Children’s Nutrition Research Center Staff Publications
Language
English
Publication Date
10-30-2023
Journal
Genome Biology
DOI
10.1186/s13059-023-03081-x
PMID
37904244
PMCID
PMC10614391
PubMedCentral® Posted Date
10-30-2023
PubMedCentral® Full Text Version
Post-print
Abstract
Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method - multiple genetic abnormality sequencing (MGA-Seq) - to simultaneously detect structural variation, copy number variation, single-nucleotide polymorphism, homogeneously staining regions, and extrachromosomal DNA (ecDNA) from a single tube. MGA-Seq directly sequences proximity-ligated genomic fragments, yielding a dataset with concurrent genome three-dimensional and whole-genome sequencing information, enabling approximate localization of genomic structural variations and facilitating breakpoint identification. Additionally, by utilizing MGA-Seq, we map focal amplification and oncogene coamplification, thus facilitating the exploration of ecDNA's transcriptional regulatory function.
Keywords
DNA Copy Number Variations, Oncogenes, Genomics, Gene Expression Regulation, DNA
Published Open-Access
yes
Recommended Citation
Lin, Da; Zou, Yanyan; Li, Xinyu; et al., "Mga-Seq: Robust Identification of Extrachromosomal DNA and Genetic Variants Using Multiple Genetic Abnormality Sequencing" (2023). Children’s Nutrition Research Center Staff Publications. 309.
https://digitalcommons.library.tmc.edu/staff_pub/309
Included in
Biochemical Phenomena, Metabolism, and Nutrition Commons, Dietetics and Clinical Nutrition Commons, Endocrinology, Diabetes, and Metabolism Commons, Nutrition Commons