Results 1 to 10 of about 1,118,249 (314)

Truvari: refined structural variant comparison preserves allelic diversity

Genome Biology, 2022
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same.
Adam C. English, Vipin K. Menon, Richard A. Gibbs, Ginger A. Metcalf, Fritz J. Sedlazeck   +4 more
doaj   +1 more source

PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation

Genome Biology, 2021
Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive ...
Medhat Mahmoud, Harshavardhan Doddapaneni, Winston Timp, Fritz J. Sedlazeck   +3 more
doaj   +1 more source

Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates

BMC Evolutionary Biology, 2020
Background Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families.
R. Alan Harris, Muthuswamy Raveendran, Kim C. Worley, Jeffrey Rogers   +3 more
doaj   +1 more source

Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation

Genome Biology, 2023
Background Systematic characterization of how  genetic variation modulates gene regulation in a cell type-specific context is essential for understanding complex traits.
Jun Wang, Xuesen Cheng, Qingnan Liang, Leah A. Owen, Jiaxiong Lu, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Yumei Li, Rui Chen   +10 more
doaj   +1 more source

Genomic variant benchmark: if you cannot measure it, you cannot improve it

Genome Biology, 2023
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges.
Sina Majidian, Daniel Paiva Agustinho, Chen-Shan Chin, Fritz J. Sedlazeck, Medhat Mahmoud   +4 more
doaj   +1 more source

SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads

BMC Genomics, 2017
Background Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing.
Oliver A. Hampton, Adam C. English, Mark Wang, William J. Salerno, Yue Liu, Donna M. Muzny, Yi Han, David A. Wheeler, Kim C. Worley, James R. Lupski, Richard A. Gibbs   +10 more
doaj   +1 more source

Community‐based recruitment and exome sequencing indicates high diagnostic yield in adults with intellectual disability

Molecular Genetics & Genomic Medicine, 2020
Background Establishing a genetic diagnosis for individuals with intellectual disability (ID) benefits patients and their families as it may inform the prognosis, lead to appropriate therapy, and facilitate access to medical and supportive services ...
Aniko Sabo, David Murdock, Shannon Dugan, Qingchang Meng, Marie‐Claude Gingras, Jianhong Hu, Donna Muzny, Richard Gibbs   +7 more
doaj   +1 more source

SVhound: detection of regions that harbor yet undetected structural variation

BMC Bioinformatics, 2023
Background Recent population studies are ever growing in number of samples to investigate the diversity of a population or species. These studies reveal new polymorphism that lead to important insights into the mechanisms of evolution, but are also ...
Luis F. Paulin, Muthuswamy Raveendran, R. Alan Harris, Jeffrey Rogers, Arndt von Haeseler, Fritz J. Sedlazeck   +5 more
doaj   +1 more source

Sequencing of a central nervous system tumor demonstrates cancer transmission in an organ transplant

Life Science Alliance, 2021
This study uses DNA sequencing to trace a donor organ transplant–mediated cancer transmission and illustrates how precise molecular pathology profiles might reduce future risk for transplant recipients.
Marie-Claude Gingras, Aniko Sabo, Maria Cardenas, Abbas Rana, Sadhna Dhingra, Qingchang Meng, Jianhong Hu, Donna M Muzny, Harshavardhan Doddapaneni, Lesette Perez, Viktoriya Korchina, Caitlin Nessner, Xiuping Liu, Hsu Chao, John Goss, Richard A Gibbs   +15 more
doaj   +1 more source

FixItFelix: improving genomic analysis by fixing reference errors

Genome Biology, 2023
The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions.
Sairam Behera, Jonathon LeFaive, Peter Orchard, Medhat Mahmoud, Luis F. Paulin, Jesse Farek, Daniela C. Soto, Stephen C. J. Parker, Albert V. Smith, Megan Y. Dennis, Justin M. Zook, Fritz J. Sedlazeck   +11 more
doaj   +1 more source