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

The effect of repeated freeze-thaw cycles on human muscle tissue visualized by postmortem computed tomography (PMCT)

The aim of this study was to determine whether effects of repetitive freeze-thaw cycles, with various thawing temperatures, on human muscle tissue can be quantified using postmortem computed tomography (PMCT) technology. An additional objective was to determine the preferred thawing temperature for muscle tissue in this study. Human cadaver upper extremities were divided into two different thawing temperature groups and underwent a series of four freeze-thaw cycles in total. Axial CT scans were performed after each cycle. CT attenuation (in Hounsfield units, HU) was measured in four muscles of the upper extremities. HU values changed significantly with the introduction of each subsequent freeze-thaw cycle. Moreover, the changes in HU values were different for each thawing group. There was a significant increase of HU values in both groups between t0 and t1 . Unfrozen tissue showed large variation of HU values in all samples. It was possible to distinguish between samples thawed at different thawing temperatures based on their respective HU values. It is advisable to keep the number of freeze-thaw cycles to just one, if the human cadaveric tissue is to be used for educational purposes. The preferred thawing temperature in this study is 2°C. Clin. Anat. 30:799-804, 2017. © 2017Wiley Periodicals, In

The importance of processing procedures and threshold values in CT scan segmentation of skeletal elements: An example using the immature os coxa

As the accessibility and utility of virtual databases of skeletal collections continues to grow, the impact that scan processing procedures has on the accuracy of data obtained from virtual databases remains relatively unknown. This study quantifies the intra- and inter-observer error generated from varying computed tomography (CT) scan processing protocols, including re-segmentation, incrementally varying thresholding value, and data collectors’ selection of the threshold value on a set of virtual subadult pelves. Four observers segmented the subadult ossa coxarum from postmortem CT scans of the fully-fleshed bodies of eleven individuals of varying ages. Segmentation protocol was set, with the exception of each observer selecting their own thresholding value for each scan. The resulting smoothed pelvic surfaces were then compared using deviation analyses. Root mean square error (RMSE), average distance deviation, and maximum deviation distances demonstrated that thresholding values of ∼50 HU (Hounsfield units) are easily tolerated, the surfaces generated are robust to error, and threshold value selection does not systematically vary with user experience. The importance of consistent methodology during segmentation protocol is highlighted here, especially with regards to consistency in both selected thresholding value as well as smoothing protocol, as these variables can affect subsequent measurements of the resultant surfaces

The accuracy of 3D virtual bone models of the pelvis for morphological sex estimation

It is currently unknown whether morphological sex estimation traits are accurately portrayed on virtual bone models, and this hampers the use of virtual bone models as an alternative source of contemporary skeletal reference data. This study determines whether commonly used morphological sex estimation traits can be accurately scored on virtual 3D pelvic bone elements. Twenty-seven intact cadavers from the body donation program of the Amsterdam UMC, University of Amsterdam, were CT scanned; this data was used to produce virtual bone models. Thereafter, the dry bones were obtained. Three traits by Klales (2012) and five traits from the Workshop of European Anthropologists (WEA) (1980) were scored on the virtual bone models and their dry skeletal counterparts. Intra- and inter-observer agreement and the agreement between the scores for each virtual bone model-dry bone pair were calculated using weighted Cohen’s kappa (K). For all Klales (2012) traits, intra- and inter-observer agreement was substantial to almost perfect for the virtual- and dry bones (K = 0.62–0.90). The agreement in scores in the virtual-dry bone pairs ranged from moderate to almost perfect (K = 0.58–0.82). For the WEA (1980) traits, intra-observer agreement was substantial to almost perfect (K = 0.64–0.91), but results were less unambiguous for inter-observer agreement (K = 0.24–0.88). Comparison of the scores between the virtual bone models and the dry bones yielded kappa values of 0.42–0.87. On one hand, clinical CT data is a promising source for contemporary forensic anthropological reference data, but the interchangeability of forensic anthropological methods between virtual bone models and dry skeletal elements needs to be tested further.http://link.springer.com/journal/414hj2020Anatom

The accuracy of 3D virtual bone models of the pelvis for morphological sex estimation

It is currently unknown whether morphological sex estimation traits are accurately portrayed on virtual bone models, and this hampers the use of virtual bone models as an alternative source of contemporary skeletal reference data. This study determines whether commonly used morphological sex estimation traits can be accurately scored on virtual 3D pelvic bone elements. Twenty-seven intact cadavers from the body donation program of the Amsterdam UMC, University of Amsterdam, were CT scanned; this data was used to produce virtual bone models. Thereafter, the dry bones were obtained. Three traits by Klales (2012) and five traits from the Workshop of European Anthropologists (WEA) (1980) were scored on the virtual bone models and their dry skeletal counterparts. Intra- and inter-observer agreement and the agreement between the scores for each virtual bone model-dry bone pair were calculated using weighted Cohen’s kappa (K). For all Klales (2012) traits, intra- and inter-observer agreement was substantial to almost perfect for the virtual- and dry bones (K = 0.62–0.90). The agreement in scores in the virtual-dry bone pairs ranged from moderate to almost perfect (K = 0.58–0.82). For the WEA (1980) traits, intra-observer agreement was substantial to almost perfect (K = 0.64–0.91), but results were less unambiguous for inter-observer agreement (K = 0.24–0.88). Comparison of the scores between the virtual bone models and the dry bones yielded kappa values of 0.42–0.87. On one hand, clinical CT data is a promising source for contemporary forensic anthropological reference data, but the interchangeability of forensic anthropological methods between virtual bone models and dry skeletal elements needs to be tested further

The geometrical precision of virtual bone models derived from clinical computed tomography data for forensic anthropology

Almost all European countries lack contemporary skeletal collections for the development and validation of forensic anthropological methods. Furthermore, legal, ethical and practical considerations hinder the development of skeletal collections. A virtual skeletal database derived from clinical computed tomography (CT) scans provides a potential solution. However, clinical CT scans are typically generated with varying settings. This study investigates the effects of image segmentation and varying imaging conditions on the precision of virtual modelled pelves. An adult human cadaver was scanned using varying imaging conditions, such as scanner type and standard patient scanning protocol, slice thickness and exposure level. The pelvis was segmented from the various CT images resulting in virtually modelled pelves. The precision of the virtual modelling was determined per polygon mesh point. The fraction of mesh points resulting in point-to-point distance variations of 2 mm or less (95% confidence interval (CI)) was reported. Colour mapping was used to visualise modelling variability. At almost all (>97%) locations across the pelvis, the point-to-point distance variation is less than 2mm(CI = 95%). In >91% of the locations, the point-to-point distance variation was less than 1 mm (CI = 95%). This indicates that the geometric variability of the virtual pelvis as a result of segmentation and imaging conditions rarely exceeds the generally accepted linear error of 2 mm. Colour mapping shows that areas with large variability are predominantly joint surfaces. Therefore, results indicate that segmented bone elements from patient-derived CT scans are a sufficiently precise source for creating a virtual skeletal database.http://link.springer.com/journal/414am2017Anatom