Article
Oncology
Louisa Lepkes, Mohamad Kayali, Britta Bluemcke, Jonas Weber, Malwina Suszynska, Sandra Schmidt, Julika Borde, Katarzyna Klonowska, Barbara Wappenschmidt, Jan Hauke, Piotr Kozlowski, Rita K. Schmutzler, Eric Hahnen, Corinna Ernst
Summary: The study evaluated the performance of four in silico CNV prediction tools in identifying germline copy number variants in cancer predisposition genes in female patients with familial breast and/or ovarian cancer. While some CNVs were missed by the prediction tools, it was found that CNV detection should not be limited to BRCA1/2 genes due to the presence of CNVs in other cancer predisposition genes. Experimental verification of in silico predicted CNVs is necessary due to high rates of false positive predictions.
Article
Microbiology
Sabino Pacheco, Isabel Gomez, Marcos Chinas, Jorge Sanchez, Mario Soberon, Alejandra Bravo
Summary: Bacillus thuringiensis (Bt) are soil bacteria that produce insecticidal proteins used for pest control. Genomic characterization of Bt strains provides valuable pesticidal protein resources with potential biotechnological applications. The sequenced Bt GR007 strain contains multiple genes coding for pesticidal proteins and virulent factors, which show differential toxicity against different insect larvae.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Seth I. Berger, Georgia Pitsava, Andrea J. Cohen, Emmanuele C. Delot, Jonathan LoTempio, Erin Hallie Andrew, Gloria Mas Martin, Sofia Marmolejos, Jessica Albert, Beatrix Meltzer, Jamie Fraser, Debra S. Regier, Amanda H. Kahn-Kirby, Erica Smith, Susan Knoblach, Arthur Ko, Vincent A. Fusaro, Eric Vilain
Summary: We evaluated the diagnostic yield of genome-slice panel reanalysis using an automated phenotype/gene ranking system in a clinical setting. We analyzed whole genome sequencing (WGS) data from 16 undiagnosed cases referred to a research center. We discovered potentially clinically significant variants in 5 out of 16 cases, including variants in genes not included in the original panel.
Article
Genetics & Heredity
Yanjing Wu, Yongle Wu, Kun Liu, Hui Liu, Shanshan Wang, Jian Huang, Huiguo Ding
Summary: It was found that the prevalence of MRC in NCPH patients was significantly higher than in cirrhotic patients, with distinguishable clinical characteristics. Rare putative pathogenic variants were identified in early-onset patients, and potential disease-related genes were discovered in the remaining patients through scRNA-seq data analysis.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Yuanhao Li, Bo Jiang, Weijun Dai
Summary: Essential genes are crucial for bacterial viability and new drug discovery, but some false positives generated by Tn-seq may result from gene deletions by bacteria themselves. Deleting genes should be considered when evaluating essentiality, as it has been underestimated in previous studies.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Food Science & Technology
Hongbiao Li, Lidan Guo, Xiaoyan Zhang, Haoqiang Mu, Shenfei Sha, Yi Lin, Hongwei Hou, Liping Wang
Summary: The study analyzed and purified the genes of Lactobacillus plantarum WUH3 and M4L1, and discovered the genes encoding Plantaricin EF and a novel bacteriocin-M4L1. The results showed that several genes encoding other bacteriocins were silent. Mining silenced genes can provide useful functional gene donors for improving production and regulating bacteriocin synthesis.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Immunology
Sara Bohnstedt Morup, Lusine Nazaryan-Petersen, Migle Gabrielaite, Joanne Reekie, Hanne Marquart, Hans Jakob Hartling, Rasmus L. Marvig, Terese L. Katzenstein, Tania N. Masmas, Jens Lundgren, Daniel D. Murray, Marie Helleberg, Line Borgwardt
Summary: This study suggests that reassessing WES/WGS data from patients with suspected PID may lead to improved diagnostic rates. Reasons for the potential gain in diagnosis include expanding the gene panel, adding structural variant analysis, and improved knowledge of genotype-phenotype correlations.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ayman Al Saati, Pierre Vande Perre, Julien Plenecassagnes, Julia Gilhodes, Nils Monselet, Bastien Cabarrou, Norbert Lignon, Thomas Filleron, Dominique Telly, Emilie Perello-Lestrade, Viviane Feillel, Anne Staub, Mathilde Martinez, Edith Chipoulet, Gaelle Collet, Fabienne Thomas, Laurence Gladieff, Christine Toulas
Summary: A study found that rare genetic variants related to DNA repair, genomic stability, and cell adhesion were detected in male breast cancer patients without BRCA1/BRCA2/PALB2 mutations. These variants were more prevalent in male breast cancer patients compared to female breast cancer patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Acoustics
E. Westenius, E. Sahlin, P. Conner, A. Lindstrand, E. Iwarsson
Summary: The objective of this study was to evaluate the diagnostic yield of clinical whole-genome sequencing (WGS) in prenatal diagnosis of non-immune hydrops fetalis (NIHF). The results showed that 52% of the fetuses in the study achieved a molecular diagnosis through WGS. However, caution is needed in interpreting the results due to the small sample size and possible over-representation of severe phenotypes.
ULTRASOUND IN OBSTETRICS & GYNECOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kimberley C. Batley, Jonathan Sandoval-Castillo, Catherine M. Kemper, Nikki Zanardo, Ikuko Tomo, Luciano B. Beheregaray, Luciana M. Moller
Summary: The study analyzed the whole genome data set of dolphins exposed to a CeMV-related mortality event and identified genetic regions and pathways associated with immune responses to CeMV. The findings suggest that levels of inbreeding in the dolphin population have minimal impact on individual outcomes. This research contributes to understanding the immune responses of dolphins to CeMV and highlights the value of whole genome data sets in conservation efforts.
Article
Allergy
Craig D. Platt, Fatima Zaman, Wayne Bainter, Kelsey Stafstrom, Abuarahman Almutairi, Margot Reigle, Sabrina Weeks, Raif S. Geha, Janet Chou
Summary: This study compared targeted next-generation sequencing with whole-exome sequencing in a global population of patients with primary immunodeficiency. The results showed that whole-exome sequencing had advantages in diagnostic yield, cost savings, and the potential for identification of novel diseases.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2021)
Article
Medicine, General & Internal
Marcella Nunziato, Federica Di Maggio, Matilde Pensabene, Maria Valeria Esposito, Flavio Starnone, Carmine De Angelis, Alessandra Calabrese, Massimiliano D'Aiuto, Gerardo Botti, Sabino De Placido, Valeria D'Argenio, Francesco Salvatore
Summary: Breast cancer, especially the hereditary/familial form, is associated with DNA variants in cancer-predisposing genes such as BRCA1/BRCA2. However, these variants only explain a portion of the cases. Researchers have developed a custom panel of 44 genes, using NGS techniques, to improve diagnostic sensitivity. A study conducted in Southern Italy found pathogenic variants in 19% of the tested patients, with MUTYH gene being the most frequently altered. These findings highlight the importance of expanding molecular testing beyond BRCA genes and may guide precision oncology therapy.
FRONTIERS IN MEDICINE
(2022)
Article
Genetics & Heredity
Jiani Guo, Yu Yang, Zhuqing Ji, Mengchu Yao, Xiaotian Xia, Xiaofeng Sha, Mingde Huang
Summary: This study focused on a 78-year-old Chinese woman with multiple cancer types, finding that the RPGRIP1L gene may be associated with various types of cancers, especially pancreatic adenocarcinoma, potentially affecting patient survival and sensitivity to paclitaxel via the TGF-beta signaling pathway.Further research is needed to determine the significance of RPGRIP1L in this family and in multiple primary tumors.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Yichuan Liu, Hui-Qi Qu, Xiao Chang, Frank D. Mentch, Haijun Qiu, Kenny Nguyen, Xiang Wang, Amir Hossein Saeidian, Deborah Watson, Joseph Glessner, Hakon Hakonarson
Summary: This study identified genetic variants associated with cancer in non-chromosomal BD patients through whole genome sequencing, providing insights for early detection of malignant tumors in children with BD.
BIOMARKER RESEARCH
(2022)
Article
Oncology
Fenfen Fu, Dongjie Zhang, Li Hu, Senthil Sundaram, Dingge Ying, Ying Zhang, Shuna Fu, Juan Zhang, Lu Yao, Ye Xu, Yuntao Xie
Summary: The study identified high-risk and moderate-risk breast cancer susceptibility genes in Chinese women, providing valuable data for genetic testing and clinical management of hereditary breast cancer in China. Patients with pathogenic variants in TP53, BRCA1, BRCA2, and PALB2 were more likely to have early onset and family history of breast cancer. Pathogenic variants of NBN, RAD50, BRIP1, and RAD51C did not show increased risk of breast cancer in Chinese women.
CANCER BIOLOGY & MEDICINE
(2022)
Article
Genetics & Heredity
Raymond H. Kim, Xiangling Wang, Andrew J. Evans, Steven C. Campbell, Jane K. Nguyen, Kirsten M. Farncombe, Charis Eng
NPJ GENOMIC MEDICINE
(2020)
Article
Urology & Nephrology
Roderick Clark, Miran Kenk, Kristen McAlpine, Emily Thain, Kirsten M. Farncombe, Colin C. Pritchard, Robert Nussbaum, Alexander W. Wyatt, Johann de Bono, Danny Vesprini, Yvonne Bombard, Justin Lorentz, Steven Narod, Raymond Kim, Neil Fleshner
Summary: The conference highlighted the importance of increasing funding for genetic testing for common genetic disorders associated with prostate cancer risk, conducting research on genetic factors affecting risk stratification and treatment outcomes in Canadian populations at higher genetic risk, raising awareness about genetic risk factors among the Canadian public, developing patient-specific care for those at increased genetic risk of prostate cancer, and establishing multidisciplinary clinics for tailored care.
CUAJ-CANADIAN UROLOGICAL ASSOCIATION JOURNAL
(2021)
Article
Genetics & Heredity
Nika Maani, Karen Panabaker, Jeanna M. McCuaig, Kathleen Buckley, Kara Semotiuk, Kirsten M. Farncombe, Peter Ainsworth, Seema Panchal, Bekim Sadikovic, Susan Randall Armel, Hanxin Lin, Raymond H. Kim
Summary: This retrospective study identified 24 cases of incidental findings in NGS-MGP testing, with pathogenic variants detected in genes such as TP53 and ATM. The majority of patients (75%) were classified as clonal hematopoiesis, while only 4.2% were confirmed as true germline variants.
NPJ GENOMIC MEDICINE
(2021)
Article
Genetics & Heredity
Roozbeh Manshaei, Sean DeLong, Veronica Andric, Esha Joshi, John B. A. Okello, Priya Dhir, Cherith Somerville, Kirsten M. Farncombe, Kelsey Kalbfleisch, Rebekah K. Jobling, Stephen W. Scherer, Raymond H. Kim, S. Mohsen Hosseini
Summary: GeneTerpret is a flexible platform that streamlines the variant interpretation process by integrating data from multiple databases and tools, applying phenotype-driven queries and validation criteria, and providing a prioritized list of potentially causal variants/genes. Comparisons with expert-curated databases and internal clinical datasets demonstrate high concordance and accuracy of GeneTerpret.
BMC MEDICAL GENOMICS
(2022)
Editorial Material
Cardiac & Cardiovascular Systems
Eriskay J. Liston, Kelsey J. Kalbfleisch, Kaitlin J. Stanley, Rajiv R. Chaturvedi, Iris Cohn, Kirsten M. Farncombe, Robin Z. Hayeems, Marci L. B. Schwartz, Cherith B. Somerville, Raymond H. Kim, Rebekah K. Jobling
Summary: Genetic testing in cardiology can improve patient and family management, and genome sequencing is a reliable method in precision medicine. However, there are challenges in integrating genome sequencing into cardiology, such as a lack of genomic literacy and difficulty in data interpretation. By adopting a multidisciplinary model, the integration of genome sequencing can be supported, leading to new diagnoses and improved medication management.
CANADIAN JOURNAL OF CARDIOLOGY
(2022)
Article
Genetics & Heredity
Andreea Chiorean, Kirsten M. Farncombe, Sean Delong, Veronica Andric, Safa Ansar, Clarissa Chan, Kaitlin Clark, Arpad M. Danos, Yizhuo Gao, Rachel H. Giles, Anna Goldenberg, Payal Jani, Kilannin Krysiak, Lynzey Kujan, Samantha Macpherson, Eamonn R. Maher, Liam G. McCoy, Yasser Salama, Jason Saliba, Lana Sheta, Malachi Griffith, Obi L. Griffith, Lauren Erdman, Arun Ramani, Raymond H. Kim
Summary: The study aims to collect information on VHL disease by screening articles and analyzing genotype-phenotype data of VHL patients. Relationship trends and existing associations were identified, which can help identify new patterns and associations in VHL disease.
Article
Oncology
Salma Shickh, Leslie E. Oldfield, Marc Clausen, Chloe Mighton, Agnes Sebastian, Alessia Calvo, Nancy N. Baxter, Lesa Dawson, Lynette S. Penney, William Foulkes, Mark Basik, Sophie Sun, Kasmintan A. Schrader, Dean A. Regier, Aly Karsan, Aaron Pollett, Trevor J. Pugh, Raymond H. Kim, Yvonne Bombard
Summary: This study explores the views of health professionals on the utility of circulating tumor DNA (ctDNA) testing in the management of hereditary cancer syndromes (HCS). The study finds that professionals have varying opinions on the use of ctDNA testing, with some optimistic about its potential to transform early cancer detection, while others are hesitant due to concerns about invasiveness and limited utility.
Article
Genetics & Heredity
Leslie E. Oldfield, Jessica Grzybowski, Sylvie Grenier, Elizabeth Chao, Gregory S. Downs, Kirsten M. Farncombe, Tracy L. Stockley, Ozgur Mete, Raymond H. Kim
Summary: This report highlights the importance of tissue testing in VHL variant negative cases, using a rare case of VHL mosaicism as an example.
NPJ GENOMIC MEDICINE
(2022)
Article
Genetics & Heredity
Kirsten M. Farncombe, Emily Thain, Carolina Barnett-Tapia, Hamid Sadeghian, Raymond H. Kim
Summary: This study reviews the contribution of LZTR1 in Noonan syndrome and describes a patient with a novel mutation in the LZTR1 gene. The patient, initially diagnosed with clinical NS, was found to have plexiform neurofibromas on brain and spine MRI, but did not meet the criteria for Neurofibromatosis type 1.
BMC MEDICAL GENOMICS
(2022)
Article
Genetics & Heredity
Safa Ansar, Janet Malcolmson, Kirsten M. Farncombe, Karen Yee, Raymond H. Kim, Hassan Sibai
Summary: This study established genetic testing criteria for adult hematology patients and demonstrated the utility of a broad approach to germline testing. The results showed a considerable proportion of patients carrying actionable variants associated with an increased risk of cancer, as well as the identification of incidental findings.
GENETICS IN MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Kilannin Krysiak, Arpad M. Danos, Jason Saliba, Joshua F. McMichael, Adam C. Coffman, Susanna Kiwala, Erica K. Barnell, Lana Sheta, Cameron J. Grisdale, Lynzey Kujan, Shahil Pema, Jake Lever, Sarah Ridd, Nicholas C. Spies, Veronica Andric, Andreea Chiorean, Damian T. Rieke, Kaitlin A. Clark, Caralyn Reisle, Ajay C. Venigalla, Mark Evans, Payal Jani, Hideaki Takahashi, Avila Suda, Peter Horak, Deborah Ritter, Xin Zhou, Benjamin J. Ainscough, Sean Delong, Chimene Kesserwan, Mario Lamping, Haolin Shen, Alex R. Marr, My H. Hoang, Kartik Singhal, Mariam Khanfar, Brian Li, Wan-Hsin Lin, Panieh Terraf, Laura B. Corson, Yasser Salama, Katie M. Campbell, Kirsten M. Farncombe, Jianling Ji, Xiaonan Zhao, Xinjie Xu, Rashmi Kanagal-Shamanna, Ian King, Kelsy C. Cotto, Zachary L. Skidmore, Jason R. Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y. Patel, Rachel H. Giles, Raymond H. Kim, Lynn M. Schriml, Elaine R. Mardis, Steven J. M. Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H. Wagner, Malachi Griffith, Obi L. Griffith
Summary: CIVIC is a crowd-sourced, public domain knowledgebase that provides literature-derived evidence characterizing the clinical utility of cancer variants. It supports variant interpretation guidelines, increases interoperability with other variant resources, and promotes widespread dissemination of structured curated data. It currently includes over 300 contributors and represents >3200 variants in >470 genes from >3100 publications.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Dena Salehipour, Kirsten M. Farncombe, Veronica Andric, Safa Ansar, Sean Delong, Eric Li, Samantha Macpherson, Sarah Ridd, Deborah I. Ritter, Courtney Thaxton, Raymond H. Kim
Summary: The article introduces the rarity and autosomal dominant inheritance of Von Hippel-Lindau (VHL) disease, as well as the challenges in studying this disease. To address these challenges, a crowd-sourced approach combined with an open-access web annotation tool was used for variant annotation and research, with training provided to community curators. These efforts have contributed to understanding the genotype-phenotype correlation in VHL disease.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Genetics & Heredity
Brittany Gillies, Hatem Krema, Anning Chao, Leonardo Lando, Kirsten M. Farncombe, Marcus Butler, Filiberto Altomare, Raymond H. Kim
Summary: This study reports the results of genetic testing and phenotype analysis of a cohort of unselected uveal melanoma patients. The collaboration between the medical genetics clinic and oncologists in a mainstreaming model plays a central role in facilitating genetic testing and counseling for patients with hereditary cancer predisposition.
OPHTHALMIC GENETICS
(2023)
Article
Genetics & Heredity
Kirsten M. Farncombe, Derek Wong, Maia L. Norman, Leslie E. Oldfield, Julia A. Sobotka, Mark Basik, Yvonne Bombard, Victoria Carile, Lesa Dawson, William D. Foulkes, David Malkin, Aly Karsan, Patricia Parkin, Lynette S. Penney, Aaron Pollett, Kasmintan A. Schrader, Trevor J. Pugh, Raymond H. Kim
Summary: At least 5% of cancer diagnoses in individuals with hereditary cancer syndrome (HCS) are attributed to genetic variants. Cell-free DNA sequencing has shown potential as a non-invasive strategy for monitoring cancer in HCS individuals. The CHARM Consortium in Canada aims to assess the clinical validity of cfDNA in HCS and explore opportunities for its incorporation into surveillance protocols.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)