Article
Multidisciplinary Sciences
Jonas Schmidt, Sandro Berghaus, Frithjof Blessing, Holger Herbeck, Josef Blessing, Peter Schierack, Stefan Rodiger, Dirk Roggenbuck, Folker Wenzel
Summary: Nanopore sequencing has great potential for clinical diagnostics, but further validation and certification are required.
Article
Biotechnology & Applied Microbiology
Nicholas P. Howard, Michela Troggio, Charles-Eric Durel, Helene Muranty, Caroline Denance, Luca Bianco, John Tillman, Eric van de Weg
Summary: This study assessed the concordance and accuracy of Illumina Infinium and Affymetrix Axiom SNP array data in apple genomes. The majority of the data was found to be compatible, although intense data filtering and curation were required for data integration. This in-depth analysis may provide valuable insights for future work on SNP array data integration and interpretation, as well as for probe/platform development.
Article
Horticulture
Elizabeth Straley, Jen Colcol Marzu, Michael J. Havey
Summary: This study successfully validated onion resistance to Fusarium basal rot through genetic analysis and selective breeding. Quantitative trait loci (QTLs) regulating resistance were identified, and genomic regions associated with resistance on chromosomes 2 and 4 were validated. A QTL that decreased resistance was also discovered.
Article
Biochemistry & Molecular Biology
Katherine Beigel, Alix E. Matthews, Katrin Kellner, Christine Pawlik, Matthew Greenwold, Jon N. Seal
Summary: Recent studies on fungus-gardening ants and their symbiotic fungi have revealed varying degrees of fungal sharing among unrelated ant lineages, challenging the previous assumption of strong concordance between ants and their symbiotic fungi within major clades. Genomic analysis suggests that each ant species tends to exhibit fidelity to its own fungal subclade, supporting a pattern of codivergence between the ants and fungi. This implies that symbiont exchange within clades may be less common than previously thought.
Article
Genetics & Heredity
Xiaoqing Wu, Baojia Huang, Xiaorui Xie, Meiying Cai, Yuqin Chen, Bin Liang, Qingmei Shen, Danhua Guo, Na Lin, Linjuan Su, Liangpu Xu
Summary: This study aimed to evaluate chromosomal abnormalities in twin pregnancies using karyotyping and SNP array analysis. The results showed that aneuploidies were the primary abnormalities in twin pregnancies, with higher detection rates in DCDA pregnancies. Ultrasound abnormalities and advanced maternal age were common indications, while cardiac defects and increased nuchal translucency were common anomalies.
Article
Biochemistry & Molecular Biology
Tingting Hua, Chang Zhang, Yating Fu, Na Qin, Su Liu, Congcong Chen, Linnan Gong, Huimin Ma, Yue Ding, Xiaoxia Wei, Chenying Jin, Chen Jin, Meng Zhu, Erbao Zhang, Juncheng Dai, Hongxia Ma
Summary: N6-methyladenosine (m6A) modification is identified as an important epigenetic mechanism in human cancer development. This study investigates the association between m(6)A-associated single-nucleotide polymorphisms (m(6)A-SNPs) and lung cancer risk. The findings reveal several novel susceptibility loci linked to lung cancer, which may affect cancer development through gene expression and m6A modification levels.
MOLECULAR CARCINOGENESIS
(2023)
Article
Biodiversity Conservation
Nicholas P. Howard, Diego Micheletti, James J. Luby, Charles-Eric Durel, Caroline Denance, Helene Muranty, Matthew Ordidge, Dirk C. Albach
Summary: This study clarified the genetic origin of triploid apple cultivars and resolved the pedigrees of many apple cultivars. The research found that historical triploids are mostly the product of diploid parentage and have limited impact on breeding efforts.
PLANTS PEOPLE PLANET
(2023)
Article
Cell Biology
Huili Xue, Aili Yu, Xuemei Chen, Na Lin, Min Lin, Hailong Huang, Liangpu Xu
Summary: A family with a history of Pelizaeus-Merzbacher disease utilized SNP array technology for prenatal diagnosis, revealing that the male fetus did not have PLP1 gene duplication, unlike the affected boy and the mother. Further analysis showed that the non-duplicated infant is developing normally, confirming the reliability and accuracy of this technology in diagnosing PMD.
Article
Biochemistry & Molecular Biology
Maria Radanova, Mariya Levkova, Galya Mihaylova, Rostislav Manev, Margarita Maneva, Rossen Hadgiev, Nikolay Conev, Ivan Donev
Summary: There is a growing interest in studying single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, as they may be associated with susceptibility, prognosis, and treatment response in colorectal cancer (CRC). These miRNA-SNPs could serve as non-invasive biomarkers for early detection of CRC. However, contradictory findings have been reported when different research groups investigated the same SNP in a gene for a specific miRNA, highlighting the need for more case-control studies involving participants from different ethnic backgrounds. According to our review, three miRNA-SNPs - miR-146a rs2910164, miR-27a rs895819, and miR-608 rs4919510 - appear to be promising prognostic, diagnostic, and predictive biomarkers for CRC.
Article
Genetics & Heredity
Haiwei Wang, Bin Liang, Yan Wang, Hailong Huang, Na Lin, Liangpu Xu
Summary: This retrospective analysis examined the types and characteristics of sex chromosomal abnormalities in 186 fetuses in Fujian Province, China. The study found various abnormalities, such as Turner syndrome, triple X syndrome, Klinefelter syndrome, and XYY syndrome, as well as mosaic variants and large-scale deletions/duplications. The use of single nucleotide polymorphism (SNP) array analysis was shown to be important for prenatal diagnosis of sex chromosomal abnormalities.
FRONTIERS IN GENETICS
(2022)
Review
Plant Sciences
Zheng Ying, Muhammad Awais, Reshmi Akter, Fengjiao Xu, Sul Baik, Daehyo Jung, Deok Chun Yang, Gi-Young Kwak, Wenying You
Summary: Discriminating plant species, cultivars, and landraces is challenging, but SNP markers have proven to be a reliable tool for differentiating Panax ginseng and similar species. This article provides a cost-effective guide for SNP marker analysis in a traditional laboratory setting.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Fisheries
Jiaying Wang, Lingwei Miao, Baohua Chen, Ji Zhao, Qiaozhen Ke, Fei Pu, Tao Zhou, Peng Xu
Summary: To promote genetic selective breeding of large yellow croaker, a liquid single nucleotide polymorphism (SNP) array called NingXin-III was developed. It is based on genotyping by target sequencing (GBTS) technology and the 55 K high-throughput solid chip-based array (NingXin-II SNP array) of large yellow croaker. NingXin-III SNP array contains 98.85% of the loci on NingXin-II SNP array and 1535 new loci, with a total of 54,990 loci distributed on 24 chromosomes. It has high genotyping accuracy, reproducibility, and can replace NingXin-II SNP array completely to support genetic improvement of important economic traits of large yellow croaker.
Article
Cardiac & Cardiovascular Systems
Matthew R. Alexander, Samuel Hank, Bethany L. Dale, Lauren Himmel, Xue Zhong, Charles D. Smart, Daniel J. Fehrenbach, Yuhan Chen, Nitin Prabakaran, Brian Tirado, Megan Centrella, Mingfang Ao, Liping Du, Yu Shyr, Daniel Levy, Meena S. Madhur
Summary: Research suggests that the Trp encoding allele of rs3184504 may be causal for hypertension and renal dysfunction, in part due to the loss of SH2B3-mediated repression of T cell IL-12 signaling leading to enhanced IFNg production.
CIRCULATION RESEARCH
(2022)
Article
Immunology
Romain Coppee, Veronique Sarrasin, Rizwana Zaffaroulah, Azza Bouzayene, Marc Thellier, Harold Noel, Jerome Clain, Sandrine Houze
Summary: This study investigates nosocomial malaria transmissions in French hospitals using genomic analysis. The results demonstrate the effectiveness of genomic analysis in resolving these transmissions despite uncertainties in the mode of contamination. The study highlights the importance of considering nosocomial transmission of life-threatening parasites when universal precautions are not rigorously followed.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Justyna Basak, Danuta Piotrzkowska, Ireneusz Majsterek, Ewa Kucharska
Summary: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system with no cure and unclear etiology. This study aimed to identify SNPs associated with an increased risk of developing MS. The findings suggest that the GG AGO1 rs636832 and AA GEMIN4 rs7813 genotypes are associated with an increased risk of MS.
Article
Oncology
Elsa Arbajian, Jakob Hofvander, Linda Magnusson, Fredrik Mertens
GENES CHROMOSOMES & CANCER
(2020)
Article
Pathology
Jakob Hofvander, Vickie Y. Jo, Christopher D. M. Fletcher, Florian Puls, Uta Flucke, Jenny Nilsson, Linda Magnusson, Fredrik Mertens
Article
Hematology
Minjun Yang, Setareh Safavi, Eleanor L. Woodward, Nicolas Duployez, Linda Olsson-Arvidsson, Jonas Ungerback, Mikael Sigvardsson, Marketa Zaliova, Jan Zuna, Thoas Fioretos, Bertil Johansson, Karolin H. Nord, Kajsa Paulsson
Review
Cell Biology
Henryk. A. Domanski
Article
Pathology
Karim H. Saba, Louise Cornmark, Jakob Hofvander, Linda Magnusson, Jenny Nilsson, Hilda van den Bos, Diana C. J. Spierings, Floris Foijer, Johan Staaf, Otte Brosjo, Vaiyapuri P. Sumathi, Suk Wai Lam, Karoly Szuhai, Judith V. M. G. Bovee, Michal Kovac, Daniel Baumhoer, Emelie Styring, Karolin H. Nord
JOURNAL OF PATHOLOGY CLINICAL RESEARCH
(2020)
Article
Cell Biology
Jan Koster, Iman Ghanei, Henryk A. Domanski
Summary: FNA cytology is a suitable tool for assessing the malignant potential of sampled soft tissue/bone lesions, but is less effective than CNB in defining the correct histopathological entity. A standardized reporting system may enhance the clinical management of patients with soft tissue tumors primarily examined by FNA cytology.
Article
Oncology
Saskia Sydow, Yvonne M. H. Versleijen-Jonkers, Magnus Hansson, Anke E. M. van Erp, Melissa H. S. Hillebrandt-Roeffen, Winette T. A. van Der Graaf, Paul Piccinelli, Pehr Rissler, Uta E. Flucke, Fredrik Mertens
Summary: Desmoplastic small round cell tumor (DSRCT) is a highly aggressive soft tissue tumor primarily affecting children and young adults, with most cases displaying a pathognomonic gene fusion. Copy number alterations were found in all DSRCT patient samples, with common imbalances including gain of chromosomes/chromosome arms 1/1q and 5/5p and loss of 6/6q and 16/16q. Global gene expression analysis revealed a distinct transcriptomic profile with enrichment of genes involved in neural differentiation, and two genes, GJB2 and GAL, showed potential as diagnostic markers at the protein level in DSRCT.
GENES CHROMOSOMES & CANCER
(2021)
Article
Oncology
Shamik Mitra, Saskia Sydow, Linda Magnusson, Paul Piccinelli, Lisa Tornudd, Ingrid Ora, Gustaf Ljungman, Johanna Sandgren, David Gisselsson, Fredrik Mertens
Summary: The ERBB2 gene is frequently amplified and overexpressed in breast cancer, which can be targeted with drugs like trastuzumab. In children, especially in alveolar and embryonal rhabdomyosarcoma, increased expression of ERBB2 can be used as a treatment target.
GENES CHROMOSOMES & CANCER
(2022)
Article
Medicine, Research & Experimental
Jan Koster, Paul Piccinelli, Linda Arvidsson, Fredrik Vult von Steyern, Camila Bedeschi Rego De Mattos, Martin Almquist, Jenny Nilsson, Linda Magnusson, Fredrik Mertens
Summary: Morphologic and immunohistochemical analysis of preoperative core needle biopsies is crucial for the management of soft tissue and bone tumors. The use of single nucleotide polymorphism array analysis can provide diagnostic information about copy number aberrations.
LABORATORY INVESTIGATION
(2022)
Article
Oncology
Natalie Andersson, Karim H. Saba, Linda Magnusson, Jenny Nilsson, Jenny Karlsson, Karolin H. Nord, David Gisselsson
Summary: Chromosomal instability is a common feature in malignant tumors, and previous studies have shown that inactivation of RB1, CDKN2A, and TP53 can contribute to this instability. In this study, the researchers used CRISPR-Cas9 technology to individually knock out these genes in immortalized cells and observed their effects on chromosomal stability over time. The results revealed that RB1 and CDKN2A loss had minimal impact on chromosomal stability, while TP53 loss led to massive chromosomal alterations. These findings suggest that RB1 and CDKN2A alone are not sufficient to cause detectable aneuploid clones, while TP53 inactivation can result in chromosomal instability and evolution.
GENES CHROMOSOMES & CANCER
(2023)
Review
Cell Biology
Bharat Rekhi, Xiaohua Qian, Henryk A. Domanski, Jerzy Klijanienko, Andrew Field
Summary: Fine needle aspiration biopsy (FNAB) is an effective method for evaluating suspicious soft tissue masses, but accurately subtyping primary soft tissue tumors can be difficult. This review discusses the diagnostic challenges in soft tissue cytopathology, including pitfalls and strategies for overcoming these challenges by integrating clinical details, key cytomorphological features, and ancillary techniques.
Editorial Material
Cell Biology
Elwira Bakula-Zalewska, Henryk A. Domanski
Review
Pathology
Henryk A. Domanski
Summary: This article summarizes the cytomorphologic criteria and presents rare and divergent cytological features of small round cell sarcomas (SRCSs). Accurate diagnosis requires careful assessment of clinical presentation, cytological features, immunohistochemical patterns, and molecular alterations. Understanding the complexity of cytological features and being aware of rare findings that differ from established diagnostic criteria are essential for correct diagnosis.
Article
Pathology
Jeffrey M. Cloutier, Gregory W. Charville, Fredrik Mertens, William Sukov, Karen Fritchie, Kyle D. Perry, Mark Edgar, Ross A. Rowsey, Andrew L. Folpe
Summary: Inflammatory leiomyosarcoma (ILMS) and histiocyte-rich rhabdomyoblastic tumor (HRRMT) share similar morphological features and gene expression profiles, with both types of tumors showing indolent behavior and primarily affecting young to middle-aged males in the deep soft tissues of the extremities. The proposal to reclassify ILMS and HRRMT as inflammatory rhabdomyoblastic tumor reflects the relationship between these two rare soft tissue tumors and their distinctive clinical characteristics.
Article
Pathology
Baptiste Ameline, Karim H. Saba, Michal Kovac, Linda Magnusson, Olaf Witt, Stefan Bielack, Michaela Nathrath, Karolin H. Nord, Daniel Baumhoer
JOURNAL OF PATHOLOGY CLINICAL RESEARCH
(2020)