Joint tests for quantitative trait loci in experimental crosses

Selective genotyping is common because it can increase the expected correlation between QTL genotype and phenotype and thus increase the statistical power of linkage tests (i.e., regression-based tests). Linkage can also be tested by assessing whether the marginal genotypic distribution conforms to its expectation, a marginal-based test. We developed a class of joint tests that, by constraining intercepts in regression-based analyses, capitalize on the information available in both regression-based and marginal-based tests. We simulated data corresponding to the null hypothesis of no QTL effect and the alternative of some QTL effect at the locus for a backcross and an F2 intercross between inbred strains. Regression-based and marginal-based tests were compared to corresponding joint tests. We studied the effects of random sampling, selective sampling from a single tail of the phenotypic distribution, and selective sampling from both tails of the phenotypic distribution. Joint tests were nearly as powerful as all competing alternatives for random sampling and two-tailed selection under both backcross and F2 intercross situations. Joint tests were generally more powerful for one-tailed selection under both backcross and F2 intercross situations. However, joint tests cannot be recommended for one-tailed selective genotyping if segregation distortion is suspected.     

Choice versus no-choice test interpretation and the role of biology and behavior in parasitoid host specificity tests

The need to improve methods and interpretation of host specificity tests for arthropod natural enemies has been clearly identified, yet there remains a paucity of empirical evidence upon which to base recommendations. Factors influencing test outcomes and the mechanisms underlying them must be understood so they can be controlled, and test results can be interpreted correctly. In this study, an established exotic host/parasitoid system was used to assess the outcomes and predictive accuracy of no-choice compared to paired choice tests within small laboratory arenas. Host acceptance by two egg parasitoids, Enoggera nassaui and Neopolycystus insectifurax (Pteromalidae), was interpreted in light of percent parasitism, offspring sex ratios and observed parasitoid behavior. No-choice tests showed that the four host species, Paropsis charybdis, Dicranosterna semipunctata, Trachymela catenata and Trachymela sloanei (Coleoptera: Chrysomelidae) were within the physiological host ranges of both parasitoids. The results of paired choice tests with the first three species supported this interpretation, with two exceptions. Trachymela catenata eggs were not accepted by E. nassaui and were accepted significantly less often by N. insectifurax when compared to no-choice tests. Both test designs predicted that D. semipunctata is within the ecological host range of the two parasitoid species, whereas field evidence suggests this is a false positive result. Percent parasitism of all hosts was higher in no-choice compared to choice tests and was predictive of rank order of host preference in choice tests. Presence of the most preferred host did not increase attack on lower ranked hosts. Offspring sex ratios of E. nassaui were independent of host preference. In contrast, N. insectifurax allocated more females to P. charybdis and mostly males to D. semipunctata and T. catenata. The results support our assertion that both no-choice and choice tests along with detailed behavioral studies should be conducted for correct interpretation of pre-release host specificity tests. This will enable more accurate predictions of parasitoid host ranges and risks parasitoids may pose to non-target organisms in the field.     

A study on the analytical sensitivity of 6 BSE tests used by the Canadian BSE reference laboratory

Bovine spongiform encephalopathy (BSE) surveillance programs have been employed in numerous countries to monitor BSE prevalence and to protect animal and human health. Since 1999, the European Commission (EC) authorized the evaluation and approval of 20 molecular based tests for the rapid detection of the pathological prion protein (PrP^sc) in BSE infection. The diagnostic sensitivity, convenience, and speed of these tests have made molecular diagnostics the preferred method for BSE surveillance. The aim of this study was to determine the analytical sensitivity of 4 commercially available BSE rapid-test kits, including the Prionics®-Check WESTERN, the Prionics® Check-PrioSTRIP™, the BioRad® TeSeE™ ELISA, and the IDEXX® HerdChek™ EIA. Performances of these tests were then compared to 2 confirmatory tests, including the BioRad® TeSeE™ Western Blot and the modified Scrapie Associated Fibrils (SAF)/OIE Immunoblot. One 50% w/v homogenate was made from experimentally generated C-type BSE brain tissues in ddH₂O. Homogenates were diluted through a background of BSE-negative brainstem homogenate. Masses of both positive and negative tissues in each dilution were calculated to maintain the appropriate tissue amounts for each test platform. Specific concentrated homogenization buffer was added accordingly to maintain the correct buffer condition for each test. ELISA-based tests were evaluated using their respective software/detection platforms. Blot-protocols were evaluated by manual measurements of blot signal density. Detection limitations were determined by fitted curves intersecting the manufacturers'' positive/negative criteria. The confirmatory SAF Immunoblot displayed the highest analytical sensitivity, followed by the IDEXX® HerdChek™ EIA, Bio-Rad® TeSeE™ Western Blot, the Bio-Rad® TeSeE™ ELISA, Prionics®-Check PrioSTRIP™, and Prionics®-Check WESTERN™, respectively. Although the tests performed at different levels of sensitivity, the most sensitive and least sensitive of the rapid tests were separated by 2 logs in analytical sensitivity, meeting European performance requirements. All rapid tests appear suitable for targeted BSE surveillance programs, as implemented in Canada.     

In Vivo Screening of Hepatocellular Carcinoma Using AC Susceptibility of Anti-Alpha Fetoprotein-Activated Magnetic Nanoparticles

With antibody-mediated magnetic nanoparticles (MNPs) applied in cancer examinations, patients must pay at least twice for MNP reagents in immunomagnetic reduction (IMR) of in vitro screening and magnetic resonance imaging (MRI) of in vivo tests. This is because the high maintenance costs and complex analysis of MRI have limited the possibility of in vivo screening. Therefore, this study proposes novel methods for in vivo screening of tumors by examining the AC susceptibility of bound MNPs using scanning superconducting-quantum-interference-device (SQUID) biosusceptometry (SSB), thereby demonstrating high portability and improved economy. The favorable agreement between in vivo tests using SSB and MRI demonstrated the feasibility of in vivo screening using SSB for hepatocellular carcinoma (HCC) targeted by anti-alpha fetoprotein (AFP)-mediated MNPs. The magnetic labeling was also proved by in vitro tests using SSB and biopsy assays. Therefore, patients receiving bioprobe-mediated MNPs only once can undergo in vivo screening using SSB in the future.     

Novel sulfonamides against Botrytis cinerea with no positive cross-resistance to commercial fungicides: Design,synthesis and SAR study

Thirty-four novel compounds were synthesized using chesulfamide (N-(2-trifluoromethyl-4-chlorophenyl)-2-oxocyclohexyl sulfonamide), a high-profile fungicide, as the lead compound, and their structures were characterized by ¹H NMR, ¹³C NMR, MS and elemental analysis. Additionally, the structure of (1S,2R)-2-((3-bromophenethyl)amino)-N-(4-chloro-2-trifluoromethylphenyl)cyclohexane-1-sulfonamide (IV-9) was confirmed by X-ray single crystal diffraction. The mycelium inhibition tests, spore germination inhibition tests, tomato pot tests and field trials were performed against strains of B. cinerea. Bioassay results showed that most of target compounds had good fungicidal activity against B. cinerea, in particular, IV-9 exhibited similar or superior effects to procymidone, boscalid and pyrisoxazole in all in vitro and in vivo tests. Moreover, there was no positive cross-resistance found between the compound IV-9 and eight commercial fungicides (azoxystrobin, boscalid, chlorothalonil, diethofencarb, fludioxonil, procymidone, pyrimethanil and pyrisoxazole) in the cross-resistance validation test performed by an innovative method.     

A review of safety tests on baculoviruses

In the late 1960's the degree of safety testing required of new candidate pesticides reached a climax. During this period, the nuclear polyhedrosis virus (NPV) ofHeliothis zea (Boddie) underwent a series of tests as thorough as those required for chemicals by the Environmental Protection Agency (E.P.A.) in the U.S.A. and by guidelines recommended by W.H.O. These included long term carcinogenicity and teratogenicity tests, tests on primates and tests on man. Indeed, the tests were far more demanding than the tests for chemicals because they examined the possibility of infection of test animals by the insect viruses. They led to the registration of a pioneer viral insecticide containing this NPV produced in caterpillars. Two other products from Lepidoptera, containing NPVs ofOrgyia pseudotsugata (McDunn) andLymantria dispar L. have satisfied the E.P.A. registration requirements. The NPV ofNeodiprion sertifer (Geoffr.) (Hym.) has proved harmless in extensive tests, including long term tests. Another 3 NPVs, those ofAutographa californica (Speyer)Spodoptera littoralis Boisd. andS. exempta (Walk.) passed tests not including the long term tests. Also a non-occluded baculovirus of a coleopteran,Oryctes rhinoceros L., has passed extensive pathogenicity tests and tests in cell lines. A number of other NPVs have been partially tested and limited tests have been made on 2 granulosis viruses (GV). The NPVs proved harmless to—and unable to replicate in—microorganisms, non-insect invertebrate cell lines vertebrate cell lines, vertebrates, plants and non-arthropod invertebrates. Replication was unusual in insects outside the insect family in which the virus was first found. GVs occur only in Lepidoptera, most are believed to be very specific and none have replicated in cell lines from insects or other animals. In addition, the rapidly expanding discipline of Invertebrate Pathology has failed to find incidence of NPVs and GVs infecting hosts outside the above stated host ranges. This is in reality a vast body of evidence matched only in extent by the absence of incidence of NPVs and GVs from the publications of medical, veterinary and phytopathology science. This evidence, and the accrued data from specific safety testing, gives increasing confidence that individual NPVs and GVs of Lepidoptera and Hymenoptera are very specific. This confidence suggests that new NPVs and GVs in these orders need be subjected only to a reduced range of the more challenging tests and to tests designed to reveal harm originating from the insect species used for virus production and from contaminants.     

Combined effects of temperature and interspecific competition on the mortality of the invasive garden ant,Lasius neglectus: A laboratory study

The invasive garden ant, Lasius neglectus, is a dominant species due to its capacity to form large supercolonies. This species was assumed to possess a wide thermal niche since it is able to adapt to cold climates, which is a factor that boosted its rapid expansion from south to many central-northern European Countries. However, the effect of variations in environmental temperatures on its competitive ability against other species has still not been investigated. In this paper, we analyzed the change in survival ability of Lasius neglectus during encounters with two Mediterranean dominant ants (Crematogaster scutellaris and Tapinoma nigerrimum) at four different temperatures (15, 20, 25 and 30 °C). Firstly, control tests were performed to provide the baseline survival ability of the three species at different temperatures. Secondly, competition tests were carried out at the same temperatures. Lasius neglectus survival was negatively affected by high temperature (30 °C) in control tests, and this impairment was much more pronounced in competition tests. On the contrary, the two opponent species were only marginally affected by temperatures in control tests. Crematogaster scutellaris was a better competitor than L. neglectus, particularly at high temperatures. Tapinoma nigerrimum was a weaker competitor and was always outcompeted by L. neglectus, particularly at low temperatures. This result could suggest that L. neglectus is at a disadvantage during interspecific encounters when temperatures are high and that the predicted future increase in environmental temperatures may potentially enhance this handicap.     

Population Dynamics of Meloidogyne incognita on Corn Grown in Soil in Fested with Arthrobotrys conoides

Microplot and greenhouse experiments were conducted to evaluate the effects of soil incorporation of the nematophagous fungus Arthrobotrys conoides and green alfalfa mulch on the population dynamics of Meloidogyne incognita on corn. Reproduction of M. incognita and the incidence of root galling were reduced by the addition of A. conoides and/or green alfalfa in all tests. Numbers of juveniles were reduced by as much as 84%, and eggs were fewest in early to mid-season soil samples from microplots. Yields increased in treatments with A. conoides and/or green alfalfa in greenhouse tests and in the microplot tests in 1979. No interaction was found between the fungus and green alfalfa in the reduction of the nematode population.     

Comparative Study of the Efficacy of Seven Paper-Reagent Strips and Conventional Biochemical Tests in Identifying Gram-negative Organisms

Gram-nagative organisms were tested with commercially available reagentimpregnated strips (PATHO-TEC). Of the 291 strains, all were tested by using seven paper tests and their conventional counterparts. Excellent correlation was obtained with the oxidase, phenylalanine-deaminase, and Voges-Proskauer tests. Indole tests made on liquid medium cultures also gave complete correlation, but some false-negative results with indole-positive Proteus strains were obtained when growth from solid medium was tested by the strip method. Paper strip urease tests were positive within 2 hr with all Klebsiella and some Serratia, Herellea, and Citrobacter strains as well as with Proteus strains. Approximately 15% of citrate strip test results differed from those of the conventional tests, and reproducibility was poor on retest. The lysine decarboxylase strip test showed a number of discrepancies and posed problems of interpretation and readability. Paper reagent strip methods are simple and convenient and merit further development to increase the specificity of those which depend on pH change up to that achieved with the Voges-Proskauer, oxidase, phenylalanine, and indole methods.     

Development of mutagenicity test using Escherichia coli K-12 as indicator organism

A derivative of Escherichia coli K-12 (strain $\text{343}\text{113}$) has been developed in which mutations in several genes can be detected simultaneously by plating parts of the bacterial population on different selective media. The mutation types include reversions from differently induced auxotrophies (nad^-, arg^-) aand (forward) mutations leading to resistance against 5-methytryptophan and to gal⁺ phenotype. It is assumed that many types of DNA alteration, including deletions and changes involving gross DNA regions, will lead to viable detectable mutants.The usefulness of strain E. coli$\text{343}\text{113}$ was tested in spot tests, in liquid tests, in tests with extracts of mammalian organs, and in mammalian-mediated tests. It is concluded that strain $\text{343}\text{113}$ is at least as useful in routine mutagenicity testing (especially in mammalian-mediated assays) as other present bacterial strains.     

So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests

Contemporary genetic association studies may test hundreds of thousands of genetic variants for association, often with multiple binary and continuous traits or under more than one model of inheritance. Many of these association tests may be correlated with one another because of linkage disequilibrium between nearby markers and correlation between traits and models. Permutation tests and simulation-based methods are often employed to adjust groups of correlated tests for multiple testing, since conventional methods such as Bonferroni correction are overly conservative when tests are correlated. We present here a method of computing P values adjusted for correlated tests (P_ACT) that attains the accuracy of permutation or simulation-based tests in much less computation time, and we show that our method applies to many common association tests that are based on multiple traits, markers, and genetic models. Simulation demonstrates that P_ACT attains the power of permutation testing and provides a valid adjustment for hundreds of correlated association tests. In data analyzed as part of the Finland–United States Investigation of NIDDM Genetics (FUSION) study, we observe a near one-to-one relationship (r²>.999) between P_ACT and the corresponding permutation-based P values, achieving the same precision as permutation testing but thousands of times faster.     

The timing of mu activity in maize

The timing of mutator activity of Mu in maize was tested in three ways: (1) by allelism tests of phenotypically similar male-transmitted mutants, (2) by studying the clustering of phenotypically similar mutants as demonstrated by ear maps and the subsequent allelism tests of these mutants, and (3) by the induction of somatic sectors in Mu plants heterozygous for plant and endosperm marker genes. Allelism tests of phenotypically similar mutants in outcrosses of Mu plants as males established that 18.6% were allelic and that premeiotic mutants are induced. This conclusion was supported by ear maps of Mu-bearing plants, which revealed sectors of seeds that produced plants bearing phenotypically similar allelic mutants. The smallness of these sectors indicated that the premeiotic activity of Mu that gave rise to them occurred very late. The lack of visible sectors in mature sporophytic, endosperm and aleurone tissue in plants carrying Mu supports the conclusion that the mutator activity of Mu does not occur throughout the ontogeny of the plant and seems to be restricted to a time shortly before and/or during meiosis.     

Pair-wise analyses of the effects of demographic processes, vital rates, and life stages on the spatiotemporal variation in the population dynamics of the riparian tree Aesculus turbinata Blume

Population growth rates (λ) of the riparian tree Aesculus turbinata varied from 0.9988 to 1.0524 spatiotemporally. We conducted a series of pair-wise demographic and matrix analyses, including randomization tests, three types of life table response experiments (LTREs), analysis of variance and χ² tests, to test which life stages had the greatest effect on this variation in λ. Randomization tests detected significant variations in λ between plots affected or not by typhoons in three habitats and between periods with high and low recruitment in one habitat. Mixed-level LTREs identified that the demographic processes and life stages that had the strongest effect on the actual variation in λ were: (1) progressions of small and intermediate juveniles and (2) founding process from seeds to 1-year-old seedlings. These juvenile stages had medium sensitivities and variances that explained high upper-level LTRE contributions. Lower-level LTREs showed that the vital rates contributing the most were the growth rates of these juvenile stages. These findings demonstrate that progression from one stage to the next, growth rates of 1-year-old seedlings, and stunted aging juveniles are the most important stages in the population dynamics of this long-lived primary tree species. Transition matrix elements with high elasticities had little effect on the variation in λ, indicating that high-elasticity vital rates do not necessarily drive variation in population growth. As compared with the results of randomization tests, significant differences in vital rates examined using ANOVA or χ² tests showed that typhoon disturbance had the greatest effect on the demographic parameters of individual trees.     

Post hoc assessment of host plant use in a generalist invader: implications for understanding insect–plant interactions and weed biocontrol

Structured host-choice and no-choice tests were conducted to help clarify the host plant interactions of an insect herbivore that is simultaneously seen as broadly polyphagous and pestiferous (in Africa) and host restricted/beneficial (in Australia). The research reported here involves specification of the host range of the invasive population of Scirtothrips aurantii found on Bryophyllum in Australia and included tests involving three separate lists of plant species considered to have the potential for thrips attack (plants of horticultural concern, native species at risk of attack and species listed for screening in the search for specialist B. delagoense biocontrol agents). This procedure was developed specifically to deal with the S. aurantii situation in Australia. Because the test species is already present in the field, the conclusions from the tests could be evaluated independently against field sampling results. Host testing revealed that the fundamental host range of the Bryophyllum population of S. aurantii includes Macadamia integrifolia, Mangifera indica and Kalanchoe blossfeldianna. However, the choice tests (involving B. delagoense) and a field survey of Man. indica demonstrated conclusively that the realised host range of S. aurantii in the field is restricted to Crassulaceae. We recommend that host testing of generalist insects not be discounted out of hand (for biological control) because of their perceived polyphagy. Any evidence of populations being strongly associated with the weed species of interest (through quantified host association studies in the native range) suggests further scrutiny of that population is warranted, by means of the host testing methods developed here and in conjunction with appropriate tests of the population’s species status.     

Antigenic Relationship of Brucella ovis and Brucella melitensis

Immune sera were prepared in rabbits by the injection of living and acetone-killed cells of Brucella ovis and smooth and rough B. melitensis. The use of whole-cell antigens in agglutination and agglutinin-absorption tests revealed little relationship between B. ovis and smooth B. melitensis, although there was extensive cross-agglutination between B. ovis and rough B. melitensis. The use of water-soluble antigens prepared from ultrasonically treated cells of the three strains revealed extensive cross-reactions in indirect hemagglutination, agar gel precipitation, and immunoelectrophoresis tests, as well as in allergic skin tests in rabbits. The most definitive results were obtained with the immunoelectrophoresis technique. B. ovis antigen produced at least 11 lines with its homologous serum. All were removed by absorption of the serum with rough B. melitensis antigen. All but three were removed by absorption with smooth B. melitensis antigen. Smooth B. melitensis antigen produced 11 lines with its homologous serum, and all but 3 were removed by absorption with B. ovis antigen. Rough B. melitensis produced nine lines with its homologous serum, and eight were removed by B. ovis antigen. The extensive cross-reactions between soluble antigens of B. ovis and B. melitensis are added evidence that B. ovis belongs in the genus Brucella.     

Fungal Parasitism of Heterodera glycines Eggs as Influenced by Egg Age and Pre-colonization of Cysts by Other Fungi

The objective of this study was to determine the effect of egg age and pre-colonization of cysts by a saprophytic or parasitic fungus on parasitism of Heterodera glycines eggs by other parasitic fungi. In agar and in soil tests, fungi generally parasitized more eggs in early developmental stages than eggs containing a juvenile. The effect of pre-colonization of cysts by a fungus on parasitism of eggs by other fungi depended on the fungi involved. In most cases, pre-colonization of cysts by an unidentified, saprophytic fungal isolate (A-1-24) did not affect parasitism of eggs in the cysts subsequently treated with other fungi. However, pre-colonization of cysts by A-1-24 reduced fungal parasitism of eggs in cysts subsequently treated with Cylindrocarpon destructans isolate 3. In agar tests, pre-colonization of cysts by Chaetomium cochliodes, a saprophytic or weakly parasitic fungus, reduced parasitism of eggs in cysts subsequently treated with Verticillium chlamydosporium Florida isolate, Fusarium oxysporum, Fusarium solani, ARF18, and another sterile fungus. However, in soil tests, pre-colonization of cysts by C. cochliodes had no effect on parasitism of eggs by subsequent fungal parasites. In another test, parasitism of eggs by V. chlamydosporium in cysts was not affected by pre-colonizing fungi C. destructans, F. oxysporum, and F. solani but was reduced by Mortierella sp., Pyrenochaeta terrestris, and C. cochliodes. Parasitism of eggs in cysts by ARF18 was reduced by pre-colonizing fungi C. destructans, F. oxysporum, F. solani, P. terrestris, and C. cochliodes but not Mortierella sp.     

Dual biocontrol potential of the entomopathogenic fungus Akanthomyces muscarius against Thaumetopoea pityocampa and plant pathogenic fungi

Akanthomyces spp. species are known for their capacity to biocontrol of certain insects and plant pathogens; however, their ability to biocontrol the pine processionary (Thaumetopoea pityocampa) and certain phytopathogenic fungi belonging to the genera Fusarium and Curvularia have not been studied before. In this study, a strain from Akanthomyces muscarius was isolated from wheat grains and then identified by morphological and molecular tests. The strain was further studied for its capacity to control Thaumetopoea pityocampa larvae through dose-mortality tests, and its ability to control some phytopathogenic fungi strains of the genera Fusarium and Curvularia was studied through direct confrontation tests. Dose-mortality tests at three concentrations of Akanthomyces muscarius against the first instar larvae revealed a mortality of 92.15% after 11 days for the concentration of 2.3 × 10⁶ conidia.ml⁻¹, with a median lethal concentration of 7.6 x10³ conidia.ml^1. Our isolate also showed antifungal activity against these phytopathogenic fungi with inhibition rates ranging from 39.61% to 52.94%. Akanthomyces muscarius proved to be a promising biocontrol agent for plant pests and diseases.     

A new potential spreading factor: Streptomyces koganeiensis hyaluronidase. A comparative study with bovine testes hyaluronidase and recombinant human hyaluronidase of the HA degradation in ECM

BackgroundRecombinant human hyaluronidase has been used in the interstitial matrix to promote the dispersion of therapeutics. The production and isolation of an extracellular hyaluronidase from Streptomyces koganeiensis (rHyal_Sk) has recently been described.MethodsThe specificity of rHyal_Sk has been assessed against heparan sulfate, chondroitin sulfates and sulfated HAs. The oligomers generated by HA degradation have been investigated by MALDI-TOF MS analysis. rHyal_Sk has been compared with BTH and PH20 in vitro, against cross-linked HA (ACP) and HA–aggrecan complex, and in vivo, by means of a diffusion assay in nude mice.ResultsDepolymerization of HA by rHyal_Sk gave tetra-, hexa- and octasaccharides in high yields. The reaction mechanism and the high HA specificity were demonstrated. The in vivo diffusion assay, supported by the in vitro tests, evidenced an initially enhanced enzymatic activity of rHyal_Sk compared to BTH and PH20.ConclusionsrHyal_Sk, compared to BTH and PH20, showed higher substrate specificity and no inhibition from GAGs sulfate, together with a superior performance for HA depolymerization in ECM. As better predictive tests for the in vivo activity of hyaluronidase we developed two assays based on the degradation of ACP or of the HA–aggrecan complex.General significancerHyal_Sk is a new potential spreading factor for intradermal drug administration. Hyaluronidases of distinct classes, that show equivalent activities in a common turbidimetric assay, could have different potencies and dose-efficacies in vivo which influences the therapeutic effect. The new proposed in vitro tests are designed to obtain a predictive characterization of the enzyme activity in vivo.     

Etude comparee de la detection chimique des proies par Proteus anguinus,cavernicole, et son parent de surface Necturus maculosus (proteidae,urodela)

Do the blind cave salamander Proteus and its epigean relative Necturus use the chemical sense in searching for prey? Proteus shows a significant, and Necturus only a weak, preference for water which passes living prey before entering a choice chamber. Prey which was frozen before the test also gave the same result in both species. However, with this immobilized prey the time for a decision in the test was much longer. The results of ten series of tests demonstrate the importance of chemoreception for prey detection in Proteus. The weaker reactions in Necturus can be explained probably by the different biotope.Six other series of tests have been conducted to show that our results are not influenced by stimuli relating to mechanoreception, thigmotaxis and rheotropism.     

Building a Robust Tumor Profiling Program: Synergy between Next-Generation Sequencing and Targeted Single-Gene Testing

Next-generation sequencing (NGS) is a powerful platform for identifying cancer mutations. Routine clinical adoption of NGS requires optimized quality control metrics to ensure accurate results. To assess the robustness of our clinical NGS pipeline, we analyzed the results of 304 solid tumor and hematologic malignancy specimens tested simultaneously by NGS and one or more targeted single-gene tests (EGFR, KRAS, BRAF, NPM1, FLT3, and JAK2). For samples that passed our validated tumor percentage and DNA quality and quantity thresholds, there was perfect concordance between NGS and targeted single-gene tests with the exception of two FLT3 internal tandem duplications that fell below the stringent pre-established reporting threshold but were readily detected by manual inspection. In addition, NGS identified clinically significant mutations not covered by single-gene tests. These findings confirm NGS as a reliable platform for routine clinical use when appropriate quality control metrics, such as tumor percentage and DNA quality cutoffs, are in place. Based on our findings, we suggest a simple workflow that should facilitate adoption of clinical oncologic NGS services at other institutions.