Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

Preview Day Welcome

Geoffrey Winship, Senior in the School of Business, gave the Preview Day Welcome talk to those assembled

VEX Robotics Club

The VEX Robotics Club is a competition-based group of students at Embry-Riddle Aeronautical University, Prescott Campus. The team designs and constructs robots using standard VEX parts and competes in university-level VEX Robotics competitions. The club is divided into three competition teams: Blue, White, and Gold teams. Each team builds one robot and represents Embry-Riddle Aeronautical University at VEX Competitions. The VEX game for the 2017-2018 season is called “In the Zone.” In the game, two competing robots score as many yellow plastic cones on red and blue stationary or mobile bases and can also move the mobile bases into scoring zones on two corners of the competition field during the two-minute matches. The robots must operate autonomously for the first 45 seconds of each match, then drivers can take over control of the robots. The teams began the season by researching different scoring ideas, building prototypes, and conducting research to determine the best designs. Then the teams built their robots and programmed them using the RobotC language, then competing in the first competition of the season in early November on campus and the second competition in early Marchon campus. The club is also responsible for hosting these two competitions, the second of which invites over seventy teams to compete in high school and university level divisions. Poster format preferred. Poster Presentation EAGLE PRIZE AWAR

Vex Robotics

The Vex Robotics Team is an E-Prize competition team. The team is comprised of students of all class standings and from all the colleges on campus. They competes in the VexU competition circuit in the state of Arizona and the competition this year is called Toss Up and is played on a 12 ft by 12 ft field. The game involves the moving or tossing of game elements, which for this year are large 16\u27 diameter beach balls and 5\u27 diameter bucky balls, into several different goal zones on the field. The game is played between two teams, each with two robots. For this years planning, building, and testing stage we used the Engineering Design Process to help guide us in solving the problem at hand. Using this method we were able to construct, program, and test our two robots for competition. The team will be competing on March 1st, 2014 in Tempe, Arizona

2015-2016 VEX Robotics Team

The VEX Robotics Team is a competition-based group on the Embry-Riddle Aeronautical University, Prescott Campus. The team designs and constructs robots using standard VEX parts, and competes in university-level VEX Robotics competitions. This year, the organization had two teams: Blue Team and Gold Team. Each team builds two robots and represents Embry-Riddle Aeronautical University at competitions. The VEX game for the 2015-2016 season is named “Nothing But Net.” In the game, each robot alliance scores as many 4-inch foam balls as possible into its respective net, which lies at the opposite corner of the 12’ by 12’ field. Then, during the last 30 seconds of the 2-minute match, one robot from each alliance elevates its partner robot off the ground either 4 inches for a low elevation, or 12 inches for a high elevation. The teams began the year with brainstorming ideas for robot designs, conducting research, and constructing prototypes. Then, the teams constructed their final designs, programmed their robots using the RobotC programming language, and conducted final testing in preparation for competition. The VEX Robotics Team successfully hosted its first VEX-U competition at Embry-Riddle Aeronautical University, Prescott Campus in November of 2015, and is planning on hosting future competitions. Additionally, the team competed at the Southwest VEX-U Tournament on March 5th, 2016 at Arizona State University in Tempe, AZ. Poster Presentation EAGLE PRIZE AWAR

Red cells from ferrochelatase-deficient erythropoietic protoporphyria patients are resistant to growth of malarial parasites

Many red cell polymorphisms are a result of selective pressure by the malarial parasite. Here, we add another red cell disease to the panoply of erythrocytic changes that give rise to resistance to malaria. Erythrocytes from individuals with erythropoietic protoporphyria (EPP) have low levels of the final enzyme in the heme biosynthetic pathway, ferrochelatase. Cells from these patients are resistant to the growth of Plasmodium falciparum malarial parasites. This phenomenon is due to the absence of ferrochelatase and not an accumulation of substrate, as demonstrated by the normal growth of P falciparum parasites in the EPP phenocopy, X-linked dominant protoporphyria, which has elevated substrate, and normal ferrochelatase levels. This observation was replicated in a mouse strain with a hypomorphic mutation in the murine ferrochelatase gene. The parasite enzyme is not essential for parasite growth as Plasmodium berghei parasites carrying a complete deletion of the ferrochelatase gene grow normally in erythrocytes, which confirms previous studies. That ferrochelatase is essential to parasite growth was confirmed by showing that inhibition of ferrochelatase using the specific competitive inhibitor, N-methylprotoporphyrin, produced a potent growth inhibition effect against cultures of P falciparum. This raises the possibility of targeting human ferrochelatase in a host-directed antimalarial strategy.8 page(s

Erythropoietic protoporphyric red blood cells are resistant to the growth of malarial parasites

Many red cell polymorphisms are a result of selective pressure by the malarial parasite. Here we add another red cell disease to the panoply of erythrocytic changes that give rise to resistance to malaria. Erythrocytes from individuals with erythropoietic protoporphyria (EPP) have low levels of the final enzyme in the heme biosynthetic pathway, ferrochelatase. Cells from these patients are resistant to the growth of the human malarial parasite, Plasmodium falciparum. We first compared the growth and replication rates of P. falciparum cultured in red cells from EPP patients (n=4) and normal erythrocytes. There was a two to three-fold reduction in parasite growth in the patient cells. Next we sought to exclude the possible negative effects on the parasite due to elevated porphyrins and reduced cell hemoglobin. To do this we employed the EPP phenocopy, X-linked dominant protoporphyria (XLDPP), which has normal ferrochelatase activity. Cells from three individuals with XLDPP supported completely normal rates of parasite growth, proving that the EPP resistance phenomenon was due to the absence of ferrochelatase. We also tested the requirement of host ferrochelatase during malarial infection by using mice with a hypomorphic mutation in the murine ferrochelatase gene and the rodent malarial species, P. chabaudi. Mice homozygous for the mutation, Fechm1Pas, have 5% residual ferrochelatase activity compared to wild-type littermates. Following infection, we observed an almost two fold reduction in peak parasitemia levels and two to three times greater rates of survival in the homozygous mice. Host ferrochelatase is therefore also necessary to sustain a normal malarial infection in mice. To determine the requirement of parasite-expressed ferrochelase, we produced a P. berghei parasite line carrying a complete deletion of the ferrochelatase gene. This strain grew normally in wild-type mouse erythrocytes, indicating that parasite ferrochelatase is dispensable during the erythrocytic stage of infection. A complete absence of ferrochelatase in humans (and mice) is not compatible with life, and therefore testing parasite growth in complete knockout cells was not possible. Instead, we used a specific competitive inhibitor of the enzyme, N-methylprotoporphyrin (NMPP) to eliminate all ferrochelatase activity from the parasite and red cell. Treatment of P. falciparum cultures with NMPP resulted in potent cytocidal and growth inhibition effects against both antimalarial drug-sensitive and drug-resistant parasite lines. The activity of NMPP could be competitively removed by titration of the ferrochelatase substrate, protoporphyrin IX, proving that the effects of NMPP were due to specific enzyme inhibition and not off-target effects. Therefore ferrochelatase activity is also essential for the Plasmodium parasite. We conclude that the refractoriness of ferrochelatse-deficient red cells to Plasmodium is due to the parasite's reliance on the host enzyme. Host ferrochelatase is probably utilized by the parasite for the biosynthesis of heme. In support of this hypothesis, others have observed that red cell ferrochelatase is imported by intraerythrocytic Plasmodium and enzymatic is retained. Finally, based on this collective data, we propose human ferrochelatase is a valid and novel "host-directed" target for an antimalarial therapy.1 page(s

VEX Robotics Team

The VEX Robotics Team is a competition-based group of students at Embry-Riddle Aeronautical University, Prescott Campus. The team designs and constructs robots using standard VEX parts, and competes in university-level VEX Robotics competitions. This year, the organization separated into three teams: Blue, White, and Gold Teams. Each team built one robot and represented Embry-Riddle Aeronautical University at VEX competitions. The VEX game for the 2016-2017 season is named “Starstruck.” In the game, each robot scores as many 6-pronged foam stars and 12 in cubes as possible over a 2ft high fence, which divides the field in half. Then, during the last 30 seconds of the 2-minute match, each robot has the opportunity to suspend itself off the ground using a 2 ft high pole located in one of the corners on its side of the field, either 4 inches for a low hang, or 12 inches for a high hang. The teams began the year with brainstorming ideas for robot designs, conducting research, and constructing prototypes. Then the teams constructed their final designs, programmed their robots using the RobotC programming language, and conducted final testing in preparation for the competition. The VEX Robotics Team successfully hosted its second VEX-U competition at Embry-Riddle Aeronautical University, Prescott Campus in November of 2016, and competed in the Southwest VEX-U Tournament on March 4th, 2017– also held at Embry-Riddle’s Prescott Campus. Eagle Prize Awar