Journal of Molecular Diagnostics最新文献

{"title":"A Cost-Effective and Labor-Saving Method for Detecting Human Leukocyte Antigen B27 Status via Sequence-Encoded Fluorescence Amplification Assay","authors":"Nan Sheng ,&nbsp;Li Zhao ,&nbsp;Shuyun Pang ,&nbsp;Wenwen Wang ,&nbsp;Panfeng Feng ,&nbsp;Jing Zhao ,&nbsp;Xiaoxiang Chen ,&nbsp;Yingying Gao","doi":"10.1016/j.jmoldx.2024.03.010","DOIUrl":"10.1016/j.jmoldx.2024.03.010","url":null,"abstract":"<div><p>Identification of human leukocyte antigen B27 (HLA-B27) by flow cytometry (FCM) has been widely applied in clinical practice for auxiliary diagnosis of ankylosing spondylitis (AS). However, FCM requires freshly prepared samples and relies on expensive equipment, reagents, and an experienced operator. To provide a cheaper and more convenient method for HLA-B27 detection, we proposed a new method termed sequence-encoded fluorescence amplification assay (SEFA), which specially recognized sequences of HLA-B27 gene (<em>HLA-B∗27</em>) covering current common subtypes in a single closed tube. SEFA could detect as low as 10 pg (equal to 3 copies) genomic DNA per reaction and distinguish <em>HLA-B∗27</em> from other <em>HLA-B</em> alleles with highly similar sequences. A total of 288 clinical samples were tested by SEFA, including 181 patients with AS and 107 healthy controls. Compared with the detection results from FCM, two controversial samples of patients with AS were obtained and further confirmed to be consistent with SEFA by Sanger sequencing, indicating that this method was more accurate than FCM. Moreover, SEFA could detect HLA-B27 status by using supernatant from crude extract of 10-μL blood without commercial reagents. Overall, SEFA has the potential to be an alternative for HLA-B27 identification with the advantage of convenience and low cost, especially suitable for early diagnosis of AS in areas with limited medical resources.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 7","pages":"Pages 574-582"},"PeriodicalIF":4.1,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824000862/pdfft?md5=0e5435d29978f475544976e51506f1e0&pid=1-s2.0-S1525157824000862-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140839502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EarlyTect BCD, a Streamlined PENK Methylation Test in Urine DNA, Effectively Detects Bladder Cancer in Patients with Hematuria","authors":"Bo-Ram Bang ,&nbsp;Jin Zhong ,&nbsp;Tae Jeong Oh ,&nbsp;Ji Yong Lee ,&nbsp;Yangyei Seo ,&nbsp;Min A Woo ,&nbsp;Jae Sung Lim ,&nbsp;Yong Gil Na ,&nbsp;Ki Hak Song ,&nbsp;Ju Hyun Shin ,&nbsp;Justin Junguek Lee ,&nbsp;Chan Su Im ,&nbsp;Seoyong Kim ,&nbsp;Safedin Beqaj ,&nbsp;Joseph D. Shirk ,&nbsp;Katelyn W. Ke ,&nbsp;John Vallone ,&nbsp;Sungwhan An","doi":"10.1016/j.jmoldx.2024.04.001","DOIUrl":"10.1016/j.jmoldx.2024.04.001","url":null,"abstract":"<div><p>The current noninvasive diagnostic approaches for detecting bladder cancer (BC) often exhibit limited clinical performance, especially for the initial diagnosis. This study aims to evaluate the validity of a streamlined urine-based <em>PENK</em> methylation test called EarlyTect BCD in detecting BC in patients with hematuria scheduled for cystoscopy in Korean and American populations. The test seamlessly integrates two steps, linear target enrichment and quantitative methylation-specific PCR within a single closed tube. The detection limitation of the test was approximately two genome copies of methylated <em>PENK</em> per milliliter of urine. In the retrospective training set (<em>n</em> = 105), an optimal cutoff value was determined to distinguish BC from non-BC, resulting in a sensitivity of 87.3% and a specificity of 95.2%. In the prospective validation set (<em>n</em> = 210, 122 Korean and 88 American patients), the overall sensitivity for detecting all stages of BC was 81.0%, with a specificity of 91.5% and an area under the curve value of 0.889. There was no significant difference between the two groups. The test achieved a sensitivity of 100% in detecting high-grade Ta and higher stages of BC. The negative predictive value of the test was 97.7%, and the positive predictive value was 51.5%. The findings of this study demonstrate that EarlyTect BCD is a highly effective noninvasive diagnostic tool for identifying BC among patients with hematuria.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 7","pages":"Pages 613-623"},"PeriodicalIF":4.1,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824000849/pdfft?md5=658c074c489a613f86fee293902bd538&pid=1-s2.0-S1525157824000849-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140764120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance Characteristics of a Real-Time PCR Assay for Direct Detection of Streptococcus pneumoniae in Clinical Specimens","authors":"Subathra Marimuthu,&nbsp;Rocio B. Damiano,&nbsp;Leslie A. Wolf","doi":"10.1016/j.jmoldx.2024.03.009","DOIUrl":"10.1016/j.jmoldx.2024.03.009","url":null,"abstract":"<div><p>Community-acquired pneumonia and complications, such as bacteremia and meningitis due to <em>Streptococcus pneumoniae</em> infection, still occur in at-risk populations, despite the availability of effective vaccines. Laboratory confirmation of <em>S. pneumoniae</em> remains challenging despite advances in blood culture techniques and the availability of nucleic acid–amplification tests. The goal of this study was to determine the performance characteristics of a molecular assay designed as a diagnostic test using primary clinical specimens for invasive pneumococcal disease. The molecular assay adapted for the Luminex Aries instrument targets an <em>S. pneumoniae</em>–specific gene (autolysin, <em>lytA</em>) in clinical specimens. Using real-time PCR MultiCode technology, four different clinical specimen types were evaluated. Specimen types included bronchoalveolar lavage, whole blood, cerebrospinal fluid, and urine to cover the various presentations and appropriate specimen types for invasive pneumococcal infections. The lower limit of detection in urine was 10 colony forming units (CFU)/mL, while in bronchoalveolar lavage, cerebrospinal fluid, and whole blood, it was 100 CFU/mL. Accuracy and specificity were both 100%, and all specimen types were stable for 8 days at 4°C. Finally, 38 clinical specimens were tested to further evaluate the assay. The performance characteristics met Clinical Laboratory Improvement Amendments standards for a clinical diagnostic assay, and the assay offers a sensitive and specific real-time PCR test for direct detection of <em>S. pneumoniae</em> in relevant clinical specimens.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 7","pages":"Pages 552-562"},"PeriodicalIF":4.1,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824000837/pdfft?md5=f7740dbec1e4718e9eacf1f2079ba9c8&pid=1-s2.0-S1525157824000837-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140788169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeted Linked-Read Sequencing for Direct Haplotype Phasing of Parental GJB2/SLC26A4 Alleles","authors":"Bo Gao ,&nbsp;Yi Jiang ,&nbsp;Mingyu Han ,&nbsp;Xiaowen Ji ,&nbsp;Dejun Zhang ,&nbsp;Lihua Wu ,&nbsp;Xue Gao ,&nbsp;Shasha Huang ,&nbsp;Chaoyue Zhao ,&nbsp;Yu Su ,&nbsp;Suyan Yang ,&nbsp;Xin Zhang ,&nbsp;Na Liu ,&nbsp;Lu Han ,&nbsp;Lihai Wang ,&nbsp;Lina Ren ,&nbsp;Jinyuan Yang ,&nbsp;Jian Wu ,&nbsp;Yongyi Yuan ,&nbsp;Pu Dai","doi":"10.1016/j.jmoldx.2024.04.002","DOIUrl":"10.1016/j.jmoldx.2024.04.002","url":null,"abstract":"<div><p>Noninvasive prenatal diagnosis (NIPD) for autosomal recessive nonsyndromic hearing loss (ARNSHL) has been rarely reported until recent years. Additionally, the existing method can not be used for challenging genome loci (eg, copy number variations, deletions, inversions, or gene recombinants) or on families without proband genotype. This study assessed the performance of relative haplotype dosage analysis (RHDO)–based NIPD for identifying fetal genotyping in pregnancies at risk of ARNSHL. Fifty couples carrying pathogenic variants associated with ARNSHL in either <em>GJB2</em> or <em>SLC26A4</em> were recruited. The RHDO-based targeted linked-read sequencing combined with whole gene coverage probes was used to genotype the fetal cell-free DNA of 49 families who met the quality control standard. Fetal amniocyte samples were genotyped using invasive prenatal diagnosis (IPD) to assess the performance of NIPD. The NIPD results showed 100% (49/49) concordance with those obtained through IPD. Two families with copy number variation and recombination were also successfully identified. Sufficient specific informative single-nucleotide polymorphisms for haplotyping, as well as the fetal cell-free DNA concentration and sequencing depth, are prerequisites for RHDO-based NIPD. This method has the merits of covering the entire genes of <em>GJB2</em> and <em>SLC26A4</em>, qualifying for copy number variation and recombination analysis with remarkable sensitivity and specificity. Therefore, it has clinical potential as an alternative to traditional IPD for ARNSHL.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 7","pages":"Pages 638-651"},"PeriodicalIF":4.1,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824000850/pdfft?md5=2c05568e8e29de7c9cb3a981d946d6eb&pid=1-s2.0-S1525157824000850-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140839462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cost-Effective and Scalable Clonal Hematopoiesis Assay Provides Insight into Clonal Dynamics","authors":"Taralynn Mack ,&nbsp;Caitlyn Vlasschaert ,&nbsp;Kelly von Beck ,&nbsp;Alexander J. Silver ,&nbsp;J. Brett Heimlich ,&nbsp;Hannah Poisner ,&nbsp;Henry R. Condon ,&nbsp;Jessica Ulloa ,&nbsp;Andrew L. Sochacki ,&nbsp;Travis P. Spaulding ,&nbsp;Ashwin Kishtagari ,&nbsp;Cosmin A. Bejan ,&nbsp;Yaomin Xu ,&nbsp;Michael R. Savona ,&nbsp;Angela Jones ,&nbsp;Alexander G. Bick","doi":"10.1016/j.jmoldx.2024.03.007","DOIUrl":"10.1016/j.jmoldx.2024.03.007","url":null,"abstract":"<div><p>Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related phenomenon in which hematopoietic stem cells acquire mutations in a select set of genes commonly mutated in myeloid neoplasia which then expand clonally. Current sequencing assays to detect CHIP mutations are not optimized for the detection of these variants and can be cost-prohibitive when applied to large cohorts or to serial sequencing. In this study, an affordable (approximately US $8 per sample), accurate, and scalable sequencing assay for CHIP is introduced and validated. The efficacy of the assay was demonstrated by identifying CHIP mutations in a cohort of 456 individuals with DNA collected at multiple time points in Vanderbilt University's biobank and quantifying clonal expansion rates over time. A total of 101 individuals with CHIP/clonal cytopenia of undetermined significance were identified, and individual-level clonal expansion rate was calculated using the variant allele fraction at both time points. Differences in clonal expansion rate by driver gene were observed, but there was also significant individual-level heterogeneity, emphasizing the multifactorial nature of clonal expansion. Additionally, mutation co-occurrence and clonal competition between multiple driver mutations were explored.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 7","pages":"Pages 563-573"},"PeriodicalIF":4.1,"publicationDate":"2024-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S152515782400076X/pdfft?md5=0ab108ca768d09e1ad3350d15036a2d7&pid=1-s2.0-S152515782400076X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140623197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical Validation of a Targeted Next-Generation Sequencing Panel for Lymphoid Malignancies","authors":"Cody J. Artymiuk ,&nbsp;Shubham Basu ,&nbsp;Tejaswi Koganti ,&nbsp;Pratyush Tandale ,&nbsp;Jagadheshwar Balan ,&nbsp;Michelle A. Dina ,&nbsp;Emily G. Barr Fritcher ,&nbsp;Xianglin Wu ,&nbsp;Taylor Ashworth ,&nbsp;Rong He ,&nbsp;David S. Viswanatha","doi":"10.1016/j.jmoldx.2024.03.008","DOIUrl":"10.1016/j.jmoldx.2024.03.008","url":null,"abstract":"<div><p>Lymphoid malignancies are a heterogeneous group of hematological disorders characterized by a diverse range of morphologic, immunophenotypic, and clinical features. Next-generation sequencing (NGS) is increasingly being applied to delineate the complex nature of these malignancies and identify high-value biomarkers with diagnostic, prognostic, or therapeutic benefit. However, there are various challenges in using NGS routinely to characterize lymphoid malignancies, including pre-analytic issues, such as sequencing DNA from formalin-fixed, paraffin-embedded tissue, and optimizing the bioinformatic workflow for accurate variant calling and filtering. This study reports the clinical validation of a custom capture-based NGS panel to test for molecular markers in a range of lymphoproliferative diseases and histiocytic neoplasms. The fully validated clinical assay represents an accurate and sensitive tool for detection of single-nucleotide variants and small insertion/deletion events to facilitate the characterization and management of patients with hematologic cancers specifically of lymphoid origin.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 7","pages":"Pages 583-598"},"PeriodicalIF":4.1,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824000771/pdfft?md5=86c736afba27feef36ac99c811b8c918&pid=1-s2.0-S1525157824000771-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140623108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Focused Exome Sequencing Gives a High Diagnostic Yield in the Indian Subcontinent","authors":"Arul J. Duraisamy ,&nbsp;Ruby Liu ,&nbsp;Shruti Sureshkumar ,&nbsp;Rajiv Rose ,&nbsp;Lakshmanan Jagannathan ,&nbsp;Cristina da Silva ,&nbsp;Adam Coovadia ,&nbsp;Vinish Ramachander ,&nbsp;Sathyapriya Chandrasekar ,&nbsp;Indu Raja ,&nbsp;Manisha Sajnani ,&nbsp;Sreekanth M. Selvaraj ,&nbsp;Bhuvandeep Narang ,&nbsp;Katayoon Darvishi ,&nbsp;Amar C. Bhayal ,&nbsp;Lavanya Katikala ,&nbsp;Fen Guo ,&nbsp;Xiangwen Chen-Deutsch ,&nbsp;Jorune Balciuniene ,&nbsp;Zeqiang Ma ,&nbsp;Madhuri Hegde","doi":"10.1016/j.jmoldx.2024.03.005","DOIUrl":"10.1016/j.jmoldx.2024.03.005","url":null,"abstract":"<div><p>The genetically isolated yet heterogeneous and highly consanguineous Indian population has shown a higher prevalence of rare genetic disorders. However, there is a significant socioeconomic burden for genetic testing to be accessible to the general population. In the current study, we analyzed next-generation sequencing data generated through focused exome sequencing from individuals with different phenotypic manifestations referred for genetic testing to achieve a molecular diagnosis. Pathogenic or likely pathogenic variants are reported in 280 of 833 cases with a diagnostic yield of 33.6%. Homozygous sequence and copy number variants were found as positive diagnostic findings in 131 cases (15.7%) because of the high consanguinity in the Indian population. No relevant findings related to reported phenotype were identified in 6.2% of the cases. Patients referred for testing due to metabolic disorder and neuromuscular disorder had higher diagnostic yields. Carrier testing of asymptomatic individuals with a family history of the disease, through focused exome sequencing, achieved positive diagnosis in 54 of 118 cases tested. Copy number variants were also found in <em>trans</em> with single-nucleotide variants and mitochondrial variants in a few of the cases. The diagnostic yield and the findings from this study signify that a focused exome test is a good lower-cost alternative for whole-exome and whole-genome sequencing and as a first-tier approach to genetic testing.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 6","pages":"Pages 510-519"},"PeriodicalIF":4.1,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140570421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Vitro Functional Analysis Can Aid Precision Diagnostics of HNF1B-MODY","authors":"Aishwarya Pavithram ,&nbsp;Haichen Zhang ,&nbsp;Kristin A. Maloney ,&nbsp;Monika Ringdal ,&nbsp;Alba Kaci ,&nbsp;Jørn V. Sagen ,&nbsp;Jeffrey Kleinberger ,&nbsp;Linda J.B. Jeng ,&nbsp;Pål R. Njølstad ,&nbsp;Toni I. Pollin ,&nbsp;Janne Molnes ,&nbsp;Bente B. Johansson","doi":"10.1016/j.jmoldx.2024.03.006","DOIUrl":"10.1016/j.jmoldx.2024.03.006","url":null,"abstract":"<div><p>Precision medicine relies on accurate and consistent classification of sequence variants. A correct diagnosis of hepatocyte nuclear factor (HNF) 1B maturity-onset diabetes of the young, caused by pathogenic variants in the <em>HNF1B</em> gene, is important for optimal disease management and prognosis, and it has implications for genetic counseling and follow-up of at-risk family members. We hypothesized that the functional characterization could provide valuable information to assist the interpretation of pathogenicity of <em>HNF1B</em> variants. Using different <em>in vitro</em> functional assays, variants identified among 313 individuals, suspected to have monogenic diabetes with or without kidney disease, were characterized. The data from the functional assays were subsequently conjugated with obtained clinical, biochemical, and <em>in silico</em> data. Two variants (p.A167P, p.H336Pfs∗22) showed severe loss of function due to impaired transactivation, reduced DNA binding (p.A167P), and mRNA instability (p.A167P). Although both these variant carriers were diagnosed with diabetes, the p.H336Pfs∗22 carrier also had congenital absence of a kidney, which is a characteristic trait for HNF1B maturity-onset diabetes of the young. Functional analysis of the p.A167P variant revealed damaging effects on HNF-1B protein function, which may warrant imaging of the kidneys and/or pancreas. In addition, the current study has generated important data, including evidence supporting the benign functional impact of five variants (p.D82N, p.T88A, p.N394D, p.V458G, and p.T544A), and piloting new approaches that will prove critical for the growth of HNF1B-diabetes diagnosis.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 6","pages":"Pages 530-541"},"PeriodicalIF":4.1,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824000758/pdfft?md5=5e2fc7bd58ea3d469c63b2288fc470f1&pid=1-s2.0-S1525157824000758-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140570380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Application of Knowledge Engineering via the Use of a Biomimetic Digital Twin Ecosystem, Phenotype-Driven Variant Analysis, and Exome Sequencing to Understand the Molecular Mechanisms of Disease","authors":"William G. Kearns ,&nbsp;Georgios Stamoulis ,&nbsp;Joseph Glick ,&nbsp;Lawrence Baisch ,&nbsp;Andrew Benner ,&nbsp;Dalton Brough ,&nbsp;Luke Du ,&nbsp;Bradford Wilson ,&nbsp;Laura Kearns ,&nbsp;Nicholas Ng ,&nbsp;Maya Seshan ,&nbsp;Raymond Anchan","doi":"10.1016/j.jmoldx.2024.03.004","DOIUrl":"10.1016/j.jmoldx.2024.03.004","url":null,"abstract":"<div><p>Applied artificial intelligence, particularly large language models, in biomedical research is accelerating, but effective discovery and validation requires a toolset without limitations or bias. On January 30, 2023, the National Academies of Sciences, Engineering, and Medicine (NAS) appointed an ad hoc committee to identify the needs and opportunities to advance the mathematical, statistical, and computational foundations of digital twins in applications across science, medicine, engineering, and society. On December 15, 2023, the NAS released a 164-page report, “Foundational Research Gaps and Future Directions for Digital Twins.” This report described the importance of using digital twins in biomedical research. The current study was designed to develop an innovative method that incorporated phenotype-ranking algorithms with knowledge engineering via a biomimetic digital twin ecosystem. This ecosystem applied real-world reasoning principles to nonnormalized, raw data to identify hidden or \"dark\" data. Clinical exome sequencing study on patients with endometriosis indicated four variants of unknown clinical significance potentially associated with endometriosis-related disorders in nearly all patients analyzed. One variant of unknown clinical significance was identified in all patient samples and could be a biomarker for diagnostics. To the best of our knowledge, this is the first study to incorporate the recommendations of the NAS to biomedical research. This method can be used to understand the mechanisms of any disease, for virtual clinical trials, and to identify effective new therapies.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 7","pages":"Pages 543-551"},"PeriodicalIF":4.1,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S152515782400062X/pdfft?md5=2eced04f2604074e0e758338fecfe11e&pid=1-s2.0-S152515782400062X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140332277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Leveraging Off-Target Reads in Panel Sequencing for Homologous Recombination Repair Deficiency Screening in Tumor","authors":"Markus Ball ,&nbsp;Iordanis Ourailidis ,&nbsp;Klaus Kluck ,&nbsp;Michael Menzel ,&nbsp;Martina Kirchner ,&nbsp;Michael Allgäuer ,&nbsp;Timothy Kwang Yong Tay ,&nbsp;Fabian Schnecko ,&nbsp;Anna-Lena Volckmar ,&nbsp;Hannah Goldschmid ,&nbsp;Olaf Neuman ,&nbsp;Stefan Fröhling ,&nbsp;Peter Schirmacher ,&nbsp;Jan Budczies ,&nbsp;Albrecht Stenzinger ,&nbsp;Daniel Kazdal","doi":"10.1016/j.jmoldx.2024.02.008","DOIUrl":"10.1016/j.jmoldx.2024.02.008","url":null,"abstract":"<div><p>Targeted tumor only sequencing has become a standard practice in cancer diagnostics. This study aims to develop an approach for robust copy number variant calling in tumor samples using only off-target region (OTR) reads. We also established a clinical use case for homologous recombination deficiency (HRD) score estimation (HRDest) using the sum of telomeric-allelic imbalance and large-scale state transition scores without the need for loss of heterozygosity information. A strong correlation was found between HRD score and the sum of telomeric-allelic imbalance + large-scale state transition in The Cancer Genome Atlas cohort (ρ = 0.99, <em>P</em> &lt; 2.2 × 10⁻¹⁶) and in a clinical in-house cohort of 34 tumors (ρ = 0.9, <em>P</em> = 5.1 × 10⁻¹³) comparing whole-exome sequencing and targeted sequencing data. HRDest scores from 1086 clinical cases were compared with The Cancer Genome Atlas data set. There were no significant differences in HRD score distribution within the analyzed tumor types. As a control, commercially available HRD standards were also sequenced, and the HRDest scores obtained from the OTR reads were well within the HRD reference range provided by the manufacturer. In conclusion, OTR reads of tumor-only panel sequencing can be used to determine genome-wide copy number variant profiles and to approximate HRD scores.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 6","pages":"Pages 479-486"},"PeriodicalIF":4.1,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824000606/pdfft?md5=7a06fe716ddff0a70ffe3ef747d45c52&pid=1-s2.0-S1525157824000606-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}