Featured Publications

Featured Publication

Insights into the evolution of longevity from the bowhead whale genome.


The bowhead whale (Balaena mysticetus) is possibly the longest living mammal with an estimated lifespan of over 200 years. Researchers performed whole-genome sequencing with the HiSeq 2000 System to investigate potential bowhead-specific molecular adaptations relevant to age-related diseases. They found gene variants involved in DNA repair, cell-cycle regulation, cancer, and aging.

Read more at PubMed »

 
 
Insights into the evolution of longevity from the bowhead whale genome.
 
 
Whole genome sequencing in cats, identifies new models for blindness in AIPL1 somite segmentation in HES7.
 
 
Cell-free DNA testing of an extended range of chromosomal anomalies: clinical experience with 6388 consecutive cases.
 
 
Sleeping beauty screen reveals Pparg activation in metastatic prostate cancer.
 
 

Insights into the evolution of longevity from the bowhead whale genome.

The bowhead whale (Balaena mysticetus) is possibly the longest living mammal with an estimated lifespan of over 200 years. Researchers performed whole-genome sequencing with the HiSeq 2000 System to investigate potential bowhead-specific molecular adaptations relevant to age-related diseases. They found gene variants involved in DNA repair, cell-cycle regulation, cancer, and aging.

Read more at PubMed »

Keane M, Semeiks J, Webb AE, et al. Insights into the evolution of longevity from the bowhead whale genome. - Cell Reports

Potential mechanisms for cancer resistance in Elephants and comparative response to DNA damage in humans.

Researchers used Illumina sequencing technology to investigate low rates of cancer mortality in elephants and molecular mechanisms of the Peto paradox – the observation that cancer incidence across species does not increase as expected for larger body size and longer lifespan. By sequencing African elephants, they found elephants have more than 20 copies of the TP53 gene, a major tumor suppressor. This could explain their low rates of cancer mortality.

Read more at PubMed »

Abegglen LM, Caulin AF, Chan A, et al. Potential mechanisms for cancer resistance in Elephants and comparative response to DNA damage in humans - JAMA

Whole genome sequencing in cats, identifies new models for blindness in AIPL1 somite segmentation in HES7.

As part of the 99 Lives Cat Genome Sequencing Initiative, researchers performed whole-genome sequencing using Illumina technology to identify disease-causing variants in the domestic cat. Sequencing Persian cats identified a novel variant in AIPL1, a gene that is frequently mutated in Leber’s congenital amaurosis, a heterogenous group of early-onset retinal dystrophies.

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Lyons LA, Creighton EK, Alhaddad H, et al. Whole genome sequencing in cats, identifies new models for blindness in AIPL1 somite segmentation in HES7. - BMC Genomics

Cell-free DNA testing of an extended range of chromosomal anomalies: clinical experience with 6388 consecutive cases.

To increase the identification of clinically relevant aneuploidies by cell-free DNA (cfDNA) prenatal screening, researchers analyzed > 6000 cases sequenced with Illumina technology. They found novel rare autosomal trisomies (RATs) and maternally inherited copy number variations (CNVs). Confirmation by amniocentesis indicates that this method of analysis is valuable to include in cfDNA screening.

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Pescia G, Guex N, Iseli C, et al. Cell-free DNA testing of an extended range of chromosomal anomalies: clinical experience with 6388 consecutive cases. - Genet Med

Sleeping beauty screen reveals Pparg activation in metastatic prostate cancer.

Using the Sleeping Beauty mutagenesis screen and the NextSeq 550 System, researchers identified alterations in peroxisome proliferator-activated receptor gamma (Pparg). Mutations in this critical regulator of lipid metabolism have been shown to drive metastatic prostate cancer in mice. The study also shows that elevated levels of Pparg correlate with poor prognosis in human patients. PPARG inhibition may represent a possible new target for prostate cancer therapy.

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Ahmad I, Mui E, Galbraith L, et al. Sleeping beauty screen reveals Pparg activation in metastatic prostate cancer. - PNAS

Composition of the gut microbiota modulates the severity of malaria.

Plasmodium infections cause > 200 million cases of malaria and ~ 1 million deaths annually. Using a mouse model and bacterial 16S rRNA sequencing on the MiSeq System, researchers found that certain strains of host gut microbes conferred resistance to Plasmodium infection, indicating a new potential avenue of therapy.

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Villarino NF, LeClair GR, Denny JE, et al. Composition of the gut microbiota modulates the severity of malaria. - PNAS

Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse.

Researchers used Illumina array technology to perform expression profiling of a mouse model with increased circulating estrogen/androgen ratio. These mice had significantly altered expression of genes related to liver lipid metabolism linked to changes in phospholipid (PL) levels in blood plasma. This altered plasma PL profile is linked to diseases such as liver cancer and diabetes.

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Vehmas AP, Adam M, Laajala TD, et al. Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse. - J Proteomics

Worldwide patterns of genomic variation and admixture in gray wolves.

Though known to be a descendant of the gray wolf, the specific region of origin of the domestic dog is still controversial. Researchers used the HiSeq 2000 System to assemble a data set of full genome sequences for 24 wolves from around the globe and 7 dogs. Analysis revealed that dogs diverged from an extinct Old World (Eurasian) wolf population.

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Fan Z, Silva P, Gronau I, et al.Worldwide patterns of genomic variation and admixture in gray wolves. - Genome Res

Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach.

Researchers used 16S rRNA sequencing on the MiSeq System to profile the diverse microbial community responsible for degradation of petroleum hydrocarbons into nontoxic compounds at 4 bioremediation sites. They found that Gram-negative strains of bacteria were prevalent and critical for success. 16S rRNA sequencing can be used to monitor microbial populations and guide efforts to enhance the bioremediation process.

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Shahi A, Aydin S, Ince B, and Ince O.Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach. - Ecotoxicol Environ Saf

The impact of oil spill to lung health – Insights from an RNA-seq study of human airway epithelial cells.

Researchers performed RNA-Seq on human airway epithelial cells treated with oil, dispersants, and oil-dispersant mixtures. They found strong effects on gene expression from oil or dispersants alone, and synergistic effects in combination. The observed expression profiles correspond to pathological features common in lung diseases such as asthma and cystic fibrosis.

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Liu YZ. Roy-Engel AM, Baddoo MC, et al.The impact of oil spill to lung health – Insights from an RNA-seq study of human airway epithelial cells. - Gene

Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes.

Using microdissection of seminiferous tubules and Illumina sequencing, researchers found new gain-of-function mutations in the male germline. These de novo point mutations occurred in genes involved in growth factor signaling and RAS oncogenes. Such “paternal age effect” mutations have known associations with congenital or perinatal lethal disorders and cancers.

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Mather GJ, McGowan SJ, Giannoulatou E, et al.Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes. - PNAS

Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice.

Researchers characterized a novel probiotic mixture that prevents tumor growth in hepatocellular carcinoma mouse models. Shotgun-metagenome sequencing revealed that the mechanism of tumor suppression is via modulation of the gut microbiota toward strains that secrete antiinflammatory metabolites. This prevents differentiation of intestinal immune cells to proinflammatory fates that promote tumor growth.

Read more at PubMed »

Li J, Sung CY, Lee N, et al.Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. - PNAS