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| http://dx.doi.org/10.1212/NXG.0000000000000642 | DOI Listing |
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Long-read genome sequencing resolves complex genomic rearrangements in rare genetic syndromes.
NPJ Genom Med
December 2024
The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
Long-read sequencing can often overcome the deficiencies in routine microarray or short-read technologies in detecting complex genomic rearrangements. Here we used Pacific Biosciences circular consensus sequencing to resolve complex rearrangements in two patients with rare genetic anomalies. Copy number variants (CNVs) identified by clinical microarray -chr8p deletion and chr8q duplication in patient 1, and interstitial deletions of chr18q in patient 2-were suggestive of underlying rearrangements.
View Article and Find Full Text PDFThe QTL and Candidate Genes Regulating the Early Tillering Vigor Traits of Late-Season Rice in Double-Cropping Systems.
Int J Mol Sci
January 2024
Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of China, Nanchang 330045, China.
Rice effective panicle is a major trait for grain yield and is affected by both the genetic tiller numbers and the early tillering vigor (ETV) traits to survive environmental adversities. The mechanism behind tiller bud formation has been well described, while the genes and the molecular mechanism underlying rice-regulating ETV traits are unclear. In this study, the candidate genes in regulating ETV traits have been sought by quantitative trait locus (QTL) mapping and bulk-segregation analysis by resequencing method (BSA-seq) conjoint analysis using rice backcross inbred line (BIL) populations, which were cultivated as late-season rice of double-cropping rice systems.
View Article and Find Full Text PDFHigh-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification.
HGG Adv
January 2023
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
Article Synopsis
- Phasing of heterozygous alleles is essential for interpreting the effects of genetic variations related to cystic fibrosis (CF), and researchers sequenced 477 CF individuals to construct haplotypes using linked-read sequencing.
- The resulting haplotypes are visualized in an interactive web app called CFTbaRcodes, allowing for exploration of complex CF gene variations.
- Fine-mapping revealed that a specific 20-kb deletion and a missense variant are linked to an increased risk of CF-related meconium ileus and pancreatic issues, providing insights into the genetic mechanisms involved in both CF and non-CF pancreatitis.
The genotype and phenotype of chromosome 18p deletion syndrome: Case series.
Medicine (Baltimore)
May 2021
Center of Medical Genetics, Northwest Women's and Children's Hospital, Xi'an, Shaanxi, PR China.
Rationale: The chromosome 18p deletion syndrome is a syndrome with a deletion of all or a portion of the short arm of the chromosome 18. The phenotypes of the chromosome 18p deletion syndrome vary widely among individuals due to differences in size and breakpoints and the involved genes on the deletions. Given the varied and untypical clinical presentation of this syndrome, the prenatal diagnosis of the syndrome still presents as a challenge.
View Article and Find Full Text PDFRisk stratification of cervical lesions using capture sequencing and machine learning method based on HPV and human integrated genomic profiles.
Carcinogenesis
October 2019
Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China.
Article Synopsis
- Cervical cancer develops over decades starting from HPV infection, necessitating high-sensitivity HPV DNA testing for primary screening and improved triage methods for HPV-positive women.
- A custom capture panel targeting 17 HPV types and 522 cervical cancer-related genes was utilized in a study involving 34 paired samples to analyze HPV integration status, somatic mutations, and copy number variations.
- The use of machine learning (Random Forest) helped create a risk stratification model based on biomarkers associated with cervical precursor lesions, achieving an average accuracy score of 0.814 by identifying crucial genetic features linked to the progression from HPV infection to more severe conditions.
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