Journal of Molecular Diagnostics最新文献

{"title":"Uncovering the Genetic Etiology of Inherited Bone Marrow Failure Syndromes Using a Custom-Designed Next-Generation Sequencing Panel","authors":"Fumin Lin ,&nbsp;Kajia Cao ,&nbsp;Fengqi Chang ,&nbsp;Joseph H. Oved ,&nbsp;Minjie Luo ,&nbsp;Zhiqian Fan ,&nbsp;Jeffrey Schubert ,&nbsp;Jinhua Wu ,&nbsp;Yiming Zhong ,&nbsp;Daniel J. Gallo ,&nbsp;Elizabeth H. Denenberg ,&nbsp;Jiani Chen ,&nbsp;Elizabeth A. Fanning ,&nbsp;Michele P. Lambert ,&nbsp;Michele E. Paessler ,&nbsp;Lea F. Surrey ,&nbsp;Kristin Zelley ,&nbsp;Suzanne MacFarland ,&nbsp;Peter Kurre ,&nbsp;Timothy S. Olson ,&nbsp;Marilyn M. Li","doi":"10.1016/j.jmoldx.2023.11.010","DOIUrl":"10.1016/j.jmoldx.2023.11.010","url":null,"abstract":"<div><p>Inherited bone marrow failure syndromes (IBMFS) are a group of heterogeneous disorders that account for ∼30% of pediatric cases of bone marrow failure and are often associated with developmental abnormalities and cancer predisposition. This article reports the laboratory validation and clinical utility of a large-scale, custom-designed next-generation sequencing panel, Children's Hospital of Philadelphia (CHOP) IBMFS panel, for the diagnosis of IBMFS in a cohort of pediatric patients. This panel demonstrated excellent analytic accuracy, with 100% sensitivity, ≥99.99% specificity, and 100% reproducibility on validation samples. In 269 patients with suspected IBMFS, this next-generation sequencing panel was used for identifying single-nucleotide variants, small insertions/deletions, and copy number variations in mosaic or nonmosaic status. Sixty-one pathogenic/likely pathogenic variants (54 single-nucleotide variants/insertions/deletions and 7 copy number variations) and 24 hypomorphic variants were identified, resulting in the molecular diagnosis of IBMFS in 21 cases (7.8%) and exclusion of IBMFS with a diagnosis of a blood disorder in 10 cases (3.7%). Secondary findings, including evidence of early hematologic malignancies and other hereditary cancer-predisposition syndromes, were observed in 9 cases (3.3%). The CHOP IBMFS panel was highly sensitive and specific, with a significant increase in the diagnostic yield of IBMFS. These findings suggest that next-generation sequencing–based panel testing should be a part of routine diagnostics in patients with suspected IBMFS.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157823002957/pdfft?md5=810ee804aa415caabd9d7ebe634a53ea&pid=1-s2.0-S1525157823002957-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138716462","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":"Quantification of Measurable Residual Disease Detection by Next-Generation Sequencing–Based Clonality Testing in B-Cell and Plasma Cell Neoplasms","authors":"Ying Liu ,&nbsp;Caleb Ho ,&nbsp;Wayne Yu ,&nbsp;Ying Huang ,&nbsp;Jeffrey Miller ,&nbsp;Qi Gao ,&nbsp;Mustafa Syed ,&nbsp;Yuanyuan Ma ,&nbsp;Meiyi Wang ,&nbsp;Lidia Maciag ,&nbsp;Kseniya Petrova-Drus ,&nbsp;Menglei Zhu ,&nbsp;JinJuan Yao ,&nbsp;Chad Vanderbilt ,&nbsp;Benjamin Durham ,&nbsp;Jamal Benhamida ,&nbsp;Mark D. Ewalt ,&nbsp;Ahmet Dogan ,&nbsp;Mikhail Roshal ,&nbsp;Khedoudja Nafa ,&nbsp;Maria E. Arcila","doi":"10.1016/j.jmoldx.2023.11.009","DOIUrl":"10.1016/j.jmoldx.2023.11.009","url":null,"abstract":"<div><p>Next-generation sequencing (NGS)–based measurable residual disease (MRD) monitoring in post-treatment settings can be crucial for relapse risk stratification in patients with B-cell and plasma cell neoplasms. Prior studies have focused on validation of various technical aspects of the MRD assays, but more studies are warranted to establish the performance characteristics and enable standardization and broad utilization in routine clinical practice. Here, the authors describe an NGS-based IGH MRD quantification assay, incorporating a spike-in calibrator for monitoring B-cell and plasma cell neoplasms based on their unique IGH rearrangement status. Comparison of MRD status (positive or undetectable) by NGS and flow cytometry (FC) assays showed high concordance (91%, 471/519 cases) and overall good linear correlation in MRD quantitation, particularly for chronic lymphocytic leukemia and B-lymphoblastic leukemia/lymphoma (<em>R</em> = 0.85). Quantitative correlation was lower for plasma cell neoplasms, where underestimation by FC is a known limitation. No significant effects on sequencing efficiency by the spike-in calibrator were observed, with excellent inter- and intra-assay reproducibility within the authors’ laboratory, and in comparison to an external laboratory, using the same assay and protocols. Assays performed both at internal and external laboratories showed highly concordant MRD detection (100%) and quantitation (<em>R</em> = 0.97). Overall, this NGS-based MRD assay showed highly reproducible results with quantitation that correlated well with FC MRD assessment, particularly for B-cell neoplasms.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157823002945/pdfft?md5=d9ff2b87c9f3c551526a243ec8fafa64&pid=1-s2.0-S1525157823002945-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138716540","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":"Slice Testing—Considerations from Ordering to Reporting","authors":"Jeffrey A. SoRelle ,&nbsp;Birgit H. Funke ,&nbsp;Celeste C. Eno ,&nbsp;Jianling Ji ,&nbsp;Avni Santani ,&nbsp;Pinar Bayrak-Toydemir ,&nbsp;Megan Wachsmann ,&nbsp;Karen E. Wain ,&nbsp;Rong Mao","doi":"10.1016/j.jmoldx.2023.11.008","DOIUrl":"10.1016/j.jmoldx.2023.11.008","url":null,"abstract":"<div><p>As the number of genes associated with various germline disorders continues to grow, it is becoming more difficult for clinical laboratories to maintain separate assays for interrogating disease-focused gene panels. One solution to this challenge is termed slice testing, where capture backbone is used to analyze data specific to a set of genes, and for this article, we will focus on exome. A key advantage to this strategy is greater flexibility by adding genes as they become associated with disease or the ability to accommodate specific provider requests. Here, we provide expert consensus recommendations and results from an Association for Molecular Pathology–sponsored survey of clinical laboratories performing exome sequencing to compare a slice testing approach with traditional static gene panels and comprehensive exome analysis. We explore specific considerations for slices, including gene selection, analytic performance, coverage, quality, and interpretation. Our goal is to provide comprehensive guidance for clinical laboratories interested in designing and using slice tests as a diagnostic.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157823002933/pdfft?md5=77cd55be79b3b8d5d5f3748b49b642f4&pid=1-s2.0-S1525157823002933-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138716539","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":"Operationalizing Quality Assurance for Clinical Illumina Somatic Next-Generation Sequencing Pipelines","authors":"Joshua Bridgers,&nbsp;Kenyon Alexander,&nbsp;Aly Karsan","doi":"10.1016/j.jmoldx.2023.11.006","DOIUrl":"10.1016/j.jmoldx.2023.11.006","url":null,"abstract":"<div><p>Quality assurance (QA) is essential for precision oncology workflows, in particular in the clinical setting. However, because of numerous variations in laboratory and bioinformatics pipelines, QA practices remain non-standardized, are often ad hoc, and are lacking longitudinal tracking. A selected review of existing software was performed for quality control of Illumina next-generation sequencing data, focusing specifically on generalizable tools that can be integrated into any bioinformatics workflow to easily develop a QA workflow with longitudinal tracking. Although all implementations need to be integrated, validated, and iterated upon to suit individual operations, providing a base suite of options will enable better validation and use of QA in clinical somatic mutation testing for workflows using Illumina next-generation sequencing and beyond.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S152515782300288X/pdfft?md5=5f4d7770319085c13a59a7a1c87cd2e8&pid=1-s2.0-S152515782300288X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138566588","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":"MLH1 Promotor Hypermethylation in Colorectal and Endometrial Carcinomas from Patients with Lynch Syndrome","authors":"Noah C. Helderman ,&nbsp;Katarina D. Andini ,&nbsp;Monique E. van Leerdam ,&nbsp;Liselotte P. van Hest ,&nbsp;Daniël R. Hoekman ,&nbsp;Aysel Ahadova ,&nbsp;Sanne W. Bajwa-ten Broeke ,&nbsp;Tjalling Bosse ,&nbsp;Elise M.J. van der Logt ,&nbsp;Floris Imhann ,&nbsp;Matthias Kloor ,&nbsp;Alexandra M.J. Langers ,&nbsp;Vincent T.H.B.M. Smit ,&nbsp;Diantha Terlouw ,&nbsp;Tom van Wezel ,&nbsp;Hans Morreau ,&nbsp;Maartje Nielsen","doi":"10.1016/j.jmoldx.2023.10.005","DOIUrl":"10.1016/j.jmoldx.2023.10.005","url":null,"abstract":"<div><p>Screening for Lynch syndrome (LS) in colorectal cancer (CRC) and endometrial cancer patients generally involves immunohistochemical staining of the mismatch repair (MMR) proteins. In case of MLH1 protein loss, <em>MLH1</em> promotor hypermethylation (<em>MLH1</em>-PM) testing is performed to indirectly distinguish the constitutional <em>MLH1</em> variants from somatic epimutations. Recently, multiple studies have reported that <em>MLH1</em>-PM and pathogenic constitutional MMR variants are not mutually exclusive. This study describes 6 new and 86 previously reported <em>MLH1</em>-PM CRCs or endometrial cancers in LS patients. Of these, methylation of the <em>MLH1</em> gene promotor C region was reported in 30 <em>MLH1</em>, 6 <em>MSH2</em>, 6 <em>MSH6</em>, and 3 <em>PMS2</em> variant carriers at a median age at diagnosis of 48.5 years [interquartile range (IQR), 39–56.75 years], 39 years (IQR, 29–51 years), 58 years (IQR, 53.5–67 years), and 68 years (IQR, 65.6–68.5 years), respectively. For 31 <em>MLH1</em>-PM CRCs in LS patients from the literature, only the B region of the <em>MLH1</em> gene promotor was tested, whereas for 13 cases in the literature the tested region was not specified. Collectively, these data indicate that a diagnosis of LS should not be excluded when <em>MLH1</em>-PM is detected. Clinicians should carefully consider whether follow-up genetic MMR gene testing should be offered, with age &lt;60 to 70 years and/or a positive family history among other factors being suggestive for a potential constitutional MMR gene defect.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157823002891/pdfft?md5=2e7a9ca1f3f2cd0f7ba583a3ee4b71a7&pid=1-s2.0-S1525157823002891-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138548622","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":"Droplet Digital PCR for Fast and Accurate Characterization of NF1 Locus Deletions","authors":"Laurence Pacot ,&nbsp;Manuela Ye ,&nbsp;Juliette Nectoux ,&nbsp;Ingrid Laurendeau ,&nbsp;Audrey Briand-Suleau ,&nbsp;Audrey Coustier ,&nbsp;Théodora Maillard ,&nbsp;Cécile Barbance ,&nbsp;Lucie Orhant ,&nbsp;Nicolas Vaucouleur ,&nbsp;Hélène Blanché ,&nbsp;Béatrice Parfait ,&nbsp;Pierre Wolkenstein ,&nbsp;Michel Vidaud","doi":"10.1016/j.jmoldx.2023.11.005","DOIUrl":"10.1016/j.jmoldx.2023.11.005","url":null,"abstract":"<div><p>Neurofibromatosis type-1 is a genetic disorder caused by loss-of-function variants in the tumor-suppressor <em>NF1</em>. Approximately 4% to 11% of neurofibromatosis type-1 patients have a <em>NF1</em> locus complete deletion resulting from nonallelic homologous recombination between low copy repeats. Codeleted genes probably account for the more severe phenotype observed in <em>NF1</em>-deleted patients. This genotype–phenotype correlation highlights the need for a detailed molecular description. A droplet digital PCR (ddPCR) set along the <em>NF1</em> locus was designed to delimitate the three recurrent <em>NF1</em> deletion breakpoints. The ddPCR was tested in 121 samples from nonrelated <em>NF1</em>-deleted patients. Classification based on ddPCR versus multiplex ligation-dependent probe amplification (MLPA) was compared. In addition, microsatellites were analyzed to identify parental origin of deletions. ddPCR identified 77 type-1 (64%), 20 type-2 (16%), 7 type-3 (6%), and 17 atypical deletions (14%). The results were comparable with MLPA, except for three atypical deletions misclassified as type-2 using MLPA, for which the <em>SUZ12</em> gene was not deleted. A significant maternal bias (25 of 30) in the origin of deletions was identified. This study proposes a fast and efficient ddPCR quantification to allow fine <em>NF1</em> deletion classification. It indicates that ddPCR can be implemented easily into routine diagnosis to complement the techniques dedicated to <em>NF1</em> point variant identification. This new tool may help unravel the genetic basis conditioning phenotypic variability in <em>NF1</em>-deleted patients and offer tailored genetic counseling.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157823002763/pdfft?md5=57654943895205e96425f468799dde72&pid=1-s2.0-S1525157823002763-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138441574","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":"Variant Classification Discordance","authors":"Hamid Ghaedi ,&nbsp;Scott K. Davey ,&nbsp;Harriet Feilotter","doi":"10.1016/j.jmoldx.2023.11.002","DOIUrl":"10.1016/j.jmoldx.2023.11.002","url":null,"abstract":"<div><p>An ever-growing catalog of human variants is hosted in the ClinVar database. In this database, submissions on a variant are combined into a multisubmitter record; and in the case of discordance in variant classification between submitters, the record is labeled as conflicting. The current study used ClinVar data to identify characteristics that would make variants more likely to be associated with the conflict class of variants. Furthermore, the Extreme Gradient Boosting algorithm was used to train classifier models to provide prediction of classification discordance for single submission variants in ClinVar database. Population allele frequency, the gene harboring the variant, variant type, consequence on protein, variant deleteriousness score, first submitter identity, and submission count were associated with conflict in variant classification. Using such features, the optimized classifier showed accuracy on the test set of 88% with the weighted average of precision, recall, and f1-score of 0.84, 0.88, and 0.85, respectively. There were pronounced associations between variant classification discordance and allele frequency, gene type, and the identity of the first submitter. The study provides the predicted discordance status for single-submitter variants deposited in ClinVar. This approach can be used to assess whether single-submitter variants are likely to be supported, or in conflict with, future entries; this knowledge may help laboratories with clinical variant assessment.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157823002738/pdfft?md5=e89086f67f83997c28d16831557eb9b2&pid=1-s2.0-S1525157823002738-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138441576","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":"An Exome Capture-Based RNA-Sequencing Assay for Genome-Wide Identification and Prioritization of Clinically Important Fusions in Pediatric Tumors","authors":"Jonathan Buckley ,&nbsp;Ryan J. Schmidt ,&nbsp;Dejerianne Ostrow ,&nbsp;Dennis Maglinte ,&nbsp;Moiz Bootwalla ,&nbsp;David Ruble ,&nbsp;Ananthanarayanan Govindarajan ,&nbsp;Jianling Ji ,&nbsp;Alexandra E. Kovach ,&nbsp;Etan Orgel ,&nbsp;Gordana Raca ,&nbsp;Fariba Navid ,&nbsp;Leo Mascarenhas ,&nbsp;Bruce Pawel ,&nbsp;Nathan Robison ,&nbsp;Xiaowu Gai ,&nbsp;Jaclyn A. Biegel","doi":"10.1016/j.jmoldx.2023.11.003","DOIUrl":"10.1016/j.jmoldx.2023.11.003","url":null,"abstract":"<div><p>This study reports the development of an exome capture-based RNA-sequencing assay to detect recurring and novel fusions in hematologic, solid, and central nervous system tumors. The assay used Twist Comprehensive Exome capture with either fresh or formalin-fixed samples and a bioinformatic platform that provides fusion detection, prioritization, and downstream curation. A minimum of 50 million uniquely mapped reads, a consensus read alignment/fusion calling approach using four callers (Arriba, FusionCatcher, STAR-Fusion, and Dragen), and custom software were used to integrate, annotate, and rank the candidate fusion calls. In an evaluation of 50 samples, the number of calls varied substantially by caller, from a mean of 24.8 with STAR-Fusion to 259.6 with FusionCatcher; only 1.1% of calls were made by all four callers. Therefore a filtering and ranking algorithm was developed based on multiple criteria, including number of supporting reads, calling consensus, genes involved, and cross-reference against databases of known cancer-associated or likely false-positive fusions. This approach was highly effective in pinpointing known clinically relevant fusions, ranking them first in 47 of 50 samples (94%). Detection of pathogenic gene fusions in three diagnostically challenging cases highlights the importance of a genome-wide and nontargeted method for fusion detection in pediatric cancer.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S152515782300274X/pdfft?md5=ab42f3f9f1a40de6374220941740add4&pid=1-s2.0-S152515782300274X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138441626","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 Cas9-Mediated Targeted Sequencing of Spinocerebellar Ataxia Repeat Expansions","authors":"Keiji Tachikawa ,&nbsp;Takahiro Shimizu ,&nbsp;Takeshi Imai ,&nbsp;Riyoko Ko ,&nbsp;Yosuke Kawai ,&nbsp;Yosuke Omae ,&nbsp;Katsushi Tokunaga ,&nbsp;Martin C. Frith ,&nbsp;Yoshihisa Yamano ,&nbsp;Satomi Mitsuhashi","doi":"10.1016/j.jmoldx.2023.10.004","DOIUrl":"10.1016/j.jmoldx.2023.10.004","url":null,"abstract":"<div><p><span><span>Hereditary repeat diseases are caused by an abnormal expansion of short tandem repeats in the genome. Among them, </span>spinocerebellar ataxia<span> (SCA) is a heterogeneous disease, and currently, 16 responsible repeats are known. Genetic diagnosis is obtained by analyzing the number of repeats through separate testing of each repeat. Although simultaneous detection of candidate repeats using current massively parallel sequencing technologies has been developed to avoid complicated multiple experiments, these methods are generally expensive. This study developed a cost-effective SCA repeat panel [Flongle SCA repeat panel sequencing (FLO-SCAp)] using Cas9-mediated targeted long-read sequencing and the smallest long-read sequencing apparatus, Flongle. This panel enabled the detection of repeat copy number changes, internal repeat sequences, and DNA methylation in seven patients with different repeat expansion diseases. The median (interquartile range) values of coverage and on-target rate were 39.5 (12 to 72) and 11.6% (7.5% to 16.5%), respectively. This approach was validated by comparing repeat copy number changes measured by FLO-SCAp and short-read whole-genome sequencing. A high correlation was observed between FLO-SCAp and short-read whole-genome sequencing when the repeat length was ≤250 bp (</span></span><em>r</em> = 0.98; <em>P</em> &lt; 0.001). Thus, FLO-SCAp represents the most cost-effective method for conducting multiplex testing of repeats and can serve as the first-line diagnostic tool for SCA.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138441573","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":"FindDNAFusion","authors":"Xiaokang Pan ,&nbsp;Huolin Tu ,&nbsp;Nehad Mohamed ,&nbsp;Matthew Avenarius ,&nbsp;Sean Caruthers ,&nbsp;Weiqiang Zhao ,&nbsp;Dan Jones","doi":"10.1016/j.jmoldx.2023.11.004","DOIUrl":"10.1016/j.jmoldx.2023.11.004","url":null,"abstract":"<div><p>Detection of cancer-associated gene fusions is crucial for diagnosis, prognosis, and treatment selection. Many bioinformatics tools are available for the detection of fusion transcripts by RNA sequencing, but there are fewer well-validated software tools for DNA next-generation sequencing (NGS). A 542-gene solid tumor NGS panel was designed, with exonic probes supplemented with intronic bait probes against genes commonly involved in oncogenic fusions, with a focus on lung cancer. Three software tools for the detecting gene fusions in this DNA-NGS panel were selected and evaluated. The performance of these tools was compared after a pilot study, and each was configured for optimal batch analysis and detection rate. A blacklist for filtering common tool-specific artifacts, and criteria for selecting clinically reportable fusions, were established. Visualization tools for annotating and confirming somatic fusions were applied. Subsequently, a full clinical validation was used for comparing the results to those from <em>in situ</em> hybridization and/or RNA sequencing. With JuLI, Factera, and GeneFuse, 94.1%, 88.2%, and 66.7% of expected fusions were detected, respectively. With a combinatorial pipeline (termed FindDNAFusion), developed by integrating fusion-calling tools with methods for fusion filtering, annotating, and flagging reportable calls, the accuracy of detection of intron-tiled genes was improved to 98.0%. FindDNAFusion is an accurate and efficient tool in detecting somatic fusions in DNA-NGS panels with intron-tiled bait probes when RNA is unavailable.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157823002751/pdfft?md5=7ffc0cf0a98d4d83957d178b88b5c556&pid=1-s2.0-S1525157823002751-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138441575","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}