To analytically and clinically validate a circulating cell-free tumor DNA sequencing test for comprehensive tumor genotyping and demonstrate its clinical feasibility. Analytic validation was conducted according to established principles and guidelines. Blood-to-blood clinical validation comprised blinded external comparison with clinical droplet digital PCR across 222 consecutive biomarker-positive clinical samples. Blood-to-tissue clinical validation comprised comparison of digital sequencing calls to those documented in the medical record of 543 consecutive lung cancer patients. Clinical experience was reported from 10,593 consecutive clinical samples. Digital sequencing technology enabled variant detection down to 0.02% to 0.04% allelic fraction/2.12 copies with ≤0.3%/2.24-2.76 copies 95% limits of detection while maintaining high specificity [prevalence-adjusted positive predictive values (PPV) >98%]. Clinical validation using orthogonal plasma- and tissue-based clinical genotyping across >750 patients demonstrated high accuracy and specificity [positive percent agreement (PPAs) and negative percent agreement (NPAs) >99% and PPVs 92%-100%]. Clinical use in 10,593 advanced adult solid tumor patients demonstrated high feasibility (>99.6% technical success rate) and clinical sensitivity (85.9%), with high potential actionability (16.7% with FDA-approved on-label treatment options; 72.0% with treatment or trial recommendations), particularly in non-small cell lung cancer, where 34.5% of patient samples comprised a directly targetable standard-of-care biomarker. High concordance with orthogonal clinical plasma- and tissue-based genotyping methods supports the clinical accuracy of digital sequencing across all four types of targetable genomic alterations. Digital sequencing's clinical applicability is further supported by high rates of technical success and biomarker target discovery. .

Abstract-The goal of this paper is to establish which practical routing schemes for wireless networks are most suitable for power-limited and bandwidth-limited communication regimes. We regard channel state information (CSI) at the receiver and point-to-point capacity-achieving codes for the additive white Gaussian noise (AWGN) channel as practical features, interference cancellation (IC) as possible, but less practical, and synchronous cooperation (CSI at the transmitters) as impractical. We consider a communication network with a single source node, a single destination node, and 1 intermediate nodes placed equidistantly on a line between them. We analyze the minimum total transmit power needed to achieve a desired end-to-end rate for several schemes and demonstrate that multihop communication with spatial reuse performs very well in the power-limited regime, even without IC. However, within a class of schemes not performing IC, single-hop transmission (directly from source to destination) is more suitable for the bandwidth-limited regime, especially when higher spectral efficiencies are required. At such higher spectral efficiencies, the gap between single-hop and multihop can be closed by employing IC, and we present a scheme based upon backward decoding that can remove all interference from the multihop system with an arbitrarily small rate loss. This new scheme is also used to demonstrate that rates of (log ) are achievable over linear wireless networks even without synchronous cooperation.

Purpose: To analytically and clinically validate microsatellite instability (MSI) detection using cell-free DNA (cfDNA) sequencing. Experimental Design: Pan-cancer MSI detection using Guardant360 was analytically validated according to established guidelines and clinically validated using 1,145 cfDNA samples for which tissue MSI status based on standard-of-care tissue testing was available. The landscape of cfDNA-based MSI across solid tumor types was investigated in a cohort of 28,459 clinical plasma samples. Clinical outcomes for 16 patients with cfDNA MSI-H gastric cancer treated with immunotherapy were evaluated. Results: cfDNA MSI evaluation was shown to have high specificity, precision, and sensitivity, with a limit of detection of 0.1% tumor content. In evaluable patients, cfDNA testing accurately detected 87% (71/82) of tissue MSI-H and 99.5% of tissue microsatellite stable (863/867) for an overall accuracy of 98.4% (934/949) and a positive predictive value of 95% (71/75). Concordance of cfDNA MSI with tissue PCR and next-generation sequencing was significantly higher than IHC. Prevalence of cfDNA MSI for major cancer types was consistent with those reported for tissue. Finally, robust clinical activity of immunotherapy treatment was seen in patients with advanced gastric cancer positive for MSI by cfDNA, with 63% (10/16) of patients achieving complete or partial remission with sustained clinical benefit. Conclusions: cfDNA-based MSI detection using Guar-dant360 is highly concordant with tissue-based testing, enabling highly accurate detection of MSI status concurrent with comprehensive genomic profiling and expanding access to immunotherapy for patients with advanced cancer for whom current testing practices are inadequate. See related commentary by Wang and Ajani, p. 6887

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A dedicated, efficient Monte Carlo (MC) accelerator head model for intensity modulated stereotactic radiosurgery treatment planning is needed to afford a highly accurate simulation of tiny IMRT fields. A virtual source model (VSM) of a mini multi-leaf collimator (MLC) (the Elekta Beam Modulator (EBM)) is presented, allowing efficient generation of particles even for small fields. The VSM of the EBM is based on a previously published virtual photon energy fluence model (VEF) (Fippel et al 2003 Med. Phys. 30 301) commissioned with large field measurements in air and in water. The original commissioning procedure of the VEF, based on large field measurements only, leads to inaccuracies for small fields. In order to improve the VSM, it was necessary to change the VEF model by developing (1) a method to determine the primary photon source diameter, relevant for output factor calculations, (2) a model of the influence of the flattening filter on the secondary photon spectrum and (3) a more realistic primary photon spectrum. The VSM model is used to generate the source phase space data above the mini-MLC. Later the particles are transmitted through the mini-MLC by a passive filter function which significantly speeds up the time of generation of the phase space data after the mini-MLC, used for calculation of the dose distribution in the patient. The improved VSM model was commissioned for 6 and 15 MV beams. The results of MC simulation are in very good agreement with measurements. Less than 2% of local difference between the MC simulation and the diamond detector measurement of the output factors in water was achieved. The X, Y and Z profiles measured in water with an ion chamber (V = 0.125 cm(3)) and a diamond detector were used to validate the models. An overall agreement of 2%/2 mm for high dose regions and 3%/2 mm in low dose regions between measurement and MC simulation for field sizes from 0.8 x 0.8 cm(2) to 16 x 21 cm(2) was achieved. An IMRT plan film verification was performed for two cases: 6 MV head&neck and 15 MV prostate. The simulation is in agreement with film measurements within 2%/2 mm in the high dose regions (> or = 0.1 Gy = 5% D(max)) and 5%/2 mm in low dose regions (<0.1 Gy).

-We consider a wireless communication system with a single source node, a single destination node, and multiple relay nodes placed equidistantly between them. We limit our analysis to the case of coded TDMA multihop transmission, i.e., the nodes do not cooperate and do not try to access the channel simultaneously. Given a global constraint on bandwidth, we determine the number of hops that achieves the desired end-to-end rate with the least transmission power. Furthermore, we examine how the optimum hop number changes when an end-toend delay con-straint is introduced using the spherepacking bound and computer simulations. The analysis demonstrates that the optimum number of hops depends on the end-to-end spectral efficiency and the path-loss exponent. Specifically, we show the existence of an asymptotic per-link spectral efficiency, which is the most preferable spectral efficiency in TDMA multihop transmission.

The most efficient way of generating particles for Monte Carlo (MC) dose calculation is through a virtual source model (VSM) of the linear accelerator head. We have previously developed a VSM based on three sources: a primary photon source, a secondary photon source and an electron contamination source (Sikora et al 2007). In this work, we present an improvement of the electron contamination source. The VSM of contamination electrons (eVSM) is derived from a full MC simulation of the accelerator head with the BEAMnrc MC system. It comprises a Gaussian source located at the base of the flattening filter. The eVSM models two effects: an energy-dependent source diameter and an angular dependence of the particle fluence. The air scatter of the contamination electrons is approximated by energetic properties of the eVSM so that explicit in-air transport is not required during MC simulation of the dose distributions in the patient. The calculations of electron dose distributions were compared between the eVSM and the full MC simulation. Good agreement was achieved for various rectangular field sizes as well as for complex conformal segment shapes for the contamination electrons of 6 and 15 MV beams. The 3D dose evaluation of the surface dose in a CT-based patient geometry shows high accuracy (2%/2 mm) of the eVSM for both energies. The model has one tunable parameter, the mean energy of the spectrum at the patient surface. High accuracy and efficiency of particle generation make the eVSM a valuable virtual source of contamination electrons for MC treatment planning systems.

Examination of bovine pituitary gland transcriptome by strand-specific RNA-seq allows detection of putative single nucleotide polymorphisms (SNPs) within potential candidate genes (CGs) or QTLs regions as well as to understand the genomics variations that contribute to economic trait. Here we report a breed-specific model to successfully perform the detection of SNPs in the pituitary gland of young growing bulls representing Polish Holstein-Friesian (HF), Polish Red, and Hereford breeds at three developmental ages viz., six months, nine months, and twelve months. A total of 18 bovine pituitary gland polyA transcriptome libraries were prepared and sequenced using the Illumina NextSeq 500 platform. Sequenced FastQ databases of all 18 young bulls were submitted to NCBI-SRA database with NCBI-SRA accession numbers SRS1296732. For the investigated young bulls, a total of 113,882,3098 raw paired-end reads with a length of 156 bases were obtained, resulting in an approximately 63 million paired-end reads per library. Breed-wise, a total of 515.38, 215.39, and 408.04 million paired-end reads were obtained for Polish HF, Polish Red, and Hereford breeds, respectively. Burrows-Wheeler Aligner (BWA) read alignments showed 93.04%, 94.39%, and 83.46% of the mapped sequencing reads were properly paired to the Polish HF, Polish Red, and Hereford breeds, respectively. Constructed breed-specific SNP-db of three cattle breeds yielded at 13,775,885 SNPs. On an average 765,326 breed-specific SNPs per young bull were identified. Using two stringent filtering parameters, i.e., a minimum 10 SNP reads per base with an accuracy ≥ 90% and a minimum 10 SNP reads per base with an accuracy = 100%, SNP-db records were trimmed to construct a highly reliable SNP-db. This resulted in a reduction of 95,7% and 96,4% cut-off mark of constructed raw SNP-db. Finally, SNP discoveries using RNA-Seq data were validated by KASP™ SNP genotyping assay. The comprehensive QTLs/CGs analysis of 76 QTLs/CGs with RNA-seq data identified KCNIP4, CCSER1, DPP6, MAP3K5 and GHR CGs with highest SNPs hit loci in all three breeds and developmental ages. However, CAST CG with more than 100 SNPs hits were observed only in Polish HF and Hereford breeds.These findings are important for identification and construction of novel tissue specific SNP-db and breed specific SNP-db dataset by screening of putative SNPs according to QTL db and candidate genes for bovine growth and reproduction traits, one can develop genomic selection strategies for growth and reproductive traits.