Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Clinical Neurology
Aurelien Perrin, Raul Juntas Morales, Francoise Chapon, Corinne Theze, Delphine Lacourt, Henri Pegeot, Emmanuelle Uro-Coste, Diane Giovannini, Nicolas Leboucq, Martial Mallaret, Emmeline Lagrange, Valerie Rigau, Karen Gaudon, Pascale Richard, Michel Koenig, Corinne Metay, Mireille Cossee
Summary: This study analyzed patients from two distinct families with a novel distal titinopathy phenotype associated with the same CNV in the TTN gene. The CNV reported in this study is the most proximal out-of-frame TTN variant and leads to aberrant splicing transcripts, resulting in frameshift and possibly dominant effects. This data represents a novel phenotype-genotype association and provides hypotheses for its dominant effects.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2021)
Article
Genetics & Heredity
Heming Wu, Qingyan Huang, Xia Zhang, Zhikang Yu, Zhixiong Zhong
Summary: This study identified a high rate of chromosomal abnormalities in fetuses with miscarriage during early and middle pregnancy, with a significantly higher numerical chromosomal abnormality rate in pregnant women aged >=35 compared to <35. The early fetal chromosomal abnormality rate was higher than the middle fetal rate, and there were 168 genes enriched in the VOUS + pCNV regions, associated with 41 functions and 12 pathways.
FRONTIERS IN GENETICS
(2021)
Article
Immunology
Manuela Moraru, Adriana Perez-Portilla, Karima Al-Akioui Sanz, Alfonso Blazquez-Moreno, Antonio Arnaiz-Villena, Hugh T. Reyburn, Carlos Vilches
Summary: Fc gamma receptors (FcγR) are cell-surface glycoproteins that play a role in immune responses. The CNR5 deletion on the FCGR locus can lead to loss and recombination of FCGR genes, potentially affecting immune function. The distribution of FCGR polymorphism shows significant variation in the highlands of Ecuador, with CNR5 deletion being relatively common.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Nora Laseca, Antonio Molina, Mercedes Valera, Alicia Antonini, Sebastian Demyda-Peyras
Summary: This study provides a detailed characterization of CNV regions in the Pura Raza Espanola horse breed, revealing a unique pattern of genomic regions enriched in CNVs and the incidence of CNVs across the entire genome. The study also identifies genes related to olfactory pathways and immune response. The findings contribute to our understanding of CNVs in equines and their impact on genetic and phenotypic variations.
Article
Biochemical Research Methods
Lingxi Chen, Yuhao Qing, Ruikang Li, Chaohui Li, Hechen Li, Xikang Feng, Shuai Cheng Li
Summary: The recent advance of single-cell copy number variation (CNV) analysis is important in addressing intratumor heterogeneity and restoring tumor-evolving trajectories. However, existing tools lack real-time interaction and are hard to reproduce. We present an online platform for real-time interactive visualization of single-cell genomics data to accelerate the understanding of cancer clonal evolution.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Microbiology
Chantal Renau-Minguez, Paula Herrero-Abadia, Paula Ruiz-Rodriguez, Vicente Sentandreu, Eduard Torrents, Alvaro Chiner-Oms, Manuela Torres-Puente, Inaki Comas, Esther Julian, Mireia Coscolla
Summary: This study describes the genome of M. brumae and compares it with other strains. M. brumae is a non-pathogenic rapidly growing mycobacterium with high immunogenicity but lacks virulence-related genes. This work provides important genomic data for studying the therapeutic potential of this bacterium.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Marie Saitou, Naoki Masuda, Omer Gokcumen
Summary: This study developed a new method to identify potentially adaptive structural variants and discovered hundreds of such variants using various analytical approaches. The study also revealed the associations of these variants with genotype frequency, coding sequences, and GWAS traits, and introduced new evolutionary models to explain the complexity of structural variant evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Editorial Material
Multidisciplinary Sciences
Roberto H. Herai, Ryan A. Szeto, Cleber A. Trujillo, Alysson R. Muotri
Summary: Researchers conducted an undisclosed in silico-only whole-exome sequencing analysis of the data, identifying genomic alterations in some clones previously undetected. However, most of these alterations could not be experimentally validated, with only one alteration remaining unconfirmed and having no impact on previous results or data interpretation.
Article
Psychiatry
Camillo Thomas Gualtieri
Summary: The genetic origins of neuropsychiatric disorders such as autism and schizophrenia are complex and characterized by irregular behavior and variable expression. High-resolution genomewide analysis techniques have begun to illuminate the unpredictable behavior of the human genome, revealing a high degree of structural and behavioral variability that is especially relevant to brain development and function. Genomic variability is a key window into the origins of complex diseases, particularly neuropsychiatric disorders and neurodevelopmental disorders. Evolutionary genomic events are over-represented in patients with autism and schizophrenia, suggesting that the special qualities of the human genome that drove evolution might play a role in the development of these disorders.
FRONTIERS IN PSYCHIATRY
(2021)
Article
Genetics & Heredity
Foad J. Rouhani, Xueqing Zou, Petr Danecek, Tauanne Dias Amarante, Gene Koh, Qianxin Wu, Yasin Memari, Richard Durbin, Inigo Martincorena, Andrew R. Bassett, Daniel Gaffney, Serena Nik-Zainal
Summary: The study explores human induced pluripotent stem cells derived from different tissues, finding UV-related damage and mutations in skin fibroblast-derived cells, while blood-derived cells show a high prevalence of acquired mutations.
Article
Biotechnology & Applied Microbiology
Huibin Shi, Taotao Li, Manchun Su, Huihui Wang, Qiao Li, Xia Lang, Youji Ma
Summary: In this study, the distribution characteristics of copy number variations (CNVs) in Tibetan sheep were investigated using whole-genome resequencing. The results showed a large number of CNV events in Tibetan sheep, which were associated with their adaptability and complex traits. Functional enrichment analysis revealed that these CNV regions were related to organ development, neural regulation, immune regulation, digestion, and metabolism. In addition, some CNV regions overlapped with quantitative trait loci (QTLs) associated with body weight and growth traits in sheep. Furthermore, significant differences were observed between different breeds, indicating that CNVs may play an important role in population differences in sheep.
Article
Biochemistry & Molecular Biology
David Porubsky, Wolfram Hoeps, Hufsah Ashraf, PingHsun Hsieh, Bernardo Rodriguez-Martin, Feyza Yilmaz, Jana Ebler, Pille Hallast, Flavia Angela Maria Maggiolini, William T. Harvey, Barbara Henning, Peter A. Audano, David S. Gordon, Peter Ebert, Patrick Hasenfeld, Eva Benito, Qihui Zhu, Charles Lee, Francesca Antonacci, Matthias Steinrucken, Christine R. Beck, Ashley D. Sanders, Tobias Marschall, Evan E. Eichler, Jan O. Korbel
Summary: Unlike copy number variants, inversions are a less studied form of genetic variation. Through the integration of multiple genomic technologies, researchers have discovered 729 inversions in 41 human genomes. The majority of these inversions are formed through twin-priming during L1 retrotransposition. It is found that inversions have an excess of common variants and a high percentage of them are flanked by segmental duplications or retrotransposons. Additionally, researchers have identified 40 recurrent inversions, accounting for 0.6% of the genome, which exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. Recurrent inversions lead to an increase in mutability in the population and predispose specific haplotypes to disease-causing copy number variants.
Article
Biochemistry & Molecular Biology
David R. Porubsky, Mitchell T. Vollger, William N. Harvey, Allison Rozanski, Peter Ebert, Glenn Hickey, Patrick D. Hasenfeld, Ashley Sanders, Catherine O. Stober, Jan Korbel, Benedict E. Paten, Tobias Marschall, Evan Eichler
Summary: There has been significant progress in phased genome assembly by combining long-read data with parental information or linked-read data. However, the typical phased genome assembly still has over 140 gaps. A detailed analysis of 182 haploid assemblies reveals that the majority of assembly gaps cluster near large and identical repeats, resulting in disrupted protein-coding genes. Misorientations and alignment discontinuities are also identified, highlighting the need for algorithmic development and pangenome representation.
Article
Biochemistry & Molecular Biology
Hong Xue, Zhenggang Wu, Xi Long, Ata Ullah, Si Chen, Wai-Kin Mat, Peng Sun, Ming-Zhou Gao, Jie-Qiong Wang, Hai-Jun Wang, Xia Li, Wen-Jun Sun, Ming-Qi Qiao
Summary: The study analyzed CNVs from genomic sequencing data to classify PMDD patient genomes into D and V groups, correlated with depression and invasion clinical types. The application of diagnostic CNV features selected by machine learning enabled efficient classification and molecular diagnosis of CNVs.
JOURNAL OF GENETICS AND GENOMICS
(2021)