic regions associated with terpene modulation in grape berries. These findings provide insights into the molecular mechanisms of terpene accumulation and offer potential applications in developing grape cultivars with desired terpene profiles.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Seongmin Hong, Yong Pyo Lim, Suk-Yoon Kwon, Ah-Young Shin, Yong-Min Kim
Summary: In polyploids, whole genome duplication plays a significant role in genome expansion, evolution, and diversification. The flowering-time gene family, one of the largest expanded gene families in plants, has functionally diversified through evolution, providing advantages for plant adaptation and survival.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Cell Biology
Aditi Hazra, Andrea O'Hara, Kornelia Polyak, Faina Nakhlis, Beth T. Harrison, Antonio Giordano, Beth Overmoyer, Filipa Lynce
Summary: The goal of this study was to identify biomarkers associated with de novo inflammatory breast cancer (IBC). Through examination of breast biopsies, significant copy number variations (CNVs) on chromosome 7p11.2 and 21 were identified. These findings provide insights into the biology of IBC and may lead to the optimization of treatment strategies.
Article
Genetics & Heredity
Jill Rafalko, Erica Soster, Samantha Caldwell, Eyad Almasri, Thomas Westover, Vivian Weinblatt, Philip Cacheris
Summary: This study found that genome-wide cfDNA screening can detect chromosomal abnormalities beyond traditional screening, with an overall PPV of >70% for cases with subchromosomal CNVs. Isolated CNVs had a lower PPV of 61.0% compared to complex CNVs at 93.9%. Detected abnormalities included isolated deletions/duplications and unbalanced structural rearrangements.
GENETICS IN MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Iris J. M. Levink, Malgorzata I. Srebniak, Walter G. De Valk, Monique M. van Veghel-Plandsoen, Anja Wagner, Djuna L. Cahen, Gwenny M. Fuhler, Marco J. Bruno
Summary: This study evaluates the feasibility and performance of shallow sequencing for detecting copy number variations in cell-free DNA from pancreatic juice for pancreatic cancer detection. The presence of an 8q24 gain in pancreatic juice shows promise as a biomarker for the detection of pancreatic cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Chongjuan Gu, Huan Gao, Kuanrong Li, Xinyu Dai, Zhao Yang, Ru Li, Canliang Wen, Yaojuan He
Summary: The study aims to investigate the distribution and potential clinical significance of CNVs less than 3 Mb in pregnancy loss/fetal death. The research found that CNVs less than 3 Mb were unevenly distributed in euploid POCs, with higher density in the pericentromeric and sub-telomeric regions. The genes involved in these CNVs were significantly enriched in biological processes and pathways important for embryonic/fetal development. The most common CNV was found at 19p13.3.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Yue Zhang, Jung-Young Park, Fan Zhang, Sara H. Olson, Irene Orlow, Yirong Li, Robert C. Kurtz, Marc Ladanyi, Jie Chen, Amanda E. Toland, Liying Zhang, Paul R. Andreassen
Summary: This study identified two novel PALB2 missense variants that impacted DNA damage responses, leading to defective PALB2 and RAD51 recruitment to DNA damage foci and compromised homologous recombination. These variants also increased cellular sensitivity to ionizing radiation and PARP inhibitor, suggesting personalized treatment possibilities for cancers carrying deleterious PALB2 variants.
Article
Oncology
Weiqiang Li, Robert J. Klein
Summary: A genome-wide association study (GWAS) on BPH identified 35 significant variants in a discovery cohort and validated 4 significant variants, including one related to the PGR gene, in a validation cohort. The study suggests that genetic variants identified from BPH GWAS can be used to identify pharmacologic targets for BPH treatment.
PROSTATE CANCER AND PROSTATIC DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Rosalie Griffin Waller, Robert J. Klein, Joseph Vijai, James D. McKay, Alyssa Clay-Gilmour, Xiaomu Wei, Michael J. Madsen, Douglas W. Sborov, Karen Curtin, Susan L. Slager, Kenneth Offit, Celine M. Vachon, Steven M. Lipkin, Charles Dumontet, Nicola J. Camp
Summary: The study identified six genes that play a role in the risk of multiple myeloma, supporting genetic pleiotropy between lymphoid neoplasm subtypes, and demonstrating the utility of sequencing genetically enriched cases to identify functionally relevant variants near GWAS loci.
HUMAN MOLECULAR GENETICS
(2021)
Article
Oncology
Danielle R. Davari, Irene Orlow, Peter A. Kanetsky, Li Luo, Sharon N. Edmiston, Kathlee Conway, Eloise A. Parrish, Honglin Hao, Klaus J. Busam, Ajay Sharma, Anne Kricker, Anne E. Cust, Hod Ahton-Culver, Stephen B. Gruber, Richard P. Gallagher, Robert Zabetti, Stefano Rosso, Lidia Sacchetto, Terence Dwyer, David W. Ollita, Colin B. Begg, Marianne Berwick, Nancy E. Thomas
Summary: ANRIL rs564398 was found to be associated with the presence of tumor-infiltrating lymphocytes (TILs) in primary melanomas, particularly among cases with NRAS/BRAF mutations, with no significant associations with Breslow thickness or ulceration. Further exploration of pathways related to ANRIL variants in relation to TILs in melanoma is warranted, considering the impact of TILs on immunotherapy and survival.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2021)
Editorial Material
Urology & Nephrology
Robert J. Klein
Article
Oncology
Xiaoyu Song, Meng Ru, Zoe Steinsnyder, Kaitlyn Tkachuk, Ryan P. Kopp, John Sullivan, Zeynep H. Gumus, Kenneth Offit, Vijai Joseph, Robert J. Klein
Summary: This study found that SNP rs2702185 at the SMG7 locus is associated with time from biochemical recurrence to prostate cancer death, and its LD partner rs10737246 is predicted to be functional. These results suggest that future association studies of prostate cancer survival should consider various intervals over the course of disease.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Review
Oncology
Robert J. Klein, Zeynep H. Gumus
Summary: In order to achieve the goals of precision medicine in complex diseases, discriminative clinical risk models are necessary. Polygenic risk scores (PRSs) have been proposed as one approach with potential clinical utility in cancer. However, the utility of PRSs depends on their actionability, discriminative power, and comparison with existing practice.
TRANSLATIONAL LUNG CANCER RESEARCH
(2022)
Article
Oncology
Robert J. Klein, Emily Vertosick, Dan Sjoberg, David Ulmert, Ann-Charlotte Ronn, Christel Haggstrom, Elin Thysell, Goran Hallmans, Anders Dahlin, Par Stattin, Olle Melander, Andrew Vickers, Hans Lilja
Summary: Polygenic risk scores (PRS) for prostate cancer incidence were evaluated and compared to PSA and a commercialized model in predicting lethal prostate cancer. The study found that PRS was associated with incident prostate cancer, but was not a stronger predictor of lethal disease compared to PSA. The combination of PRS and PSA did not contribute additional risk stratification for lethal prostate cancer.
NPJ PRECISION ONCOLOGY
(2022)
Article
Oncology
Li Luo, Ronglai Shen, Arshi Arora, Irene Orlow, Klaus J. Busam, Cecilia Lezcano, Tim K. Lee, Eva Hernando, Ivan Gorlov, Christopher Amos, Marc S. Ernstoff, Venkatraman E. Seshan, Anne E. Cust, James Wilmott, Richard A. Scolyer, Graham Mann, Eduardo Nagore, Pauline Funchain, Jennifer Ko, Peter Ngo, Sharon N. Edmiston, Kathleen Conway, Paul B. Googe, David Ollila, Jeffrey E. Lee, Shenying Fang, Judy R. Rees, Cheryl L. Thompson, Meg Gerstenblith, Marcus Bosenberg, Bonnie Gould Rothberg, Iman Osman, Yvonne Saenger, Adam Z. Reynolds, Matthew Schwartz, Tawny Boyce, Sheri Holmen, Elise Brunsgaard, Paul Bogner, Pei Fen Kuan, Charles Wiggins, Nancy E. Thomas, Colin B. Begg, Marianne Berwick
Summary: This study examines the genomic landscape of early-stage melanomas and identifies different driver mutation sub-types, highlighting the clinical and pathological characteristics associated with each subtype. These findings provide important insights into the development and metastasis of melanoma.
PIGMENT CELL & MELANOMA RESEARCH
(2022)
Article
Multidisciplinary Sciences
Xiaoyu Song, Jiayi Ji, Joseph H. Rothstein, Stacey E. Alexeeff, Lori C. Sakoda, Adriana Sistig, Ninah Achacoso, Eric Jorgenson, Alice S. Whittemore, Robert J. Klein, Laurel A. Habel, Pei Wang, Weiva Sieh
Summary: Researchers have developed a new cell-type-aware transcriptome-wide association study approach to predict cell-type level gene expression and identify disease-associated genes. This approach provides insights into the genetic and cellular etiology of diseases such as breast cancer.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Myvizhi Esai Selvan, Kenan Onel, Sacha Gnjatic, Robert J. Klein, Zeynep H. Gumus
Summary: Recent studies have shown that rare, deleterious variants (RDVs) in specific genes play a critical role in heritable cancer risk. By analyzing whole-exome sequencing data of 20,789 participants, we identified associations between cancer risk and RDVs in DNA repair, cancer predisposition, and somatic cancer drivers. Moreover, we found that personal RDV load in these gene-sets is associated with increased risk, earlier onset, increased M1 macrophages in tumor, and increased tumor mutational burden in specific cancers. These findings can be used to identify high-risk individuals and improve prognosis through increased surveillance, earlier screening, and targeted treatments.
NPJ PRECISION ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Irene Orlow, Keimya D. Sadeghi, Sharon N. Edmiston, Jessica M. Kenney, Cecilia Lezcano, James S. Wilmott, Anne E. Cust, Richard A. Scolyer, Graham J. Mann, Tim K. Lee, Hazel Burke, Valerie Jakrot, Ping Shang, Peter M. Ferguson, Tawny W. Boyce, Jennifer S. Ko, Peter Ngo, Pauline Funchain, Judy R. Rees, Kelli O'Connell, Honglin Hao, Eloise Parrish, Kathleen Conway, Paul B. Googe, David W. Ollila, Stergios J. Moschos, Eva Hernando, Douglas Hanniford, Diana Argibay, Christopher Amos, Jeffrey E. Lee, Iman Osman, Li Luo, Pei-Fen Kuan, Arshi Aurora, Bonnie E. Gould Rothberg, Marcus W. Bosenberg, Meg R. Gerstenblith, Cheryl Thompson, Paul N. Bogner, Ivan P. Gorlov, Sheri L. Holmen, Elise K. Brunsgaard, Yvonne M. Saenger, Ronglai Shen, Venkatraman Seshan, Eduardo Nagore, Marc S. Ernstoff, Klaus J. Busam, Colin B. Begg, Nancy E. Thomas, Marianne Berwick
Summary: This study aims to identify prognostic classifiers for melanoma patients, using small-sized tumor samples. The findings show that multiple omics analyses can be successfully conducted on these samples, providing valuable insights for future research.
Article
Oncology
James C. Root, Yuelin Li, Elizabeth Schofield, Irene Orlow, Elizabeth Ryan, Tiffany Traina, Sunita K. Patel, Tim A. Ahles
Summary: The impact of cancer and cancer treatment on longer-term cognitive aging trajectories is currently unknown. Older breast cancer survivors showed lower learning and memory performance compared to non-cancer controls, and younger survivors exhibited more prominent differences in learning and memory as well as attention, processing speed, and executive function. These differences suggest a mechanism of cognitive aging and emphasize the importance of prevention and intervention in cancer survivorship.
Article
Oncology
David Corley Gibbs, Nancy E. Thomas, Peter A. Kanetsky, Li Luo, Klaus J. Busam, Anne E. Cust, Hoda Anton-Culver, Richard P. Gallagher, Roberto Zanetti, Stefano Rosso, Lidia Sacchetto, Sharon N. Edmiston, Kathleen Conway, David W. Ollila, Colin B. Begg, Marianne Berwick, Sarah Ward, Irene Orlow
Summary: This study found that the Gc1f haplotype in the GC gene is associated with a reduced risk of melanoma-specific death. In melanoma patients, those with the Gc1f haplotype had a 37% lower risk of melanoma-specific death compared to those without the Gc1f haplotype, based on two population-based studies.
JNCI CANCER SPECTRUM
(2023)
Article
Oncology
Danielle R. Davari, Irene Orlow, Peter A. Kanetsky, Li Luo, Klaus J. Busam, Ajay Sharma, Anne Kricker, Anne E. Cust, Hoda Anton-Culver, Stephen B. Gruber, Richard P. Gallagher, Roberto Zanetti, Stefano Rosso, Lidia Sacchetto, Terence Dwyer, David C. Gibbs, David W. Ollila, Colin B. Begg, Marianne Berwick, Nancy E. Thomas
Summary: GWAS and candidate pathway studies have identified low-penetrant genetic variants associated with cutaneous melanoma, showing associations with primary melanoma tumor prognostic characteristics and melanoma-specific survival. Further research into these genetic variants and their related biological pathways is warranted.