Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit

Currently, the most commonly used method for human identification and kinship analysis in forensic genetics is the detection of length polymorphism in short tandem repeats (STRs) using polymerase chain reaction (PCR) and capillary electrophoresis (CE). However, numerous studies have shown that considerable sequence variations exist in the repeat and flanking regions of the STR loci, which cannot be identified by CE detection. Comparatively, massively parallel sequencing (MPS) technology can capture these sequence differences, thereby enhancing the identification capability of certain STRs. In this study, we used the ForenSeq™ DNA Signature Prep Kit to sequence 58 STRs and 94 individual identification SNPs (iiSNPs) in a sample of 220 unrelated individuals from the Eastern Chinese Han population. Our aim is to obtain MPS-based STR and SNP data, providing further evidence for the study of population genetics and forensic applications. The results showed that the MPS method, utilizing sequence information, identified a total of 486 alleles on autosomal STRs (A-STRs), 97 alleles on X-chromosome STRs (X-STRs), and 218 alleles on Y-chromosome STRs (Y-STRs). Compared with length polymorphism, we observed an increase of 260 alleles (157, 31, and 72 alleles on A-STRs, X-STRs, and Y-STRs, respectively) across 36 STRs. The most substantial increments were observed in DYF387S1 and DYS389II, with increases of 287.5% and 250%, respectively. The most increment in the number of alleles was found at DYF387S1 and DYS389II (287.5% and 250%, respectively). The length-based (LB) and sequence-based (SB) combined random match probability (RMP) of 27 A-STRs were 6.05E-31 and 1.53E-34, respectively. Furthermore, other forensic parameters such as total discrimination power (TDP), cumulative probability of exclusion of trios (CPEtrio), and duos (CPEduo) were significantly improved when using the SB data, and informative data were obtained for the 94 iiSNPs. Collectively, these findings highlight the advantages of MPS technology in forensic genetics, and the Eastern Chinese Han genetic data generated in this study could be used as a valuable reference for future research in this field.

Percutaneous Magnetic Resonance Imaging-Guided Coaxial Cutting Needle Biopsy of Pancreatic Lesions: Diagnostic Accuracy and Safety

PURPOSE

To appraise the diagnostic performance of magnetic resonance imaging-guided percutaneous coaxial cutting needle biopsy of pancreatic lesions using a 0.4-T open magnetic resonance imaging scanner with optical tracking navigation.

MATERIALS AND METHODS

This retrospective study included 158 patients who underwent magnetic resonance imaging-guided pancreatic lesion biopsy procedures from May 2019 to December 2020. Two to four specimens were collected from each patient. Pathological diagnosis and clinical follow-ups were conducted to establish the final diagnosis. The procedures were evaluated for sensitivity, specificity, positive and negative predictive values, diagnostic accuracy, and complications. The Cardiovascular and Interventional Radiological Society of Europe guidelines were used to classify complications.

RESULTS

Biopsy pathology revealed 139 pancreatic tumor malignancies and 19 benign pancreatic lesions. Finally, 151 patients were diagnosed with pancreatic malignancy and 7 with benign disease confirmed by surgery, re-biopsy, and clinical follow-up. The sensitivity, specificity, positive and negative predictive value, and accuracy for diagnosis of pancreatic diseases were 92.1%, 100%, 100%, 36.8%, and 92.4%, respectively. The biopsy accuracy was significantly related to the size (≤ 2 cm, 76.2%; 2-4 cm, 94.0%; > 4 cm, 96.2%, P = .02) and not the lesion's location (head of pancreas, 90.7%; neck of pancreas, 88.9%; body of pancreas, 94.3%; tail of pancreas, 96.7%, P = .73). Minor complications included two patients experiencing mild abdominal pain and two with a minor occurrence of hemorrhage.

CONCLUSIONS

Percutaneous magnetic resonance imaging-guided pancreatic lesion biopsy combined with optical navigation has high diagnostic accuracy and is safe for clinical practice. Level of Evidence Level 4, Case-series.

DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations

Driver mutations can contribute to the initial processes of cancer, and their identification is crucial for understanding tumorigenesis as well as for molecular drug discovery and development. Allostery regulates protein function away from the functional regions at an allosteric site. In addition to the known effects of mutations around functional sites, mutations at allosteric sites have been associated with protein structure, dynamics, and energy communication. As a result, identifying driver mutations at allosteric sites will be beneficial for deciphering the mechanisms of cancer and developing allosteric drugs. In this study, we provided a platform called DeepAlloDriver to predict driver mutations using a deep learning method that exhibited >93% accuracy and precision. Using this server, we found that a missense mutation in RRAS2 (Gln72 to Leu) might serve as an allosteric driver of tumorigenesis, revealing the mechanism of the mutation in knock-in mice and cancer patients. Overall, DeepAlloDriver would facilitate the elucidation of the mechanisms underlying cancer progression and help prioritize cancer therapeutic targets. The web server is freely available at: https://mdl.shsmu.edu.cn/DeepAlloDriver.

AlloReverse: multiscale understanding among hierarchical allosteric regulations

Increasing data in allostery are requiring analysis of coupling relationships among different allosteric sites on a single protein. Here, based on our previous efforts on reversed allosteric communication theory, we have developed AlloReverse, a web server for multiscale analysis of multiple allosteric regulations. AlloReverse integrates protein dynamics and machine learning to discover allosteric residues, allosteric sites and regulation pathways. Especially, AlloReverse could reveal hierarchical relationships between different pathways and couplings among allosteric sites, offering a whole map of allostery. The web server shows a good performance in re-emerging known allostery. Moreover, we applied AlloReverse to explore global allostery on CDC42 and SIRT3. AlloReverse predicted novel allosteric sites and allosteric residues in both systems, and the functionality of sites was validated experimentally. It also suggests a possible scheme for combined therapy or bivalent drugs on SIRT3. Taken together, AlloReverse is a novel workflow providing a complete regulation map and is believed to aid target identification, drug design and understanding of biological mechanisms. AlloReverse is freely available to all users at https://mdl.shsmu.edu.cn/AlloReverse/ or http://www.allostery.net/AlloReverse/.

Internal validation of an improved system for forensic application: a 41-plex Y-STR panel

Y-chromosome short tandem repeats (Y-STRs) have a unique role in forensic investigation. However, low-medium mutating Y-STRs cannot meet the requirements for male lineage differentiation in inbred populations, whereas rapidly mutating (RM) high-resolution Y-STRs might cause unexpected exclusion of paternal lineages. Thus, combining Y-STRs with low and high mutation rates helps to distinguish male individuals and lineages in family screening and analysis of genetic relationships. In this study, a novel 6-dye, 41-plex Y-STR panel was developed and validated, which included 17 loci from the Yfiler kit, nine RM Y-STR loci, 15 low-medium mutating Y-STR loci, and three Y-InDels. Developmental validation was performed for this panel, including size precision testing, stutter analysis, species specificity analysis, male specificity testing, sensitivity testing, concordance evaluation, polymerase chain reaction inhibitors analysis, and DNA mixture examination. The results demonstrated that the novel 41-plex Y-STR panel, developed in-house, was time efficient, accurate, and reliable. It showed good adaptability to directly amplify a variety of case-type samples. Furthermore, adding multiple Y-STR loci significantly improved the system's ability to distinguish related males, making it highly informative for forensic applications. In addition, the data obtained were compatible with the widely used Y-STR kits, facilitating the search and construction of population databases. Moreover, the addition of Y-Indels with short amplicons improves the analyses of degraded samples.

Key Points

A novel multiplex comprising 41 Y-STR and 3 Y-InDel was developed for forensic application.The multiplex included rapidly mutating Y-STRs and low-medium mutating Y-STRs, which is compatible with many commonly used Y-STR kits.The multiplex is a powerful tool for distinguishing related males, familial searching, and constructing DNA databases.

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

Extrachromosomal mobile genetic elements (eMGEs), including phages and plasmids, that can move across different microbes, play important roles in genome evolution and shaping the structure of microbial communities. However, we still know very little about eMGEs, especially their abundances, distributions and putative functions in microbiomes. Thus, a comprehensive description of eMGEs is of great utility. Here we present mMGE, a comprehensive catalog of 517 251 non-redundant eMGEs, including 92 492 plasmids and 424 759 phages, derived from diverse body sites of 66 425 human metagenomic samples. About half the eMGEs could be further grouped into 70 074 clusters using relaxed criteria (referred as to eMGE clusters below). We provide extensive annotations of the identified eMGEs including sequence characteristics, taxonomy affiliation, gene contents and their prokaryotic hosts. We also calculate the prevalence, both within and across samples for each eMGE and eMGE cluster, enabling users to see putative associations of eMGEs with human phenotypes or their distribution preferences. All eMGE records can be browsed or queried in multiple ways, such as eMGE clusters, metagenomic samples and associated hosts. The mMGE is equipped with a user-friendly interface and a BLAST server, facilitating easy access/queries to all its contents easily. mMGE is freely available for academic use at: https://mgedb.comp-sysbio.org.

Degradation of the In-plane Shear Modulus of Structural BFRP Laminates Due to High Temperature

The behavior of fiber reinforced polymer (FRP) composites at high temperature is a critical issue that needs to be clearly understood for their structural uses in civil engineering. However, due to technical difficulties during testing at high temperature, limited experimental investigations have been conducted regarding the thermal behavior of basalt fiber reinforced polymer (BFRP) composites, especially for the in-plane shear modulus of BFRP laminates. To this end, both an analytical derivation and an experimental program were carried out in this work to study the in-plane shear modulus of BFRP laminates. After the analytical derivation, the in-plane shear modulus was investigated as a function of the elastic modulus in different directions (0°, 45° and 90° of the load-to-fiber angle) and Poisson's ratio in the fiber direction. To obtain the in-plane shear modulus, the four parameters were tested at different temperatures from 20 to 250 °C. A novel non-contacting digital image correlation (DIC) sensing system was adopted in the high-temperature tests to measure the local strain field on the FRP samples. Based on the test results, it was found that the elastic moduli in different directions were reduced to a very low level (less than 20%) from 20 to 250 °C. Furthermore, the in-plane shear modulus of BFRP at 250 °C was only 3% of that at 20 °C.