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
Oncology
Adam Szpechcinski, Malgorzata Szolkowska, Sebastian Winiarski, Urszula Lechowicz, Piotr Wisniewski, Magdalena Knetki-Wroblewska
Summary: The molecular dysregulation of thymic epithelial tumors, including thymomas and thymic carcinomas, is poorly understood. Through next-generation sequencing, this study identified more single nucleotide variants (SNVs) in thymic carcinomas compared to thymomas. Somatic pathogenic gene variants in TP53, ERBB2, KIT, or KRAS were found in a subset of thymic carcinomas, while uncertain clinical significance variants in KIT, ERBB2, and FOXL2 were exclusively found in thymomas. The presence of somatic pathogenic variants was associated with shorter disease-free survival in thymic carcinoma patients. This study expands our understanding of the genetic alterations in these tumors and highlights potential therapeutic targets.
Article
Pediatrics
Haiyan Luo, Yan Yang, Xinrong Wang, Fangping Xu, Cheng Huang, Danping Liu, Liuyang Zhang, Ting Huang, Pengpeng Ma, Qing Lu, Shuhui Huang, Bicheng Yang, Yongyi Zou, Yanqiu Liu
Summary: This study aimed to explore the efficacy of combining conventional hearing screening with genetic screening among a large number of newborns in Jiangxi Province, China. The results showed that GJB2 and SLC26A4 are the most common genes associated with hearing loss among newborns in Jiangxi Province. Concurrent screening provides a more comprehensive approach for the management and prevention of hearing loss in newborns.
FRONTIERS IN PEDIATRICS
(2022)
Article
Biochemistry & Molecular Biology
Claudia Maria Hattinger, Chiara Casotti, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: This study investigated the relationship between SNPs and CDDP resistance in high-grade osteosarcoma cells, providing a basis for further research on the topic.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Biochemical Research Methods
Mihai Lefter, Jonathan K. Vis, Martijn Vermaat, Johan T. den Dunnen, Peter E. M. Taschner, Jeroen F. J. Laros
Summary: The Human Genome Variation Society provides guidelines on accurately describing genetic variants, with the Mutalyzer tool suite being able to automatically apply these guidelines for users to check and correct their descriptions. Mutalyzer has successfully processed over 133 million descriptions, with around 50% being reported as correct and able to automatically correct descriptions for approximately 7% of cases.
Article
Pharmacology & Pharmacy
Chiara Casotti, Claudia Maria Hattinger, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Michela Pasello, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: In this study, an innovative mmNGS approach was used to investigate SNPs associated with MTX resistance in HGOS cell lines. The results showed that allele changes in TP53, SLC19A1, and MTHFR were functionally involved in the development of MTX resistance. In addition, a fusion transcript of DHFR and MSH3 was identified in the cells with the highest MTX resistance level.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Oncology
Yoon Ji Choi, Jung Yoon Choi, Ju Won Kim, Ah Reum Lim, Youngwoo Lee, Won Jin Chang, Soohyeon Lee, Jae Sook Sung, Hee-Joon Chung, Jong Won Lee, Eun Joo Kang, Jung Sun Kim, Taekyu Lim, Hye Sook Kim, Yu Jung Kim, Mi Sun Ahn, Young Saing Kim, Ji Hyun Park, Seungtaek Lim, Sung Shim Cho, Jang Ho Cho, Sang Won Shin, Kyong Hwa Park, Yeul Hong Kim
Summary: The K-MASTER project aims to be a Korean national precision medicine platform that screens actionable mutations in solid tumor patients through analyzing NGS. The comparison between NGS panel and orthogonal methods showed a different degree of agreement for each genetic alteration, but generally had a high agreement rate.
CANCER RESEARCH AND TREATMENT
(2022)
Article
Oncology
Moonsik Kim, Changseon Lee, Juyeon Hong, Juhee Kim, Ji Yun Jeong, Nora Jee-Young Park, Ji-Eun Kim, Ji Young Park
Summary: The purpose of this study was to validate a targeted hybridization capture-based DNA panel (ONCOaccuPanel) for the simultaneous detection of genetic alterations in solid tumors using the Illumina MiSeq sequencing platform. The panel showed high sensitivity, reproducibility, and repeatability in detecting clinically relevant mutations, as demonstrated through validation using known genetic mutations and additional sequencing of tumor samples. The clinical application of ONCOaccuPanel also showed robust detection of oncogenic alterations and targetable genetic alterations in a significant percentage of cases.
CANCER RESEARCH AND TREATMENT
(2023)
Review
Pharmacology & Pharmacy
Jia Sen Tan, Muhamad Norizwan Bin Jaffar Ali, Bee Koon Gan, Wen Siang Tan
Summary: This article comprehensively reviews the fundamentals, challenges, and solutions of virus-based nanocarriers (VNPs) for biomedical applications. It examines different types of VNPs and their biomedical applications, cargo loading and targeted delivery strategies, and the latest developments in controlled release of cargoes. Challenges faced by VNPs in biomedical applications are identified, and solutions are provided to overcome them.
EXPERT OPINION ON DRUG DELIVERY
(2023)
Article
Biochemistry & Molecular Biology
Aimi Zafira Razman, Yung-An Chua, Noor Alicezah Mohd Kasim, Alyaa Al-Khateeb, Siti Hamimah Sheikh Abdul Kadir, Siti Azma Jusoh, Hapizah Nawawi
Summary: Familial hypercholesterolaemia (FH) is caused by mutations in genes related to lipid metabolism. This study focused on Malaysian FH patients and found that mutations in low-density lipoprotein receptor and apolipoprotein B genes were the most common, while novel variants in the PCSK9 gene were identified. The prevalence of genetically confirmed FH in the Malaysian community is relatively high, emphasizing the importance of genetic confirmation in both potential and possible FH cases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Hsien-Yu Fan, Wan-Yu Lin, Tzu-Pin Lu, Yun-Yu Chen, Justin BoKai Hsu, Sung-Liang Yu, Ta-Chen Su, Hung-Ju Lin, Yang-Ching Chen, Kuo-Liong Chien
Summary: This study used targeted next-generation sequencing to investigate the association between genetic variants and left ventricular mass, and identified candidate genes including CASQ2, COL5A1, and FXN. These findings provide important insights into the functional mechanisms of these genes and variants.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Manal Alaamery, Jahad Alghamdi, Salam Massadeh, Mona Alsawaji, Nora Aljawini, Nour Albesher, Bader Alghamdi, Mansour Almutairi, Fayez Hejaili, Majid Alfadhel, Batoul Baz, Bader Almuzzaini, Adel F. Almutairi, Mubarak Abdullah, Francisco J. Quintana, Abdullah Sayyari
Summary: This study aimed to investigate the genetic causes of end-stage renal disease (ESRD) in Saudi kidney disease patients, using a targeted next-generation sequencing gene panel. The results identified several genetic variants associated with ESRD and CKD in this population, including novel variants not previously reported in other populations. Further studies are needed to validate these findings in larger sample sizes and different ethnic groups.
FRONTIERS IN GENETICS
(2022)
Review
Biotechnology & Applied Microbiology
Xinran Wang, Xiaozhou Luo
Summary: Food is crucial for human survival, but traditional agriculture faces challenges in meeting the sustainable environmental development and increasing population's food demand. Synthetic biology, particularly using engineered microbial cell factories, offers great advantages in producing food alternatives and additives, contributing to healthy and sustainable food supply. This review summarizes quantitation methods for cellular biosynthetic precursors, providing guidance for precise pathway engineering.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Oncology
Anisha Luthra, Brooke Mastrogiacomo, Shaleigh A. Smith, Debyani Chakravarty, Nikolaus Schultz, Francisco Sanchez-Vega
Summary: NGS technologies have been widely adopted in cancer research and clinical care in the past decade, enabling patient stratification, biomarker identification, heritable cancer risk assessment, and treatment monitoring. The development of novel algorithms, computational pipelines, and structured knowledge bases has been crucial for downstream data processing and interpretation. Collaborations across institutions have led to the creation of large pooled datasets that offer valuable insights into the genomics of rare cancers.
GENES CHROMOSOMES & CANCER
(2022)
Article
Cell Biology
Maximiliaan Schillebeeckx, Marjut Pihlajoki, Elisabeth Gretzinger, Wei Yang, Franziska Thol, Theresa Hiller, Ann-Kathrin Loebs, Theresa Roehrig, Anja Schrade, Rebecca Cochran, Patrick Y. Jay, Markku Heikinheimo, Robi D. Mitra, David B. Wilson
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2015)
Retraction
Medicine, Research & Experimental
Haiyang Yu, Mykyta Artomov, Sebastian Braehler, M. Christine Stander, Ghaidan Shamsan, Matthew G. Sampson, J. Michael White, Matthias Kretzler, Jeffrey H. Miner, Sanjay Jain, Cheryl A. Winkler, Robi D. Mitra, Jeffrey B. Kopp, Mark J. Daly, Andrey S. Shaw
JOURNAL OF CLINICAL INVESTIGATION
(2016)
Article
Biochemical Research Methods
Gabe Haller, David Alvarado, Kevin McCall, Robi D. Mitra, Matthew B. Dobbs, Christina A. Gurnett
Article
Biochemistry & Molecular Biology
Erin B. Styles, Karen J. Founk, Lee A. Zamparo, Tina L. Sing, Dogus Altintas, Cyril Ribeyre, Virginie Ribaud, Jacques Rougemont, David Mayhew, Michael Costanzo, Matej Usaj, Adrian J. Verster, Elizabeth N. Koch, Daniele Novarina, Marco Graf, Brian Luke, Marco Muzi-Falconi, Chad L. Myers, Robi David Mitra, David Shore, Grant W. Brown, Zhaolei Zhang, Charles Boone, Brenda J. Andrews
Article
Biochemistry & Molecular Biology
Zongtai Qi, Michael Nathaniel Wilkinson, Xuhua Chen, Sumithra Sankararaman, David Mayhew, Robi David Mitra
NUCLEIC ACIDS RESEARCH
(2017)
Article
Genetics & Heredity
Matthew Yen, Zongtai Qi, Xuhua Chen, John A. Cooper, Robi D. Mitra, Michael D. Onken
BMC MEDICAL GENOMICS
(2018)
Article
Multidisciplinary Sciences
Christian A. Shively, Jiayue Liu, Xuhua Chen, Kaiser Loell, Robi D. Mitra
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Yiming Kang, Nikhil R. Patel, Christian Shively, Pamela Samantha Recio, Xuhua Chen, Bernd J. Wranik, Griffin Kim, R. Scott McIsaac, Robi Mitra, Michael R. Brent
Article
Biochemistry & Molecular Biology
Jiayue Liu, Christian A. Shively, Robi D. Mitra
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Alexander J. Cammack, Arnav Moudgil, Jiayang Chen, Michael J. Vasek, Mark Shabsovich, Katherine McCullough, Allen Yen, Tomas Lagunas, Susan E. Maloney, June He, Xuhua Chen, Misha Hooda, Michael N. Wilkinson, Timothy M. Miller, Robi D. Mitra, Joseph D. Dougherty
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemical Research Methods
Christian A. Shively, Fengping Dong, Robi D. Mitra
Summary: Numerous tools for gene expression knockdown have been developed and characterized in the model organism Saccharomyces cerevisiae and extended to facilitate studies in multicellular models. In this study, the researchers systematically evaluated the efficacy of seven constitutive and inducible knockdown strategies using a panel of essential genes. They also created a tagging vector collection for improved strain construction and successfully adapted an improved protein degradation strategy for one-step strain construction in yeast. This work provides a toolbox for endogenous gene expression knockdown and recommendations for perturbing essential genes.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pamela S. Recio, Nikhil J. Mitra, Christian A. Shively, David Song, Grace Jaramillo, Kristine Shady Lewis, Xuhua Chen, Robi D. Mitra
Summary: Gene expression changes are regulated by transcription factors (TFs) that bind to DNA. Existing models of TF function often do not match experimental measurements, indicating unknown biology. In this study, we analyzed a well-studied TF called Gal4 and built a thermodynamic model to describe its binding. We found that the model failed to predict binding in many cases, but experimental observations showed substantial binding. Further investigation revealed a novel mode of binding in which Gal4 binds unexpectedly to DNA sequences with high densities of half sites. This mode of binding was also found in other zinc cluster TFs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Matthew Lalli, Allen Yen, Urvashi Thopte, Fengping Dong, Arnav Moudgil, Xuhua Chen, Jeffrey Milbrandt, Joseph D. Dougherty, Robi D. Mitra
Summary: The calling cards technology using self-reporting transposons allows the identification of DNA-protein interactions through RNA sequencing. By introducing a DNA barcode and additional barcode during reverse transcription, the cost and labor requirements of bulk calling card experiments can be reduced, and simultaneous transcriptome measurement can be achieved. This method is efficient and powerful for inferring gene regulatory networks in a population of cells.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Meeting Abstract
Clinical Neurology
Alexander J. Cammack, Arnav Moudgil, Tomas Lagunas, Michael J. Vasek, Mark Shabsovich, June He, Xuhua Chen, Michael N. Willkinson, Timothy M. Miller, Robi D. Mitra, Joseph D. Dougherty
ANNALS OF NEUROLOGY
(2019)
Article
Cell Biology
Theresa Roehrig, Marjut Pihlajoki, Ricarda Ziegler, Rebecca S. Cochran, Anja Schrade, Maximiliaan Schillebeeckx, Robi D. Mitra, Markku Heikinheimo, David B. Wilson
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2015)