Next Generation Sequencing

Novel tool enables high-precision, low-cost pediatric leukemia diagnostics

An upgrade to U-M developed tech enables researchers to see even finer transcription detail inside cells

Seq-Scope-eXpanded allows researchers to see even finer transcription detail, enabling discoveries that weren't possible with previous methods. The technology has been expanded to capture transcriptome from tissue with greater resolution.

Pediatric investigation review highlights the future of newborn screening with next-generation sequencing

The use of next-generation sequencing in newborn screening can detect a wide range of genetic disorders, some of which are not currently testable through traditional means. This approach enables earlier disease detection and long-term health planning.

Skeletal muscle epigenetic clocks developed using postmortem tissue from an Asian population

A new study introduced epigenetic clocks in skeletal muscle from an Asian population, identifying DNA methylation sites associated with age and developing accurate age prediction models using NGS and SBE. The findings offer a reliable method for estimating age and its potential applications in forensic science.

Island ant communities show signs of ‘insect apocalypse’

A study by Okinawa Institute of Science and Technology researchers found that 79% of endemic ant species in Fiji are declining over the past few hundred years, coinciding with European contact and modern agricultural techniques. In contrast, non-native ant species are exploding in population.

New AI tool illuminates “dark side” of the human genome

Researchers at Salk Institute launched a machine learning framework called ShortStop to explore overlooked DNA regions and discover microproteins with potential roles in disease. The tool identified 210 new microprotein candidates in lung cancer data, including one validated target for therapeutic treatment.

dpMIG-seq: a game-changer in genetic mapping of tetraploid crops

A new PCR-based sequencing method, dpMIG-seq, simplifies genetic mapping of tetraploid crops by offering high reproducibility and accuracy. The method enables the construction of a comprehensive linkage map across 12 linkage groups in a tetraploid blueberry F1 population.

Study identifies key genetic alterations and biomarker for blastic plasmacytoid dendritic cell neoplasm

A recent study discovered that the mutational landscape of blastic plasmacytoid dendritic cell neoplasm (BPDCN) is similar to other myeloid neoplasms. The researchers identified CCDC50 as a potential biomarker for this disease, which showed promising results in tracking disease activity and monitoring treatment success.

Machine learning algorithm brings long-read sequencing to the clinic

A new machine learning algorithm, SAVANA, has been developed to accurately detect structural variations in cancer genomes using long-read sequencing data. The algorithm was tested on 99 human tumour samples and showed high consistency with current clinical standards.

Relationship between mutation profile detected by next-generation sequencing and histopathological parameters in lung squamous cell carcinoma

The study evaluated the mutation profiles of lung squamous cell carcinoma (LSCC) detected by next-generation sequencing to assess relationships with clinicopathological parameters. Detection of mutations revealed associations between certain genes, such as PIK3CA and NF1, with specific histopathological features.

Study: DNA test detects three times more lung pathogens than traditional methods

A recent study found that Metagenomic next-generation sequencing (mNGS) can detect pathogens in 86% of cases, outperforming conventional microbiological tests which identified pathogens in only 67% of cases. mNGS guides treatment decisions and improves patient outcomes by detecting rare/atypical pathogens.

Australian Academy of Science honors Murdoch University agricultural researcher

Rajeev Varshney, a Murdoch University professor, has been elected as a Fellow of the Australian Academy of Science. He is recognized for his groundbreaking work in genomics, genetics, and pre-breeding, helping to secure food production in the face of climate change.

A new technique to use generative AI to design RNA

A new generative AI technique allows for the design of RNA molecules with improved functions, opening up potential for novel therapeutics and diagnostics. The SANDSTORM and GARDN systems enable the prediction and generation of RNA sequences tailored for specific tasks in cells or diagnostic assays.

EpiAge: A new test to measure biological age using saliva or blood

A new test called EpiAgePublic estimates biological age using only three DNA sites in the ELOVL2 gene, simplifying traditional methods while maintaining accuracy. The study found that EpiAgePublic accurately tracks aging patterns and can identify factors accelerating the aging process.

New genetic mutation linked to drug resistance in non-small cell lung cancer patient

A new genetic mutation, RUFY1-RET fusion, was discovered in a patient with stage IV CD-74-ROS1 fusion NSCLC who developed resistance to lorlatinib. The finding highlights the importance of ongoing genetic testing to guide therapy decisions.

Gene variant common in individuals of African ancestry may lead to reduced metabolism of the thiopurine class of drugs

A novel study found that the TPMT∗8 allele is associated with reduced metabolism of thiopurine drugs, which can lead to toxicity. The research emphasizes the importance of understanding the function of TPMT∗8 to ensure effective pharmacogenomic testing across all ancestries.

Epitope binning-seq: A game-changer in antibody drug discovery

Researchers developed Epitope Binning-seq to analyze epitopes in monoclonal antibodies. The method accurately classified antibodies into distinct epitope bins, providing valuable insights into their binding patterns and streamlining early antibody drug development.

Genetic and therapeutic landscapes in cohort of pancreatic adenocarcinomas using NGS and machine learning

A study published in Oncotarget has identified specific mutational and therapeutic landscapes of pancreatic cancer in the Russian population. By applying machine learning models to full exome individual data, researchers received personalized recommendations for targeted treatment options for each clinical case.

Advanced viral diagnostics tool closer to widespread use

VirCapSeq-VERT, a next-generation sequencing-based screening and surveillance system, can detect any virus that can potentially infect humans with greater sensitivity and speed than other NGS platforms. The technology achieved clinical sensitivity of 99 percent and 100 percent clinical specificity in a validation study.

Improving the diagnosis of infection: a prospective study clarifies the role of an innovative metagenomic tool

A new metagenomics tool has improved the diagnosis of infections by detecting rare pathogens with high accuracy. The tool was tested on 742 samples from 523 patients and showed a diagnostic yield of over 25% in cases where infection was strongly suspected.

Genetic predisposition to early breast cancer in Kazakh women

Researchers identified 38 unique pathogenic variants in 57 patients, including novel variants specific to the Kazakh population. These variants were associated with an increased risk of triple-negative breast cancer and family history of breast cancer.

Uncovering thalassemia diversity in southern china through next-generation sequencing

A large-scale thalassemia screening project involving 136,312 individuals revealed a high prevalence of thalassemia in Ganzhou, with 14.545% carriers identified. Next-generation sequencing techniques outperformed conventional methods in identifying novel and rare mutations.

First defence against devastating ToCSV tomato virus explored

A team of researchers at the University of Johannesburg has made a groundbreaking discovery about how tomato plants defend themselves against the devastating ToCSV virus. By studying the molecular genetics of infected tomato varieties, they found that viral DNA methylation plays a crucial role in resistance to ToCSV.

De-code of the crop

A research group at Kyoto University has successfully developed a self-fertile buckwheat variety and a new type of the crop with a sticky texture. This breakthrough could contribute to the efficient breeding of less-common orphan crops, addressing the world's growing food demands.

Loss of a particular protein causes growth defects in mice and humans

Researchers identified a mutation in the TMCO3 gene in two sisters with short stature, and found it regulates expression of proteins controlling bone growth. A mouse model lacking the gene confirmed its role in longitudinal growth.

Case Report: Intrathoracic synovial sarcoma with BRAF V600E mutation

Researchers report a case of a 15-year-old boy with recurrent intrathoracic synovial sarcoma who achieved partial response with BRAF inhibitor Vemurafenib treatment. The study highlights the importance of routine next-generation sequencing to drive treatment choice and investigate BRAF mutations in SS tumors.

New algorithm for quicker detection of antibiotic resistances

Researchers have developed a new method to detect antibiotic resistances in Proteus mirabilis, enabling faster identification of potentially resistant strains. The algorithm uses cutting-edge molecular biology methods and can determine whether a bacterial strain is susceptible to carbapenem antibiotics.

AMP offers evidence-based recommendations for next-generation sequencing germline variant confirmation

The Association for Molecular Pathology (AMP) has published a report establishing evidence-based recommendations for orthogonal confirmation practices of germline variants detected by next-generation sequencing. The guidelines aim to promote standardization, transparency, and quality improvement among laboratories.

Automated, accurate reporting for NGS-based clonality testing

Researchers have developed an automated calling algorithm for determining B and T cell clonality from NGS data with greater sensitivity than previous models. The new model increases the assay's sensitivity in detecting clonality, allowing for more accurate diagnosis and monitoring of lymphoproliferative disorders.

New method of clustering colorectal cancer patients using DPE sequencing

Researchers propose a new method of clustering colorectal cancer patients using differential presence of exons (DPE) sequencing, which can provide valuable information on CRC progression and response to therapy. This analysis may also reduce costs and time required for staging CRC patients.

mNGS outperforms microbiological tests to diagnose bloodstream infections – BGI Insight

A study published in the Journal of Infection found that mNGS was significantly more effective at detecting bloodstream infections than conventional microbiological tests (CMTs), identifying 187 infection cases compared to CMTs' 81. Viral infections were the most common type, with CMV being the leading cause.

Performance of OncoK9® in real-world veterinary practice mirrors clinical validation study

A new study from PetDx shows OncoK9 performs similarly to its landmark clinical validation study in real-world settings, detecting 26 types of cancer in high-risk dogs. The test also provides peace of mind for veterinarians and families by detecting cancer in over 94% of negative cases.

Humans are leaving behind a ‘frozen signature’ of microbes on Mount Everest

Scientists discover human-associated microbes in soil samples from Mount Everest's South Col, highlighting the impact of tourism on high-altitude environments. The findings also shed light on the potential for life beyond Earth, particularly on Mars and other cold moons.

Researchers decode 95.6% of the genome of Nicotiana benthamiana

A research group at Nagoya University has sequenced 95.6% of the Nicotiana benthamiana genome using next-generation sequencing technology. The findings provide insight into the plant's ability to perform grafting, a rare phenomenon in plants.

Faster genomics-based diagnosis may accelerate targeted treatment of patients with myeloid neoplasms

Researchers evaluate an integrated NGS system, delivering accurate diagnoses in under 24 hours and expanding targeted treatments available to patients with myeloid neoplasms. The assay identified 80-92% of genetic variants, demonstrating promising results for accelerating precision therapies.

Dogs’ average age at cancer diagnosis is associated with size, sex, breed

A new study analyzed 3,452 dogs with cancer to determine median ages of diagnosis based on characteristics such as weight, breed, and sex. The findings suggest that giant breeds, males, and purebred dogs tend to receive a cancer diagnosis at relatively younger ages.

Oncoscience | Association between tumor mutations and meningioma recurrence in Grade I/II disease

A study of 184 grade I and II meningiomas found associations between specific tumor mutations and increased or decreased recurrence rates. Mutations in ATM and CREBBP were linked to accelerated recurrence, while POLE mutations showed protective effects, highlighting potential targets for intervention.

Oncotarget | Treasures from trash in cancer research

A new study explores the value of 'trash data' from cancer genome sequencing, identifying new strategies to uncover previously unexplored information. The researchers found that genomic and transcriptomic data contain relevant information that can help elucidate carcinogenesis and discover putative biomarkers with clinical applications.

Perennial rice’s next steps: Large-scale localization to adapt across different climates

A new report showcases perennial rice strains that can thrive in various climate conditions, offering labor and cost savings for farmers. The research emphasizes the need for large-scale localization of perennial rice to tailor it to local climates, with potential applications in Africa and other regions.

Oncotarget | Mutation analysis performed on tumor biopsies from patients with newly-diagnosed germinal center aggressive B cell lymphomas

A new study analyzed tumor biopsies from patients with newly-diagnosed germinal center B cell lymphoma and found that CREBBP mutations were associated with lower disease-free survival rates. The researchers identified CLMA as a practical tool to translate experimental findings into clinical applications.

Association for molecular pathology offers recommendations for in silico approaches for validating next-generation sequencing analysis pipelines

The Association for Molecular Pathology (AMP) has published consensus recommendations for using in silico approaches to validate Next-Generation Sequencing (NGS) data analysis pipelines. The guidelines provide expert opinion on the advantages and disadvantages of different types of in silico data and offer general recommendations for s...

Chromosome-scale genome of a gentle giant

Researchers have completed and released a chromosome-scale genome sequence of the Aldabra giant tortoise, providing a much-needed genetic resource for rescue efforts. The data will aid in breeding efforts, comparative studies with other tortoise species, and understanding the species' remarkable size.

Genetic sequencing could be key to containing future COVID-19 variant outbreaks

A new study suggests that genetic sequencing can detect emerging COVID-19 variants with enough time to contain them at their source. This approach requires coordinated global efforts to prevent the spread of new variants.

CU Cancer Center study aims to predict critical markers for lung cancer treatments

Researchers used Guardant NGS to analyze nearly 17,000 lung cancer samples and found MET amplification in 1.2% of cases, with 20.8% having overlapping oncogenic drivers. The study suggests that high gene copy numbers and smaller amplified regions can be used to enrich for the true MET-sensitive population.

A blueprint for life forms on Mars?

Researchers at McGill University have discovered microbes that can survive in conditions similar to those on Mars. These microorganisms thrive in extremely salty, cold, and oxygen-free environments by eating and breathing simple inorganic compounds. The study provides insights into the possibility of life on Mars.

Genetic test can diagnose certain immune system disorders

Researchers developed a genetic test that diagnoses primary immunodeficiency disorders (PID), revealing inherited genetic defects in nearly half of patients. The test uses next-generation sequencing technology to identify specific gene variants associated with PID, enabling targeted treatment and earlier intervention for family members.

New method can easily identify viruses in tumors in a routine clinical genomic sequencing assay

Researchers developed a digital subtraction technique to identify viral DNA in tumor samples, achieving comparable results to standard clinical methods. The study discovered novel associations between specific tumors and viruses, warranting further investigation.

Analysis of 2,658 tumors sheds new light on mutations in cancer

A recent study by KU Leuven and The Francis Crick Institute analyzed 2,658 tumor samples and found that 21% exhibited double mutations in both maternal and paternal DNA copies. This discovery sheds new light on the origin of mutations and their role in cancer development.

Inventory of the world belowground: Using DNA to study fungal communities

A new study published in Applications in Plant Sciences highlights the negative effects of clearcutting on mycorrhizal fungi, showing less diversity in formerly deforested areas. High-throughput sequencing reveals over 300 distinct fungal lineages in soil and root samples, shedding light on ecosystem health.

Vaping – not prior smoking – is associated with changes in gene regulation linked to disease

A new study from Keck School of Medicine of USC shows that vaping is associated with dysregulation of mitochondrial genes and immune response genes, similar to smoking. The research found that over 80% of gene dysregulation in vapers correlated with the intensity and duration of current vaping.

Cutting-edge molecular tools reveal potential COVID-19 diagnostic and therapeutic targets

Using next-generation sequencing, researchers identified four major regulatory pathways and specific molecular effectors behind COVID-19 symptoms. The study may pave the way for a more personalized approach to diagnosis and treatment.

CDC/ClinGen collaboration results in a significant new genetic variant resource

A new list of 546 expert-curated pathogenic variants in 84 genes has been developed for use in next-generation sequencing (NGS) genetic testing. This curated resource addresses the complexities of large assays and provides a scalable solution for test developers and laboratories.

Taking the guesswork out of genetic engineering

A team of Harvard researchers created an integrated pipeline, STAMPScreen, to help genetic engineers identify target genes and perform screening studies. The protocol combines computational tools with lab experiments to quickly and efficiently test gene function in living cells.

Integrative approach by NUS biologists increases accuracy of mosquito vector surveillance

A team of researchers from NUS developed an integrative approach to boost accuracy in mosquito surveillance by including larvae and species identification using mini-barcodes. This approach improves overall diversity estimates by 38% compared to adult-only data, contributing to baseline knowledge on potential vectors in Singapore.

New versatile genetic test for lymphoid neoplasms supports personalized management of patients and further research

Researchers have developed a new integrative genetic test, LYNX, that analyzes standard and novel molecular markers in common lymphoid neoplasms. The test provides accurate detection of mutations, identification of large genome-wide chromosomal aberrations, and assessment of immunoglobulin and T-cell receptor gene rearrangements.

Automated next generation sequencing platform can accurately screen thousands for COVID-19

A new COVID-19 screening platform, C19-SPAR-Seq, has been developed to rapidly analyze thousands of samples for variants. The platform boasts a sensitivity rate greater than 95%, making it a crucial tool in the fight against the pandemic.

World's first next-generation protein sequencing device to accelerate the study of diseases and pandemics

The Quantum-Si ecosystem enables sensitive and accurate research tools and diagnostics through digital proteomics, transforming the study of proteins on a large scale. The company's platform offers a complete solution for sample preparation, sequencing, and data analysis, reducing costs and increasing accessibility.

Biochip advances enable next-generation sequencing technologies

Researchers review advances in biochip technology, which is driving groundbreaking discoveries in biology and medicine. Biochips are being applied to real-world settings, enabling single-cell analysis and preprocessing for high-throughput sequencing.

A novel method of isolating infecting organisms after joint replacement

Researchers developed a method using next-generation genomic sequencing to isolate infecting organisms after joint replacement surgery. The technique identified pathogens in over 80% of cases that previously went undetected, revolutionizing treatment for patients with joint-replacement infections.

Next-generation gene sequencing helps diagnose rare diseases in newborns

New research suggests that next-generation gene sequencing can rapidly diagnose rare diseases in newborns, providing timely molecular diagnoses and potentially life-saving interventions. The technique has shown diagnostic success rates of up to 40% in a pilot study of 20 infants with complex medical issues.