Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Validation of computed tomography-based attenuation correction of deviation between theoretical and actual values for four computed tomography scanners

Objective: In this study, we aimed to validate the accuracy of computed tomography-based attenuation correction (CTAC) using the bilinear scaling method.Methods: The measured attenuation coefficient (μm) was compared to a theoretical attenuation coefficient (μt ) using four different CT scanners and an RMI 467 phantom. The effective energy of the CT beam X-rays was calculated, using the aluminum half-value layer method, and was used in conjunction with an attenuation map to convert the CT numbers to μm values for the photon energy of 140 keV. We measured the CT number of the RMI 467 phantom for each of four scanners, and compared the μm and μt values for the effective energies of the CT beam X-rays, effective atomic numbers, and physical densities.Results: The μm values for CT beam X-rays with low effective energies decreased in high construction elements, compared with CT beam X-rays of high effective energies . As the physical density increased, the μm values elevated linearly. Compared with other scanners, the μm values obtained from the scanner with CT beam X-rays of the maximal effective energy increased once the effective atomic number exceeded 10.00. The μm value of soft tissue was equivalent to the μt value. However, the ratios of the maximal differences between the μm value and the μt value were 25.4% (lung) and 21.5% (bone) respectively. Additionally, the maximal differences in the μm values were 6.0% in the bone tissue for each scanner.Conclusion: The bilinear scaling method could accurately convert CT numbers to μ values within the soft tissues

Use of a digital phantom developed by QIBA for harmonizing SUVs obtained from the state-of-the-art SPECT/CT systems: a multicenter study

Abstract Background Although quantitative analysis using standardized uptake value (SUV) becomes realistic in clinical single-photon emission computed tomography/computed tomography (SPECT/CT) imaging, reconstruction parameter settings can deliver different quantitative results among different SPECT/CT systems. This study aims to propose a use of the digital reference object (DRO), which is a National Electrical Manufacturers Association (NEMA) phantom-like object developed by the Quantitative Imaging Biomarker Alliance (QIBA) fluorodeoxyglucose-positron emission tomography technical committee, for the purpose of harmonizing SUVs in Tc-99m SPECT/CT imaging. Methods The NEMA body phantom with determined Tc-99m concentration was scanned with the four state-of-the-art SPECT/CT systems. SPECT data were reconstructed using different numbers of the product of subset and iteration numbers (SI) and the width of 3D Gaussian filter (3DGF). The mean (SUVmean), maximal (SUVmax), and peak (SUVpeak) SUVs for six hot spheres (10, 13, 17, 22, 28, and 37 mm) were measured after converting SPECT count into SUV using Becquerel calibration factor. DRO smoothed by 3DGF with a FWHM of 17 mm (DRO17 mm) was generated, and the corresponding SUVs were measured. The reconstruction condition to yield the lowest root mean square error (RMSE) of SUVmeans for all the spheres between DRO17 mm and actual phantom images was determined as the harmonized condition for each SPECT/CT scanner. Then, inter-scanner variability in all quantitative metrics was measured before (i.e., according to the manufacturers’ recommendation or the policies of their own departments) and after harmonization. Results RMSE was lowest in the following reconstruction conditions: SI of 100 and 3DGF of 13 mm for Brightview XCT, SI of 160 and 3DGF of 3 pixels for Discovery NM/CT, SI of 60 and 3DGF of 2 pixels for Infinia, and SI of 140 and 3DGF of 15 mm for Symbia. In pre-harmonized conditions, coefficient of variations (COVs) among the SPECT/CT systems were greater than 10% for all quantitative metrics in three of the spheres, SUVmax and SUVmean, in one of the spheres. In contrast, all metrics except SUVmax in the 17-mm sphere yielded less than 10% of COVs after harmonization. Conclusions Our proposed method clearly reduced inter-scanner variability in SUVs. A digital phantom developed by QIBA would be useful for harmonizing SUVs in multicenter trials using SPECT/CT