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Human Genomics May 2024Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative,...
Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India.
BACKGROUND
Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India.
RESULTS
903 smMIPs were designed to target exon and exon-intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood.
CONCLUSION
We developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.
Topics: Humans; Lysosomal Storage Diseases; India; DNA Copy Number Variations; Genetic Testing; High-Throughput Nucleotide Sequencing; Polymorphism, Single Nucleotide; Female; Male; Molecular Probes
PubMed: 38730490
DOI: 10.1186/s40246-024-00613-9 -
Phytomedicine : International Journal... Jul 2024It has been a current research hospots using fingerprinting technology for quality control of Chinese herbal medicines (CHMs), which provides a scientific basis for...
BACKGROUND
It has been a current research hospots using fingerprinting technology for quality control of Chinese herbal medicines (CHMs), which provides a scientific basis for establishment of overall quality control in accordance with the characteristics of CHMs. The fingerprinting technology for CHMs is diverse, and the research field covers many disciplines, such as analytical chemistry, pharmacology, pharmaceutics, biochemistry, and molecular biology.
PURPOSE
To effectively understand the key areas and future directions of research regarding the fingerprint and adulteration of CHMs.
METHODS/RESULTS
this paper analyzed 879 articles in this field in the Web of Science Core Collection from 2000 to 2023 with CiteSpace and VOSviewer, and systematically assessed the research process, hotspots, topic distribution among disciplines, etc. The most prominent contributors of fingerprint and adulteration of CHMs research are mainly from China, India, the United States, England, and Brazil. The knowledge domains of fingerprint and adulteration of CHMs research focus mainly on the topics of molecular authentication, DNA barcoding, HPLC, near-infrared spectroscopy, manage data, chemometrics, and electrochemical fingerprinting. Most countries have recognized the pharmaceutical potential of natural products, and have paid more attention to the fingerprint and adulteration of CHMs in the past decade. Future the research tends to focus more on molecular identification and authentication, and electrochemical and chromatographic fingerprinting in controlling the adulteration of CHMs.
CONCLUSION
This research provides a valuable reference for scholars in related fields to analyze existing research results, understand the development trend, and explore new research directions.
Topics: Drugs, Chinese Herbal; Drug Contamination; Quality Control; Chromatography, High Pressure Liquid; DNA Barcoding, Taxonomic
PubMed: 38728918
DOI: 10.1016/j.phymed.2024.155667 -
Forensic Science International. Genetics Jul 2024The Forensic Databases Advisory Board (FDAB), an independent board that assists the International Society for Forensic Genetics (ISFG), has presented a First Report on...
The Forensic Databases Advisory Board (FDAB), an independent board that assists the International Society for Forensic Genetics (ISFG), has presented a First Report on ethical aspects of the following Forensic Genetic Frequency Databases (FGFD): EMPOP, STRidER and YHRD. The FDAB designed an ethical framework to evaluate the content of these FGFD, and the factors to be considered for retention and acceptance of submissions. The FDAB framework proposes to categorize submissions according to the risk of having contravened the universal ethical principles outlined by international organizations, and the guidelines adopted by the ISFG. The report has been open to discussion by the scientific community since 2023. Herein we present the conception and development of the First Report along with a summary of its content, with consideration of the feedback received.
Topics: Humans; Forensic Genetics; Gene Frequency; Databases, Genetic; Databases, Nucleic Acid; DNA Fingerprinting
PubMed: 38728819
DOI: 10.1016/j.fsigen.2024.103053 -
Forensic Science International Jul 2024Research into the recovery of DNA from illicit drug samples has shown it is possible to get forensically useful profiles from such substrates. However, it is not yet...
Research into the recovery of DNA from illicit drug samples has shown it is possible to get forensically useful profiles from such substrates. However, it is not yet known if the different physical states that drugs can be found in influences the quantity and quality of DNA that can be recovered or what is the best sampling method to adopt for powdered samples. This research used acetaminophen in four different states - large crystalline, powder, in solution, or residue - to determine the efficacy of current DNA technology in recovery and analysis of the resulting sample. Five replicates of each were prepared. Human blood was deposited on or mixed with the drug and left for 1 hour. The surface of the drug was sampled by wet/dry swabbing (where appropriate), or the entire sample was deposited in a tube, and the DNA then extracted using DNA-IQ™. The amount of DNA recovered (ng), degradation index, number of PCR cycles (Ct) required for the IPC to reach threshold, number of alleles in the DNA profile and average peak height (APH) were assessed. All samples, irrespective of the physical state they were collected from, returned full DNA profiles that corresponded to the DNA profile of the blood donor, with no degradation or inhibition detected. It was also found the wet/dry swabbing method returned higher levels of DNA than inclusion of the entire sample into the tube for powdered acetaminophen and the appropriate method to use will be dependent on casework circumstances. The findings of this research further develops our understanding of the recovery of DNA from drugs, and supports the need for further investigation to understand under what conditions DNA can be recovered from illicit substances.
Topics: Acetaminophen; Humans; DNA; Specimen Handling; DNA Fingerprinting; Polymerase Chain Reaction; Powders; Microsatellite Repeats; Analgesics, Non-Narcotic; DNA Degradation, Necrotic
PubMed: 38718526
DOI: 10.1016/j.forsciint.2024.112046 -
Microbial Genomics May 2024infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of...
infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of ribotypes (RTs) 014/020 (=169), 002 (=77) and 056 (=36), the three most prominent strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLS agents , but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, =36) to 115.6 (RT002, ST8, =77) and 315.9 (RT014/020, STs 2, 13, 14, 49, =169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, =14; RT002, =3; RT056, =2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.
Topics: Clostridioides difficile; Australia; Ribotyping; Humans; Clostridium Infections; Phylogeny; Genome, Bacterial; Drug Resistance, Bacterial; Anti-Bacterial Agents; Polymorphism, Single Nucleotide; Genotype
PubMed: 38717815
DOI: 10.1099/mgen.0.001232 -
Frontiers in Plant Science 2024Oak decline is a complex disorder that seriously threatens the survival of Zagros forests. In an extensive study on taxonomy and pathology of fungi associated with oak...
Oak decline is a complex disorder that seriously threatens the survival of Zagros forests. In an extensive study on taxonomy and pathology of fungi associated with oak decline in the central and northern part of Zagros forests, 462 fungal isolates were obtained from oak trees showing canker, gummosis, dieback, defoliation, and partial or total death symptoms. Based on inter-simple sequence repeat (ISSR) fingerprinting patterns, morphological characteristics, and sequences of ribosomal DNA (28S rDNA and ITS) and protein coding loci (, , , , , , and ), 24 fungal species corresponding to 19 genera were characterized. Forty percent of the isolates were placed in eight coelomycetous species from seven genera, namely, , , , , , , and . Of these, four species are new to science, which are introduced here as taxonomic novelties: sp. nov., sp. nov., sp. nov., and sp. nov. According to pathogenicity trials on leaves and stems of 2-year-old Persian oak () seedlings, spp. (, , and ), , and were recognized as nonpathogenic. All coelomycetous species were determined as pathogenic in both pathogenicity trials on leaves and seedling stems, of which sp. nov., , and were recognized as the most virulent species followed by .
PubMed: 38708399
DOI: 10.3389/fpls.2024.1377441 -
Forensic Science International Jul 2024Weak and partial DNA profiles are commonly encountered within forensic casework due to amplification of low DNA input samples. One option for increasing allelic...
Weak and partial DNA profiles are commonly encountered within forensic casework due to amplification of low DNA input samples. One option for increasing allelic detection in such samples is the purification of amplified PCR product using commercially available column-based methods. In this study, four commercially available post-PCR purification methods, QIAGEN MinElute®, Independent Forensics Amplicon™ Rx, Millipore Microcon® and Thermo Fisher Scientific ExoSAP-IT™ were evaluated, comparing the quality of PowerPlex® 21 DNA profiles produced to the standard DNA profile generated prior to purification. An increased detection of alleles above the analytical threshold was observed following purification with the MinElute®, Amplicon™ Rx and Microcon® methods, allowing informative DNA profiles to be recovered using as little as 8 pg DNA. However, post-PCR purification using the ExoSAP-IT™ kit was unsuccessful, with no alleles detected above analytical threshold in samples with ≤16 pg DNA. The MinElute® kit was selected for optimisation on the basis of DNA profile quality, including increased detection of alleles and minimal artefacts. The MinElute® method was optimised by evaluating the number of washes and final elution buffer volume, resulting in a further increase in detection of alleles by reducing the elution buffer volume. Overall, this study showed that PowerPlex® 21 DNA profiles from low input DNA can be successfully enhanced by employing the MinElute® post-PCR purification method.
Topics: Humans; DNA Fingerprinting; Polymerase Chain Reaction; DNA; Microsatellite Repeats; Alleles
PubMed: 38705055
DOI: 10.1016/j.forsciint.2024.112043 -
Journal of Forensic Sciences Jul 2024The potential evidential value of male underwear in cases of alleged sexual assault is often overlooked. Male underwear can be a critical item in the investigation of...
The potential evidential value of male underwear in cases of alleged sexual assault is often overlooked. Male underwear can be a critical item in the investigation of alleged sexual assaults. Body fluids/DNA, which may transfer to the penis during sexual contact, may in turn transfer to the inside front of the underwear, and persist for months or years, provided the underwear are not washed. Here, we demonstrate how the case circumstances drive the sampling strategy of male underwear, in order to maximize the effectiveness of the forensic analysis. Sampling considerations including recovery methods and sampling sequence are discussed, and a methodical examination strategy of male underwear is proposed. To highlight the pertinence of male underwear to the investigation of alleged sexual assaults, three real-life cases are discussed, in which male underwear were examined for multiple body fluids/DNA, and the findings obtained proved evidentially significant. The different cases demonstrate the versatility of male underwear examination in situations, where different body fluids and DNA may transfer based on the specific allegation, and emphasize how targeted sampling can allow the scientist to assess the probability of the findings based on two competing propositions. Accurate sampling strategies are imperative for robust probability assignment in evaluative reporting of scientific findings.
Topics: Humans; Male; Specimen Handling; DNA; Clothing; Adult; DNA Fingerprinting; Sex Offenses; Female; Semen; Cervix Mucus; Polymerase Chain Reaction; Young Adult
PubMed: 38703136
DOI: 10.1111/1556-4029.15539 -
Journal of Integrative Plant Biology May 2024In the present study, we have successfully established a gene editing platform in broomcorn millet, one of the oldest crops originating from China, by using our...
In the present study, we have successfully established a gene editing platform in broomcorn millet, one of the oldest crops originating from China, by using our CRISPR/Cas12i.3, and we also created new elite germplasm for this crop.
PubMed: 38695642
DOI: 10.1111/jipb.13669 -
Chemistry & Biodiversity Jun 2024Salvia lanigera Poir. is a small herbaceous perennial species with violet flowers that grows in low-altitude deserts, and sandy loam. During the collection of S....
Salvia lanigera Poir. is a small herbaceous perennial species with violet flowers that grows in low-altitude deserts, and sandy loam. During the collection of S. lanigera, unusual populations with white flowers were found. Therefore, the two populations (violet- and white-flowered) were subjected to comparative investigations, including DNA fingerprinting, chemical composition, and biological evaluation. The two populations showed DNA variations, with 6.66 % polymorphism in ISSR and 25 % in SCoT markers. GC/MS and UHPLC/HRMS of aqueous methanol extracts, led to the tentative identification of 43 and 50 compounds in both populations. In addition, the structures of nine compounds, including four first-time reported compounds in the species, were confirmed by NMR. Furthermore, the total extracts exhibited weak radical scavenging activity against DPPH and a lower inhibitory effect towards acetylcholinesterase. In conclusion, the obtained data suggested that the white-colored flower could be an additional important character record for the Egyptian S. lanigera.
Topics: Salvia; Egypt; Flowers; Metabolomics; DNA Fingerprinting; Plant Extracts; Biphenyl Compounds; Gas Chromatography-Mass Spectrometry; Picrates; Acetylcholinesterase; Cholinesterase Inhibitors; Chromatography, High Pressure Liquid
PubMed: 38680104
DOI: 10.1002/cbdv.202400619