Featured Publications

Featured Publication

Epigenome and transcriptome reprogramming in muscle after training


Scientists used arrays and RNA sequencing to study how exercise affects DNA methylation in human skeletal muscle. Genes upregulated after training were involved in morphological changes and associated with a decrease in methylation. This is the first evidence that cells exhibit a controlled response to exercise via changes in methylation and gene expression.

Read more at PubMed »

 
 
Epigenome and transcriptome reprogramming in muscle after training
 
 
Prediction of breast cancer risk based on profiling with genetic variants
 
 
Genomic signatures of disease in Streptococcus suis
 
 
Fine mapping of type 1 diabetes susceptibility loci
 
 

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

Scientists used arrays and RNA sequencing to study how exercise affects DNA methylation in human skeletal muscle. Genes upregulated after training were involved in morphological changes and associated with a decrease in methylation. This is the first evidence that cells exhibit a controlled response to exercise via changes in methylation and gene expression.

Read more at PubMed »

Lindholm ME, Marabita F, Gomez-Cabrero D, et al. An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training - Epigenetics

Prediction of breast cancer risk based on profiling with common genetic variants

Investigators genotyped thousands of breast cancer samples and controls to identify lifetime risk estimates. Using 77 SNPs, they constructed risk scores for the disease overall and by estrogen receptor status. Findings include risk stratification for women with and without a family history of breast cancer.

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Mavaddat N, Pharoah PD, Michailidou K, et al.Prediction of breast cancer risk based on profiling with common genetic variants - Journal of the National Cancer Institute

Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS

The role of genetic variation in sporadic amyotrophic lateral sclerosis (ALS) is largely unknown. To find causative variants, scientists sequenced the exomes of 44 trios with unaffected parents and identified homozygous, heterozygous, and de novo coding variants implicated in the disease. This study indicates that rare variants and de novo mutations are likely mechanisms underlying sporadic ALS.

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Steinberg KM, Yu B, Koboldt DC, Mardis ER, Pamphlett R. Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS. - Scientific Reports

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

To investigate the tuberculosis strains responsible for widespread infection in 18th century Europe, researchers isolated samples from human remains in a Hungarian crypt. Sequencing using HiSeq and MiSeq Systems revealed that most individuals contained multiple M. tuberculosis genotypes, which were mapped to contemporary lineages. These findings might inform current and future disease monitoring.

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Kay GL, Sergeant MJ, Zhou Z, et al. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. - Nature Communications

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

To understand zoonotic Streptococcus suis infections, researchers sequenced 375 bacterial isolates from pigs and humans. Disease-associated isolates typically contained fewer genes than others but were more likely to encode virulence factors. Results showed little geographical clustering and high recombination rates, implying that an increase in virulence could spread quickly.

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Weinert LA, Chaudhuri RR, Wang J, et al. Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis - Nature Communications

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

Researchers used the custom Immunochip array to analyze risk loci for type 1 diabetes. Comparison to 15 immune diseases showed that type 1 diabetes is genetically most similar to juvenile idiopathic arthritis. The study also identified 3 novel risk loci localized to enhancer sequences active in thymus, T, B, and CD34+ cells.

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Onengut-Gumuscu S, Chen WM, Burren O, et al. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers - Nature Communications

Whole-genome sequence-based analysis of thyroid function

To understand the role of genetic variation in thyroid function, researchers used whole-genome sequencing data from the UK10K project and imputed genotyping data. The study identified 3 new loci associated with thyroid function and uncovered a rare functional variant in the transthyretin gene TTR. These findings might account for the missing heritability of thyroid function.

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Taylor PN, Porcu E, Chew S, et al. Whole-genome sequence-based analysis of thyroid function - Nature Communications