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Borsinger T, Torchia M, Malskis B, Levy BA, Werth PM, Moschetti WE. Characterizing the Native Microbiome Using Next-Generation Sequencing of Bilateral 'Aseptic' Knees. J Arthroplasty 2024; 39:1317-1322. [PMID: 37952737 DOI: 10.1016/j.arth.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Next generation sequencing (NGS) has proven ability to identify organisms beyond those identified through traditional culture-based techniques in cases of suspected prosthetic joint infection. However, there is concern that some microorganisms identified may represent the natural joint microbiome rather than pathogenic agents. This work sought to evaluate the presence of microorganisms identified with NGS in bilateral native, presumed "aseptic" knees with osteoarthritis. METHODS There were 40 patients undergoing primary unilateral (30) or bilateral (10) total knee arthroplasty enrolled prospectively. During surgery, samples of fluid and tissue were obtained from operative knees, and joint fluid was obtained from nonoperative knees. Samples were sent for NGS analysis and processed according to manufacturer protocols. Patient age, body mass index, comorbidities, prior history of injections, and grade of arthritis were evaluated for association with positive NGS results. RESULTS There were 3 of 80 samples (3.8%) that demonstrated positive NGS. There were two of these that had multiple microorganisms identified (1 knee with 4 microorganisms; 1 knee with 2 microorganisms). An additional 2 samples had positive NGS results below the manufacturer's threshold for reporting. The most common organism identified was Cutibacterium acnes, present in 2 of the 3 positive samples. No patient baseline characteristics were associated with positive NGS results. CONCLUSIONS Some native knee joints with osteoarthritis have positive microorganisms identified with NGS. The presence of microorganisms in the native knee has important implications for better understanding the native joint microbiome as well as utilization of NGS in cases of suspected prosthetic joint infection.
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Affiliation(s)
- Tracy Borsinger
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Michael Torchia
- Department of Orthopaedics, Essentia Health Duluth Clinic, Duluth, Minnesota
| | - Bethany Malskis
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Benjamin A Levy
- Department of Orthopaedics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Paul M Werth
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Wayne E Moschetti
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
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Aydin Mericoz C, Eren OC, Kulac I, Firat P. Fusion of old and new: Employing touch imprint slides for next generation sequencing in solid tumors. Diagn Cytopathol 2024; 52:264-270. [PMID: 38339821 DOI: 10.1002/dc.25283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Cytomorphological evaluation of tissue touch imprints during rapid on-site evaluation or intraoperative pathology consultation has crucial value. However, literature on their utility for molecular testing is limited. In this study, we emphasize a further benefit of touch imprint slides and scrutinize our institutional experience on their use in molecular testing, specifically next generation sequencing (NGS). MATERIALS AND METHODS NGS-based reports (2019-2023) of Koç University Hospital were retrospectively analyzed and circumstances in which sequencing was conducted on touch imprint slides were retrieved (n = 18). Type/location of the biopsy, diagnosis, results, and quality metrics were recorded. RESULTS Touch imprints were addressed when they harbored more neoplastic cells compared with permanent biopsies, when suboptimal fixation mitigated deoxyribonucleic acid/ribonucleic acid (DNA/RNA) yield in resections or when the sample was obtained from bone and required decalcification. Diagnoses were diverse, namely non-small-cell lung cancer, gastric adenocarcinoma, glial tumor, Ewing sarcoma, and carcinoma of unknown primary. The percentage of tumor cells on slides stretched between 15% and 70%. Molecular findings ranged from KRAS mutations to TRIM1::NTRK2 and EWSR::FLI1 fusions. For five cases, sequencing did not yield any alteration, one study was not completed because it did not yield high-quality RNA. CONCLUSION Touch imprint slides provide a reliable alternative, especially when neoplastic cells are scarce in permanent biopsies or decalcification deters nucleic acid quality. Based on our experience, we suggest making touch imprints on a routine basis, especially for every bone biopsy. Once digitally scanned duplicates are made, original slides can be safely used for DNA-/RNA-based molecular studies.
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Affiliation(s)
- Cisel Aydin Mericoz
- Department of Pathology, Koç University School of Medicine, Istanbul, Turkey
| | - Ozgur Can Eren
- Department of Pathology, Koç University School of Medicine, Istanbul, Turkey
- Department of Immunology, Graduate School of Health Sciences, Koç University, Istanbul, Turkey
- Koç University IsBank Research Center for Infectious Diseases, Istanbul, Turkey
| | - Ibrahim Kulac
- Department of Pathology, Koç University School of Medicine, Istanbul, Turkey
- Research Center for Translational Medicine, Koç University, Istanbul, Turkey
| | - Pinar Firat
- Department of Pathology, Koç University School of Medicine, Istanbul, Turkey
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Wei H, Qing-Zhen Z, Jing Y, Zhe Z. A DNA typing panel of 201 genetic markers for degraded samples: development and validation. Yi Chuan 2024; 46:306-318. [PMID: 38632093 DOI: 10.16288/j.yczz.23-253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
With the increasing number of complex forensic cases in recent years, it's more important to combine the different types of genetic markers such as short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (InDels), and microhaplotypes (MHs) to provide more genetic information. In this study, we selected totally 201 genetic markers, including 24 autosomes STRs (A-STRs), 24 Y chromosome STRs (Y-STRs), 110 A-SNPs, 24 Y-SNPs, 9 A-InDels, 1 Y-InDel, 8 MHs, and Amelogenin to establish the HID_AM Panel v1.0, a Next-Generation Sequencing (NGS) detection system. According to the validation guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), the repeatability, accuracy, sensitivity, suitability for degraded samples, species specificity, and inhibitor resistance of this system were assessed. The typing results on 48 STRs and Amelogenin of this system were completely consistent with those obtained using capillary electrophoresis. This system accurately detected 79 SNPs as parallelly confirmed by a FGx sequencer with the ForenSeq™ DNA Signature Prep Kit. Complete allele typing results could be obtained with a DNA input of no less than 200 pg. The detection success rate of this system was significantly higher than that of the GlobalFiler™ kit when the degradation index of mock degraded sample was greater than 15.87. When the concentration of hematin in the amplification system was ≤40 µmol/L, indigo blue was ≤2 mmol/L, or humic acid was ≤15 ng/µL, amplification was not significantly inhibited. The system barely amplified the DNA extract from duck, mouse, cow, rabbit, and chick. The detection rate of STRs on routine samples of this panel is 99.74%, while all the SNPs, InDels, and MHs were successfully detected. In summary, we setup a NGS individual typing panel including 201 genetic markers with the high accuracy, sensitivity, species specificity, and inhibitors resistance, which is applicable for individual identification of degraded samples.
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Affiliation(s)
- Han Wei
- Bioinformatics Center of Academy of Military Medical Sciences, Beijing 100850, China
| | - Zhang Qing-Zhen
- Bioinformatics Center of Academy of Military Medical Sciences, Beijing 100850, China
| | - Yang Jing
- Bioinformatics Center of Academy of Military Medical Sciences, Beijing 100850, China
| | - Zhou Zhe
- Bioinformatics Center of Academy of Military Medical Sciences, Beijing 100850, China
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Han H, Lee HJ, Kim KS, Chung J, Na HS. Comparison of the performance of MiSeq and NovaSeq in oral microbiome study. J Oral Microbiol 2024; 16:2344293. [PMID: 38645704 PMCID: PMC11028001 DOI: 10.1080/20002297.2024.2344293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 04/23/2024] Open
Abstract
Objective Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study. Methods Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens. Results NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades. Conclusion Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.
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Affiliation(s)
- Hyejung Han
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Jin Chung
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| | - Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
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Maekawa F, Hayashida M, Takeoka K, Fukutsuka K, Nakagawa M, Akasaka T, Sakamoto S, Sumiyoshi S, Kobashi Y, Ohno H. Two recurrent types of IGH::5' BCL2 breakpoints representing cytogenetic ins(14;18)(q32;q21q21) and t(14;18)(q32;q21), mediated by the VDJ and class switch recombination processes, respectively. Leuk Lymphoma 2024:1-10. [PMID: 38608254 DOI: 10.1080/10428194.2024.2341333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
We describe two types of IGH::BCL2 breakpoints involving the 5' region of BCL2 (5' BCL2). One was ins(14;18)(q32;q21q21) observed in 2 follicular lymphoma (FL) cases, in which IGH was cleaved at 3' of IGHD and 5' of IGHJ and BCL2 was cleaved at 5' BCL2 and downstream regions, and a 281- or 201-kilobase pair fragment containing the BCL2 protein-coding sequences was invertedly inserted into IGH. In another type observed in 2 FL and 2 chronic lymphocytic leukemia (CLL) cases, breakage and reunion occurred within the switch region associated with IGHM (Sµ) and 5' BCL2, creating IGH Sµ::5' BCL2 fusion sequences on der(18)t(14;18)(q32;q21). The former is considered to be mediated by VDJ-recombination, while the latter by the class switch recombination process. There were no particular features in FL or CLL cases with IGH::5' BCL2 breakpoints compared with those with t(14;18)(q32;q21)/IGH::BCL2 involving the 3' breakpoint cluster regions.
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Affiliation(s)
- Fumiyo Maekawa
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | | | - Kayo Takeoka
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | | | - Miho Nakagawa
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
| | - Takashi Akasaka
- Department of Hematology, Tenri Hospital, Tenri, Nara, Japan
| | - Shinichi Sakamoto
- Department of Diagnostic Pathology, Tenri Hospital, Tenri, Nara, Japan
| | - Shinji Sumiyoshi
- Department of Diagnostic Pathology, Tenri Hospital, Tenri, Nara, Japan
| | - Yoichiro Kobashi
- Department of Diagnostic Pathology, Tenri Hospital, Tenri, Nara, Japan
| | - Hitoshi Ohno
- Tenri Institute of Medical Research, Tenri Hospital, Tenri, Nara, Japan
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Bonnot Ruget M, Moulin P, Pagan C, Cheillan D, Marmontel O, Raverot G, Benlian P, Di Filippo M. Diagnostic challenge between a frequent polygenic hypocholesterolemia and an unusual Smith Lemli Opitz syndrome related to bi-allelic DHCR7 mutations. Clin Chem Lab Med 2024; 0:cclm-2024-0162. [PMID: 38581293 DOI: 10.1515/cclm-2024-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/28/2024] [Indexed: 04/08/2024]
Affiliation(s)
- Mathilde Bonnot Ruget
- 26900 Service de Biochimie et Biologie moléculaire, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon , Lyon Cedex, France
| | - Philippe Moulin
- CarMen Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Pierre-Bénite, France
- 26900 Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, GHE, Hospices Civils de Lyon , Bron Cedex, France
| | - Cécile Pagan
- 26900 Service de Biochimie et Biologie moléculaire, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon , Lyon Cedex, France
| | - David Cheillan
- 26900 Service de Biochimie et Biologie moléculaire, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon , Lyon Cedex, France
- CarMen Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Oriane Marmontel
- 26900 Service de Biochimie et Biologie moléculaire, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon , Lyon Cedex, France
- CarMen Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Pierre-Bénite, France
| | - Gerald Raverot
- Lyon 1 University, Villeurbanne, France
- Endocrinology Department, 26900 Reference Center for Rare Pituitary Diseases HYPO, "Groupement Hospitalier Est" Hospices Civils de Lyon , Bron, France
- Inserm U1052, CNRS UMR5286, Cancer Research Center of Lyon, Lyon, France
| | - Pascale Benlian
- Univ. Lille, INSERM, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 1283 - EGID, Lille, France
| | - Mathilde Di Filippo
- 26900 Service de Biochimie et Biologie moléculaire, Laboratoire de Biologie Médicale Multi-sites, Hospices Civils de Lyon , Lyon Cedex, France
- CarMen Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Pierre-Bénite, France
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Mosca I, Freri E, Ambrosino P, Belperio G, Granata T, Canafoglia L, Ragona F, Solazzi R, Filareto I, Castellotti B, Messina G, Gellera C, DiFrancesco JC, Soldovieri MV, Taglialatela M. Case report: Marked electroclinical improvement by fluoxetine treatment in a patient with KCNT1-related drug-resistant focal epilepsy. Front Cell Neurosci 2024; 18:1367838. [PMID: 38644974 PMCID: PMC11027738 DOI: 10.3389/fncel.2024.1367838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
Variants in KCNT1 are associated with a wide spectrum of epileptic phenotypes, including epilepsy of infancy with migrating focal seizures (EIMFS), non-EIMFS developmental and epileptic encephalopathies, autosomal dominant or sporadic sleep-related hypermotor epilepsy, and focal epilepsy. Here, we describe a girl affected by drug-resistant focal seizures, developmental delay and behavior disorders, caused by a novel, de novo heterozygous missense KCNT1 variant (c.2809A > G, p.S937G). Functional characterization in transiently transfected Chinese Hamster Ovary (CHO) cells revealed a strong gain-of-function effect determined by the KCNT1 p.S937G variant compared to wild-type, consisting in an increased maximal current density and a hyperpolarizing shift in current activation threshold. Exposure to the antidepressant drug fluoxetine inhibited currents expressed by both wild-type and mutant KCNT1 channels. Treatment of the proband with fluoxetine led to a prolonged electroclinical amelioration, with disappearance of seizures and better EEG background organization, together with an improvement in behavior and mood. Altogether, these results suggest that, based on the proband's genetic and functional characteristics, the antidepressant drug fluoxetine may be repurposed for the treatment of focal epilepsy caused by gain-of-function variants in KCNT1. Further studies are needed to verify whether this approach could be also applied to other phenotypes of the KCNT1-related epilepsies spectrum.
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Affiliation(s)
- Ilaria Mosca
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, Campobasso, Italy
| | - Elena Freri
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Paolo Ambrosino
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Giorgio Belperio
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Tiziana Granata
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Laura Canafoglia
- Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Francesca Ragona
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Roberta Solazzi
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Ilaria Filareto
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, Milan, Italy
| | - Barbara Castellotti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Giuliana Messina
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | | | - Maria Virginia Soldovieri
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, Campobasso, Italy
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LaPelusa M, Cann C, Ciombor KK, Eng C. Mutational Signature Changes in Patients With Metastatic Squamous Cell Carcinoma of the Anal Canal. Oncologist 2024; 29:e475-e486. [PMID: 38103030 PMCID: PMC10994269 DOI: 10.1093/oncolo/oyad326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
PURPOSE We examined the concordance of genetic mutations between pretreatment tumor tissue and posttreatment circulating tumor DNA (ctDNA) in patients with metastatic squamous cell carcinoma of the anal canal (SCCA) and assessed the impact of therapy on this concordance. METHODS We analyzed next-generation sequencing reports from pretreatment tumor tissue and posttreatment ctDNA in 11 patients with metastatic SCCA treated at Vanderbilt University Medical Center between 2017 and 2021. RESULTS Among the mutations identified in posttreatment ctDNA, 34.5% were also found in pretreatment tumor tissue, while 47.6% of pretreatment tumor tissue mutations were found in posttreatment ctDNA. Four patients had preservation of potentially actionable mutations in both pretreatment tissue and posttreatment ctDNA, while 7 patients had newly identified mutations in posttreatment ctDNA that were not present in pretreatment tumor tissue. CONCLUSION Patients with SCCA demonstrate a high degree of temporal mutational heterogeneity. This supports the hypothesis that ctDNA can serve as a real-time tracking mechanism for solid tumors' molecular evolution in response to therapy. Our findings highlight the potential of ctDNA in identifying emerging actionable mutations, supplementing information from tissue-based genomic assessments. Further research, ideally with larger and multi-institutional cohorts, is needed to validate our findings in this relatively rare tumor type.
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Affiliation(s)
- Michael LaPelusa
- Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher Cann
- Division of Hematology and Oncology, Department of Internal Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristen K Ciombor
- Division of Hematology and Oncology, Department of Internal Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cathy Eng
- Division of Hematology and Oncology, Department of Internal Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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de Oliveira AML, Massi FP, Stelet VN, Hirata BKB, Visentainer JEL. The novel HLA-DPA1*01:182 allele identified in a Brazilian bone marrow donor. HLA 2024; 103:e15470. [PMID: 38566403 DOI: 10.1111/tan.15470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
The new HLA-DPA1*01:182 allele differs from HLA-DPA1*01:03:01:04 by a single mismatch in exon 4.
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Affiliation(s)
- Anthony Marçal Leão de Oliveira
- Department of Clinical Analysis and Biomedicine (DAB), Postgraduate Program in Biosciences and Physiopathology (PBF), Laboratory of Immunogenetics at the State University of Maringá (LIG-UEM), Maringá, Brazil
| | - Fernanda Pelisson Massi
- Department of Clinical Analysis and Biomedicine (DAB), Postgraduate Program in Biosciences and Physiopathology (PBF), Laboratory of Immunogenetics at the State University of Maringá (LIG-UEM), Maringá, Brazil
- Department of Basic Health Sciences (DBS), Laboratory of Immunogenetics at the State University of Maringá (LIG-UEM), Maringá, Brazil
| | | | - Bruna Karina Banin Hirata
- Department of Basic Health Sciences (DBS), Laboratory of Immunogenetics at the State University of Maringá (LIG-UEM), Maringá, Brazil
| | - Jeane Eliete Laguila Visentainer
- Department of Basic Health Sciences (DBS), Laboratory of Immunogenetics at the State University of Maringá (LIG-UEM), Maringá, Brazil
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Cowzer D, Shah RH, Chou JF, Kundra R, Punn S, Fiedler L, DeMore A, Capanu M, Berger MF, Reidy-Lagunes D, Raj N. Clinical utility of plasma cell-free DNA in pancreatic neuroendocrine neoplasms. Endocr Relat Cancer 2024; 31:e230292. [PMID: 38252063 DOI: 10.1530/erc-23-0292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/22/2024] [Indexed: 01/23/2024]
Abstract
In advanced pancreatic neuroendocrine neoplasms (PanNEN), there are little data detailing the frequency of genetic alterations identified in cell free DNA (cfDNA), plasma-tissue concordance of detected alterations, and clinical utility of cfDNA. Patients with metastatic PanNENs underwent cfDNA collection in routine practice. Next-generation sequencing (NGS) of cfDNA and matched tissue when available was performed. Clinical actionability of variants was annotated by OncoKB. Thirty-two cfDNA samples were analyzed from 25 patients, the majority who had well-differentiated intermediate grade disease (13/25; 52%). Genomic alterations were detected in 68% of patients and in 66% of all cfDNA samples. The most frequently altered genes were DAXX (28%), TSC2 (24%), MEN1 (24%), ARID1B (20%), ARID1A (12%), and ATRX (12%). Twenty-three out of 25 (92%) patients underwent tumor tissue NGS. Tissue-plasma concordance for select genes was as follows:DAXX (95.7%), ARID1A (91.1%), ATRX (87%), TSC2 (82.6%), MEN1 (69.6%). Potentially actionable alterations were identified in cfDNA of 8 patients, including TSC2 (4; level 3b), ATM (1; level 3b), ARID1A (2; level 4), and KRAS (1; level 4). An ETV6:NTRK fusion detected in tumor tissue was treated with larotrectinib; at progression, sequencing of cfDNA identified an NTRK3 G623R alteration as the acquired mechanism of resistance; the patient enrolled in a clinical trial of a second-generation TRK inhibitor with clinical benefit. In metastatic PanNENs, cfDNA-based NGS identified tumor-associated mutations in 66% of plasma samples with a high level of plasma-tissue agreement in PanNEN-associated genes. Clonal evolution, actionable alterations, and resistance mechanisms were detected through circulating cfDNA genotyping.
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Affiliation(s)
- Darren Cowzer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ronak H Shah
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Joanne F Chou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ritika Kundra
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sippy Punn
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Laura Fiedler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - April DeMore
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pathology and laboratory medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Diane Reidy-Lagunes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Medical College of Cornell University, New York, New York, USA
| | - Nitya Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Medical College of Cornell University, New York, New York, USA
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Tanimoto S, Hirata Y, Ishizu S, Wang R, Furuta A, Mabuchi R, Okada G. Changes in the Quality and Microflora of Yellowtail Seriola quinqueradiata Muscles during Cold Storage. Foods 2024; 13:1086. [PMID: 38611390 PMCID: PMC11012079 DOI: 10.3390/foods13071086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
We evaluated the changes in the quality and microflora of yellowtail flesh cold-stored until spoilage. Based on the sensory evaluation, odor palatability was deemed unacceptable for dark muscle (DM) and the dorsal part of the ordinary muscle (OD) after >10 days and 14 of storage, respectively. Log 7 CFU/g in DM as well as OD was obtained on days 10 (Aeromonas spp.) and 14 (Enterobacteriaceae and Pseudomonas spp.) of storage, whereas log 5 (Brocothrix thermosphacta) and 6 (H2S-producing bacteria) CFU/g in them were obtained on day 14 of storage. In these bacteria, the viable bacterial counts of Pseudomonas spp. and Aeromonas spp. in DM were significantly higher than those in OD only at some storage times. Amplicon sequencing revealed that in both muscles, Pseudomonas became predominant after storage, with greater than 90% recorded after more than 10 days of storage. The relative abundances of Acinetobacter, Unclassified Gammaproteobacter, and Shewanella were relatively high in both muscles after more than 10 days of storage; however, these values were less than 5%. Ethyl butyrate in the OD and DM and 2,3-butanedione in the OD were first detected on days 14 and 10 of storage, respectively. Acetoin in the OD increased by 81-fold after 14 days of storage and was significantly increased in the DM after more than 10 days compared with the amount detected pre-storage. Volatiles, such as (E)-2-pentenal in the OD and 1-pentanol in the DM, decreased and increased linearly, respectively, throughout the 14-day storage period. Altogether, these volatile components may cause quality deterioration due to spoilage and/or lipid oxidation during cold storage of the OD and DM.
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Affiliation(s)
- Shota Tanimoto
- Faculty of Regional Development, Prefectural University of Hiroshima, Hiroshima 734-0003, Japan; (A.F.); (G.O.)
| | - Yuka Hirata
- Faculty of Human Culture and Science, Prefectural University of Hiroshima, Hiroshima 734-0003, Japan;
| | - Shinta Ishizu
- Graduate School of Comprehensive Scientific Research, Prefectural University of Hiroshima, Shobara 734-0003, Japan; (S.I.); (R.W.)
| | - Run Wang
- Graduate School of Comprehensive Scientific Research, Prefectural University of Hiroshima, Shobara 734-0003, Japan; (S.I.); (R.W.)
| | - Ayumi Furuta
- Faculty of Regional Development, Prefectural University of Hiroshima, Hiroshima 734-0003, Japan; (A.F.); (G.O.)
| | - Ryota Mabuchi
- Faculty of Bioresource Sciences, Prefectural University of Hiroshima, Shobara 727-0023, Japan;
| | - Genya Okada
- Faculty of Regional Development, Prefectural University of Hiroshima, Hiroshima 734-0003, Japan; (A.F.); (G.O.)
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12
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Foley MM, Koehler G, Fu J, Allen R, Wagner JR. An exploratory view into allelic drop-out of sequenced autosomal STRs. J Forensic Sci 2024. [PMID: 38505986 DOI: 10.1111/1556-4029.15504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/30/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024]
Abstract
As massively parallel sequencing is implemented in forensic genetics, an understanding of sequence data must accompany these advancements, that is, accurate modeling of data for proper statistical analysis. Allelic drop-out, a common stochastic effect seen in genetic data, is often modeled in statistical analysis of STR results. This proof-of-concept study sequenced several serial dilutions of a standard sample ranging from 4 ng to 7.82 pg to evaluate allelic drop-out trends on a select panel of autosomal STRs using the ForenSeq™ DNA Signature Prep Kit, Primer Set A on the Illumina MiSeq FGx. Parameters assessed included locus, profile, and run specific information. A majority of the allelic drop-out occurred in DNA concentrations less than 31.25 pg. Statistical results indicated a need for locus-specific modeling based on STR descriptors, like simple versus compound repeat patterns. No correlation was seen between average read count of scored alleles and allelic drop-out at a locus. A statistical correlation was observed between the amount of allelic drop-out and the starting amount of DNA in a sample, average read count of a sample, and total read count generated on a flow cell. This study supports using common allelic drop-out factors used in fragment length analysis on sequenced STRs while including additional locus, sample, and run specific information. Results demonstrate multiple factors that can be considered when developing probability of allelic drop-out models for sequenced autosomal STRs including locus-specific analysis, total read count of a profile, and total read count sequenced on a flow cell.
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Affiliation(s)
- Megan M Foley
- School of Forensic Sciences, Oklahoma State University, Tulsa, Oklahoma, USA
- Department of Forensic Sciences, George Washington University, Washington, DC, USA
| | - Gerwald Koehler
- Department of Biochemistry & Microbiology, Oklahoma State University, Tulsa, Oklahoma, USA
| | - Jun Fu
- School of Forensic Sciences, Oklahoma State University, Tulsa, Oklahoma, USA
| | - Robert Allen
- School of Forensic Sciences, Oklahoma State University, Tulsa, Oklahoma, USA
| | - Jarrad R Wagner
- School of Forensic Sciences, Oklahoma State University, Tulsa, Oklahoma, USA
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13
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Wojciechowska D, Salamon S, Wróblewska-Seniuk K. It's time to shed some light on the importance of fungi in neonatal intensive care units: what do we know about the neonatal mycobiome? Front Microbiol 2024; 15:1355418. [PMID: 38567073 PMCID: PMC10985264 DOI: 10.3389/fmicb.2024.1355418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
The 21st century, thanks to the development of molecular methods, including DNA barcoding, using Sanger sequencing, and DNA metabarcoding, based on next-generation sequencing (NGS), is characterized by flourishing research on the human microbiome. Microbial dysbiosis is perceived as a new pathogenetic factor for neonatal diseases. Fungi are crucial, but neglected, components of the neonatal microbiome, which, despite their low abundance, significantly impact morbidity and mortality rates of premature infants hospitalized in Neonatal Intensive Care Units (NICUs). The neonatal mycobiome's composition and effect on health remain poorly studied research areas. Our knowledge about neonatal mycobiome, composed of limited genera, is mainly based on research on the bacterial microbiome. We presume it is influenced by clinical factors, including prematurity, antibiotic therapy, and type of delivery. Understanding these risk factors may be useful in prevention strategies against dysbiosis and invasive fungal infections. Despite the methodological challenges resulting from the biology of the fungal cell, this topic is an attractive area of research that may contribute to more effective treatment, especially of newborns from risk groups. In this mini review, we discuss the current state of knowledge, research gaps, study difficulties, and future research directions on the neonatal mycobiome, concerning potential future clinical applications.
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Affiliation(s)
- Dobrochna Wojciechowska
- II Department of Neonatology, Poznan University of Medical Sciences, Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, Poznan, Poland
| | - Sylwia Salamon
- Department of Plant Microbiomics, Institute of Plant Genetics, Academy of Sciences, Poznan, Poland
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14
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Budurlean L, Tukaramrao DB, Zhang L, Dovat S, Broach J. Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection. J Pers Med 2024; 14:291. [PMID: 38541033 PMCID: PMC10971281 DOI: 10.3390/jpm14030291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
Structural variants drive tumorigenesis by disrupting normal gene function through insertions, inversions, translocations, and copy number changes, including deletions and duplications. Detecting structural variants is crucial for revealing their roles in tumor development, clinical outcomes, and personalized therapy. Presently, most studies rely on short-read data from next-generation sequencing that aligns back to a reference genome to determine if and, if so, where a structural variant occurs. However, structural variant discovery by short-read sequencing is challenging, primarily because of the difficulty in mapping regions of repetitive sequences. Optical genome mapping (OGM) is a recent technology used for imaging and assembling long DNA strands to detect structural variations. To capture the structural variant landscape more thoroughly in the human genome, we developed an integrated pipeline that combines Bionano OGM and Illumina whole-genome sequencing and applied it to samples from 29 pediatric B-ALL patients. The addition of OGM allowed us to identify 511 deletions, 506 insertions, 93 duplications/gains, and 145 translocations that were otherwise missed in the short-read data. Moreover, we identified several novel gene fusions, the expression of which was confirmed by RNA sequencing. Our results highlight the benefit of integrating OGM and short-read detection methods to obtain a comprehensive analysis of genetic variation that can aid in clinical diagnosis, provide new therapeutic targets, and improve personalized medicine in cancers driven by structural variation.
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Affiliation(s)
- Laura Budurlean
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | | | - Lijun Zhang
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sinisa Dovat
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
- Department of Pediatrics, Penn State Cancer Institute, Hershey, PA 17033, USA
| | - James Broach
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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15
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Lan Y, Zhou H, He S, Shu J, Liang L, Wei H, Luo J, Wang C, Zhao X, Qiu Q, Huang P. Appropriate whole genome amplification and pathogenic loci detection can improve the accuracy of preimplantation genetic diagnosis for deletional α-thalassemia. Front Endocrinol (Lausanne) 2024; 14:1176063. [PMID: 38523870 PMCID: PMC10957767 DOI: 10.3389/fendo.2023.1176063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 11/13/2023] [Indexed: 03/26/2024] Open
Abstract
Objective To improve the accuracy of preimplantation genetic testing (PGT) in deletional α-thalassemia patients. Design Article. Patients fifty-two deletional α-thalassemia couples. Interventions Whole genome amplification (WGA), Next-generation sequencing (NGS) and PCR mutation loci detection. Main outcome measures WGA, Single nucleotide polymorphism (SNP) and PCR mutation loci detection results; Analysis of embryo chromosome copy number variation (CNV). Results Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) methods for PGT for deletional α-thalassemia. Blastocyst biopsy samples (n = 253) were obtained from 52 deletional α-thalassemia couples. The results of the comparison of experimental data between groups MALBAC and MDA are as follows: (i) The average allele drop-out (ADO) rate, MALBAC vs. MDA = 2.27% ± 3.57% vs. 0.97% ± 1.4%, P=0.451); (ii) WGA success rate, MALBAC vs. MDA = 98.61% vs. 98.89%, P=0.851; (iii) SNP haplotype success rate, MALBAC vs. MDA = 94.44% vs. 96.68%, P=0.409; (iv) The result of SNP haplotype analysis is consistent with that of Gap-PCR/Sanger sequencing results, MALBAC vs. MDA = 36(36/72, 50%) vs. 151(151/181, 83.43%), P=0; (v) Valid SNP loci, MALBAC vs. MDA = 30 ± 9 vs. 34 ± 10, P=0.02; (vi) The mean CV values, MALBAC vs. MDA = 0.12 ± 0.263 vs. 0.09 ± 0.40, P=0.916; (vii) The average number of raw reads, MALBAC vs. MDA =3244259 ± 999124 vs. 3713146 ± 1028721, P=0; (viii) The coverage of genome (%), MALBAC vs. MDA = 5.02 ± 1.09 vs. 5.55 ± 1.49, P=0.008. Conclusions Our findings indicate that MDA is superior to MALBAC for PGT of deletional α-thalassemia. Furthermore, SNP haplotype analysis combined with PCR loci detection can improve the accuracy and detection rate of deletional α-thalassemia.
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Affiliation(s)
- Yueyun Lan
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Hong Zhou
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Sheng He
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Nanning, China
| | - Jinhui Shu
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Lifang Liang
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Nanning, China
| | - Hongwei Wei
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Nanning, China
| | - Jingsi Luo
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Caizhu Wang
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Xin Zhao
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Qingming Qiu
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
| | - Peng Huang
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
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16
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Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS, Patel JA, Duncan P, Mazumder R. Communicating computational workflows in a regulatory environment. Drug Discov Today 2024; 29:103884. [PMID: 38219969 DOI: 10.1016/j.drudis.2024.103884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 01/16/2024]
Abstract
The volume of nucleic acid sequence data has exploded recently, amplifying the challenge of transforming data into meaningful information. Processing data can require an increasingly complex ecosystem of customized tools, which increases difficulty in communicating analyses in an understandable way yet is of sufficient detail to enable informed decisions or repeats. This can be of particular interest to institutions and companies communicating computations in a regulatory environment. BioCompute Objects (BCOs; an instance of pipeline documentation that conforms to the IEEE 2791-2020 standard) were developed as a standardized mechanism for analysis reporting. A suite of BCOs is presented, representing interconnected elements of a computation modeled after those that might be found in a regulatory submission but are shared publicly - in this case a pipeline designed to identify viral contaminants in biological manufacturing, such as for vaccines.
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Affiliation(s)
- Jonathon G Keeney
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
| | - Naila Gulzar
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | | | - Ondrej Klempir
- R&D Informatics Solutions, MSD Czech Republic, Prague, Czech Republic
| | | | - Danny A Bitton
- R&D Informatics Solutions, MSD Czech Republic, Prague, Czech Republic
| | - Julia M Maritz
- Exploratory Science Center, Merck & Co., Cambridge, MA, USA
| | - Charles H S King
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Janisha A Patel
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | | | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
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17
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Pepe F, Giordano C, Russo G, Palumbo L, Vincenzi A, Acanfora G, Lisi D, Picardi M, Pane F, Troncone G, Vigliar E. Liquid biopsy: A promising tool for driving strategies and predicting failures in patients with classic Hodgkin lymphoma. Cytopathology 2024; 35:182-187. [PMID: 37340989 DOI: 10.1111/cyt.13255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/04/2023] [Indexed: 06/22/2023]
Abstract
Classic Hodgkin lymphoma (cHL) consists of a heterogeneous group of haematological disorders that covers undifferentiated B cell neoplasms originating from germinal centre B cells. The HL molecular characterization still represents an ongoing challenge due to the low fraction of tumour Hodgkin and Reed-Sternberg cells mixed with a plethora of non-tumour haematological cells. In this scenario, next generation sequencing of liquid biopsy samples is emerging as a useful tool in HL patients' management. In this review, we aimed to overview the clinical and methodological topics regarding the implementation of molecular analysis in cHL, focusing on the role of liquid biopsy in diagnosis, follow-up, and response prediction.
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Affiliation(s)
- Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudia Giordano
- Department of Clinical Medicine and Surgery, Hematology Unit, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Lucia Palumbo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Annamaria Vincenzi
- Department of Clinical Medicine and Surgery, Hematology Unit, University of Naples Federico II, Naples, Italy
| | - Gennaro Acanfora
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Dario Lisi
- Department of Clinical Medicine and Surgery, Hematology Unit, University of Naples Federico II, Naples, Italy
| | - Marco Picardi
- Department of Clinical Medicine and Surgery, Hematology Unit, University of Naples Federico II, Naples, Italy
| | - Fabrizio Pane
- Department of Clinical Medicine and Surgery, Hematology Unit, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
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18
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Wener ER, McLennan JD, Papsin BC, Cushing SL, Stavropoulos DJ, Mendoza-Londono R, Quercia N, Gordon KA. Variants in Genes Associated with Hearing Loss in Children: Prevalence in a Large Canadian Cohort. Laryngoscope 2024. [PMID: 38426810 DOI: 10.1002/lary.31373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The objective of this study was to assess the prevalence of genetic variants associated with hearing loss in a large cohort of children in Canada using high throughput next generation sequencing (NGS). METHODS A total of 485 children with hearing loss underwent NGS testing with an 80 gene panel of syndromic and non-syndromic variants known to be associated with hearing loss. Genetic variants were classified as pathogenic, likely pathogenic, likely benign, benign, or variants of uncertain significance (VUS), according to the American College of Medical Genetics and Genomics guidelines. RESULTS Across the 80 genes tested, 923 variants, predominantly in 28 genes, were identified in 324 children. Pathogenic variants occurred in 19/80 (23.8%) of the hearing loss related genes tested and confirmed the etiology of hearing loss in 73/485 (15.1%) of children. GJB2 was the most prevalent gene, affecting 28/73 (38.4%) children with confirmed genetic hearing loss in our cohort. Most identified variants (748/923, 81.0%, in 76/80 genes) were of uncertain significance. CONCLUSION Genetic testing using NGS identified the etiology in approximately 15% of childhood hearing loss in a Canadian cohort which is lower than what is typically reported. GJB2 was the most common genetic cause of hearing loss. VUS are commonly identified, presenting clinical challenges for counseling. LEVEL OF EVIDENCE Level 4 Laryngoscope, 2024.
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Affiliation(s)
- Emily R Wener
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacob D McLennan
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Blake C Papsin
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sharon L Cushing
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dimitri James Stavropoulos
- Genome Diagnostics Paediatric Laboratory Medicine, Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Genome Diagnostics Paediatric Laboratory Medicine, Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nada Quercia
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Karen A Gordon
- Archie's Cochlear Implant Laboratory, Neuroscience & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
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19
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Nørgaard M, Drechsler LØ, Møller BK. Characterization of the novel HLA-DPB1*1584:01 allele, identified by next-generation sequencing. HLA 2024; 103:e15435. [PMID: 38488774 DOI: 10.1111/tan.15435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024]
Abstract
HLA-DPB1*1584:01 differs from HLA-DPB1*104:01:01:03 by one nucleotide substitution in exon 2.
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Affiliation(s)
- Maja Nørgaard
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Bjarne Kuno Møller
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
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20
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Malakar S, Sutaoney P, Madhyastha H, Shah K, Chauhan NS, Banerjee P. Understanding gut microbiome-based machine learning platforms: A review on therapeutic approaches using deep learning. Chem Biol Drug Des 2024; 103:e14505. [PMID: 38491814 DOI: 10.1111/cbdd.14505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/21/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Human beings possess trillions of microbial cells in a symbiotic relationship. This relationship benefits both partners for a long time. The gut microbiota helps in many bodily functions from harvesting energy from digested food to strengthening biochemical barriers of the gut and intestine. But the changes in microbiota composition and bacteria that can enter the gastrointestinal tract can cause infection. Several approaches like culture-independent techniques such as high-throughput and meta-omics projects targeting 16S ribosomal RNA (rRNA) sequencing are popular methods to investigate the composition of the human gastrointestinal tract microbiota and taxonomically characterizing microbial communities. The microbiota conformation and diversity should be provided by whole-genome shotgun metagenomic sequencing of site-specific community DNA associating genome mapping, gene inventory, and metabolic remodelling and reformation, to ease the functional study of human microbiota. Preliminary examination of the therapeutic potency for dysbiosis-associated diseases permits investigation of pharmacokinetic-pharmacodynamic changes in microbial communities for escalation of treatment and dosage plan. Gut microbiome study is an integration of metagenomics which has influenced the field in the last two decades. And the incorporation of artificial intelligence and deep learning through "omics-based" methods and microfluidic evaluation enhanced the capability of identification of thousands of microbes.
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Affiliation(s)
- Shilpa Malakar
- Department of Microbiology, Kalinga University, Raipur, Chhattisgarh, India
| | - Priya Sutaoney
- Department of Microbiology, Kalinga University, Raipur, Chhattisgarh, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kamal Shah
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Nagendra Singh Chauhan
- Department of Medical education, Drugs Testing Laboratory Avam Anusandhan Kendra, Raipur, Chhattisgarh, India
| | - Paromita Banerjee
- Department of Cardiology, AIIMS Rishikesh, Rishikesh, Uttarkhand, India
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21
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Frolov A, Guzman MA, Hayat G, Martin JR. Two Cases of Sporadic Amyotrophic Lateral Sclerosis With Contrasting Clinical Phenotypes: Genetic Insights. Cureus 2024; 16:e56023. [PMID: 38606235 PMCID: PMC11008550 DOI: 10.7759/cureus.56023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 04/13/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disease that affects individuals of diverse racial and ethnic backgrounds. There is currently no cure for ALS, and the number of efficient disease-modifying drugs for ALS is limited to a few, despite the large number of clinical trials conducted in recent years. The latter could be attributed to the significant heterogeneity of ALS clinical phenotypes even in their familial forms. To address this issue, we conducted postmortem genetic screening of two female patients with sporadic ALS (sALS) and contrasting clinical phenotypes. The results demonstrated that despite their contrasting clinical phenotypes, both patients had rare pathologic/deleterious mutations in five genes: ACSM5, BBS12, HLA-DQB1, MUC20, and OBSCN, with mutations in three of those genes being identical: BBS12, HLA-DQB1, and MUC20. Additional groups of mutated genes linked to ALS, other neurologic disorders, and ALS-related pathologies were also identified. These data are consistent with a hypothesis that an individual could be primed for ALS via mutations in a specific set of genes not directly linked to ALS. The disease could be initiated by a concerted action of several mutated genes linked to ALS and the disease's clinical phenotype will evolve further through accessory gene mutations associated with other neurological disorders and ALS-related pathologies.
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Affiliation(s)
- Andrey Frolov
- Center for Anatomical Science and Education, Saint Louis University School of Medicine, Saint Louis, USA
| | - Miguel A Guzman
- Department of Pathology, Saint Louis University School of Medicine, Saint Louis, USA
| | - Ghazala Hayat
- Department of Neurology, Saint Louis University School of Medicine, Saint Louis, USA
- ALS Center of Excellence, Saint Louis University School of Medicine, Saint Louis, USA
| | - John R Martin
- Center for Anatomical Science and Education, Saint Louis University School of Medicine, Saint Louis, USA
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22
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Pellegrino F, Tirtei E, Divincenzo F, Campello A, Rubino C, Augustoni E, Linari A, Asaftei SD, Fagioli F. An integrative morpho-molecular approach in malignant ectomesenchymoma diagnosis: report of a new paediatric case and a review of the literature. Front Oncol 2024; 14:1320541. [PMID: 38496756 PMCID: PMC10940369 DOI: 10.3389/fonc.2024.1320541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction Malignant ectomesenchymoma (MEM) is a soft tissue tumour, consisting of both malignant neuroectodermal elements and one or more mesenchymal elements. Case presentation and review of the literature Here we describe the case of a 6-months-old male, previously treated in another hospital for abdominal rhabdomyosarcoma (RMS). Histological re-examination demonstrated that the tumour had mesenchymal and neuroectodermal elements components, with a new diagnosis of abdominal-pelvic MEM. A Next-Generation Sequencing (NGS) analysis was performed on a surgical tumour specimen and revealed the presence of a somatic mutation, already reported in MEM cases. We carried out a review of the literature and we found 33 new cases of MEM since the last review. We reported the clinic-pathologic features of new cases of MEM, highlighting the role of molecular studies in supporting the diagnosis of this ambiguous tumours. Conclusion We promote the importance of a diagnosis based on an integrative morpho-molecular approach, that routinely include molecular analysis and the use of bioinformatic mutation detection tools, to support diagnostic and therapeutical queries and to highlight tumour biology and behaviour.
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Affiliation(s)
- Francesco Pellegrino
- Department of Pediatric and Public Health Sciences, Postgraduate School of Pediatrics, Regina Margherita Children Hospital, University of Turin, Turin, Italy
| | - Elisa Tirtei
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children’s Hospital, City of Health and Science of Turin, Torino, Italy
| | - Federico Divincenzo
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children’s Hospital, City of Health and Science of Turin, Torino, Italy
| | - Anna Campello
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children’s Hospital, City of Health and Science of Turin, Torino, Italy
| | - Carlotta Rubino
- Department of Pediatric and Public Health Sciences, Postgraduate School of Pediatrics, Regina Margherita Children Hospital, University of Turin, Turin, Italy
| | - Elisabetta Augustoni
- Department of Pediatric and Public Health Sciences, Postgraduate School of Pediatrics, Regina Margherita Children Hospital, University of Turin, Turin, Italy
| | - Alessandra Linari
- Department of Pathology, Azienda Ospedaliera Città della Salute e della Scienza, Turin, Italy
| | - Sebastian Dorin Asaftei
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children’s Hospital, City of Health and Science of Turin, Torino, Italy
| | - Franca Fagioli
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children’s Hospital, City of Health and Science of Turin, Torino, Italy
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23
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Novkovic M, Banovic Djeri B, Ristivojevic B, Knezevic A, Jankovic M, Tanasic V, Radojicic V, Keckarevic D, Vidanovic D, Tesovic B, Skakic A, Tolinacki M, Moric I, Djordjevic V. Genome sequence diversity of SARS-CoV-2 in Serbia: insights gained from a 3-year pandemic study. Front Microbiol 2024; 15:1332276. [PMID: 38476954 PMCID: PMC10929721 DOI: 10.3389/fmicb.2024.1332276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 03/14/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been evolving rapidly causing emergence of new variants and health uncertainties. Monitoring the evolution of the virus was of the utmost importance for public health interventions and the development of national and global mitigation strategies. Here, we report national data on the emergence of new variants, their distribution, and dynamics in a 3-year study conducted from March 2020 to the end of January 2023 in the Republic of Serbia. Nasopharyngeal and oropharyngeal swabs from 2,398 COVID-19-positive patients were collected and sequenced using three different next generation technologies: Oxford Nanopore, Ion Torrent, and DNBSeq. In the subset of 2,107 SARS-CoV-2 sequences which met the quality requirements, detection of mutations, assignment to SARS-CoV-2 lineages, and phylogenetic analysis were performed. During the 3-year period, we detected three variants of concern, namely, Alpha (5.6%), Delta (7.4%), and Omicron (70.3%) and one variant of interest-Omicron recombinant "Kraken" (XBB1.5) (<1%), whereas 16.8% of the samples belonged to other SARS-CoV-2 (sub)lineages. The detected SARS-CoV-2 (sub)lineages resulted in eight COVID-19 pandemic waves in Serbia, which correspond to the pandemic waves reported in Europe and the United States. Wave dynamics in Serbia showed the most resemblance with the profile of pandemic waves in southern Europe, consistent with the southeastern European location of Serbia. The samples were assigned to sixteen SARS-CoV-2 Nextstrain clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F and six different Omicron recombinants (XZ, XAZ, XAS, XBB, XBF, and XBK). The 10 most common mutations detected in the coding and untranslated regions of the SARS-CoV-2 genomes included four mutations affecting the spike protein (S:D614G, S:T478K, S:P681H, and S:S477N) and one mutation at each of the following positions: 5'-untranslated region (5'UTR:241); N protein (N:RG203KR); NSP3 protein (NSP3:F106F); NSP4 protein (NSP4:T492I); NSP6 protein (NSP6: S106/G107/F108 - triple deletion), and NSP12b protein (NSP12b:P314L). This national-level study is the most comprehensive in terms of sequencing and genomic surveillance of SARS-CoV-2 during the pandemic in Serbia, highlighting the importance of establishing and maintaining good national practice for monitoring SARS-CoV-2 and other viruses circulating worldwide.
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Affiliation(s)
- Mirjana Novkovic
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Bojana Banovic Djeri
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Bojan Ristivojevic
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Knezevic
- Institute of Microbiology and Immunology, Department of Virology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marko Jankovic
- Institute of Microbiology and Immunology, Department of Virology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vanja Tanasic
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Verica Radojicic
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dusan Keckarevic
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dejan Vidanovic
- Veterinary Specialized Institute “Kraljevo”, Kraljevo, Serbia
| | - Bojana Tesovic
- Veterinary Specialized Institute “Kraljevo”, Kraljevo, Serbia
| | - Anita Skakic
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Tolinacki
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Ivana Moric
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Valentina Djordjevic
- Center for Genome Sequencing and Bioinformatics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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24
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Lin DI, Huang RSP, Ladas I, Keller RB, Patel NR, Lakis S, Decker B, Janovitz T, Mata DA, Ross JS, Vergilio JA, Elvin JA, Herbst RS, Mack PC, Killian JK. Precision needle-punch tumor enrichment from paraffin blocks improves the detection of clinically actionable genomic alterations and biomarkers. Front Oncol 2024; 14:1328512. [PMID: 38444675 PMCID: PMC10912171 DOI: 10.3389/fonc.2024.1328512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/11/2024] [Indexed: 03/07/2024] Open
Abstract
Background While many molecular assays can detect mutations at low tumor purity and variant allele frequencies, complex biomarkers such as tumor mutational burden (TMB), microsatellite instability (MSI), and genomic loss of heterozygosity (gLOH) require higher tumor purity for accurate measurement. Scalable, quality-controlled, tissue-conserving methods to increase tumor nuclei percentage (TN%) from tumor specimens are needed for complex biomarkers and hence necessary to maximize patient matching to approved therapies or clinical trial enrollment. We evaluated the clinical utility and performance of precision needle-punch enrichment (NPE) compared with traditional razor blade macroenrichment of tumor specimens on molecular testing success. Methods Pathologist-directed NPE was performed manually on formalin-fixed, paraffin embedded (FFPE) blocks. Quality control of target capture region and quantity of residual tumor in each tissue block was determined via a post-enrichment histologic slide recut. Resultant tumor purity and biomarker status were determined by the computational analysis pipeline component of the FDA-approved next-generation sequencing (NGS) assay, FoundationOne®CDx. Following NPE implementation for real-world clinical samples, assay performance and biomarker (MSI, TMB, gLOH) detection were analyzed. Results In real-world clinical samples, enrichment rate via NPE was increased to ~50% over a 2.5-year period, exceeding the prior use of razor blade macro-enrichment (<30% of cases) prior to NPE implementation due to proven efficacy in generating high quality molecular results from marginal samples and the ease of use for both pathologist and histotechnologists. NPE was associated with lower test failures, higher computational tumor purity, and higher rates of successful TMB, MSI and gLOH determination when stratified by pre-enriched (incipient) tumor nuclei percentage. In addition, challenging cases in which tumor content was initially insufficient for testing were salvaged for analysis of biomarker status, gene amplification/deletion, and confident mutant or wild-type gene status determination. Conclusions Pathologist-directed precision enrichment from tissue blocks (aka NPE) increases tumor purity, and consequently, yields a greater number of successful tests and complex biomarker determinations. Moreover, this process is rapid, safe, inexpensive, scalable, and conserves patient surgical pathology material. NPE may constitute best practice with respect to enriching tumor cells from low-purity specimens for biomarker detection in molecular laboratories.
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Affiliation(s)
- Douglas I Lin
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Richard S P Huang
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Ioannis Ladas
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Rachel B Keller
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Nimesh R Patel
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Sotirios Lakis
- Foundation Medicine GmbH, Pathology Department, Penzberg, Germany
| | - Brennan Decker
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Tyler Janovitz
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Douglas A Mata
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Jeffrey S Ross
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Jo-Anne Vergilio
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Julia A Elvin
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Roy S Herbst
- Department of Medical Oncology, Yale School of Medicine, Yale Cancer Center, New Haven, CT, United States
| | - Philip C Mack
- Division of Hematology and Oncology, Department of Medicine, Tisch Cancer Institute at Mount Sinai, New York, NY, United States
| | - Jonathan K Killian
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
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25
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Desai AN, Kurian CJ, Rafferty W, Behrens DL, Khrizman P. Case report: An unusual presentation of intra-abdominal desmoplastic small round cell tumor. Front Oncol 2024; 14:1260474. [PMID: 38440227 PMCID: PMC10910504 DOI: 10.3389/fonc.2024.1260474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
Background Intra-abdominal desmoplastic small round cell tumor (IDSRCT) is a rare entity (0.2-0.74 cases per million people per year), which predominantly occurs in young men. It may present as an abdominal mass with pain, distention, and constipation. IDSRCT has a very poor prognosis, with 5-year overall survival estimated at 15%-30%. Diagnosis is made with tissue biopsy. Case description We present a case of a 28-year-old man with a history of schizophrenia and depression who presented to an emergency room (ER) in November 2022 with constipation and pelvic pain. The patient was sent home with a bowel regimen after radiography showed no obstruction. He re-presented for evaluation due to persistent pain. A computerized tomography scan of the abdomen and pelvis (CT A/P) revealed numerous pelvic masses with severe colitis, bilateral moderate hydronephrosis, and metastatic disease in the liver. A colonoscopy showed a mass extending 3 cm from the anus to 10 cm causing a partial obstruction. Biopsy was read as squamous cell carcinoma (SCC). The patient was subsequently admitted to our institution with pelvic pain, nausea, and vomiting. Colorectal surgery performed a colectomy with end-ileostomy due to colonic obstruction. He was evaluated by a medical oncologist, with previous slides requested for review. Initial review was concerning metastatic basaloid SCC with neuroendocrine features and a Ki67 of 70%. Given his recent abdominal surgeries, chemotherapy was delayed until February 2023 when he was started on reduced dose carboplatin and paclitaxel. Tumor specimen was sent for next generation sequencing (NGS) and programmed death-1 ligand 1 (PD-L1) testing. NGS results returned after the first dose of chemotherapy was given and showed a t(11;22) EWSR-WT1 translocation characteristic of desmoplastic small round cell tumor. The patient was supported in the hospital and discharged with oncology follow-up. Discussion As seen in this case, pathology review is essential to ensuring correct diagnosis and appropriate treatment plan. This is especially true when the clinical scenario does not match the listed pathology. Additional diagnostics such as NGS are invaluable in establishing correct diagnosis.
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Affiliation(s)
- Akshay Nilesh Desai
- Department of Internal Medicine at Cooper University Healthcare, Camden, NJ, United States
| | - Christine Jane Kurian
- Department of Medical Oncology and Hematology at MD Anderson Cancer Center at Cooper University Healthcare, Camden, NJ, United States
| | - William Rafferty
- Department of Pathology at Cooper University Healthcare, Camden, NJ, United States
| | - Danielle Lajoie Behrens
- Department of Medical Oncology and Hematology at MD Anderson Cancer Center at Cooper University Healthcare, Camden, NJ, United States
| | - Polina Khrizman
- Department of Medical Oncology and Hematology at MD Anderson Cancer Center at Cooper University Healthcare, Camden, NJ, United States
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26
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Sreedharanunni S, Singla S, Balakrishnan A, Singh A, Jamwal M, Singh N, Singh C, Jandial A, Lad D, Sharma P, Sachdeva MUS, Malhotra P, Das R. The frequency and clinical outcome of mono-hit and multi-hit TP53 aberrations in newly diagnosed multiple myeloma. Pathology 2024:S0031-3025(24)00057-6. [PMID: 38413253 DOI: 10.1016/j.pathol.2023.12.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/01/2023] [Accepted: 12/06/2023] [Indexed: 02/29/2024]
Abstract
We investigated the frequency and outcome of mono-hit and multi-hit TP53 aberrations [biallelic or ≥1 TP53 mutations (TP53mut) or TP53mut with variant allele frequency (VAF) ≥55%] in an Indian cohort of newly diagnosed multiple myeloma (NDMM) patients. We employed fluorescence insitu hybridisation (FISH; n=457) and targeted next-generation sequencing (NGS; n=244) on plasma cell-enriched samples. We also studied the impact of TP53mut in cases with and without TP53 deletions (TP53del). In our cohort with a median age of 60 years, TP53del and TP53mut were seen in 12.9% (n=59/457; 14-95% cells) and 10.2% (n=25/244; 30 variants; VAF 3.4-98.2%; median 38.2%) respectively. Mono-hit and multi-hit-TP53 aberrations were observed in 10.2% and 7.8%, respectively. Compared to TP53-wild-type (TP53wt), mono-hit and multi-hit TP53 aberrations were associated with significantly poorer progression-free survival (PFS) (22.6 vs 12.1 vs 9.5 months; p=0.004) and overall survival (OS) [not reached (NR) vs 13.1 vs 15.6 months respectively; p=0.024]. However, multi-hit TP53 did not significantly differ in OS/PFS compared to mono-hit cases. Compared to TP53wt, PFS and OS were significantly poorer in patients with TP53mut only (9.5 vs 22.6 months and 12.1 months vs NR, respectively; p=0.020/0.004). TP53mut retained its significance even in the presence of any Revised International Staging System (HR 2.1; 95% CI 1.1-3.8; p=0.015) for OS. The detection of additional cases with TP53 aberrations, as well as poor survival associated with the presence of mutation alone, supports TP53mut testing in NDMM at least in patients without TP53del and other high-risk cytogenetic abnormalities.
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Affiliation(s)
- Sreejesh Sreedharanunni
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | - Shelly Singla
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anand Balakrishnan
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Archana Singh
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manu Jamwal
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Namrata Singh
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Charanpreet Singh
- Department of Clinical Haematology and Medical Oncology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aditya Jandial
- Department of Clinical Haematology and Medical Oncology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Deepesh Lad
- Department of Clinical Haematology and Medical Oncology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Praveen Sharma
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Man Updesh Singh Sachdeva
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Department of Clinical Haematology and Medical Oncology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Reena Das
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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27
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Firdaus Z, Li X. Unraveling the Genetic Landscape of Neurological Disorders: Insights into Pathogenesis, Techniques for Variant Identification, and Therapeutic Approaches. Int J Mol Sci 2024; 25:2320. [PMID: 38396996 PMCID: PMC10889342 DOI: 10.3390/ijms25042320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic abnormalities play a crucial role in the development of neurodegenerative disorders (NDDs). Genetic exploration has indeed contributed to unraveling the molecular complexities responsible for the etiology and progression of various NDDs. The intricate nature of rare and common variants in NDDs contributes to a limited understanding of the genetic risk factors associated with them. Advancements in next-generation sequencing have made whole-genome sequencing and whole-exome sequencing possible, allowing the identification of rare variants with substantial effects, and improving the understanding of both Mendelian and complex neurological conditions. The resurgence of gene therapy holds the promise of targeting the etiology of diseases and ensuring a sustained correction. This approach is particularly enticing for neurodegenerative diseases, where traditional pharmacological methods have fallen short. In the context of our exploration of the genetic epidemiology of the three most prevalent NDDs-amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, our primary goal is to underscore the progress made in the development of next-generation sequencing. This progress aims to enhance our understanding of the disease mechanisms and explore gene-based therapies for NDDs. Throughout this review, we focus on genetic variations, methodologies for their identification, the associated pathophysiology, and the promising potential of gene therapy. Ultimately, our objective is to provide a comprehensive and forward-looking perspective on the emerging research arena of NDDs.
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Affiliation(s)
- Zeba Firdaus
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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28
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Zarka KA, Jagd LM, Douches DS. T-DNA characterization of genetically modified 3-R-gene late blight-resistant potato events with a novel procedure utilizing the Samplix Xdrop ® enrichment technology. Front Plant Sci 2024; 15:1330429. [PMID: 38419775 PMCID: PMC10900525 DOI: 10.3389/fpls.2024.1330429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Before the commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, polymerase chain reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole-genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole-genomic sequencing coverage that meets the regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234, and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.
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Affiliation(s)
- Kelly A. Zarka
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - David S. Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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29
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Holder P, Clark CC, Moody L, Boardman FK, Cowlard J, Allen L, Walter C, Bonham JR, Chudleigh J. Stakeholder Views of the Proposed Introduction of Next Generation Sequencing into the Cystic Fibrosis Screening Protocol in England. Int J Neonatal Screen 2024; 10:13. [PMID: 38390977 PMCID: PMC10885054 DOI: 10.3390/ijns10010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
The project aimed to gather, analyse, and compare the views of stakeholders about the proposed UK cystic fibrosis (CF) screening protocol incorporating next generation sequencing (NGS). The study design was based on principles of Q-methodology with a willingness-to-pay exercise. Participants were recruited from 12 CF centres in the UK. The study contained twenty-eight adults who have experience with CF (parents of children with CF (n = 21), including parents of children with CF transmembrane conductance regulator (CFTR)-related metabolic syndrome (CRMS)/CF screen positive-inconclusive diagnosis (CFSPID), an uncertain outcome (n = 3), and adults with CF (n = 4)), and nine health professionals involved in caring for children with CF. Parents and health professionals expressed a preference for a sensitive approach to NGS. This was influenced by the importance participants placed on not missing any children with CF via screening and the balance of harm between missing a case of CF compared to picking up more children with an uncertain outcome (CRMS/CFSPID). Given the preference for a sensitive approach, the need for adequate explanations about potential outcomes including uncertainty (CFSPID) at the time of screening was emphasized. More research is needed to inform definitive guidelines for managing children with an uncertain outcome following CF screening.
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Affiliation(s)
- Pru Holder
- Florence Nightingale Faculty of Nursing, Midwifery & Palliative Care, King’s College London, London SE5 9PJ, UK;
| | - Corinna C. Clark
- Warwick Medical School, Warwick University, Coventry CV4 7AL, UK; (C.C.C.); (F.K.B.)
| | - Louise Moody
- Centre for Arts, Memory and Communities, Coventry University, Coventry CV1 5FB, UK;
| | - Felicity K. Boardman
- Warwick Medical School, Warwick University, Coventry CV4 7AL, UK; (C.C.C.); (F.K.B.)
| | - Jacqui Cowlard
- Paediatric Respiratory Medicine, Royal London Children’s Hospital, London E1 1FR, UK;
| | - Lorna Allen
- Cystic Fibrosis Trust, London EC3N 1RE, UK; (L.A.); (C.W.)
| | - Claire Walter
- Cystic Fibrosis Trust, London EC3N 1RE, UK; (L.A.); (C.W.)
| | - James R. Bonham
- Pharmacy, Diagnostics and Genetics, Sheffield Children’s NHS Foundation Trust, Sheffield S10 2TH, UK;
| | - Jane Chudleigh
- Florence Nightingale Faculty of Nursing, Midwifery & Palliative Care, King’s College London, London SE5 9PJ, UK;
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Tomas C, Rodrigues P, Jønck CG, Barekzay Z, Simayijiang H, Pereira V, Børsting C. Performance of a 74-Microhaplotype Assay in Kinship Analyses. Genes (Basel) 2024; 15:224. [PMID: 38397213 PMCID: PMC10888013 DOI: 10.3390/genes15020224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory.
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Affiliation(s)
| | | | | | | | | | | | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V’s Vej 11, DK-2100 Copenhagen, Denmark; (C.T.); (P.R.); (C.G.J.); (Z.B.); (V.P.)
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Germani MM, Vetere G, Giordano M, Ciracì P, Capone I, Tamborini E, Conca E, Busico A, Pietrantonio F, Piva VM, Boccaccino A, Simionato F, Bortolot M, Manca P, Lonardi S, Conca V, Borelli B, Carullo M, Del Re M, Fontanini G, Rossini D, Cremolini C. Molecular screening with liquid biopsy for anti-EGFR retreatment in metastatic colorectal cancer: preliminary data from the randomized phase 2 PARERE trial. Front Oncol 2024; 13:1307545. [PMID: 38406172 PMCID: PMC10889120 DOI: 10.3389/fonc.2023.1307545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/17/2023] [Indexed: 02/27/2024] Open
Abstract
Background Retreatment with anti-EGFR monoclonal antibodies is a promising strategy in patients with RAS/BRAF wild-type (wt) metastatic colorectal cancer (mCRC) who achieved benefit from previous anti-EGFR exposure upon exclusion of mutations in RAS/BRAF genes according to circulating tumor DNA (ctDNA) analysis by means of liquid biopsy (LB). This treatment approach is now being investigated in the randomized phase II trial PARERE (NCT04787341). We here present preliminary findings of molecular screening. Methods Patients with RAS/BRAFV600E wt mCRC according to tissue genotyping who benefited from previous anti-EGFR-based treatment (fluoropyrimidines, oxaliplatin, irinotecan, and antiangiogenics) and then experienced disease progression to EGFR targeting were eligible for screening in the PARERE trial. The next-generation sequencing (NGS) panel Oncomine™ was employed for ctDNA testing. Results A total of 218 patients underwent LB, and ctDNA sequencing was successful in 201 of them (92%). RAS/BRAFV600E mutations were found in 68 (34%) patients and were mainly subclonal (median variant allele fraction [VAF] for KRAS, NRAS, and BRAF mutant clones: 0.52%, 0.62%, and 0.12%, respectively; p = 0.01), with KRASQ61H being the most frequently detected (31%). Anti-EGFR-free intervals did not predict ctDNA molecular status (p = 0.12). Among the 133 patients with RAS/BRAFV600E wt tumors according to LB, 40 (30%) harbored a mutation in at least another gene potentially implied in anti-EGFR resistance, mainly with subclonal expression (median VAF, 0.56%). In detail, alterations in PIK3CA, FBXW7, GNAS, MAP2K, ERBB2, BRAF (class I and II non-BRAFV600E), SMAD, EGFR, AKT1, and CTNNB1 occurred in 13%, 8%, 7%, 3%, 2%, 2%, 1%, 1%, 1%, and 1% cases, respectively. Co-mutations were detected in 13 (33%) out of 40 patients. Conclusions This is the largest prospective cohort of mCRC patients screened with LB for anti-EGFR retreatment in a randomized study. ctDNA genotyping reveals that at least one out of three patients candidate for retreatment should be excluded from this therapy, and other potential drivers of anti-EGFR resistance are found in approximately one out of three patients with RAS/BRAFV600E wt ctDNA.
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Affiliation(s)
- Marco Maria Germani
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Guglielmo Vetere
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Mirella Giordano
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Paolo Ciracì
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Iolanda Capone
- Molecular Pathology Laboratory, Department of Pathology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale Dei Tumori, Milan, Italy
| | - Elena Tamborini
- Molecular Pathology Laboratory, Department of Pathology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale Dei Tumori, Milan, Italy
| | - Elena Conca
- Molecular Pathology Laboratory, Department of Pathology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale Dei Tumori, Milan, Italy
| | - Adele Busico
- Molecular Pathology Laboratory, Department of Pathology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale Dei Tumori, Milan, Italy
| | - Filippo Pietrantonio
- Department of Medical Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Vittoria Matilde Piva
- Oncology Unit 1, Veneto Institute of Oncology - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
- Department of Surgical, Oncological, and Gastroenterological Sciences, University of Padua, Padua, Italy
| | - Alessandra Boccaccino
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Martina Bortolot
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Oncology, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Paolo Manca
- Department of Medical Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Lonardi
- Oncology Unit 3, Veneto Institute of Oncology - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Veronica Conca
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Beatrice Borelli
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Martina Carullo
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Daniele Rossini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Section of Clinical Pharmacology and Oncology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Chiara Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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Wadapurkar RM, Sivaram A, Vyas R. Computational investigations into structure and function impact of novel mutations identified in targeted exons from ovarian cancer cell lines. J Biomol Struct Dyn 2024:1-15. [PMID: 38334284 DOI: 10.1080/07391102.2024.2310776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/20/2024] [Indexed: 02/10/2024]
Abstract
The lack of sensitive and specific biomarkers for ovarian cancer leads to late stage diagnosis of the disease in a majority of the cases. Mutation accumulation is the basis for cancer progression, thus identifying mutations is an important step in the disease diagnosis. In the present study, a comprehensive analysis of fifteen Next Generation Sequencing samples from thirteen ovarian cancer cell lines was carried out for the identification of new mutations. The study revealed eight clinically significant novel mutations in six ovarian cancer oncogenes, viz. SMARCA4, ARID1A, PPP2R1A, CTNNB1, DICER1 and PIK3CA. In-depth computational analysis revealed that the mutations affected the structure of the proteins in terms of stability, solvent accessible surface area and molecular dynamics. Moreover, the mutations were present in functionally significant domains of the proteins, thereby adversely affecting the protein functionality. PPI network for SMARCA4, CTNNB1, DICER1, PIK3CA, PPP2R1A and ARID1A showed that these genes were involved in certain significant pathways affecting various hallmarks of cancer. For further validation, in vitro studies were performed that revealed hypermutability of the CTNNB1 gene. Through this study we have identified some key mutations and have analysed their structural and functional impact. The study establishes some key mutations, which can be potentially explored as biomarker and drug target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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Heilmann AM, Riess JW, McLaughlin-Drubin M, Huang RSP, Hjulstrom M, Creeden J, Alexander BM, Erlich RL. Insights of Clinical Significance From 109 695 Solid Tumor Tissue-Based Comprehensive Genomic Profiles. Oncologist 2024; 29:e224-e236. [PMID: 37682776 PMCID: PMC10836312 DOI: 10.1093/oncolo/oyad251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 08/06/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND FoundationOneCDx is approved in the US and Japan as a companion diagnostic test to identify patients with cancer who may benefit from treatment with 30 drug therapies in the US and 23 in Japan. Tumor profiling with FoundationOneCDx also detects genomic findings with evidence of clinical significance that may inform clinical care decisions beyond companion diagnostic claims. This observational study reports the breadth and impact of clinical decision insights from FoundationOneCDx solid tumor profiles. MATERIALS AND METHODS Consecutive test result reports for patients with solid tumor diagnoses (n = 109 695) were retrospectively analyzed for clinically significant predictive, prognostic, and diagnostic genomic alterations and signatures, determined in accordance with professional guidelines. Interventional clinical trials with targeted therapies or immune checkpoint inhibitors were matched to tumor profiles based on evidence that the genomic finding may be an actionable, investigational, or hypothetical target in the patient's tumor type. RESULTS In 14 predefined cancer types (80.7% of analyzed solid tumors), predictive, prognostic, and diagnostic markers were reported in 47.6%, 13.2%, and 4.5% of samples, respectively, accounting for a total of 51.2% of tumor profiles. Pan-cancer predictive markers of tumor mutational burden (TMB) of 10 or more mutations per megabase, high microsatellite instability (MSI), or NTRK1/2/3 fusions were observed in 15.6%, 2.0%, and 0.1% of solid tumors, respectively. Most solid tumor profiles (89.2%) had genomic results that could theoretically inform decisions on the selection of immunotherapy and targeted therapy clinical trials. CONCLUSION For this real-world population of patients with FoundationOneCDx solid tumor profiles in the routine course of clinical care, clinically significant findings were reported for approximately half of patients with genomic results.
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Affiliation(s)
| | - Jonathan W Riess
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
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Schmitt J, Gothot A. HLA-C*05:292N, a novel HLA-C null allele identified by next-generation sequencing. HLA 2024; 103:e15380. [PMID: 38342776 DOI: 10.1111/tan.15380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/13/2024]
Abstract
HLA-C*05:292N differs from HLA-C*05:01:01:08 by a frameshift mutation, a deletion at gDNA position 758.
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Affiliation(s)
- Justine Schmitt
- HLA Typing Laboratory, Liège University Hospital, Liège, Belgium
| | - André Gothot
- HLA Typing Laboratory, Liège University Hospital, Liège, Belgium
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de Oliveira AML, Massi FP, Pinto LDB, de Lima Neto QA, Visentainer JEL. Two novel HLA-DRB3 alleles identified in Brazilian bone marrow donors: HLA-DRB3*01:122 and -DRB3*01:123. HLA 2024; 103:e15407. [PMID: 38372613 DOI: 10.1111/tan.15407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
We identified two new HLA-DRB3 alleles in Brazilian individuals using next generation sequencing.
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Affiliation(s)
- Anthony Marçal Leão de Oliveira
- Department of Clinical Analysis and Biomedicine (DAB), Postgraduate Program in Biosciences and Physiopathology (PBF), Laboratory of Immunogenetics, State University of Maringá (LIG-UEM), Maringá, Brazil
| | - Fernanda Pelisson Massi
- Department of Clinical Analysis and Biomedicine (DAB), Postgraduate Program in Biosciences and Physiopathology (PBF), Laboratory of Immunogenetics, State University of Maringá (LIG-UEM), Maringá, Brazil
| | - Larissa Danielle Bahls Pinto
- Department of Basic Health Sciences (DBS), Laboratory of Immunogenetics, State University of Maringá (LIG-UEM), Maringá, Brazil
| | - Quirino Alves de Lima Neto
- Department of Basic Health Sciences (DBS), Laboratory of Immunogenetics, State University of Maringá (LIG-UEM), Maringá, Brazil
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Misra MK, Brown NK, Marino SG. Next-generation sequencing identifies two novel HLA-DPB1 alleles: HLA-DPB1*1069:01 and DPB1*1072:01. HLA 2024; 103:e15368. [PMID: 38342772 DOI: 10.1111/tan.15368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/13/2024]
Abstract
Characterization of two novel HLA-DPB1 alleles: HLA-DPB1*1069:01, and DPB1*1072:01 containing non-synonymous nucleotide substitutions.
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Affiliation(s)
- Maneesh K Misra
- Department of Pathology, The University of Chicago Medicine, Chicago, Illinois, USA
| | - Nicholas K Brown
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susana G Marino
- Department of Pathology, The University of Chicago Medicine, Chicago, Illinois, USA
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Cozzi-Lepri A, Dunn D, Tostevin A, Marvig RL, Bennedbaek M, Sharma S, Kozal MJ, Gompels M, Pinto AN, Lundgren J, Baxter JD. Rate of response to initial antiretroviral therapy according to level of pre-existing HIV-1 drug resistance detected by next-generation sequencing in the strategic timing of antiretroviral treatment (START) study. HIV Med 2024; 25:212-222. [PMID: 37775947 PMCID: PMC10872720 DOI: 10.1111/hiv.13556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/12/2023] [Indexed: 10/01/2023]
Abstract
OBJECTIVES The main objective of this analysis was to evaluate the impact of pre-existing drug resistance by next-generation sequencing (NGS) on the risk of treatment failure (TF) of first-line regimens in participants enrolled in the START study. METHODS Stored plasma from participants with entry HIV RNA >1000 copies/mL were analysed using NGS (llumina MiSeq). Pre-existing drug resistance was defined using the mutations considered by the Stanford HIV Drug Resistance Database (HIVDB v8.6) to calculate the genotypic susceptibility score (GSS, estimating the number of active drugs) for the first-line regimen at the detection threshold windows of >20%, >5%, and >2% of the viral population. Survival analysis was conducted to evaluate the association between the GSS and risk of TF (viral load >200 copies/mL plus treatment change). RESULTS Baseline NGS data were available for 1380 antiretroviral therapy (ART)-naïve participants enrolled over 2009-2013. First-line ART included a non-nucleoside reverse transcriptase inhibitor (NNRTI) in 976 (71%), a boosted protease inhibitor in 297 (22%), or an integrase strand transfer inhibitor in 107 (8%). The proportions of participants with GSS <3 were 7% for >20%, 10% for >5%, and 17% for the >2% thresholds, respectively. The adjusted hazard ratio of TF associated with a GSS of 0-2.75 versus 3 in the subset of participants with mutations detected at the >2% threshold was 1.66 (95% confidence interval 1.01-2.74; p = 0.05) and 2.32 (95% confidence interval 1.32-4.09; p = 0.003) after restricting the analysis to participants who started an NNRTI-based regimen. CONCLUSIONS Up to 17% of participants initiated ART with a GSS <3 on the basis of NGS data. Minority variants were predictive of TF, especially for participants starting NNRTI-based regimens.
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Affiliation(s)
| | - David Dunn
- Institute for Global Health, UCL, London, UK
| | | | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marc Bennedbaek
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark
| | - Shweta Sharma
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | | | | | - Angie N Pinto
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jens Lundgren
- Copenhagen HIV Programme, Rigs Hospitalet, University of Copenhagen, Copenhagen, Denmark
| | - John D Baxter
- Cooper Medical School of Rowan University and Cooper University Health Care, Camden, New Jersey, USA
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Amen R, Havenstein K, Kirschbaum F, Tiedemann R. Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus)-A hybrid capture/HTS metabarcoding approach. Mol Ecol 2024; 33:e17248. [PMID: 38126927 DOI: 10.1111/mec.17248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/02/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Ecological speciation within the mormyrid genus Campylomormyrus resulted in sympatric species exhibiting divergence in their feeding apparatus and electric organ discharge (EOD). This study documents the overall diet of the genus Campylomormyrus and examines the hypothesis that the Campylomormyrus radiation is caused by adaptation to different food sources. We performed diet assessment of five sympatric Campylomormyrus species (C. alces, C. compressirostris, C. curvirostris, C. tshokwe, C. numenius) and their sister taxon Gnathonemus petersii with markedly different snout morphologies and EODs using hybrid capture/HTS DNA metabarcoding of their stomach contents. Our approach allowed for high taxonomic resolution of prey items, including benthic invertebrates, allochthonous invertebrates and vegetation. Comparisons of the diet compositions using quantitative measures and diet overlap indices revealed that all species are able to exploit multiple food niches in their habitats, that is fauna at the bottom, the water surface and the water column. A major part of the diet is larvae of aquatic insects, such as dipterans, coleopterans and trichopterans, known to occur in holes and interstitial spaces of the substrate. The results indicate that different snout morphologies and the associated divergence in the EOD could translate into different prey spectra. This suggests that the diversification in EOD and/or morphology of the feeding apparatus could be under functional adaptation.
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Affiliation(s)
- Rahma Amen
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Zoology, Faculty of Science, Aswan University, Aswan, Egypt
| | - Katja Havenstein
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Frank Kirschbaum
- Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Sharma A, Bagchi S, Barwad AW, Agarwal SK, Kanga U. One nucleotide substitution in the 3'UTR generated the novel allele HLA-B*40:01:02:47 in a North Indian individual. HLA 2024; 103:e15377. [PMID: 38342777 DOI: 10.1111/tan.15377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/13/2024]
Abstract
HLA-B*40:01:02:47 differs from HLA-B*40:01:02:01 by one nucleotide change in the 3'UTR at position 2739 (A>T).
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Affiliation(s)
- Akanksha Sharma
- Department of Transplant Immunology and Immunogenetics, Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine (ICMR), All India Institute of Medical Sciences, New Delhi, India
| | - Soumita Bagchi
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Adarsh W Barwad
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Kumar Agarwal
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine (ICMR), All India Institute of Medical Sciences, New Delhi, India
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40
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Gravante C, Berka Y, Peters L, Mancini S, Liacini A. Characterization of the novel HLA-B*57:169 allele by next generation sequencing. HLA 2024; 103:e15344. [PMID: 38358022 DOI: 10.1111/tan.15344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 02/16/2024]
Abstract
HLA-B*57:169 differs from HLA-B*57:01:01:12 by one nucleotide substitution at position 2512, codon 320 located in exon 6.
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Affiliation(s)
- Chris Gravante
- Department of Pathology and Laboratory Medicine, Temple University Hospital, Philadelphia, Pennsylvania, United States
| | - Yacine Berka
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Lindsey Peters
- Department of Pathology and Laboratory Medicine, Temple University Hospital, Philadelphia, Pennsylvania, United States
| | - Shannon Mancini
- Department of Pathology and Laboratory Medicine, Temple University Hospital, Philadelphia, Pennsylvania, United States
| | - Abdelhamid Liacini
- Lewis Katz School of Medicine, Temple University Hospital, Philadelphia, Pennsylvania, United States
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41
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Ghous G, Ijaz K, Esebua M, Layfield LJ. Molecular testing of cytology specimens: Issues in specimen adequacy and clinical utility. Diagn Cytopathol 2024; 52:123-130. [PMID: 38017653 DOI: 10.1002/dc.25253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/28/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) is standard of care for workup of many neoplasms including adenocarcinomas of the lung. Molecular testing of cytology samples is used for many types of neoplasms but the value of such testing for the selection of "first"- and "second-line" treatment protocols is incompletely understood. METHODS Fifty-six sequentially performed cytology specimens (49 fine needle aspirates and 7 fluids) submitted for molecular analysis were reviewed by a medical oncologist to determine specimen adequacy and utility of results for therapy selection. Chart review was performed to determine availability of microsatellite instability status, tumor mutational burden, and presence of driver mutations treatable with targeted therapy in a "first"- or "second-line" application. RESULTS Forty of 56 cases were successfully sequenced and 34% (19/56) had targetable mutations detected by NGS. Ten of these 19 cases (53%) received targeted therapy for their tumor type with five of 10 patients receiving "first-line" therapy and five (50%) "second-line" therapy. Twenty-two mutations were detected where no targeted therapy for the patient's tumor type existed but targeted therapies were available for other tumor types. Of these specimens, only one patient received treatment using protocols associated with a second tumor type. Total mutation burden and microsatellite instability status results were obtained in 29 of 56 cases (52%). CONCLUSIONS 71% (40/56) of cytologic specimens were adequate for sequencing with 34% (19/56) demonstrating a targetable mutation and 53% of these patients receiving therapy targeted to the driver mutation of their tumor type.
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Affiliation(s)
- Ghulam Ghous
- Division of Hematology and Oncology, Department of Medicine, University of Missouri - Columbia, Columbia, Missouri, USA
| | - Komal Ijaz
- Department of Pathology and Anatomical Sciences, University of Missouri - Columbia, Columbia, Missouri, USA
| | - Magda Esebua
- Department of Pathology and Anatomical Sciences, University of Missouri - Columbia, Columbia, Missouri, USA
| | - Lester J Layfield
- Department of Pathology and Anatomical Sciences, University of Missouri - Columbia, Columbia, Missouri, USA
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42
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Sharma A, Bagchi S, Barwad AW, Agarwal SK, Kanga U. Characterization of the novel HLA-B*15:05:01:02 allele by sequence-based typing. HLA 2024; 103:e15363. [PMID: 38305067 DOI: 10.1111/tan.15363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024]
Abstract
HLA-B*15:05:01:02 differs from HLA-B*15:05:01:01 by one nucleotide change in intron 2 at position 517 (C > A).
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Affiliation(s)
- Akanksha Sharma
- Department of Transplant Immunology and Immunogenetics, Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine (ICMR), All India Institute of Medical Sciences, New Delhi, India
| | - Soumita Bagchi
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Adarsh W Barwad
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Kumar Agarwal
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine (ICMR), All India Institute of Medical Sciences, New Delhi, India
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43
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Magura T, Mizser S, Horváth R, Tóth M, Likó I, Lövei GL. Urbanization reduces gut bacterial microbiome diversity in a specialist ground beetle, Carabus convexus. Mol Ecol 2024; 33:e17265. [PMID: 38214370 DOI: 10.1111/mec.17265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
Urbanization is rapidly shaping and transforming natural environments, creating networks of modified land types. These urbanization-driven modifications lead to local extinctions of several species, but the surviving ones also face numerous novel selection pressures, including exposure to pollutants, habitat alteration, and shifts in food availability and diversity. Based on the assumption that the environmental pool of microorganisms is reduced in urban habitats due to habitat alteration, biodiversity loss, and pollution, we hypothesized that the diversity of bacterial microbiome in digestive tracts of arthropods would be lower in urban than rural habitats. Investigating the gut bacterial communities of a specialist ground beetle, Carabus convexus, in forested rural versus urban habitats by next generation high-throughput sequencing of the bacterial 16S rRNA gene, we identified 3839 bacterial amplicon sequence variants. The composition of gut bacterial samples did not significantly differ by habitat (rural vs. urban), sex (female vs. male), sampling date (early vs. late spring), or their interaction. The microbiome diversity (evaluated by the Rényi diversity function), however, was higher in rural than urban adults. Our findings demonstrate that urbanization significantly reduced the diversity of the gut bacterial microbiome in C. convexus.
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Affiliation(s)
- Tibor Magura
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Anthropocene Ecology Research Group, Debrecen, Hungary
| | - Szabolcs Mizser
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Roland Horváth
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Anthropocene Ecology Research Group, Debrecen, Hungary
| | - Mária Tóth
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Anthropocene Ecology Research Group, Debrecen, Hungary
| | - István Likó
- UD-GenoMed Medical Genomic Technologies Ltd, Clinical Centre, University of Debrecen, Debrecen, Hungary
| | - Gábor L Lövei
- HUN-REN-UD Anthropocene Ecology Research Group, Debrecen, Hungary
- Department of Agroecology, Flakkebjerg Research Centre, Aarhus University, Slagelse, Denmark
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44
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Usta Akgul S, Catalbasyan T, Demir DK, Borjkhani M, Süsal C. The novel HLA-B*39:199 allele identified in a candidate bone marrow donor. HLA 2024; 103:e15360. [PMID: 38305001 DOI: 10.1111/tan.15360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
HLA-B*39:199 differs from HLA-B*39:10:01 by a G → A substitution in exon 5 in codon 282.
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Affiliation(s)
- Sebahat Usta Akgul
- Transplant Immunology Research Center of Excellence, Koç University Hospital, Istanbul, Turkey
| | - Talin Catalbasyan
- Transplant Immunology Research Center of Excellence, Koç University Hospital, Istanbul, Turkey
| | - Demir Kaan Demir
- Transplant Immunology Research Center of Excellence, Koç University Hospital, Istanbul, Turkey
| | - Mahdis Borjkhani
- Transplant Immunology Research Center of Excellence, Koç University Hospital, Istanbul, Turkey
| | - Caner Süsal
- Transplant Immunology Research Center of Excellence, Koç University Hospital, Istanbul, Turkey
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45
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Sharma A, Bagchi S, Barwad AW, Agarwal SK, Kanga U. A single nucleotide substitution in intron 3 generated the novel HLA-A*11:01:01:68 allele. HLA 2024; 103:e15382. [PMID: 38358088 DOI: 10.1111/tan.15382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
HLA-A*11:01:01:68 differs from HLA-A*11:01:01:01 by one nucleotide change in intron 3 at position 1474 (G > A).
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Affiliation(s)
- Akanksha Sharma
- Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine (ICMR), Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Soumita Bagchi
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Adarsh W Barwad
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Kumar Agarwal
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine (ICMR), Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
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46
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Nafea AM, Wang Y, Wang D, Salama AM, Aziz MA, Xu S, Tong Y. Application of next-generation sequencing to identify different pathogens. Front Microbiol 2024; 14:1329330. [PMID: 38348304 PMCID: PMC10859930 DOI: 10.3389/fmicb.2023.1329330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/18/2023] [Indexed: 02/15/2024] Open
Abstract
Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.
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Affiliation(s)
- Aljuboori M. Nafea
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Duanyang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ahmed M. Salama
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
- Medical Laboratory at Sharkia Health Directorate, Ministry of Health, Sharkia, Egypt
| | - Manal A. Aziz
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Veshkini A, Dengler F, Bachmann L, Liermann W, Helm C, Ulrich R, Delling C, Kühn C, Hammon HM. Cryptosporidium parvum infection alters the intestinal mucosa transcriptome in neonatal calves: implications for immune function. Front Immunol 2024; 15:1351427. [PMID: 38318169 PMCID: PMC10839036 DOI: 10.3389/fimmu.2024.1351427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
One of the leading causes of infectious diarrhea in newborn calves is the apicomplexan protozoan Cryptosporidium parvum (C. parvum). However, little is known about its immunopathogenesis. Using next generation sequencing, this study investigated the immune transcriptional response to C. parvum infection in neonatal calves. Neonatal male Holstein-Friesian calves were either orally infected (N = 5) or not (CTRL group, N = 5) with C. parvum oocysts (gp60 subtype IIaA15G2R1) at day 1 of life and slaughtered on day 7 after infection. Total RNA was extracted from the jejunal mucosa for short read. Differentially expressed genes (DEGs) between infected and CTRL groups were assessed using DESeq2 at a false discovery rate < 0.05. Infection did not affect plasma immunohematological parameters, including neutrophil, lymphocyte, monocyte, leucocyte, thrombocyte, and erythrocyte counts as well as hematocrit and hemoglobin concentration on day 7 post infection. The immune-related DEGs were selected according to the UniProt immune system process database and were used for gene ontology (GO) and pathway enrichment analysis using Cytoscape (v3.9.1). Based on GO analysis, DEGs annotated to mucosal immunity, recognizing and presenting antigens, chemotaxis of neutrophils, eosinophils, natural killer cells, B and T cells mediated by signaling pathways including toll like receptors, interleukins, tumor necrosis factor, T cell receptor, and NF-KB were upregulated, while markers of macrophages chemotaxis and cytosolic pattern recognition were downregulated. This study provides a holistic snapshot of immune-related pathways induced by C. parvum in calves, including novel and detailed feedback and feedforward regulatory mechanisms establishing the crosstalk between innate and adaptive immune response in neonate calves, which could be utilized further to develop new therapeutic strategies.
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Affiliation(s)
- Arash Veshkini
- Research Institute for Farm Animal Biology, Institute of Nutritional Physiology “Oskar Kellner”, Dummerstorf, Germany
| | - Franziska Dengler
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria
| | - Lisa Bachmann
- Research Institute for Farm Animal Biology, Institute of Nutritional Physiology “Oskar Kellner”, Dummerstorf, Germany
- Faculty of Agriculture and Food Science, University of Applied Science Neubrandenburg, Neubrandenburg, Germany
| | - Wendy Liermann
- Research Institute for Farm Animal Biology, Institute of Nutritional Physiology “Oskar Kellner”, Dummerstorf, Germany
| | - Christiane Helm
- Institutue for Veterinary Pathology, Leipzig University, Leipzig, Germany
| | - Reiner Ulrich
- Institutue for Veterinary Pathology, Leipzig University, Leipzig, Germany
| | - Cora Delling
- Institute of Veterinary Parasitology, Leipzig University, Leipzig, Germany
| | - Christa Kühn
- Research Institute for Farm Animal Biology, Institute of Genome Biology, Dummerstorf, Germany
- Agricultural and Environmental Faculty, University Rostock, Rostock, Germany
| | - Harald M. Hammon
- Research Institute for Farm Animal Biology, Institute of Nutritional Physiology “Oskar Kellner”, Dummerstorf, Germany
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48
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Zhang Y, Liu W, Duan J. On the core segmentation algorithms of copy number variation detection tools. Brief Bioinform 2024; 25:bbae022. [PMID: 38340093 PMCID: PMC10858679 DOI: 10.1093/bib/bbae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/26/2023] [Indexed: 02/12/2024] Open
Abstract
Shotgun sequencing is a high-throughput method used to detect copy number variants (CNVs). Although there are numerous CNV detection tools based on shotgun sequencing, their quality varies significantly, leading to performance discrepancies. Therefore, we conducted a comprehensive analysis of next-generation sequencing-based CNV detection tools over the past decade. Our findings revealed that the majority of mainstream tools employ similar detection rationale: calculates the so-called read depth signal from aligned sequencing reads and then segments the signal by utilizing either circular binary segmentation (CBS) or hidden Markov model (HMM). Hence, we compared the performance of those two core segmentation algorithms in CNV detection, considering varying sequencing depths, segment lengths and complex types of CNVs. To ensure a fair comparison, we designed a parametrical model using mainstream statistical distributions, which allows for pre-excluding bias correction such as guanine-cytosine (GC) content during the preprocessing step. The results indicate the following key points: (1) Under ideal conditions, CBS demonstrates high precision, while HMM exhibits a high recall rate. (2) For practical conditions, HMM is advantageous at lower sequencing depths, while CBS is more competitive in detecting small variant segments compared to HMM. (3) In case involving complex CNVs resembling real sequencing, HMM demonstrates more robustness compared with CBS. (4) When facing large-scale sequencing data, HMM costs less time compared with the CBS, while their memory usage is approximately equal. This can provide an important guidance and reference for researchers to develop new tools for CNV detection.
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Affiliation(s)
- Yibo Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Wenyu Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Junbo Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
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Becken BA, Lamson DM, Gonzalez G, Patel S, St. George K, Kajon AE. A Fulminant Case of Adenovirus Genotype C108 Infection in a Pediatric Stem Cell Transplant Recipient with x-Linked Lymphoproliferative Syndrome Type 1. Viruses 2024; 16:137. [PMID: 38257837 PMCID: PMC10819400 DOI: 10.3390/v16010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
A 3-year-old male with X-linked lymphoproliferative syndrome type 1 underwent an unrelated umbilical cord blood transplant (UUCBT). The week prior to transplant the patient tested positive for adenovirus (HAdV) with a viral load of <190 copies/mL and was started on cidofovir. UUCBT proceeded as scheduled, and the patient engrafted on day +19. The patient's HAdV load in serum continued to rise with resulting hepatic dysfunction, despite ongoing therapy with cidofovir and HAdV specific T-cell infusions. The patient died 6 months after transplantation having never cleared the virus. Next generation whole genome sequencing and sequence data analyses identified an intertypic recombinant HAdV-C P1H2F2 closely related (99.6% similarity) to genotype C108 in the isolates from three blood specimens obtained during the last week of life. Incidentally, the de novo assembly strategy enabled the detection of an adeno-associated virus type 2 (AAV2) genome in the DNA purified from the plasma isolates. Proteotyping analysis revealed minor differences in the predicted amino acid sequences for E1A, E1B 19K, E1B 55K, DNA polymerase, penton base, and fiber. None of the mutations previously described for HAdV-C5 variants resistant to cidofovir were identified. In silico restriction enzyme analysis revealed a distinct Sac I profile for the identified virus, supporting its designation as a C108 variant.
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Affiliation(s)
- Bradford A. Becken
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.B.); (S.P.)
| | - Daryl M. Lamson
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; (D.M.L.); (K.S.G.)
| | - Gabriel Gonzalez
- UCD National Virus Reference Laboratory, Dublin, Ireland;
- Japan Initiative for World-Leading Vaccine Research and Development Centers, Institute for Vaccine Research and Development, Hokkaido University, Hokkaido, Japan
| | - Sachit Patel
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.B.); (S.P.)
| | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; (D.M.L.); (K.S.G.)
| | - Adriana E. Kajon
- Lovelace Biomedical Research Institute, Albuquerque, NM 87108, USA
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50
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Lou J, Chu X, Yang X, Jamil M, Zhu H. Deciphering DNA repair gene mutational landscape in uterine corpus endometrial carcinoma patients using next generation sequencing. Am J Cancer Res 2024; 14:210-226. [PMID: 38323278 PMCID: PMC10839304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/25/2023] [Indexed: 02/08/2024] Open
Abstract
Uterine Corpus Endometrial Carcinoma (UCEC) is a significant health concern with a complex genetic landscape impacting disease susceptibility and progression. This study aimed to unravel the spectrum of DNA repair gene mutations in Pakistani UCEC patients through Next Generation Sequencing (NGS) and explore their potential functional consequences via downstream analyses. NGS analysis of genomic DNA from 30 UCEC patients was conducted to identify clinically significant pathogenic mutations in DNA repair genes. This analysis revealed mutations in 4 key DNA repair genes: BRCA1, BRCA2, APC, and CDH1. Kaplan-Meier (KM) analysis was employed to assess the prognostic value of these mutations on patient overall survival (OS) in UCEC. To delve into the functional impact of these mutations, we performed RT-qPCR, immunohistochemistry (IHC), and western blot analyses on the mutated UCEC samples compared to their non-mutated counterparts. These results unveiled the up-regulation in the expression of the mutated genes, suggesting a potential association between the identified mutations and enhanced gene activity. Additionally, targeted bisulfite sequencing analysis was utilized to evaluate DNA methylation patterns in the promoters of the mutated genes. Strikingly, hypomethylation in the promoters of BRCA1, BRCA2, APC, and CDH1 was observed in the mutated UCEC samples relative to the non-mutated, indicating the involvement of epigenetic mechanisms in the altered gene expression. In conclusion, this study offers insights into the genetic landscape of DNA repair gene mutations in Pakistani UCEC patients. The presence of pathogenic mutations in BRCA1, BRCA2, APC, and CDH1, coupled with their down-regulation and hypermethylation, suggests a convergence of genetic and epigenetic factors contributing to genomic instability in UCEC cells. These findings enhance our understanding of UCEC susceptibility and provide potential avenues for targeted therapeutic interventions in Pakistani UCEC patients.
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Affiliation(s)
- Jun Lou
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Key Laboratory of Translational Research for CancerNanchang 330029, Jiangxi, China
| | - Xiaoyan Chu
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
| | - Xiaorong Yang
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Hong Zhu
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
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