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A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

To better understand the Zea mays transcriptome, scientists performed deep RNA sequencing of the maize seedling. The study improved current annotations by adding previously unannotated transcript variants as well as new transcripts, genes, and gene fusion events. These findings provide a resource for future research and breeding of the staple crop.
Read more at PubMed »
Featured Publication

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes

To better understand somatic mutations in childhood cancer, investigators sequenced 633 known epigenetic regulatory genes in over 1,000 tumors. Whole-genome, exome, and targeted sequencing identified frequently mutated genes and novel mutations in cancer subtypes, providing a resource for future cancer research.
Read more at PubMed »
Featured Publication

Single-cell genomics for dissection of complex malaria infections

Most malaria infections contain mixtures of distinct parasite lineages, which impact virulence, drug resistance, and intra-host dynamics. Using single-cell sequencing, researchers investigated Plasmodium falciparum and Plasmodium vivax malarial infections. This approach can generate parasite sequences directly from blood samples, revealing new information about species relatedness and drug resistance.
Read more at PubMed »
Featured Publication

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

Sequencing metastatic cancer tissue can be difficult due to inaccessibility and low purity. To overcome these challenges, researchers developed a process for monitoring metastatic cancer by enriching, isolating, and sequencing circulating tumor cells (CTC). Exome sequencing of CTC showed variant concordance with tumor biopsies, demonstrating a new approach for understanding metastatic prostate cancer.
Read more at PubMed »
Maize seedling transcriptome revealed from ultra-deep sequencing
The landscape of somatic mutations in epigenetic regulators across pediatric cancer
Single-cell genomics for dissection of complex malaria infections
Exome sequencing of circulating tumor cells provides window into prostate cancer

Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease

Researchers conducted a meta-analysis of genome-wide association data from Parkinson’s disease studies and then tested the significant loci. Analysis identified and replicated 28 independent risk variants for Parkinson’s disease across 24 loci, including 6 newly identified loci. The findings provide insight into the genetic basis of Parkinson’s disease.

Read more at PubMed »

Nalls MA, Pankratz N, Lill CM, Do CB, Hernandez DG, et al. Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease  Nature Genetics

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

To analyze tumor heterogeneity, researchers developed a method for sequencing the genomes and exomes of single cells from breast cancer and normal tissue. Sequencing and copy number profiling revealed changes in mutation frequencies during clonal expansion, providing insights into tumor evolution that may inform future diagnosis and treatment for breast cancer.

Read more at PubMed »

Wang Y, Waters J, Leung ML, Unruh A, Roh W, et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing  Nature

Single-cell genomics for dissection of complex malaria infections

Most malaria infections contain mixtures of distinct parasite lineages, which impact virulence, drug resistance, and intra-host dynamics. Using single-cell sequencing, researchers investigated Plasmodium falciparum and Plasmodium vivax malarial infections. This approach can generate parasite sequences directly from blood samples, revealing new information about species relatedness and drug resistance.

Read more at PubMed »

Nair S, Nkhoma SC, Serre D, Zimmerman PA, Gorena K, et al. Single-cell genomics for dissection of complex malaria infections  Genome Research

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

To investigate the diverse molecular subtypes of gastric cancer, researchers performed whole-genome sequencing and molecular profiling of 100 tumor/normal pairs. Sequencing identified both known and novel driver mutations and pathway alterations, illustrating the complex genomic landscape of gastric cancer and contributing to the development of targeted therapies.

Read more at PubMed »

Wang K, Yuen ST, Xu J, Lee SP, Yan HH, et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer  Nature Genetics

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

Sequencing metastatic cancer tissue can be difficult due to inaccessibility and low purity. To overcome these challenges, researchers developed a process for monitoring metastatic cancer by enriching, isolating, and sequencing circulating tumor cells (CTC). Exome sequencing of CTC showed variant concordance with tumor biopsies, demonstrating a new approach for understanding metastatic prostate cancer.

Read more at PubMed »

Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, et al. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer  Nature Biotechnology

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes

To better understand somatic mutations in childhood cancer, investigators sequenced 633 known epigenetic regulatory genes in over 1,000 tumors. Whole-genome, exome, and targeted sequencing identified frequently mutated genes and novel mutations in cancer subtypes, providing a resource for future cancer research.

Read more at PubMed »

Huether R, Dong L, Chen X, Wu G, Parker M, et al. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes  Nature Communications

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Researchers developed a novel algorithm for comparing the timing of gene expression changes in individual cells from the same tissue. Using the algorithm with single-cell transcriptome sequencing on the HiSeq 2500 System, they analyzed expression patterns in the development of human myoblasts. This approach can provide new insights into transcriptional regulation during time-dependent processes, including differentiation, proliferation, and tumorigenesis.

Read more at PubMed »

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells  Nature Biotechnology

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

To better understand the Zea mays transcriptome, scientists performed deep RNA sequencing of the maize seedling. The study improved current annotations by adding previously unannotated transcript variants as well as new transcripts, genes, and gene fusion events. These findings provide a resource for future research and breeding of the staple crop.

Read more at PubMed »

Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, et al. A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing  Scientific Reports