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Structural Variation Interpretation in the Genome Sequencing Era: Lessons from Cytogenetics.
Clin Chem
January 2025
Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States.
Background: Structural variation (SV), defined as balanced and unbalanced chromosomal rearrangements >1 kb, is a major contributor to germline and neoplastic disease. Large variants have historically been evaluated by chromosome analysis and now are commonly recognized by chromosomal microarray analysis (CMA). The increasing application of genome sequencing (GS) in the clinic and the relatively high incidence of chromosomal abnormalities in sick newborns and children highlights the need for accurate SV interpretation and reporting.
View Article and Find Full Text PDFA recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum.
Sci Rep
January 2025
Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible and functional foods. In this study, we compared the plastid genomes (plastomes) and 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that the PJ accessions were monophyletic within the genus Peucedanum.
View Article and Find Full Text PDFGenome-wide maps of highly-similar intrachromosomal repeats that can mediate ectopic recombination in three human genome assemblies.
HGG Adv
December 2024
International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México. Electronic address:
Repeated sequences spread throughout the genome play important roles in shaping the structure of chromosomes and facilitating the generation of new genomic variation through structural rearrangements. Several mechanisms of structural variation formation use shared nucleotide similarity between repeated sequences as substrate for ectopic recombination. We performed genome-wide analyses of direct and inverted intrachromosomal repeated sequence pairs with >200bp and >80% sequence identity in three human genome assemblies, GRCh37, GRCh38, and the T2T-CHM13 alternate assembly.
View Article and Find Full Text PDFStructural variant allelic heterogeneity in MECP2 duplication syndrome provides insight into clinical severity and variability of disease expression.
Genome Med
December 2024
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Background: MECP2 Duplication Syndrome, also known as X-linked intellectual developmental disorder Lubs type (MRXSL; MIM: 300260), is a neurodevelopmental disorder caused by copy number gains spanning MECP2. Despite varying genomic rearrangement structures, including duplications and triplications, and a wide range of duplication sizes, no clear correlation exists between DNA rearrangement and clinical features. We had previously demonstrated that up to 38% of MRXSL families are characterized by complex genomic rearrangements (CGRs) of intermediate complexity (2 ≤ copy number variant breakpoints < 5), yet the impact of these genomic structures on regulation of gene expression and phenotypic manifestations have not been investigated.
View Article and Find Full Text PDFRPA and Rad27 limit templated and inverted insertions at DNA breaks.
Nucleic Acids Res
December 2024
Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA.
Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus.
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