Aim High-resolution HLA typing plays a central role in medical decisions concerning the matching ... more Aim High-resolution HLA typing plays a central role in medical decisions concerning the matching of stem cell transplant recipients to unrelated donors. However, DNA sequencing based typing (SBT) may result with three or more allele combination. We undertook this study to validate whether luminex based PCR-SSO method can resolve these SBT ambiguities. Methods HLA medium and high resolution genotyping was performed using Luminex-based sequence-specific oligonucleotide (SSO) (Thermofiser, LabtypeSSO) and Sequencing based typing (Atria Genetics HLA SBT kits) respectively. Fluorochrome-labeled DNA fragments were electrophoresed by capillary electrophoresis on an ABI 3130 Genetic Analyzer. Heterozygous Ambiguity Resolving Primers (HARPs) were used as the gold standard method to resolve ambiguity. Results A total of 64 DNA samples typed by SSO and SBT (15 A, 14 B, 19 C and 16 DRB1) showed HLA assignments that have more than four possible antigen/allele combinations. SSO based typing resolved 57% of ambiguities for HLA-A; 51% for HLA-B, 60% for HLA-C and 65% for HLA-DRB1 locus. On the contrary, HARPS resolved 94% of ambiguities for HLA-A and -B, 90% for HLA-C and 83% for HLA-DRB1. Overall, SSO significantly resolve ambiguities for Class I (p Conclusions Significant ambiguity resolution of SBT results can be achieved by SSO, which would significantly reduce the need of additional amplifications and financial cost involved in HARP analysis. Therefore, we recommend the combination of SSO and SBT for the generation of high resolution HLA typing and advocate the use of HARPS only in cases of unresolved HLA typing by both SSO and SBT. Also, it is important that SSO probe reaction patterns be reviewed thoroughly to assure the right allele combinations.
The problem of Network Traffic Classification (NTC) has attracted significant amount of interest ... more The problem of Network Traffic Classification (NTC) has attracted significant amount of interest in the research community, offering a wide range of solutions at various levels. The core challenge is in addressing high amounts of traffic diversity found in today's networks. The problem becomes more challenging if a quick detection is required as in the case of identifying malicious network behavior or new applications like peer-to-peer traffic that have potential to quickly throttle the network bandwidth or cause significant damage. Recently, Traffic Dispersion Graphs (TDGs) have been introduced as a viable candidate for NTC. The TDGs work by forming a network wide communication graphs that embed characteristic patterns of underlying network applications. However, these patterns need to be quickly evaluated for mounting real-time response against them. This paper addresses these concerns and presents a novel solution for real-time analysis of Traffic Dispersion Metrics (TDMs) in the TDGs. We evaluate the dispersion metrics of interest and present a dedicated solution on an FPGA for their analysis. We also present analytical measures and empirically evaluate operating effectiveness of our design. The mapped design on Virtex-5 device can process 7.4 million packets/second for a TDG comprising of 10k flows at very high accuracies of over 96%.
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Papers by faisal khan