Purpose Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability. Methods This manual review standard operating procedure (SOP) consists of methods to annotate variants with four different calls and 19 tags. The calls indicate a reviewer’s confidence in each variant and the tags indicate commonly observed sequencing patterns and artifacts that inform the manual review call. Four individuals were asked to classify variants prior to, and after, reading the SOP and accuracy was assessed by comparing reviewer calls with orthogonal validation sequencing. Results After reading the SOP, average accuracy in somatic variant identification increased by 16.7% ( p value = 0.0298) and average interreviewer agreement increased by 12.7% ( p value < 0.001). Manual review conducted after reading the SOP did not significantly increase reviewer time. Conclusion This SOP supports and enhances manual somatic variant detection by improving reviewer accuracy while reducing the interreviewer variability for variant calling and annotation.
Background: Basophil activation is associated with the expression of CD63. In birch-pollen-associated food allergy to celery, carrot and apple, Bet v 1, Api g 1, Dau c 1 and Mal d 1 are major allergens. Recombinant allergens have not yet been used in the CD63-based basophil activation test (BAT). Objective: To evaluate the feasibility of using recombinant allergens in the BAT in the diagnosis of allergy to apple, carrot and celery and to compare results with routine tests, i.e. skin prick tests (SPTs) and specific IgE. Methods: Thirty-two patients with an oral allergy syndrome induced by apple, carrot or celery and 22 controls were studied. SPTs were performed with native foods. Specific IgE was determined by the CAP method and basophil activation by flowcytometry upon double staining with anti-IgE/anti-CD63 monoclonal antibodies after incubating with purified recombinant Bet v 1, Bet v 2, Api g 1, Dau c 1 and Mal d 1. Results: By the combined use of the BAT and the CAP method, sensitization to Bet v 1 and Bet v 2 was detected in 100 and 25% of all subjects, respectively. Sensitivity of specific IgE for apple, carrot and celery was 60, 70 and 75% with corresponding specificities of 64, 86 and 82%. Sensitivity of the BAT for Mal d 1, Dau c 1 and Api g 1 was 75, 65 and 75% with corresponding specificities of 68, 100 and 77%. Conclusions: The BAT using recombinant allergens provides a valuable new in vitro method for the detection of sensitization to foods. Although double-blind placebo-controlled food challenges remain the gold standard to confirm food allergy, the CD63-based BAT with recombinant allergens may supplement routine tests for allergy diagnosis.
Three strains (RT112, Du145, SCC4451) were found to have a missense-mutation in the core domain and one did not express p53 at all (HeLa), presumably due to HPV18 infection. Immunoblots of these cells showed neither a regulated p53 nor p21 expression. The cells did not arrest in G1 phase after X-irradiation but did arrest in G2/M. All cells expressing wild-type protein (LNCaP, T47D-B8, MCF-7 and sublines BB and Bus) showed an intact p53 and p21 regulation and a modest arrest in both G1 and G2/M. Thus, in contrast to other studies, all tumour cells investigated showed either a typical p53wt or mutant (mut) pattern. Protein function was compared with cell survival and DNA damage, as assessed previously. p53 wild-type cells were on average 1.3-times (n.s.) more radiosensitive than mutant cells, but there was a considerable overlap between both groups. Further, the 1.3-fold enhanced resistance of cells lacking wild-type p53 was paralleled by a 1.3-fold lower number of induced double-strand breaks. The results suggest that p53 could have impact on chromatin compaction and thus effect DNA damage induction and radiosensitivity of tumour cells.
DNA double-strand break (DSB) repair is crucial to maintain genomic stability. The fidelity of the repair depends on the complexity of the lesion, with clustered DSBs being more difficult to repair than isolated breaks. Using live cell imaging of heavy ion tracks produced at a high-energy particle accelerator we visualised simultaneously the recruitment of different proteins at individual sites of complex and simple DSBs in human cells. NBS1 and 53BP1 were recruited in a few seconds to complex DSBs, but in 40% of the isolated DSBs the recruitment was delayed approximately 5 min. Using base excision repair (BER) inhibitors we demonstrate that some simple DSBs are generated by enzymatic processing of base damage, while BER did not affect the complex DSBs. The results show that DSB processing and repair kinetics are dependent on the complexity of the breaks and can be different even for the same clastogenic agent. Repair of DNA double-strand breaks is a necessary pathway to maintain genomic stability in mammalian cells 1. The DNA damage response (DDR) signalling cascade is rapid and hierarchically coordinated, with many proteins being recruited to the damage sites at different times and depending on the repair pathway. Complex DSBs, i.e. complex lesions involving multiple strand breaks and/or oxidative damages within two helical turns 2,3 , are more difficult to repair than isolated, frank DSBs 4. Complex DSBs can be produced by ionising radiation (IR) 3,5 , and their fraction and complexity and clustering increases for densely ionising, high-linear energy transfer (LET) radiation such as α-particles and heavy ions 6. Endogenous DSBs (simple DSBs produced during replication) have much higher frequency than IR-induced DSBs at low doses, but the latter include complex DSBs 7. These complex lesions are considered ultimately responsible for the late effects of low doses of IR 8 , including environmental exposures and cosmic radiation risk in space travel. The repair of simple and complex DSBs is therefore crucial to understand the difference between endogenous and exogenous genotoxicity and for modelling the risk related to exposure to low doses IR on Earth 9 and in space 10. Delayed repair of clustered DSBs has been observed by immunostaining of markers of single strand breaks (SSBs), DSBs and base damage in mammalian cells 11. Here we measured the early protein recruitment at sites of simple and clustered, complex DSBs by live cell imaging. Immunostaining on fixed samples is unable to identify the early kinetics and cannot follow the evolution of individual foci, therefore providing only average values 12. High-charge and-energy (HZE) ions offer a unique opportunity for these studies as they simultaneously produce both clustered (along the track) and isolated (off-track) DSBs. In fact, the inner part of the ion track (core) includes primary particle ionizations and low-energy electrons, and results mostly in complex, clustered DSBs for HZE ions at high linear energy transfer (LET), whereas low-LET high-energy ionised ...
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