Anaplastic lymphoma receptor tyrosine kinase (ALK) gene rearrangements occur in a subgroup of non-small cell lung carcinomas (NSCLCs). The identification of these rearrangements is important for guiding treatment decisions. The aim of our study was to screen ALK gene fusions in NSCLCs and to compare the results detected by targeted resequencing with results detected by commonly used methods, in...

BACKGROUND Despite current knowledge of mutations in 45 genes that can cause nonsyndromic sensorineural hearing loss (SNHL), no unified clinical test has been developed that can comprehensively detect mutations in multiple genes. We therefore designed Affymetrix resequencing microarrays capable of resequencing 13 genes mutated in SNHL (GJB2, GJB6, CDH23, KCNE1, KCNQ1, MYO7A, OTOF, PDS, MYO6, SL...

PURPOSE FKBP51, (FKBP5), is a negative regulator of Akt. Variability in FKBP5 expression level is a major factor contributing to variation in response to chemotherapeutic agents including gemcitabine, a first line treatment for pancreatic cancer. Genetic variation in FKBP5 could influence its function and, ultimately, treatment response of pancreatic cancer. EXPERIMENTAL DESIGN We set out to ...

In selective repeat automatic repeat request (SRARQ) used by a transmitter-receiver pair, data packets correctly received by the receiver need to be delivered to its upper-layer protocol in the same order as they arrived at the transmitter from its upper-layer protocol. In this paper, we propose a novel discrete-time priority queueing network to model SR-ARQ, and study the performance of the re...

This study considers instant decision-making needs of the automobile manufactures for resequencing vehicles before final assembly (FA). We propose a rule-based two-stage stochastic model to determine the number of spare vehicles that should be kept in the pre-assembly buffer to restore the altered sequence due to paint defects and upstream department constraints. First stage of the model decide...

Next generation DNA sequencing (NGS) technologies have revolutionized the pace at which whole genome and exome sequences can be generated. However, despite these advances, many of the methods for targeted resequencing, such as the generation of high-depth exome sequences, are somewhat limited by the relatively large amounts of starting DNA that are normally required. In the case of tumour analy...

Protocols such as TCP requires packets to be accepted (i.e., delivered to the receiving application) in the order they are transmitted at the sender. Packets are sometimes misordered in the network. In order to deliver the arrived packets to the application in sequence, the receiver’s transport layer needs to temporarily buffer out-of-order packets and re-sequence them as more packets arrive. E...

Recent studies indicate that out-of-order arrival of data packets during downloads of resources is not pathological network behaviour (ACM/IEEE Trans. Networking 1999; 7(6):789). Though this situation is most intuitive when packets of the same resource arrive in parallel from several sources, it turns out that this phenomenon may also occur in the single source scenario. Knowledge regarding the...

Targeted resequencing of DNA at specific genes or other genomic loci is now feasible for hundreds or thousands of samples, and costs for larger-scale resequencing are decreasing rapidly. For at least the 1 2 T. LUMLEY ET AL. next few years, resequencing will need to be confined to small subsets of the large samples on which genome-wide association studies have been recently been performed. This...

Genome sequencing centers are flooding the scientific community with data. A single sequencing machine can nowadays generate more data in one day than any existing machine could have produced throughout the entire year of 2005. Therefore, the pressure for efficient sequencing data compression algorithms is very high and is being felt worldwide. Here, we describe GReEn (Genome Resequencing Encod...