Review
Biochemical Research Methods
Satoko Yoshida, Yee Jia Kee
Summary: Parasitic plants pose a serious agricultural threat, but can also be valuable resources for metabolites. Advances in sequencing technology have provided insights into the evolutionary and molecular mechanisms of plant parasitism, revealing gene losses, horizontal gene transfers, and the importance of mobile signals between parasites and hosts. Transcriptome analyses show shared processes among parasitic species, and functional analysis is beginning to uncover molecular mechanisms in host-parasite interactions.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Behavioral Sciences
Leejee Choi, Joon-Yong An
Summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component. Advances in genomic technologies have enabled researchers to identify genetic variations associated with ASD and to understand the genetic architecture of the disorder. Large-scale genetic analyses, including microarray and next-generation sequencing (NGS), have resulted in successful gene discovery and provided new insights into the neurobiology of ASD.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2021)
Article
Multidisciplinary Sciences
Negar Valizadeh, Hossein Abbasi Holasou, Seyyed Abolghasem Mohammadi, Khalid Mahmood Khawar
Summary: The CTAB method is suitable for extraction of high-quality genomic DNA from Artemisia anuua L., resulting in relatively high purity and clear polymorphic bands.
IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY TRANSACTION A-SCIENCE
(2021)
Article
Entomology
Haiguang Zhang, Wenjun Bu
Summary: Insecta is the most diverse group in the animal kingdom, and COI gene is commonly used for species delimitation. However, high intra-specific genetic variation in insects can lead to false positives in COI-based species delimitation. The threshOpt and localMinima algorithms in the Spider package are recommended for threshold-based species delimitation studies in insects. More comprehensive research is needed on the genetic variation in COI among Insecta, and the abundant COI data in BOLD provides an opportunity for such assessment.
Article
Biochemistry & Molecular Biology
Xenia Keighley, Maiken Hemme Bro-Jorgensen, Hans Ahlgren, Paul Szpak, Marta Maria Ciucani, Fatima Sanchez Barreiro, Lesley Howse, Anne Birgitte Gotfredsen, Aikaterini Glykou, Peter Jordan, Kerstin Liden, Morten Tange Olsen
Summary: The study investigated the factors influencing the preservation of ancient pinniped DNA, finding that the geographic origin of samples, skeletal element types, collagen content, and collection year significantly impact endogenous content and DNA damage. It was discovered that skeletal elements and sample context were the most influential factors in DNA preservation.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Neurosciences
Lennart Frahm, Theodore D. Satterthwaite, Peter T. Fox, Robert Langner, Simon B. Eickhoff
Summary: This study evaluated the performance of the Activation Likelihood Estimation (ALE) meta-analysis algorithm in structural neuroimaging data. The results showed that the sensitivity and specificity of the ALE algorithm in structural data were similar to those observed in functional data. To prevent significant clusters from being driven by single experiments, it is recommended to include at least 23 experiments in a VBM ALE dataset.
Review
Genetics & Heredity
Hidekazu Kato, Hiroki Kimura, Itaru Kushima, Nagahide Takahashi, Branko Aleksic, Norio Ozaki
Summary: Schizophrenia is a complex and chronic psychiatric disorder with a high heritability. Despite the lack of diagnostic tests or biomarkers, genetic research has made significant progress in our understanding of the genetic architecture of schizophrenia, including rare copy number variations (CNVs), rare single-nucleotide variants (SNVs), and common single-nucleotide polymorphisms (SNPs). These genetic variants play crucial roles in the pathogenesis of schizophrenia. New approaches such as CRISPR-based genetics and induced pluripotent stem cell technology can help further study the functional analysis of these variants. These advancements will contribute to the development of pathology-based therapeutics and a better understanding of the pathophysiology of schizophrenia.
JOURNAL OF HUMAN GENETICS
(2023)
Article
Allergy
Katri Suuronen, Katriina Ylinen, Jaakko Heikkila, Erja Makela, Raija Vastapuu, Kristiina Aalto-Korte, Maria Pesonen
Summary: This study chemically analyzed the (meth)acrylate content in 31 gel nail products and 6 acrylic nail products, and compared the results with the information on product labels. The penetration of artificial nail materials through disposable gloves was also tested. The labeling of most artificial nail products was found to be incorrect, and disposable gloves were not effective in protecting against acrylic nail liquids.
CONTACT DERMATITIS
(2023)
Review
Plant Sciences
Hilde Nybom, Gunars Lacis
Summary: Recent national and international projects have focused on large-scale genotyping of vegetatively propagated crops, aiming to identify true-to-type plant material, detect synonyms, investigate genetic diversity, and create sustainable databases for research and breeding. Different DNA markers and next-generation sequencing methods have their advantages and disadvantages, with large-scale phenotyping methods lagging behind but crucial for understanding commercially important traits. Collaborative projects with broad-scale data collection are likely to produce more reliable results in the analysis of gene action and development of robust DNA markers.
Article
Biochemistry & Molecular Biology
Changjun Peng, Dong-Dong Wu, Jin-Long Ren, Zhong-Liang Peng, Zhifei Ma, Wei Wu, Yunyun Lv, Zeng Wang, Cao Deng, Ke Jiang, Christopher L. Parkinson, Yin Qi, Zhi-Yi Zhang, Jia-Tang Li
Summary: By analyzing 14 newly assembled genomes, we investigated the genetic basis of snake phenotypes and conducted functional experiments to understand their morphological characteristics. We identified genes, regulatory elements, and structural variations that have potentially contributed to the evolution of snakes, such as limb loss, elongated body plan, asymmetrical lungs, sensory systems, and digestive adaptations. We also found genes and regulatory elements that might have shaped the evolution of vision, skeletal system and diet in blind snakes, and thermoreception in infrared-sensitive snakes. Our study provides new insights into the evolution and development of snakes and vertebrates.
Article
Genetics & Heredity
Dario Galanti, Daniela Ramos-Cruz, Adam Nunn, Isaac Rodriguez-Arevalo, J. F. Scheepens, Claude Becker, Oliver Bossdorf
Summary: Natural epigenetic variation in Thlaspi arvense is significantly associated with both DNA sequence and environment of origin. Genetic variation is generally a stronger predictor of DNA methylation variation, but the strength of environmental association varies between different sequence contexts. Epigenetic variation may play a role in the short-term climate adaptation of pennycress.
Review
Genetics & Heredity
Masahiro Nakatochi, Itaru Kushima, Norio Ozaki
Summary: Copy number variants (CNVs) are common structural variations, with recent technological advances enabling large-scale genetic studies to reveal associations with diseases, particularly psychiatric disorders. Improved detection methods are expected to provide further insights into the molecular basis of psychiatric disorders and other complex diseases.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Public, Environmental & Occupational Health
Lixian Zhong, Weiwei Chen, Tonghua Wang, Qiuting Zeng, Leizhen Lai, Junlong Lai, Junqin Lin, Shaohui Tang
Summary: An umbrella review of meta-analyses on the association between alcohol consumption and health outcomes found that while there were statistically significant beneficial associations and harmful associations, only a small number of them had high-quality evidence. Further robust and larger prospective studies are needed to confirm these results.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Genetics & Heredity
Urmo Vosa, Annique Claringbould, Harm-Jan Westra, Marc Jan Bonder, Patrick Deelen, Biao Zeng, Holger Kirsten, Ashis Saha, Roman Kreuzhuber, Seyhan Yazar, Harm Brugge, Roy Oelen, Dylan H. de Vries, Monique G. P. van der Wijst, Silva Kasela, Natalia Pervjakova, Isabel Alves, Marie-Julie Fave, Mawusse Agbessi, Mark W. Christiansen, Rick Jansen, Ilkka Seppala, Lin Tong, Alexander Teumer, Katharina Schramm, Gibran Hemani, Joost Verlouw, Hanieh Yaghootkar, Reyhan Sonmez Flitman, Andrew Brown, Viktorija Kukushkina, Anette Kalnapenkis, Sina Rueger, Eleonora Porcu, Jaanika Kronberg, Johannes Kettunen, Bernett Lee, Futao Zhang, Ting Qi, Jose Alquicira Hernandez, Wibowo Arindrarto, Frank Beutner, Julia Dmitrieva, Mahmoud Elansary, Benjamin P. Fairfax, Michel Georges, Bastiaan T. Heijmans, Alex W. Hewitt, Mika Kahonen, Yungil Kim, Julian C. Knight, Peter Kovacs, Knut Krohn, Shuang Li, Markus Loeffler, Urko M. Marigorta, Hailang Mei, Yukihide Momozawa, Martina Mueller-Nurasyid, Matthias Nauck, Michel G. Nivard, Brenda W. J. H. Penninx, Jonathan K. Pritchard, Olli T. Raitakari, Olaf Rotzschke, Eline P. Slagboom, Coen D. A. Stehouwer, Michael Stumvoll, Patrick Sullivan, Peter A. C. 't Hoen, Joachim Thiery, Anke Tonjes, Jenny van Dongen, Maarten van Iterson, Jan H. Veldink, Uwe Voelker, Robert Warmerdam, Cisca Wijmenga, Morris Swertz, Anand Andiappan, Grant W. Montgomery, Samuli Ripatti, Markus Perola, Zoltan Kutalik, Emmanouil Dermitzakis, Sven Bergmann, Timothy Frayling, Joyce van Meurs, Holger Prokisch, Habibul Ahsan, Brandon L. Pierce, Terho Lehtimaki, Dorret Boomsma, Bruce M. Psaty, Sina A. Gharib, Philip Awadalla, Lili Milani, Willem H. Ouwehand, Kate Downes, Oliver Stegle, Alexis Battle, Peter M. Visscher, Jian Yang, Markus Scholz, Joseph Powell, Greg Gibson, Tonu Esko, Lude Franke
Summary: Genetic variants associated with traits primarily affect complex phenotypes through regulatory mechanisms on the transcriptome. Most genes show cis-eQTL effects, while distal trans-eQTL effects have lower replication rates. However, single-cell RNA-seq data prioritize intracellular trans-eQTL effects mediated by transcription factors. Additionally, a subset of genes correlated with polygenic scores for various phenotypes may serve as potential drivers for those traits.
Article
Biochemical Research Methods
Teo Lemane, Rayan Chikhi, Pierre Peterlongo
Summary: Genome wide association studies aim to uncover the connections between genotypes and phenotypes. Recent research suggests the significance of using k-mers instead of single-nucleotide polymorphisms for such experiments. We introduce a tool called kmdiff, which enables faster and more memory-efficient differential k-mer analysis on large sequencing cohorts.
Article
Oncology
Kelly Offermans, Josien C. A. Jenniskens, Colinda C. J. M. Simons, Iryna Samarska, Gregorio E. Fazzi, Jaleesa R. M. van der Meer, Kim M. Smits, Leo J. Schouten, Matty P. Weijenberg, Heike Grabsch, Piet A. van den Brandt
Summary: This study investigated the prognostic value of mutational subgroups based on somatic mutations in RAS, BRAF, PIK3CA, MET, and mismatch repair (MMR) status in colorectal cancer (CRC) patients. The results showed that mutational subgroups were associated with survival differences in CRC patients, while Warburg-subtypes did not provide additional prognostic information within these mutational subgroups.
Article
Oncology
Theodore M. Brasky, Erinn M. Hade, David E. Cohn, Alison M. Newton, Stacey Petruzella, Kelli O'Connell, Kimberly A. Bertrand, Linda S. Cook, Immaculata De Vivo, Mengmeng Du, Jo L. Freudenheim, Christine M. Friedenreich, Marc T. Goodman, Jessica Gorzelitz, Torukiri I. Ibiebele, Vittorio Krogh, Linda M. Liao, Loren Lipworth, Lingeng Lu, Susan McCann, Tracy A. O'Mara, Julie R. Palmer, Jeanette Ponte, Anna Prizment, Harvey Risch, Sven Sandin, Leo J. Schouten, Veronica Wendy Setiawan, Xiao-ou Shu, Britton Trabert, Piet A. van den Brandt, Penelope M. Webb, Nicolas Wentzensen, Lynne R. Wilkens, Alicja Wolk, Herbert Yu, Marian L. Neuhouser
Summary: This study analyzed data from 12 prospective cohort studies and found that higher dietary intake of long-chain omega-3 polyunsaturated fatty acids (LCn3PUFA) may increase the risk of endometrial cancer, especially among specific subgroups characterized by body weight and tumor pathology.
GYNECOLOGIC ONCOLOGY
(2023)
Article
Obstetrics & Gynecology
Olga Tsuiko, Yasmine El Ayeb, Tatjana Jatsenko, Joke Allemeersch, Cindy Melotte, Jia Ding, Sophie Debrock, Karen Peeraer, Arne Vanhie, Anne De Leener, Celine Pirard, Candice Kluyskens, Ellen Denayer, Eric Legius, Joris Robert Vermeesch, Hilde Brems, Eftychia Dimitriadou
Summary: Long-read amplicon sequencing is a simple and cost-effective strategy for preclinical preimplantation genetic testing in couples with a de novo pathogenic variant. This approach allows for the identification of the parental origin of the mutant allele and provides access to universal genome-wide haplotyping-based PGT programs. The success rate of this method is 75%.
HUMAN REPRODUCTION
(2023)
Article
Ethics
Zoe Claesen, Neeltje Crombag, Lidewij Henneman, Joris Robert Vermeesch, Pascal Borry
Summary: In this paper, the authors evaluate the role of the child's right to an open future in setting the scope of non-invasive prenatal testing (NIPT). They find that extending the open future principle to delineate the scope of NIPT is theoretically flawed. However, they suggest that it can be used in counseling for prenatal screening to encourage parents' reflection on the implications of knowing for the sake of knowing on their future children and their relationship with them.
JOURNAL OF BIOETHICAL INQUIRY
(2023)
Article
Oncology
Kelly Offermans, Josien C. A. Jenniskens, Colinda C. J. M. Simons, Iryna Samarska, Gregorio E. Fazzi, Kim M. Smits, Leo J. Schouten, Matty P. Weijenberg, Heike I. Grabsch, Piet A. van den Brandt
Summary: In this study, the authors found that metabolic Warburg-subtypes can predict the survival benefit from adjuvant therapy in colorectal cancer patients. Patients with moderate metabolic Warburg-subtype had a survival benefit from adjuvant therapy, while patients with low metabolic Warburg-subtype did not.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Oncology
Romain Meer, Jeroen van de Pol, Piet A. van den Brandt, Leo J. J. Schouten
Summary: This study examined the association between a Healthy Lifestyle Index score and renal cell cancer risk using data from the Netherlands Cohort Study. The study found a weak, non-statistically significant association between adherence to a healthy lifestyle and a lower risk of renal cell cancer.
Article
Biochemistry & Molecular Biology
Ilse Parijs, Nathalie Brison, Leen Vancoillie, Machteld Baetens, Bettina Blaumeiser, Sebastien Boulanger, Julie Desir, Boyan Dimitrov, Nathalie Fieremans, Katrien Janssens, Sandra Janssens, Axel Marichal, Bjorn Menten, Colombine Meunier, Kim Van Berkel, Ann Van Den Bogaert, Koenraad Devriendt, Kris Van Den Bogaert, Joris Robert Vermeesch
Summary: Maternally inherited 15q11-q13 duplications are associated with more severe neurodevelopmental anomalies, while paternally inherited duplications are normal or associated with milder phenotypes. Our analysis of low coverage genome-wide cell-free DNA sequencing data from pregnant women confirms this difference in impact and recommends appropriate genetic counselling for women with 15q11-q13 duplications identified during non-invasive prenatal screening.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Maria Siermann, Ophelia Valcke, Joris Robert Vermeesch, Taneli Raivio, Olga Tsuiko, Pascal Borry
Summary: A qualitative study was conducted on healthcare professionals' perspectives towards PGT-P. Most professionals believed that it is premature to implement PGT-P due to ethical concerns and presented various considerations including validity, limitations, and potential benefits.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Public, Environmental & Occupational Health
Silvano Gallus, Alessandra Lugo, Chiara Stival, Sonia Cerrai, Luke Clancy, Filippos T. Filippidis, Giuseppe Gorini, Maria Jose Lopez, Angel Lopez-Nicolas, Sabrina Molinaro, Anna Odone, Joan B. Soriano, Olena Tigova, Piet A. van den Brandt, Constantine I. Vardavas, Esteve Fernandez
Summary: According to the survey conducted by the TackSHS project, over 8.3 million adults in 12 European countries use electronic cigarettes. The majority of users are dual users, using both electronic and conventional cigarettes, using electronic cigarettes with nicotine, and using them in smoke-free indoor areas.
JOURNAL OF EPIDEMIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jhih-Rong Lin, Yingjie Zhao, M. Reza Jabalameli, Nha Nguyen, Joydeep Mitra, Ann Swillen, Jacob A. S. Vorstman, Eva W. C. Chow, Marianne van den Bree, Beverly S. Emanuel, Joris R. Vermeesch, Michael J. Owen, Nigel M. Williams, Anne S. Bassett, Donna M. McDonald-McGinn, Raquel E. Gur, Carrie E. Bearden, Bernice E. Morrow, Herbert M. Lachman, Zhengdong D. Zhang
Summary: 22q11.2 deletion is a strong genetic risk factor for schizophrenia. Whole-genome sequencing of schizophrenia cases and controls with this deletion revealed the effects of rare coding variants in modifier genes, contributing to the pathogenesis of schizophrenia. The modifier genes affected synaptic function and developmental disorders and were coexpressed with 22q11.2 genes in specific brain regions.
MOLECULAR PSYCHIATRY
(2023)
Article
Pathology
Bartholomeus G. H. Latten, Bela Kubat, Piet A. van den Brandt, Axel zur Hausen, Leo J. Schouten
Summary: The autopsy rate is declining while major discrepancies exist between autopsies and clinical diagnoses. This study aims to investigate the relationship between the cause of death, a history of cancer, and the autopsy rate. The findings of this study are important in understanding the impact of cancer on autopsies and can help counteract the decline in the medical autopsy.
Article
Oncology
Selena Odeh, Iryna V. Samarska, Andres Matoso, Jeroen A. A. Van De Pol, Marcella M. L. L. Baldewijns, Christina A. A. Hulsbergen-Van De Kaa, Jaleesa Van Der Meer, Guido Roemen, Erik Geelkens, Manon Van Engeland, Axel Zur Hausen, Leo J. Schouten, Kim M. Smits
Summary: The aim of this study was to re-evaluate renal cell carcinoma cases from a large population-based cohort in the Netherlands, using new classifications, in order to identify newly recognized subtypes. The cases were initially evaluated using previous classifications and data on clinicopathological characteristics were obtained. Two urogenital pathologists reviewed digital slides according to new grading and classification systems. No new RCC subtypes were identified in the cases. Restaging and regrading showed the possibility of reporting newer features in an old sample collection.
Letter
Medical Laboratory Technology
Margot van Riel, Yan Zhao, Tatjana Jatsenko, Lore Lannoo, Dirk Timmerman, Joris R. Vermeesch
CLINICAL CHEMISTRY
(2023)
Article
Genetics & Heredity
Yingjie Zhao, Yujue Wang, Lijie Shi, Donna M. McDonald-McGinn, T. Blaine Crowley, Daniel E. McGinn, Oanh T. Tran, Daniella Miller, Jhih-Rong Lin, Elaine Zackai, H. Richard Johnston, Eva W. C. Chow, Jacob A. S. Vorstman, Claudia Vingerhoets, Therese van Amelsvoort, Doron Gothelf, Ann Swillen, Jeroen Breckpot, Joris R. Vermeesch, Stephan Eliez, Maude Schneider, Marianne B. M. van den Bree, Michael J. Owen, Wendy R. Kates, Gabriela M. Repetto, Vandana Shashi, Kelly Schoch, Carrie E. Bearden, M. Cristina Digilio, Marta Unolt, Carolina Putotto, Bruno Marino, Maria Pontillo, Marco Armando, Stefano Vicari, Kathleen Angkustsiri, Linda Campbell, Tiffany Busa, Damian Heine-Suner, Kieran C. Murphy, Declan Murphy, Sixto Garcia-Minaur, Luis Fernandez, Zhengdong D. Zhang, Elizabeth Goldmuntz, Raquel E. Gur, Beverly S. Emanuel, Deyou Zheng, Christian R. Marshall, Anne S. Bassett, Tao Wang, Bernice E. Morrow
Summary: Congenital heart disease (CHD) in patients with 22q11.2 deletion syndrome (22q11.2DS) may be influenced by genetic modifiers in the TBX1 gene network. Chromatin regulatory genes including EP400, KAT6A, KMT2C, KMT2D, NSD1, CHD7, and PHF21A are identified as potential modifiers. These findings suggest shared mechanisms involving the TBX1 gene network in the etiology of CHD.
NPJ GENOMIC MEDICINE
(2023)
