Editorial Material
Medicine, General & Internal
Georgeta Cardos, Nicolae Gica, Corina Gica, Anca Maria Panaitescu, Mariana Predescu, Gheorghe Peltecu, Florina Mihaela Nedelea
Summary: MCA, using DNA microarray technology, is a valuable method for diagnosing pathogenic genomic imbalances in patients with MCM, DD/ID, and ASD, with a higher resolution than the traditional G-banded karyotyping.
Review
Biochemistry & Molecular Biology
Yajie Tong, Shuqing Zhang, Suzette Riddle, Rui Song, Dongmei Yue
Summary: Circular RNA (circRNA) is a newly discovered noncoding RNA that plays important roles in gene regulation and as biomarkers for clinical disorders. It is involved in maternal-fetus risk factors and may contribute to the development of cardiopulmonary disorders. Despite being a recent area of research, some studies have already revealed the expression patterns and biological functions of circRNAs.
Article
Pathology
Ourania Parra, Joel A. Lefferts, Laura J. Tafe, Alejandro A. Gru, Konstantinos Linos
Summary: In the classification of skin tumors, melanomas and precursor lesions are divided into nine pathways based on clinical, histomorphologic, molecular, and genetic characteristics. Cross-reactivity between HRAS and NRAS proteins can create diagnostic pitfalls in assessing lesions with spitzoid characteristics.
Article
Genetics & Heredity
Peng Huang, Yueyun Lan, Hong Zhou, Luye Lin, Jinhui Shu, Caizhu Wang, Xin Zhao, Lifang Liang, Sheng He, Jingfei Mou, Xiaofei Zhang, Qingming Qiu, Hongwei Wei
Summary: This study evaluated the effectiveness of different detection technologies applied to pre-implantation genetic testing for monogenic disorders (PGT-M) through a retrospective analysis of clinical detection data. The study found that SNP array and NGS are more suitable choices compared to Gap-PCR for detecting deletional mutations. However, no significant difference was observed when detecting point mutations using any of the methods. The study also proposed a multi-technology comprehensive application scheme to improve the detection efficiency and reliability of PGT-M.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2023)
Article
Agronomy
Chon-Sik Kang, Young-Jun Mo, Kyeong-Min Kim, Kyeong-Hoon Kim, Jae-Buhm Chun, Chul-Soo Park, Seong-Woo Cho
Summary: This study identified several QTLs affecting yield potential in wheat by using a recombinant inbred line population derived from Korean wheat cultivars. Multiple stable QTLs were detected in at least two environments, including those influencing spike length, tiller number, and length of center rachis. Taejoong contributed significantly to the spike length QTLs.
Article
Agronomy
Yikun Zhao, Bin Jiang, Yongxue Huo, Hongmei Yi, Hongli Tian, Haotian Wu, Rui Wang, Jiuran Zhao, Fengge Wang
Summary: The PSNPdms is a simple yet efficient tool for plant molecular research, providing comprehensive technical support for various fields such as crop breeding and genetic analysis. It offers effective data quality control through multiple dimensions and features a simple laboratory management structure.
Article
Biochemical Research Methods
Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S. Vo
Summary: Despite the advancement of sequencing technology, SNP arrays remain the most cost-effective genotyping solution for large-scale genomic research. This study introduces a novel method called LmTag for tag SNP selection, which improves imputation performance and prioritizes highly functional SNP markers. It is particularly suitable for under-represented populations and non-model species in developing countries.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Feifei Ma, Yunfeng Xu, Ruifang Wang, Yiping Tong, Aimin Zhang, Dongcheng Liu, Diaoguo An
Summary: In this study, a high-density genetic map was constructed using the Wheat 660K SNP array, and a total of 12 stable QTLs related to yield were identified. These QTLs explained up to 34.7% of the phenotypic variation in at least three environments. Some of the validated QTLs, such as QTkw-1B.2, QPh-2D.1 (QSl-2D.2/QScn-2D.1), QPh-4B.1, and QTss-7A.3, could be novel QTLs. These findings provide important information for further breeding programs and marker-assisted selection in wheat.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
S. P. Dixit, A. K. Bhatia, Indrajit Ganguly, Sanjeev Singh, Soumya Dash, Anurodh Sharma, N. Anandkumar, A. K. Dang, S. Jayakumar
Summary: This study investigated the genomic diversity and relationships among seven different cattle breeds, showing shared ancestry and recent intermingling between breeds. Selection signatures revealed significant genetic differences between populations, with certain genes potentially affecting production traits and morphological characteristics in cattle. The presence of specific genes, such as HMGA2, may explain variations in stature among different breeds.
SCIENTIFIC REPORTS
(2021)
Review
Obstetrics & Gynecology
Vandana Kamath, Mary Purna Chacko, Richard Kirubakaran, Mariano Mascarenhas, Mohan S. Kamath
Summary: This study evaluated the incremental yield and diagnostic accuracy of SNP array compared to karyotype analysis in detecting chromosomal abnormalities for prenatal diagnosis. The results showed that SNP array had a higher incremental yield and accuracy compared to karyotype analysis. When used as a stand-alone test, SNP array performed favorably in prenatal diagnosis compared to SNP array combined with karyotype analysis.
EUROPEAN JOURNAL OF OBSTETRICS & GYNECOLOGY AND REPRODUCTIVE BIOLOGY
(2022)
Article
Plant Sciences
Ruidong Sun, Shijin He, Yuwei Qi, Yimeng Li, Xiaohang Zhou, Ying Liu, Xihang Liu, Mingyang Ding, Xiangling Lv, Fenghai Li
Summary: Tassel branch number is an important agronomic trait associated with maize kernels and yield. In this study, we identified candidate genes and quantitative trait loci associated with tassel development by analyzing samples from different growth stages. We also found differential gene expression and differences in phytohormone content between different maize lines. These findings provide theoretical insights into the mechanism of tassel branch development in maize.
FRONTIERS IN PLANT SCIENCE
(2023)
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
Genetics & Heredity
Liang-Liang Fan, Yue Sheng, Chen-Yu Wang, Ya-Li Li, Ji-Shi Liu
Summary: 7q terminal deletion syndrome is a rare condition characterized by multiple congenital malformations such as abnormal brain and facial structures, developmental delay, and intellectual disability. A rare case of a Chinese patient with this syndrome was identified, presenting with both brain structure abnormalities and cerebellar sulcus widening.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Gagandeep Singh, Niraj Singh, Ranjith Kumar Ellur, Alexander Balamurugan, G. Prakash, Rajeev Rathour, Kalyan Kumar Mondal, Prolay Kumar Bhowmick, S. Gopala Krishnan, Mariappan Nagarajan, Rakesh Seth, K. K. Vinod, Varsha Singh, Haritha Bollinedi, Ashok Kumar Singh
Summary: Pusa Basmati 1509 (PB1509) is a significant variety of Basmati rice that generates foreign exchange. However, it is vulnerable to bacterial blight and blast. To overcome this, resistance genes were incorporated into PB1509 using different donor parents. Near isogenic lines (NILs) were developed with a genomic similarity ranging from 97.38% to 98.92%. The best-performing individuals were identified and intercrossing led to the generation of improved varieties with comparable agronomy, grain, and cooking quality parameters to PB1509. Cultivating these improved varieties can reduce cultivation costs, decrease pesticide use, and increase productivity while ensuring consumer safety.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
C. Penaloza, T. Manousaki, R. Franch, A. Tsakogiannis, A. K. Sonesson, M. L. Aslam, F. Allal, L. Bargelloni, R. D. Houston, C. S. Tsigenopoulos
Summary: SNP arrays are powerful tools for studying the genetic basis of complex traits in European seabass and gilthead seabream, showing high conversion rates and repeatability. These arrays enable efficient genotyping and exploration of population structure and haplotype sharing in diverse fish populations.
Article
Hematology
Artem Kalinichenko, Giovanna Perinetti Casoni, Loic Dupre, Luca Trotta, Jakob Huemer, Donatella Galgano, Yolla German, Ben Haladik, Julia Pazmandi, Marini Thian, Ozlem Yuce Petronczki, Samuel C. Chiang, Mervi Taskinen, Anne Hekkala, Saila Kauppila, Outi Lindgren, Terhi Tapiainen, Michael J. Kraakman, Kim Vettenranta, Alexis J. Lomakin, Janna Saarela, Mikko R. J. Seppanen, Yenan T. Bryceson, Kaan Boztug
Summary: This study identifies RhoG as a novel essential regulator in aiding the retention of cytotoxic granules near the plasma membrane, facilitating their release for the elimination of infected and malignant cells. The interaction between RhoG and Munc13-4 is crucial for the docking of cytotoxic granules to the plasma membrane and subsequent membrane fusion, shedding light on the molecular pathomechanism behind genetically determined forms of hemophagocytic lymphohistiocytosis.
Article
Allergy
Meri Kaustio, Naemeh Nayebzadeh, Reetta Hinttala, Terhi Tapiainen, Pirjo Astrom, Katariina Mamia, Nora Pernaa, Johanna Lehtonen, Virpi Glumoff, Elisa Rahikkala, Minna Honkila, Paivi Olsen, Antti Hassinen, Minttu Polso, Nashat Al Sukaiti, Jalila Al Shekaili, Mahmood Al Kindi, Nadia Al Hashmi, Henrikki Almusa, Daria Bulanova, Emma Haapaniemi, Pu Chen, Maria Suo-Palosaari, Paivi Vieira, Hannu Tuominen, Hannaleena Kokkonen, Nabil Al Macki, Huda Al Habsi, Tuija Lopponen, Heikki Rantala, Vilja Pietiainen, Shen-Ying Zhang, Marjo Renko, Timo Hautala, Tariq Al Farsi, Johanna Uusimaa, Janna Saarela
Summary: This study delves into the disease mechanisms associated with loss of the DIAPH1 gene in SCBMS patients, revealing immune deficiency, defective cytoskeletal organization, and mitochondrial dysfunction as key factors. The findings suggest a complex interplay of genetic and cellular pathways contributing to the pathology of SCBMS.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2021)
Article
Dermatology
L. Harjama, V. Karvonen, K. Kettunen, O. Elomaa, E. Einarsdottir, H. Heikkila, S. Kivirikko, P. Ellonen, J. Saarela, A. Ranki, J. Kere, K. Hannula-Jouppi
Summary: Hereditary palmoplantar keratodermas (PPK) is a group of rare skin disorders characterized by epidermal hyperkeratosis of the palms and soles, with mutations in at least 69 genes implicated. In a cohort of 64 patients, pathogenic mutations were identified in five genes: AQP5, AAGAB, KRT9, SERPINB7, and SLURP1, with diffuse PPK being the most common presentation.
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2021)
Article
Clinical Neurology
Henna Jonsson, Mikko Lehto, Sampsa Vanhatalo, Eija Gaily, Tarja Linnankivi
Summary: This study investigated the prevalence of vigabatrin-attributed visual field defect (VAVFD) in infantile spasms and the utility of optical coherence tomography (OCT) in detecting vigabatrin-related damage. The study found that the overall prevalence of VAVFD is lower after exposure in infancy compared to adulthood, and the risk increases with longer treatment duration. OCT showed concomitant attenuated RNFL in some children with VAVFD. Further studies should aim to identify infants particularly susceptible to VAVFD and clarify the role of OCT.
DEVELOPMENTAL MEDICINE AND CHILD NEUROLOGY
(2022)
Article
Oncology
Maarit A. Laaksonen, Robert J. MacInnis, Karen Canfell, Jonathan E. Shaw, Dianna J. Magliano, Emily Banks, Graham G. Giles, Julie E. Byles, Tiffany K. Gill, Paul Mitchell, Vasant Hirani, Robert G. Cumming, Claire M. Vajdic
Summary: Thyroid cancer burden in the future is significantly influenced by overweight and obesity, with obesity having a more pronounced effect, particularly in men. If current obese individuals were to lose weight, nearly 10% of thyroid cancer cases could be avoided, and factors such as alcohol consumption and marital status are also associated with the burden.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Oncology
Disha Malani, Ashwini Kumar, Oscar Bruck, Mika Kontro, Bhagwan Yadav, Monica Hellesoy, Heikki Kuusanmaki, Olli Dufva, Matti Kankainen, Samuli Eldfors, Swapnil Potdar, Jani Saarela, Laura Turunen, Alun Parsons, Imre Vastrik, Katja Kivinen, Janna Saarela, Riikka Raty, Minna Lehto, Maija Wolf, Bjorn Tore Gjertsen, Satu Mustjoki, Tero Aittokallio, Krister Wennerberg, Caroline A. Heckman, Olli Kallioniemi, Kimmo Porkka
Summary: Functional precision medicine tumor board integrates clinical, molecular, and functional data to guide treatment decisions for patients with acute myeloid leukemia. A high percentage of patients have actionable drugs identified, with a significant response rate to individually tailored therapies. Integration of data across patients enables the identification of drug response biomarkers for continuous improvement in personalized cancer medicine.
Meeting Abstract
Oncology
R. Nousiainen, K. Eloranta, A. Hassinen, J. Saarela, S. Cairo, V. Pietiainen, M. Heikinheimo, M. Pihlajoki
ANNALS OF ONCOLOGY
(2022)
Article
Dermatology
V Karvonen, L. Harjama, K. Helio, K. Kettunen, O. Elomaa, J. W. Koskenvuo, J. Kere, S. Weckstrom, M. Holmstrom, J. Saarela, A. Ranki, T. Helio, K. Hannula-Jouppi
Summary: This study reports a case of focal PPK with concurrent cardiomyopathy and arrhythmias caused by a mutation in the DSP gene. The mutation was found in 9 affected family members and had no impact on unaffected members. The dermatological findings preceded the cardiac symptoms, which varied in onset and presentation.
JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY
(2022)
Article
Oncology
Marko Lukic, Idlir Licaj, Maarit A. Laaksonen, Elisabete Weiderpass, Kristin B. Borch, Charlotta Rylander
Summary: This study assessed the burden of colon cancer in Norwegian women and identified modifiable risk factors associated with the disease. The findings indicate that a significant proportion of colon cancer cases among women in Norway can be attributed to modifiable risk factors, highlighting the potential of adopting a healthy lifestyle for prevention.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Oncology
Maarit A. Laaksonen, Siqi E. Li, Karen J. Canfell, Robert J. E. MacInnis, Graham G. K. Giles, Emily Banks, Julie L. G. Byles, Dianna J. Magliano, Jonathan E. Shaw, Tiffany K. Gill, Vasant Hirani, Robert G. W. Cumming, Paul Mitchell, Michelle M. Bonello, Claire M. Vajdic, Barbara-Ann Adelstein, Anne W. Taylor, Kay Price
Summary: This study assessed the individual and joint contribution of contemporary factors to the future burden of oesophageal and stomach cancers in Australia, and found that smoking is the leading preventable cause for oesophageal cancers and overweight/obesity is the main cause for stomach cancers.
BRITISH JOURNAL OF CANCER
(2023)
Article
Immunology
Elina A. Tuovinen, Outi Kuismin, Leila Soikkonen, Timi Martelius, Meri Kaustio, Sari Hamalainen, Hanna Viskari, Jaana Syrjanen, Ulla Wartiovaara-Kautto, Kari K. Eklund, Janna Saarela, Markku Varjosalo, Juha Kere, Timo Hautala, Mikko R. J. Seppanen
Summary: The NF-κB family of transcription factors is important in cellular signaling pathways, and NFKB1 variants have been associated with CVID and immunodeficiency. However, the penetrance and prevalence of CVID are relatively low, while inflammatory manifestations are more common.
CLINICAL IMMUNOLOGY
(2023)
Article
Immunology
Wenny Santaniemi, Pirjo Astrom, Virpi Glumoff, Nora Pernaa, Ella-Noora Tallgren, Sanna Palosaari, Antti Nissinen, Meri Kaustio, Outi Kuismin, Janna Saarela, Katariina Nurmi, Kari K. Eklund, Mikko R. J. Seppanen, Timo Hautala
Summary: In this study, the impact of a heterozygous NFKB1 c.C936T/p.R157X LOF variant on immunity in sterile fasciitis patients and their family members was explored. The variant resulted in reduced p50 or p105 protein levels and elevated IL-1 beta and IL-8 levels, potentially contributing to the high neutrophil counts observed during fasciitis episodes. The variant also led to reduced phosphorylation of p65/RelA in neutrophils, suggesting defective activation of canonical NF-kappa B, and compromised oxidative burst following activation of NF-kappa B-dependent mechanisms.
JOURNAL OF CLINICAL IMMUNOLOGY
(2023)
Article
Medicine, General & Internal
Pui Y. Lee, Brad A. Davidson, Roshini S. Abraham, Blanche Alter, Juan I. Arostegui, Katherine Bell, Alexandre Belot, Jenna R. E. Bergerson, Timothy J. Bernard, Paul A. Brogan, Yackov Berkun, Natalie T. Deuitch, Dimana Dimitrova, Sophie A. Georgin-Lavialle, Marco Gattorno, Bodo Grimbacher, Hasan Hashem, Michael S. Hershfield, Rebecca N. Ichord, Kazushi Izawa, Jennifer A. Kanakry, Raju P. Khubchandani, Femke C. C. Klouwer, Evan A. Luton, Ada W. Man, Isabelle Meyts, Joris M. Van Montfrans, Seza Ozen, Janna Saarela, Gustavo C. Santo, Aman Sharma, Ariane Soldatos, Rachel Sparks, Troy R. Torgerson, Ignacio Leandro Uriarte, Taryn A. B. Youngstein, Qing Zhou, Ivona Aksentijevich, Daniel L. Kastner, Eugene P. Chambers, Amanda K. Ombrello
Summary: Deficiency of adenosine deaminase 2 (DADA2) is a recessively inherited disease characterized by systemic vasculitis, early-onset stroke, bone marrow failure, and/or immunodeficiency affecting both children and adults. This study provides consensus statements for the evaluation and management of DADA2, a potentially fatal disease that requires early diagnosis and treatment.
Article
Multidisciplinary Sciences
Adil Harroud, Pernilla J. Stridh, Jacob H. McCauley, Janna Saarela, Aletta M. R. van den Bosch, Hendrik Engelenburg, Ashley Beecham, Lars Alfredsson, Katayoun Alikhani, Lilyana Amezcua, Till F. M. Andlauer, Maria Ban, Lisa Barcellos, Nadia Barizzone, Tone Berge, Achim Berthele, Stefan Bittner, Steffan Bos, Farren B. S. Briggs, Stacy Caillier, Peter Calabresi, Domenico Caputo, David Carmona-Burgos, Paola Cavalla, Elisabeth Celius, Gabriel Cerono, Angel Chinea, Tanuja Chitnis, Ferdinando Clarelli, Manuel Comabella, Giancarlo Comi, Chris Cotsapas, Bruce C. A. Cree, Sandra D'Alfonso, Efthimios Dardiotis, Philip De Jager, Silvia Delgado, Benedicte Dubois, Sinah Engel, Federica Esposito, Marzena Fabis-Pedrini, Massimo Filippi, Kathryn Fitzgerald, Christiane Gasperi, Lissette Gomez, Refujia Gomez, Georgios Hadjigeorgiou, Joerg Hamann, Friederike Held, Roland Henry, Jan Hillert, Jesse Huang, Inge Huitinga, Talat Islam, Noriko Isobe, Maja Jagodic, Allan L. Kermode, Michael Khalil, Trevor Kilpatrick, Ioanna Konidari, Karim Kreft, Jeannette Lechner-Scott, Maurizio Leone, Felix Luessi, Sunny Malhotra, Ali Manouchehrinia, Clara Manrique, Filippo Martinelli-Boneschi, Andrea Martinez, Viviana Martinez-Maldonado, Elisabetta Mascia, Luanne Metz, Luciana Midaglia, Xavier Montalban, Jorge Oksenberg, Tomas Olsson, Annette Oturai, Kimmo Paakkonen, Grant P. Parnell, Nikolaos Patsopoulos, Margaret Pericak-Vance, Fredrik Piehl, Justin Rubio, Adam Santaniello, Silvia Santoro, Catherine Schaefer, Finn Sellebjerg, Hengameh Shams, Klementy Shchetynsky, Claudia Silva, Vasileios Siokas, Helle Sondergaard, Melissa Sorosina, Bruce Taylor, Marijne Vandebergh, Elena Vasileiou, Domizia Vecchio, Margarete Voortman, Howard Weiner, Dennis Wever, V. Wee Yong, David Hafler, Graeme Stewart, Alastair Compston, Frauke Zipp, Hanne Harbo, Bernhard Hemmer, An Goris, Joost Smolders, Stephen Hauser, Ingrid Kockum, Stephen Sawcer, Sergio Baranzini, Ingileif Jonsdottir, Yolanda Blanco, Sara Llufriu, Lohith Madireddy, Albert Saiz, Pablo Villoslada, Kari Stefansson, Hanne F. Harbo, Bernhard Hemmer, An Goris, Ingrid Kockum, Stephen J. Sawcer, Sergio E. Baranzini
Summary: Multiple sclerosis (MS) is an autoimmune disease that affects the central nervous system (CNS) and results in significant neurodegeneration. A genome-wide association study identified a significant association between the rs10191329 polymorphism in the DYSF-ZNF638 locus and MS severity. This polymorphism was also associated with earlier need for a walking aid and increased brain pathology. Another polymorphism in the DNM3-PIGC locus showed suggestive association with MS, and there was significant heritability enrichment in CNS tissues. Mendelian randomization analyses suggested a potential protective effect of higher educational attainment in MS.
Review
Clinical Neurology
An Goris, Marijne Vandebergh, Jacob L. McCauley, Janna Saarela, Chris Cotsapas
Summary: Large-scale mapping studies have identified 236 independent genetic variants associated with an increased risk of multiple sclerosis, providing crucial biological insights into the disease's causes and mechanisms. These findings have important implications for understanding the epidemiology of multiple sclerosis and guiding risk assessment and prognosis.