Identification of Disease Susceptibility Alleles in the Next Generation Sequencing Era.

The development of next generation sequencing (NGS) technologies has transformed the study of human genetic variation. In less than a decade, NGS has facilitated the discovery of causal mutations in both rare, monogenic diseases and common, heterogeneous disorders, leading to unprecedented improvements in disease diagnosis and treatment strategies. Given the rapid evolution of NGS platforms, it is now possible to analyze whole genomes and exomes quickly and affordably.

Identifying Robertsonian Translocation Carriers by Microarray-Based DNA Analysis.

Objective: To develop a noninvasive prenatal testing improvement that allows identification of Robertsonian translocation carriers.

Methods: Blood samples from 191 subjects, including 7 pregnant and 9 non-pregnant Robertsonian translocation carriers, were analyzed for fetal trisomy and Robertsonian translocation status. Digital Analysis of Selected Regions (DANSR™) assays targeting sequences common to the p arms of 5 acrocentric chromosomes were developed and added to existing DANSR assays.

Identification of novel clinical factors associated with hepatic fat accumulation in extreme obesity.

Objectives: The accumulation of lipids stored as excess triglycerides in the liver (steatosis) is highly prevalent in obesity and has been associated with several clinical characteristics, but most studies have been based on relatively small sample sizes using a limited set of variables. We sought to identify clinical factors associated with liver fat accumulation in a large cohort of patients with extreme obesity.

Methods: We analyzed 2929 patients undergoing intraoperative liver biopsy during a primary bariatric surgery.

Genome-wide analysis of hepatic lipid content in extreme obesity.

Aims: Individuals with type 2 diabetes have an increased risk of developing non-alcoholic fatty liver disease (NAFLD), and NAFLD patients are also at greater risk for developing type 2 diabetes. Although the relationship between type 2 diabetes and NAFLD is highly interconnected, the pathogenic mechanisms linking the two diseases are poorly understood. The goal of this study was to identify genetic determinants of hepatic lipid accumulation through association analysis using histological phenotypes in obese individuals.

Microarray-based cell-free DNA analysis improves noninvasive prenatal testing.

Objective: To develop a microarray-based method for noninvasive prenatal testing (NIPT) and compare it with next-generation sequencing.

Methods: Maternal plasma from 878 pregnant women, including 187 trisomy cases (18 trisomy 13, 37 trisomy 18, 132 trisomy 21), was evaluated for trisomy risk. Targeted chromosomes were analyzed using Digital Analysis of Selected Regions (DANSR™) assays.

FN14 expression correlates with MET in NSCLC and promotes MET-driven cell invasion.

The five-year survival rate in advanced non-small cell lung cancer (NSCLC) remains below ten percent. The invasive and metastatic nature of NSCLC tumor cells contributes to the high mortality rate, and as such the mechanisms that govern NSCLC metastasis is an active area of investigation. Two surface receptors that influence NSCLC invasion and metastasis are the hepatocyte growth factor receptor (HGFR/MET) and fibroblast growth factor-inducible 14 (FN14).

Prospective molecular profiling of canine cancers provides a clinically relevant comparative model for evaluating personalized medicine (PMed) trials.

Background: Molecularly-guided trials (i.e. PMed) now seek to aid clinical decision-making by matching cancer targets with therapeutic options.

Elevated expression of Fn14 in non-small cell lung cancer correlates with activated EGFR and promotes tumor cell migration and invasion.

Lung cancer is the leading cause of cancer deaths worldwide; approximately 85% of these cancers are non-small cell lung cancer (NSCLC). Patients with NSCLC frequently have tumors harboring somatic mutations in the epidermal growth factor receptor (EGFR) gene that cause constitutive receptor activation. These patients have the best clinical response to EGFR tyrosine kinase inhibitors (TKIs).

Identification of causal sequence variants of disease in the next generation sequencing era.

Over the last decade, genetic studies have identified numerous associations between single nucleotide polymorphism (SNP) alleles in the human genome and important human diseases. Unfortunately, extending these initial associative findings to identification of the true causal variants that underlie disease susceptibility is usually not a straightforward task. Causal variant identification typically involves searching through sizable regions of genomic DNA in the vicinity of disease-associated SNPs for sequence variants in functional elements including protein coding, regulatory, and structural sequences.

Tumor necrosis factor-like weak inducer of apoptosis stimulation of glioma cell survival is dependent on Akt2 function.

Malignant gliomas are the most common primary brain tumors. Despite intensive clinical investigation and significant technical advances in surgical and radiation treatment, the impact on clinical outcome for patients with malignant gliomas is disappointing. We have previously shown that tumor necrosis factor-like weak inducer of apoptosis (TWEAK), a member of the tumor necrosis factor superfamily, can stimulate glioma cell survival via binding to the Fn14 receptor, activation of the NF-kappaB pathway, and upregulation of BCL-X(L) gene expression.

Variants in the plasmacytoma variant translocation gene (PVT1) are associated with end-stage renal disease attributed to type 1 diabetes.

Objective: End-stage renal disease (ESRD) attributed to diabetes is strongly dependent on genetic factors. We previously reported association between variants in the plasmacytoma variant translocation gene (PVT1) and ESRD attributed to type 2 diabetes in Pima Indians. The objective of this study was to evaluate the extent to which these variants mediate susceptibility in other populations.