Featured Publications

Featured Publication

Alzheimer’s disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

Researchers used microarrays and bisulfite sequencing to examine the influence of DNA methylation on Alzheimer’s disease. They identified and functionally validated associations between altered DNA methylation and early disease pathology. These epigenetic patterns are hypothesized to be involved in the onset of Alzheimer's disease.
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Alzheimer’s disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
 
 
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
 
 
High-quality massively parallel sequencing of the human mitochondrial genome using MiSeq
 
 
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
 
 

Alzheimer’s disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

Researchers used microarrays and bisulfite sequencing to examine the influence of DNA methylation on Alzheimer’s disease. They identified and functionally validated associations between altered DNA methylation and early disease pathology. These epigenetic patterns are hypothesized to be involved in the onset of Alzheimer's disease.

Read more at PubMed »

De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, et al. Alzheimer’s disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci  Nature Neuroscience

Most genetic risk for autism resides with common variation

The role of genetic heritability in autism spectrum disorders is unclear. Using microarray technology, scientists investigated how rare and common genetic variants contribute to autism. Results indicated that approximately 52.4% of risk arises from genetic variation, with common variants contributing more to total heritability than rare variants.

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Gaugler T, Klei L, Sanders SJ, Bodea CA, Goldberg AP, et al. Most genetic risk for autism resides with common variation  Nature Genetics

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

Investigators examined the effect of the 2010 Deepwater Horizon oil spill on sediment microbial communities. Metagenomic shotgun sequencing and 16S rRNA sequencing showed that heavily impacted sediments were enriched in Gammaproteobacteria and Colwellia species. Genes involved in denitrification pathways were abundant in samples that exceeded the Environmental Protection Agency’s benchmarks for polycyclic aromatic hydrocarbons, suggesting that microbial response accounted for some hydrocarbon degradation.

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Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, et al. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill  ISME Journal

High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq

Current Sanger-based mitochondrial DNA typing methods used in forensic genomics are inefficient and produce limited data. To overcome these challenges, researchers generated whole-genome mitochondrial haplotypes using the MiSeq System. The approach demonstrated higher throughput and improved haplogroup assignment compared to conventional methods.

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King JL, LaRue BL, Novroski NM, Stoljarova M, Seo SB, et al. High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq  Forensic Science International:

Biological insights from 108 schizophrenia-associated genetic loci

Genetic risk for schizophrenia is conferred by many alleles. A genome-wide association study revealed a large number of novel risk loci for the disorder. Genetic associations were enriched among genes expressed in the brain and tissues involved in immunity, supporting the hypothesized role of immune dysregulation in schizophrenia.

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Schizophrenia Working Group of the Psychiatric Genomics Consortium Biological insights from 108 schizophrenia-associated genetic loci  Nature

A defect in the RNA-processing protein HNRPDL causes limb-girdle muscular dystrophy 1G (LGMD1G)

Limb-girdle muscular dystrophies (LGMD) are a heterogeneous group of genetic muscle disorders. Whole-genome sequencing of two families affected by LGMD 1G identified mutations in the HNRPDL gene. Functional studies indicated a novel association between the disorder and the RNA-processing gene, offering potential for new therapeutic approaches.

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Vieira NM, Naslavsky MS, Licinio L, Kok F, Schlesinger D, et al. A defect in the RNA-processing protein HNRPDL causes limb-girdle muscular dystrophy 1G (LGMD1G)  Human Molecular Genetics

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

An outbreak of Ebola virus recently spread through West Africa. To understand viral transmission and evolution, investigators used the HiSeq 2500 System to sequence 99 Ebola virus genomes isolated from patients. The outbreak strain showed sustained human-to-human transmission and rapid mutation rates, informing epidemiological and genomic surveillance efforts.

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Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak  Science

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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