Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(47), P. 18880 - 18889
Published: Nov. 11, 2024
A new approach to sample preparation and enzymatic digestion in bottom-up proteomics has been developed using alginate-based hydrogel entrapment of enzymes. This facilitates rapid room-temperature digestions with multienzyme capabilities. Three methodologies were tested: within microcentrifuge tubes,
Language: Английский
medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: March 26, 2024
Abstract Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read offers the advantage of better mappability and long-range phasing, which results substantial improvements germline SV detection. However, long-read detection methods do not generalize well analysis SVs tumor genomes with complex rearrangements, heterogeneity, aneuploidy. Here, we present Severus: a method for accurate different types using phased breakpoint graph approach. To benchmark various short- methods, sequenced five tumor/normal cell line pairs Illumina, Nanopore, PacBio platforms; this Severus showed highest F1 scores (harmonic mean precision recall) as compared methods. We then applied three clinical cases pediatric cancer, demonstrating concordance known genetic findings revealing clinically relevant cryptic rearrangements missed by standard genomic panels.
Language: Английский
Citations
9
Genome Research, Journal Year: 2025, Volume and Issue: 35(4), P. 572 - 582
Published: April 1, 2025
In this mini-review, we explore the advancements in genome-wide DNA methylation profiling, tracing evolution from traditional methods such as arrays and whole-genome bisulfite sequencing to cutting-edge single-molecule profiling enabled by long-read (LRS) technologies. We highlight how LRS is transforming clinical translational research, particularly its ability simultaneously measure genetic epigenetic information, providing a more comprehensive understanding of complex disease mechanisms. discuss current challenges future directions field, emphasizing need for innovative computational tools robust, reproducible approaches fully harness capabilities molecular diagnostics.
Language: Английский
Citations
1
Molecular Cancer, Journal Year: 2025, Volume and Issue: 24(1)
Published: Feb. 14, 2025
Delving into cancer dormancy has been an inherent task that may drive the lethal recurrence of after primary tumor relief. Cells in quiescence can survive for a short or long term silence, undergo genetic epigenetic changes, and initiate relapse through certain contextual cues. The state be induced by multiple conditions including drug treatment, turn, undergoes life cycle generally occurs dissemination, invasion, intravasation, circulation, immune evasion, extravasation, colonization. Throughout this cascade, cellular machinery governs fate individual cells, largely affected gene regulation. Despite its significance, precise view is yet hampered. Revolutionizing advanced single cell read sequencing analysis methodologies artificial intelligence, most recent stage research tool progress, expected to provide holistic diverse aspects dormancy.
Language: Английский
Citations
0
Nature Biotechnology, Journal Year: 2025, Volume and Issue: unknown
Published: April 4, 2025
Language: Английский
Citations
0
medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: March 18, 2024
The complexities of cancer genomes are becoming more easily interpreted due to advancements in sequencing technologies and improved bioinformatic analysis. Structural variants (SVs) represent an important subset somatic events tumors. While detection SVs has been markedly by the development long-read sequencing, variant identification annotation remains challenging. We hypothesized that use a completed human reference genome (CHM13-T2T) would improve SV calling. Our findings tumour/normal matched benchmark sample two patient samples show CHM13-T2T improves prioritization accuracy compared GRCh38, with notable reduction false positive calls. also overcame lack resources for lifting over CHM13-T2T-aligned reads GRCh38 genome, therefore combining both alignment advanced annotations. In this process, we assessed current set COLO829/COLO829BL across four replicates sequenced at different centers technologies. discovered instability cell line these replicates; 346 (1.13%) were only discoverable single replicate. identify 49 SVs, which appear be stable as they consistently present replicates. As such, propose consensus updated calling include coordinates our benchmark. is available at: 10.5281/zenodo.10819636 work demonstrates new approaches optimize potential improvements other genetic diseases.
Language: Английский
Citations
3
Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(47), P. 18880 - 18889
Published: Nov. 11, 2024
A new approach to sample preparation and enzymatic digestion in bottom-up proteomics has been developed using alginate-based hydrogel entrapment of enzymes. This facilitates rapid room-temperature digestions with multienzyme capabilities. Three methodologies were tested: within microcentrifuge tubes,
Language: Английский
Citations
1