FLEXIBLE, PRODUCTION-SCALE, HUMAN WHOLE GENOME SEQUENCING ON A BENCHTOP SEQUENCER

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 2, 2024

ABSTRACT Human whole-genome sequencing (hWGS) provides comprehensive genomic information that can potentially help guide research in disease prevention and treatment ultimately improve human health. Recent advancements technology have improved quality further reduced costs on bench-top sized instruments, making an accessible for broader use. Here, we demonstrate the feasibility of a large whole genome project using benchtop sequencer small laboratory setting, scale previously reserved production-scale factory-sized machines. In this project, 807 samples were prepared sequenced across 313 flow cells, with high at median %Q30 96.6% %Q40 89.31%. To screen library maximize sample yield, utilized 48-plex pre-pool ‘QC’ runs to provide >1x coverage per prior pooling full-depth sequencing. With strategy, consistently achieved >30x three-plex trios standard settings or up 4 run high-throughput setting. Additionally, low-pass data provided valuable sample-level insights, allowing detection chromosome copy number variations (CNV) three instruments running concurrently, >2,800 30x genomes could be year. additional flexibility present platform, also explored two different use cases 1) insert sizes (1kb+) achieve superior coverage; 2) proof concept rapid WGS minimize answer turnaround time time-critical applications. Sequencing 2×100 <12 hours subsequent generation fastq, bam vcf <1 hour. This study cost-effective flexible real-world demonstration achieving both hWGS instrument without need complex batching schemes sequencers.

Language: Английский

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Diagnostics and Therapy for Malignant Tumors

Biomedicines, Journal Year: 2024, Volume and Issue: 12(12), P. 2659 - 2659

Published: Nov. 21, 2024

Malignant tumors remain one of the most significant global health challenges and contribute to high mortality rates across various cancer types. The complex nature these requires multifaceted diagnostic therapeutic approaches. This review explores current advancements in methods, including molecular imaging, biomarkers, liquid biopsies. It also delves into evolution strategies, surgery, chemotherapy, radiation therapy, novel targeted therapies such as immunotherapy gene therapy. Although progress has been made understanding biology, future oncology lies integration precision medicine, improved tools, personalized approaches that address tumor heterogeneity. aims provide a comprehensive overview state diagnostics treatments while highlighting emerging trends lie ahead.

Language: Английский

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Permeability-Engineered Compartmentalization System Promises Next-Generation Single-Cell Analysis

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(49), P. 19155 - 19159

Published: Dec. 2, 2024

Single-cell analysis, including sequencing, imaging, and biochemical assays, has become a fundamental strategy in biomedical research. Microplates, with their open system design, facilitate multistep reagent addition, subtraction, buffer exchange, while physically isolated wells prevent cross-contamination between biomolecules, establishing them as foundational compartmentalized platform for single-cell analysis. In contrast, water-in-oil droplets, produced by microfluidic systems, create nanoliter/picoliter-sized droplets that act advanced platform. Although droplet systems offer significant advantages nearly complete isolation presents substantial limitations. This impedes the development of ex vivo requiring material complicating complex reactions hindering advancement multiomics technologies nonsequencing applications. Recent innovations permeability-engineered compartmentalization featuring unique materials structures controllable promise to overcome these We discuss latest advancements system, elucidates its underlying principles, explores potential applications field

Language: Английский

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Enhancing Clinical Applications by Evaluation of Sensitivity and Specificity in Whole Exome Sequencing

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(24), P. 13250 - 13250

Published: Dec. 10, 2024

The cost-effectiveness of whole exome sequencing (WES) remains controversial due to variant call variability, necessitating sensitivity and specificity evaluation. WES was performed by three companies (AA, BB, CC) using reference standards composed DNA from hydatidiform mole individual blood at various ratios. Sensitivity assessed the detection rate null–homozygote (N–H) alleles expected allelic fractions, while false positive (FP) errors were counted for unexpected alleles. approximately 20% in-house results BB CC around 5% AA. Dynamic Read Analysis GENomics (DRAGEN) analyses identified 1.34 1.71 times more variants, detecting over 96% with common variants increasing 5%. In-house FP varied significantly among (up 13.97 times), DRAGEN minimized this variation. Despite showing higher CC, increased highlights importance effective bioinformatic conditions. We also potential effects target enrichment proposed optimal cutoff values read depth allele fraction in WES. Optimizing analysis based on can enhance improve clinical utility

Language: Английский

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A single-center, cohort study of the mutational profile of Ukrainian patients with non-small cell lung cancer

Український радіологічний та онкологічний журнал, Journal Year: 2024, Volume and Issue: 32(4), P. 504 - 517

Published: Dec. 3, 2024

Background. Lung cancer continues to be a significant health concern globally. Due the heterogeneity of disease, using innovative strategies for effective management and treatment patients is extremely important. Purpose – characterize mutational profile group non-small cell lung (NSCLC) utilizing next-generation sequencing technique. Materials Methods. A total 42 samples that were fixed in formalin embedded paraffin (FFPE) collected from Ukrainian diagnosed with who had surgery at Sumy Regional Clinical Oncology Center. DNA was extracted FFPE Omega Bio-tek E.Z.N.A.® Kit (USA) following manufacturerʼs instructions. Sequencing performed on Illumina NextSeq 550Dx platform 550 Mid-Output Kit. The Cancer Genome Atlas Program (TCGA) database (https://portal.gdc.cancer.gov/) used comparative analysis prevalence genomic mutations cohort Caucasian NSCLC. Statistical Stata V.18.0 software (StataCorp, Texas, USA; https://www.stata.com; 2024). paper belongs «description case series» category which type study recognized by evidence based medicine does not claim statistical significance result. Results. Among NSCLC samples, 11 (26.19%) carried driver such as EGFR (n=2; L858R), KRAS (n=7; G12C, G12D, G12A A146S), BRAF (n=1; V600E) translocation EML4(exon6) ALK (exon20) chr2:42503838 chr2:29447579). All mutually exclusive. No NRAS, ROS1, RET, MET, ERBB2, PIK3CA mutation cases detected. number never smoked significantly higher than former or current smokers (p=0.046). association found between age, sex, tumor stage, histology NSCLC, mutations. Conclusions. Molecular genetic profiling revealed 26.19% radically treated Most are oncogenic sensitive tyrosine kinase inhibitors.

Language: Английский

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