Review
Biochemistry & Molecular Biology
Ludmila Volozonoka, Anna Miskova, Linda Gailite
Summary: This review provides insight into the performance and drawbacks of WGA techniques such as DOP-PCR, MDA, MALBAC, and hybrid techniques in PGT. The advantages of MDA-based solutions for comprehensive genome coverage and PCR-based solutions for uniformity of coverage are highlighted. The choice of WGA technique should take into consideration the influence of MPS parameters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Yinghui Ye, Jieliang Ma, Long Cui, Sijia Lu, Fan Jin
Summary: This study demonstrated that NGS for PGT on day-3 embryos is an effective clinical application, especially for patients with diminished ovarian reserve and limited embryos. The euploid rate for different translocations varied significantly, and double embryo transfer showed higher success rates compared to single embryo transfer.
FRONTIERS IN GENETICS
(2021)
Article
Obstetrics & Gynecology
Songchang Chen, Xuyang Yin, Sijia Zhang, Jun Xia, Ping Liu, Pingyuan Xie, Huijuan Yan, Xinming Liang, Junyu Zhang, Yiyao Chen, Hongjun Fei, Lanlan Zhang, Yuting Hu, Hui Jiang, Ge Lin, Fang Chen, Chenming Xu
Summary: WGS offers a cost-effective and reliable approach for genome-wide haplotyping and PGT for monogenic disorders, aneuploidy, and structural rearrangements without the need for additional family members, showing 100% concordance with traditional PGT methods.
HUMAN REPRODUCTION
(2021)
Article
Medicine, General & Internal
Zhiping Zhang, Lei Zhang, Yaoqin Wang, Xingyu Bi, Lixia Liang, Yuan Yuan, Dan Su, Xueqing Wu
Summary: This study aimed to investigate the effects of different factors on the euploidy of blastocysts undergoing IVF and preimplantation genetic testing (PGT). The study found that maternal age, abnormal parental karyotype, nonfirst cycles, and blastocysts number per cycle <3 were the risk factors for no euploid blastocyst.
Article
Genetics & Heredity
Jia Zhou, Ziying Yang, Jun Sun, Lipei Liu, Xinyao Zhou, Fengxia Liu, Ya Xing, Shuge Cui, Shiyi Xiong, Xiaoyu Liu, Yingjun Yang, Xiuxiu Wei, Gang Zou, Zhonghua Wang, Xing Wei, Yaoshen Wang, Yun Zhang, Saiying Yan, Fengyu Wu, Fanwei Zeng, Jian Wang, Tao Duan, Zhiyu Peng, Luming Sun
Summary: The study aimed to evaluate the utility of whole genome sequencing (WGS) compared with chromosomal microarray (CMA) and whole exome sequencing (WES) in prenatal diagnosis of fetal structural anomalies. Results showed that WGS provided more comprehensive and precise genetic information with a faster turnaround time and less DNA required than CMA plus WES, making it a potential alternative for prenatal diagnosis of fetal structural anomalies.
Article
Endocrinology & Metabolism
Han Yang, Dandan Yang, Qi Zhu, Kaijuan Wang, Chao Zhang, Beili Chen, Weiwei Zou, Yan Hao, Ding Ding, Zhaojuan Yu, Dongmei Ji, Dawei Chen, Yunxia Cao, Huijuan Zou, Zhiguo Zhang
Summary: This study compared the differences between two blastocyst biopsy strategies and analyzed the embryo development, sequencing results, pregnancy outcomes, and offspring health. The results showed that blastocyst biopsy strategy without laser-assisted zona pellucid drilling on day 3 achieves better clinical treatment effects.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Genetics & Heredity
Jesper Eisfeldt, Maria Pettersson, Anna Petri, Daniel Nilsson, Lars Feuk, Anna Lindstrand
Summary: This study reported a healthy female carrying two novel CCRs and characterized these complex rearrangements. The results were validated using multiple cytogenetic methods, revealing the highest number of breakpoint junctions (137) and indicating an association between CCR formation and active gene transcription.
Review
Biology
Anja M. Westram, Rui Faria, Kerstin Johannesson, Roger Butlin, Nick Barton
Summary: Local adaptation and parallel evolution are major topics in evolutionary genomics. Genetic structures that reduce recombination, such as chromosomal inversions, play an important role in local adaptation. However, the contribution of inversions to parallel evolution is still not well understood.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Genetics & Heredity
Francisco de Menezes Cavalcante Sassi, Geize Aparecida Deon, Alexandr Sember, Thomas Liehr, Osvaldo Takeshi Oyakawa, Orlando Moreira Filho, Luiz Antonio Carlos Bertollo, Marcelo Ricardo Vicari, Marcelo de Bello Cioffi
Summary: By using whole chromosome painting probes derived from H. carvalhoi, this study investigated the evolutionary trajectories of synteny blocks involved in the XY1Y2 sex chromosome system in six Harttia species. The results showed distinct evolutionary fates of mapped synteny blocks in different species, indicating elevated karyotype dynamics in Harttia among the three evolutionary clades.
FRONTIERS IN GENETICS
(2023)
Article
Medicine, Research & Experimental
Yidong Chen, Yuan Gao, Jialin Jia, Liang Chang, Ping Liu, Jie Qiao, Fuchou Tang, Lu Wen, Jin Huang
Summary: The discovery of embryonic cell-free DNA in spent embryo culture media has provided hope for noninvasive preimplantation genetic testing. However, the cellular origins of this DNA are not well understood, and methods for detecting maternal DNA contamination are limited. This study used whole-genome DNA methylation sequencing to identify the sources of cell-free DNA in spent embryo culture media, providing insights into noninvasive preimplantation genetic testing.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Review
Genetics & Heredity
Antonio Capalbo, Maurizio Poli, Chaim Jalas, Eric J. Forman, Nathan R. Treff
Summary: The use of aneuploidy testing in IVF cycles is increasing, with almost half of cycles in the US undergoing PGT-A. Evidence shows that embryos diagnosed with uniform whole-chromosome aneuploidy rarely result in live births, while embryos with low-level mosaicism for whole chromosomes have reproductive capabilities similar to euploid embryos. Differentiating between uniform and mosaic aneuploidy is crucial in clinical and research settings for proper management of aneuploid embryos.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Obstetrics & Gynecology
Alessandra Alteri, Greta Chiara Cermisoni, Mirko Pozzoni, Gerarda Gaeta, Paolo Ivo Cavoretto, Paola Vigano
Summary: This review examines the impact of embryo biopsy on obstetric and neonatal outcomes. Limited evidence suggests that embryo biopsy may increase the risk of preterm delivery, low birthweight, and hypertensive disorders of pregnancy. However, more research is needed to fully understand the potential consequences of this procedure and develop alternative non-invasive approaches for preimplantation genetic testing (PGT).
HUMAN REPRODUCTION UPDATE
(2023)
Article
Genetics & Heredity
Alejandra Damian, Gonzalo Nunez-Moreno, Claire Jubin, Alejandra Tamayo, Marta Rodriguez de Alba, Cristina Villaverde, Cedric Fund, Marc Delepine, Aurelie Leduc, Jean Francois Deleuze, Pablo Minguez, Carmen Ayuso, Marta Corton
Summary: In this study, long-read sequencing technology was used to uncover cryptic pathogenic structural variants (SVs) in two unresolved PAX6-negative cases of congenital aniridia. The study highlights the limitations of traditional short-read sequencing in detecting pathogenic SVs in low-complexity regions of the genome and demonstrates the value of long-read sequencing in identifying hidden sources of variation in rare genetic diseases.
Article
Obstetrics & Gynecology
Yunqiao Dong, Dun Liu, Yangyun Zou, Cheng Wan, Chuangqi Chen, Mei Dong, Yuqiang Huang, Cuiyu Huang, Huinan Weng, Xiulan Zhu, Fang Wang, Shujing Jiao, Na Liu, Sijia Lu, Xiqian Zhang, Fenghua Liu
Summary: In this study, a quantitative method, qPCT, was established to detect parental DNA contamination in conventional IVF. It was found that the maternal contamination rate was 0.83% and the risk of paternal contamination was negligible. The clinical study also showed successful pregnancies using vitrified conventional IVF embryos.
REPRODUCTIVE BIOMEDICINE ONLINE
(2023)
Article
Biochemistry & Molecular Biology
Sara Ravagni, Ines Sanchez-Donoso, Irene Jimenez-Blasco, Pedro Andrade, Manel Puigcerver, Ana Chorao Guedes, Raquel Godinho, David Goncalves, Manuel Leitao, Jennifer A. Leonard, Jose Domingo Rodriguez-Teijeiro, Carles Vila
Summary: With the use of various data, we have studied common quails in the Azores archipelago and found that they have formed a unique evolutionary lineage that differs from mainland populations. This uniqueness is the result of either genetic drift or adaptation to local conditions. Our findings show that Azorean quails are a well-differentiated lineage with small size and dark throat pigmentation, and they diverged from mainland quail lineages more than 0.8 million years ago, contrary to the idea of a recent human-mediated arrival. These results reveal the unique and long evolutionary history of the Azorean quails.
Article
Genetics & Heredity
Tamara Jarayseh, Brecht Guillemyn, Hanna De Saffel, Jan Willem Bek, Delfien Syx, Sofie Symoens, Yannick Gansemans, Filip Nieuwerburgh, Sujatha Jagadeesh, Jayarekha Raja, Fransiska Malfait, Paul J. Coucke, Adelbert De Clercq, Andy Willaert
Summary: Bi-allelic mutations in TAPT1 gene lead to a wide range of phenotypes, from severe skeletal and congenital abnormalities to isolated early-onset cataract. A frameshift mutation in the TAPT1 gene was identified in a patient with bilateral early-onset cataract and skeletal abnormalities, expanding the phenotypic spectrum. A zebrafish model with TAPT1 gene knockout exhibited eye malformations, loss of vision, increased photokinetics, and hyperpigmentation, providing insights into the ultrastructural and molecular characteristics of TAPT1 mutations.
Article
Immunology
Kai Ling Liang, Juliette Roels, Marieke Lavaert, Tom Putteman, Lena Boehme, Laurentijn Tilleman, Imke Velghe, Valentina Pegoretti, Inge van de Walle, Stephanie Sontag, Jolien Vandewalle, Bart Vandekerckhove, Georges Leclercq, Pieter Van Vlierberghe, Claude Libert, Filip Van Nieuwerburgh, Roman Fischer, Roland E. Kontermann, Klaus Pfizenmaier, Gina Doody, Martin Zenke, Tom Taghon
Summary: The interaction between thymocytes and thymic stromal cells is crucial for T cell development. This study demonstrates that intrathymic development of dendritic cells (DCs) plays a role in supporting early stages of human T cell development. The transcription factor IRF8 and transmembrane TNF are involved in this process. Selective targeting of TNFR2 has the potential to enhance the generation of T cell precursors for clinical applications.
Article
Environmental Sciences
Xiangrong Chen, Mohamed F. Abdallah, Charlotte Grootaert, Filip Van Nieuwerburgh, Andreja Rajkovic
Summary: This study investigated the combined toxicity of Aflatoxin B1 (AFB1) and fumonisin B1 (FB1) on mitochondrial and glycolytic activity in HepG2 cells. The results showed that the co-exposure, especially at high doses, significantly inhibited mitochondrial respiration. Moreover, RNA transcriptome sequencing revealed differential expression of the p53 signaling pathway and downregulation of genes encoding for Complexes I, II, III, and IV.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Annelies Raes, Eline Wydooghe, Krishna Chaitanya Pavani, Osvaldo Bogado Pascottini, Katleen Van Steendam, Maarten Dhaenens, Annekatrien Boel, Sonia Heras, Bjorn Heindryckx, Luc Peelman, Dieter Deforce, Filip Van Nieuwerburgh, Geert Opsomer, Ann Van Soom, Katrien Smits
Summary: While animal models have shown that culturing embryos in groups improves blastocyst yield and quality, the identity of the responsible embryotrophins remains largely unknown. This study identified cathepsin-L as an important embryotrophin in bovine in vitro embryo production, and demonstrated that supplementation of cathepsin-L significantly improved blastocyst development and quality.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Daniel Angel-Velez, Tim Meese, Mohamed Hedia, Andrea Fernandez-Montoro, Tine De Coster, Osvaldo Bogado Pascottini, Filip Van Nieuwerburgh, Jan Govaere, Ann Van Soom, Krishna Pavani, Katrien Smits
Summary: In the last decade, in vitro embryo production has become an established clinical practice in horses. However, the blastocyst rates from vitrified equine oocytes remain low due to cryopreservation's negative effect on oocyte developmental potential. This study compared the transcriptome profiles of vitrified equine oocytes before and after in vitro maturation. The results showed that vitrification of in vitro matured oocytes had subtle advantages in terms of the mRNA profile, highlighting the potential for further improvements in equine oocyte vitrification efficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Virology
Thomas-Wolf Verdonckt, Anton Bilsen, Filip Van Nieuwerburgh, Loes De Troij, Dulce Santos, Jozef Vanden Broeck
Summary: Insect cell expression systems are used in the medical industry for vaccine development against diseases like COVID-19. The study focuses on the characterization of a specific virus called Bombyx mori latent virus (BmLV) and its pathogenicity. The results demonstrate that a variant of BmLV causes acute infections and strong cytopathic effects in cell lines and animal models. The study also examines the RNAi-based immune response in the cell line and animal models, shedding light on the genomic diversity of BmLV.
Article
Agriculture, Dairy & Animal Science
Evy Beckers, Sofie F. M. Bhatti, Mario Van Poucke, Ingeborgh Polis, Frederic Farnir, Filip Van Nieuwerburgh, Paul Mandigers, Luc Van Ham, Luc Peelman, Bart J. G. Broeckx
Summary: A significant percentage of Dutch partridge dogs suffer from epileptic seizures, but little is known about the genetic cause. This study identified a risk locus for idiopathic epilepsy on chromosome 12 and a variant in the CCDC85A gene that increases the risk of disease in homozygous variant dogs. Further research is needed to determine the usefulness of these findings in breeding decisions.
Article
Agriculture, Dairy & Animal Science
Marielen de Souza, Venessa Eeckhaut, Evy Goossens, Richard Ducatelle, Filip Van Nieuwerburgh, Karl Poulsen, Ana Angelita Sampaio Baptista, Ana Paula Frederico Rodrigues Loureiro Bracarense, Filip Van Immerseel
Summary: Galactomannans in broiler feed can negatively impact zootechnical performance and gut microbiota composition. Mannanase supplementation can restore the gut microbiota and improve performance to normal levels.
Article
Immunology
Leen Hermans, Sofie Denaeghel, Robert J. J. Jansens, Steffi De Pelsmaeker, Filip Van Nieuwerburgh, Dieter Deforce, Everardo Hegewisch-Solloa, Emily M. Mace, Eric Cox, Bert Devriendt, Herman W. Favoreel
Summary: Two subsets of NK cells are found in the pig liver, one resembling human lrNK cells and the other resembling conventional CD8a(high) NK cells in peripheral blood. The transcriptome analysis reveals that CD8a(dim) lrNK cells exhibit an immature and anti-inflammatory phenotype, while the CD8a(high) NK cells in the liver have an intermediate phenotype expressing liver residency-associated transcripts.
FRONTIERS IN IMMUNOLOGY
(2023)
Meeting Abstract
Allergy
Sharon Van Nevel, Tim Meese, Gabriele Holtappels, Natalie De Ruyck, Stijn Vanhee, Nan Zhang, Filip Van Nieuwerburgh, Claus Bachert
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jose Manuel Salvador Lopez, Lea Vidal, Michelle Patricia Adiutama, Filip Van Nieuwerburgh, Dieter Deforce, Jean-Marc Nicaud, Inge Noelle Adrienne Van Bogaert
Summary: Comparative transcriptomics was conducted to identify proteins involved in fatty acid export through the cell wall in an engineered fatty acid secreting Yarrowia lipolytica yeast. The study revealed that the deletion of the faa1 gene led to the accumulation and secretion of free fatty acids (FFAs). By comparing the transcriptome of the mutant with a wildtype-like strain, several upregulated genes were identified, including cell wall proteins and proteins with unknown functions. However, none of these proteins had a clear role in FFA export.
FEMS YEAST RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Eva Gijbels, Kevin De Muynck, Bart Vanderborght, Tim Meese, Filip Van Nieuwerburgh, Aude Vanlander, Frederik Berrevoet, Bart Hendrikx, Anne Hoorens, Hans Van Vlierberghe, Mathieu Vinken, Lindsey Devisscher
Meeting Abstract
Nutrition & Dietetics
B. Boshuizen, L. Mare, C. De Meeus, L. Devisscher, C. Vidal Moreno de Vega, J. De Oliveira, G. Hosotani, Y. Gansemans, T. Meese, F. Van Nieuwerburgh, D. Deforce, C. Delesalle
PROCEEDINGS OF THE NUTRITION SOCIETY
(2023)
Article
Pharmacology & Pharmacy
Koen Deserranno, Laurentijn Tilleman, Kaat Rubben, Dieter Deforce, Filip Van Nieuwerburgh
Summary: Pharmacogenomics (PGx) studies the impact of genomic variation on drug response and allows personalized dosing. Current PGx testing methods cannot identify large structural variants and star-alleles. This study successfully enriched 1,036 PGx-relevant genes using Oxford Nanopore Technologies and demonstrated accurate variant and star-allele calling. It also showed that up to three samples can be multiplexed without significant decrease in variant calling performance.
FRONTIERS IN PHARMACOLOGY
(2023)