Article
Microbiology
Justin T. Landis, Razia Moorad, Linda J. Pluta, Carolina Caro-Vegas, Ryan P. McNamara, Anthony B. Eason, Aubrey Bailey, Femi Cleola S. Villamor, Angelica Juarez, Jason P. Wong, Brian Yang, Grant S. Broussard, Blossom Damania, Dirk P. Dittmer
Summary: Variants of concern (VOC) in SARS-CoV-2 are viruses with >= 3 single-nucleotide variants (SNVs) compared to the ancestor virus, with potential for higher transmissibility and/or worse clinical progression. Little is known about the frequency and circumstances of new viral variants emerging.
Review
Biochemical Research Methods
Tingting Gong, Vanessa M. Hayes, Eva K. F. Chan
Summary: This review highlights important factors affecting somatic SV detection and compares the performance of seven commonly used SV callers. By focusing on changes in sensitivity and precision for detecting different SV types and size ranges from samples with varying variant allele frequencies and sequencing depths, the evaluation findings extend beyond the seven SV callers examined in this paper.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medical Laboratory Technology
Mohammad Athar, Ibrahim S. Ghita, Amani A. Albagenny, Zainularifeen Abduljaleel, Ghulam Shadab, Ahmed Elsendiony, Saeed H. Halawani, Mohammad M. Alkazmi, Khalid Alquthami, Mohammad M. Alkhuzae, Abdulaziz A. Althebyani, Neda M. Bogari, Anas Dannoun, Faisal A. Al-Allaf
Summary: Thrombophilia is a significant cause of illness and death in certain populations, including Arabs. Next Generation Sequencing (NGS) was utilized to identify genetic variants associated with thrombophilia, uncovering known and novel variants in multiple genes. The study highlights the potential of NGS in identifying rare genetic factors predisposing individuals to thrombotic events.
CLINICA CHIMICA ACTA
(2021)
Review
Immunology
Xiaomin Chen, Yutong Kang, Jing Luo, Kun Pang, Xin Xu, Jinyu Wu, Xiaokun Li, Shengwei Jin
Summary: The ongoing COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has highlighted the importance of next-generation sequencing in understanding the virus. NGS analysis has provided insights into the origin and transmission of SARS-CoV-2, as well as related factors like ACE2 expression levels, gut microbiota dysbiosis, and immunogenetics of patients. These sequencing techniques have the potential to identify new hosts, aid in diagnostic development, and discover therapeutic targets, offering crucial support in the fight against future public health emergencies.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Urology & Nephrology
Jose Lazaro-Guevara, Julio Fierro-Morales, A. Hunter Wright, River Gunville, Christopher Simeone, Scott G. Frodsham, Melissa H. Pezzolesi, Courtney A. Zaffino, Laith Al-Rabadi, Nirupama Ramkumar, Marcus G. Pezzolesi
Summary: This study investigated the genetic basis of nondiabetic kidney disease (NDKD) and diabetic kidney disease (DKD) through targeted NGS, finding rare diagnostic variants consistent with clinical diagnoses in 19% of NDKD patients and in 22% of DKD patients. Additionally, genetic variants suggestive of NDKD were detected in 3% of diabetic patients. These findings suggest that rare variants in kidney disease-related genes may contribute to the pathogenesis of DKD and NDKD in patients with diabetes.
AMERICAN JOURNAL OF NEPHROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Richard Sather III, Jacie Ihinger, Michael Simmons, Tahsin Khundkar, Glenn P. Lobo, Sandra R. Montezuma
Summary: This retrospective study used next generation sequencing to identify genetic variants in RP patients at the Inherited Retinal Disease Clinic at UMN/M Health System. The study found that over half of the patients had a genotype consistent with their examination results, while further research is needed for the remaining patients to determine the underlying genetic etiology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Brendan O'Fallon, Jacob Durtschi, Ana Kellogg, Tracey Lewis, Devin Close, Hunter Best
Summary: This study proposes two algorithmic adaptations to improve the accuracy of CNV detection in a Hidden Markov Model (HMM) context. First, it improves the accuracy by computing target- and copy number-specific emission distributions. Second, it enhances the sensitivity for small CNV calls using the Pointwise Maximum a posteriori (PMAP) HMM decoding procedure. The prototype implementation, called Cobalt, shows similar sensitivity to other CNV detection tools but significantly reduces false positive detections.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Hye Lim Choi, Ha Rim Yang, Ha Gyeong Shin, Kyusang Hwang, Ji Woong Kim, Ji Hyun Lee, Taehoon Ryu, Yushin Jung, Sukmook Lee
Summary: Antibody phage display is a crucial technology for discovering and developing target-specific monoclonal antibodies. This study constructed a large human combinatorial single-chain variable fragment library with high diversity, which can be used for the rapid development of recombinant human monoclonal antibodies for therapeutic and diagnostic applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Shalini S. Nayak, Pauline E. Schneeberger, Siddaramappa J. Patil, Karegowda M. Arun, Pujar Suresh, Viralam S. Kiran, Sateesh Siddaiah, Shreesha Maiya, Shrikanth K. Venkatachalagupta, Neethukrishna Kausthubham, Fanny Kortum, Isabella Rau, Alexandra Wey-Fabrizius, Lotte Van den Heuvel, Josephina Meester, Lut Van Laer, Anju Shukla, Bart Loeys, Katta M. Girisha, Kerstin Kutsche
Summary: Marfan syndrome and related disorders are heritable connective tissue disorders with clinical features involving various systems. A study in India involving 53 families and 83 patients found that targeted gene sequencing was effective in diagnosing these disorders, with a high percentage of rare variants identified in genes associated with Marfan syndrome, Loeys-Dietz syndrome, and Shprintzen-Goldberg syndrome. The study also discovered novel variants in a significant portion of the patients and highlighted the spectrum of variants in Indian individuals for the first time.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Alesa Kristan, Tadej Pajic, Ales Maver, Tadeja Rezen, Tanja Kunej, Rok Kolic, Andrej Vuga, Martina Fink, Spela Zula, Helena Podgornik, Sasa Anzej Doma, Irena Preloznik Zupan, Damjana Rozman, Natasa Debeljak
Summary: An erythrocytosis is characterized by an increase in red blood cell mass, often associated with genetic variants in genes related to oxygen sensing, hematopoietic cell maturation, and oxygen transfer. Classical sequencing approaches may only provide a correct diagnosis for a fraction of patients with congenital erythrocytosis, as the genetic background of the disorder is more complex and involves additional genes. A targeted next-generation sequencing approach was used in this study to identify genetic variants in patients with unexplained erythrocytosis, leading to the discovery of pathogenic and novel variants in relevant genes, as well as the identification of potential associations with iron metabolism genes. This study contributes to improving the diagnosis and management of Slovenian patients with erythrocytosis and provides insights for future research into the etiology of this rare hematological disorder.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Angeliki Andrikopoulou, Eleni Zografos, Kleoniki Apostolidou, Anastasios Kyriazoglou, Alksistis-Maria Papatheodoridi, Maria Kaparelou, Konstantinos Koutsoukos, Michalis Liontos, Meletios-Athanasios Dimopoulos, Flora Zagouri
Summary: This study aimed to identify the molecular landscape of germline and somatic mutations in ovarian cancer patients through NGS analysis. The results revealed that TP53 and BRCA1 were the most common somatic mutations in high grade serous carcinoma patients, while BRCA1 and BRCA2 were the most common genes with pathogenic alterations in germline mutations.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Xiaonan Wu, Jun Zhao, Ling Yang, Xin Nie, Zheng Wang, Ping Zhang, Chao Li, Xueqing Hu, Min Tang, Yuting Yi, Xinhua Du, Xuefeng Xia, Yanfang Guan, Zicheng Yu, Wenguang Gu, Xiangming Quan, Lin Li, Hong Shi
Summary: This study reveals the differences in somatic genetic mutations and tumor mutation burden between young and aged lung adenocarcinoma (LUAD) patients, which may provide directions for targeted therapy and advantages of immunotherapy for the elderly in the future.
Article
Cell Biology
Jie Huang, Jun Liu, Ruiyi Tian, Kevin Liu, Patrick Zhuang, Hannah Tayla Sherman, Christoph Budjan, Michelle Fong, Min-Seo Jeong, Xue-Jun Kong
Summary: This study demonstrates the clinical feasibility and technical implementation of a WGS genetic report for patients with ASD. By using WGS data from six family trios and considering clinical symptoms and literature review, an evidence-based and transparent bioinformatics pipeline and report framework were provided. This method can contribute to a better understanding of ASD pathophysiology, early detection of associated comorbidities, and personalized treatment based on genetic information.
Article
Medical Laboratory Technology
Peng-fei Liu, Zhong-ling Zhuo, Fei Xie, Shu Wang, Xiao-tao Zhao
Summary: This study identified four novel pathogenic BRCA variants in breast cancer patients, enriching the genetic database of breast cancer in the Chinese population. These variants are genetic risk factors for hereditary breast cancer, emphasizing the importance of BRCA variant detection and genetic counseling for breast cancer patients.
CLINICA CHIMICA ACTA
(2021)
Article
Genetics & Heredity
Anna Repczynska, Katarzyna Julga, Jolanta Skalska-Sadowska, Magdalena M. Kacprzak, Alicja Bartoszewska-Kubiak, Ewelina Lazarczyk, Damian Loska, Malgorzata Drozniewska, Kamila Czerska, Jacek Wachowiak, Olga Haus
Summary: This study reports on a family with two siblings diagnosed with Fanconi anemia. Through the use of MMC test, aCGH, and NGS analysis, pathogenic alterations in the FANCA gene were identified in these patients. The study also identified a third sibling as a carrier of FANCA gene deletion.
ORPHANET JOURNAL OF RARE DISEASES
(2022)
Article
Biotechnology & Applied Microbiology
Joseph C. Forbi, Michael Dillon, Michael A. Purdy, Bakary S. Drammeh, Alexandra Tejada-Strop, Daniel McGovern, Guo-liang Xia, Yulin Lin, Lilia M. Ganova-Raeva, David S. Campo, Hong Thai, Gilberto Vaughan, Dunstan Haule, Regina P. Kutaga, Sridhar V. Basavaraju, Saleem Kamili, Yury E. Khudyakov
JOURNAL OF GENERAL VIROLOGY
(2017)
Article
Infectious Diseases
David S. Campo, Yury Khudyakov
INFECTION GENETICS AND EVOLUTION
(2018)
Article
Biochemical Research Methods
Seth Sims, Atkinson G. Longmire, David S. Campo, Sumathi Ramachandran, Magdalena Medrzycki, Lilia Ganova-Raeva, Yulin Lin, Amanda Sue, Hong Thai, Alexander Zelikovsky, Yury Khudyakov
BMC BIOINFORMATICS
(2018)
Article
Biochemical Research Methods
Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
BMC BIOINFORMATICS
(2018)
Article
Genetics & Heredity
David S. Campo, Vishal Nayak, Ganesh Srinivasamoorthy, Yury Khudyakov
BMC MEDICAL GENOMICS
(2019)
Article
Biochemical Research Methods
David S. Campo, Yury Khudyakov
BMC BIOINFORMATICS
(2020)
Article
Multidisciplinary Sciences
David S. Campo, Joseph W. Gussler, Amanda Sue, Pavel Skums, Yury Khudyakov
Article
Biochemical Research Methods
J. Walker Gussler, David S. Campo, Zoya Dimitrova, Pavel Skums, Yury Khudyakov
Summary: Background investigation of outbreaks is crucial for interrupting and preventing the transmission of infectious diseases. This study presents a new computational framework, PYCIVO, which can infer the primary case in viral outbreaks. By simulating the evolution of hepatitis C virus (HCV) variants between cases involved in direct transmission, PYCIVO constructs a probabilistic disease transmission tree. It improves upon previous work by implementing a custom heterogeneity index and identifying scenarios where the primary case may not have been sampled.
BMC BIOINFORMATICS
(2022)
Article
Microbiology
Eldin Talundzic, Stephen Scott, Simon O. Owino, David S. Campo, Naomi W. Lucchi, Venkatachalam Udhayakumar, Julie M. Moore, David S. Peterson
Summary: This study reveals the association between the genetic diversity of the Plasmodium falciparum protein VAR2CSA and immune evasion and virulence, highlighting its significance for vaccine development.
Meeting Abstract
Gastroenterology & Hepatology
Alexander Ibrahim Mosa, David S. Campo, Richard A. Urbanowicz, Atif Zahoor, Mounir G. AbouHaidar, Adam J. Gehring, Johnathan E. Tavis, Jonathan K. Ball, Jordan J. Feld
Article
Biotechnology & Applied Microbiology
Inna Rytsareva, David S. Campo, Yueli Zheng, Seth Sims, Sharma V. Thankachan, Cansu Tetik, Jain Chirag, Sriram P. Chockalingam, Amanda Sue, Srinivas Aluru, Yury Khudyakov
Proceedings Paper
Engineering, Biomedical
Viachaslau Tsyvina, David Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
2017 IEEE 7TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL ADVANCES IN BIO AND MEDICAL SCIENCES (ICCABS)
(2017)
Article
Biotechnology & Applied Microbiology
Atkinson G. Longmire, Seth Sims, Inna Rytsareva, David S. Campo, Pavel Skums, Zoya Dimitrova, Sumathi Ramachandran, Magdalena Medrzycki, Hong Thai, Lilia Ganova-Raeva, Yulin Lin, Lili T. Punkova, Amanda Sue, Massimo Mirabito, Silver Wang, Robin Tracy, Victor Bolet, Thom Sukalac, Chris Lynberg, Yury Khudyakov
Article
Biotechnology & Applied Microbiology
David S. Campo, June Zhang, Sumathi Ramachandran, Yury Khudyakov
Article
Biochemical Research Methods
Pavel Skums, Alex Zelikovsky, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev, Igor Mandric, Sumathi Ramachandran, David Campo, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhan O'Connor, Guo-Liang Xia, Yury Khudyakov