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Li Y, Ye J, Liang L, Tan X, Zheng L, Qin T, Yu L. Detection of α-thalassemia South-East Asian deletion based on a fully integrated digital polymerase chain reaction system DropXpert S6. Hematology 2024; 29:2365596. [PMID: 38864494 DOI: 10.1080/16078454.2024.2365596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
OBJECTIVES This study aimed to establish a droplet digital polymerase chain reaction (ddPCR) assay for South-East Asian (SEA) deletion based on a fully integrated digital PCR system DropXpert S6. METHODS A total of 151 whole blood samples, 10 chorionic villus samples, and 17 amniotic fluid samples were collected, including 106 SEA heterozygotes, 43 normal individuals, 10 Hb Bart's hydrops details, and 19 SEA deletions combined with other genotypes.Genotypes of these samples were determined by the Gap-PCR method. We perform a series of optimizations of the ddPCR system to ensure the performance of the entire ddPCR reaction, such as droplet stability, fluorescence clustering, sensitivity, and accuracy. RESULTS Our assay exhibited 99.4% (177/178) accuracy compared with the Gap-PCR method, and the minimum detection limit of DNA was 0.1 ng/μL.Both targets have reliable linearity, R2 = 0.9999 for the α-thalassemia SEA deletion allele and R2 = 1 for the wild-type allele. The coefficient of variation for α-thalassemia SEA deletion allele detection at 2 and 10 ng/μL concentrations was 5.42% and 1.91%, respectively. In contrast, the coefficient of variation for wild-type allele detection was 4.06% and 1.83%, demonstrating its high quantitative accuracy. In addition, the DropXpert S6 PCR system showed some advantages over other ddPCR instruments, such as reducing testing costs, simplifying and automating the workflow. CONCLUSIONS The DropXpert S6 PCR system provided a highly accurate diagnosis for α-thalassemia SEA deletion and can be used to detect α-thalassemia as an alternative method.
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Affiliation(s)
- Youqiong Li
- Center for Medical Genetics and Prenatal Diagnosis, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Junwei Ye
- Research and Development Department, Shenzhen Biorain Technology Co., Ltd, Shenzhen, People's Republic of China
| | - Liang Liang
- Center for Medical Genetics and Prenatal Diagnosis, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Xiao Tan
- Research and Development Department, Shenzhen Biorain Technology Co., Ltd, Shenzhen, People's Republic of China
| | - Lihong Zheng
- Center for Medical Genetics and Prenatal Diagnosis, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Ting Qin
- Center for Medical Genetics and Prenatal Diagnosis, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Linfen Yu
- Research and Development Department, Shenzhen Biorain Technology Co., Ltd, Shenzhen, People's Republic of China
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Oscorbin IP, Gordukova MA, Davydova NV, Zinovieva NV, Kovzel EF, Andries L, Kudlay DA, Filipenko ML. Multiplex droplet digital PCR for 22q11.2 microdeletions screening and DiGeorge syndrome diagnostics. Clin Chim Acta 2024; 563:119903. [PMID: 39127298 DOI: 10.1016/j.cca.2024.119903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/01/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND AND AIMS DiGeorge syndrome (DGS) is a genetic disorder manifesting in polymorphic symptoms related to developmental abnormalities of various organs including thymus. DGS is caused by microdeletions in the 22q11.2 region between several low copy repeats (LCR) occurring in approximately 1 in 4000 live births. Diagnosis of DGS relies on phenotypic examination, qPCR, ultrasound, FISH, MLPA and NGS which can be relatively inaccurate, time-consuming, and costly. MATERIALS AND METHODS A novel multiplex droplet digital PCR (ddPCR) assay was designed, optimized and validated for detection and mapping 22q11.2 microdeletions by simultaneous amplification of three targets - TUPLE1, ZNF74, D22S936 - within the deletion areas and one reference target - RPP30 - as an internal control. RESULTS The assay reliable identified microdeletions when the template concentration was >32 copies per reaction and successfully detected LCR22A-B, LCR22A-C, LCR22A-D, and LCR22B-C deletions in clinical samples from 153 patients with signs of immunodeficiency. In patients with the microdeletions, flow cytometry detected a significant increase in B-cell and natural killer cell counts and percentages, while T-cell percentages and T-cell receptor excision circle (TREC) numbers decreased. CONCLUSION The designed ddPCR assay is suitable for diagnosing DGS using whole blood and blood spots.
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Affiliation(s)
- Igor Petrovich Oscorbin
- Laboratory of Pharmacogenomics, The Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia.
| | | | | | | | - Elena Fedorovna Kovzel
- Clinical Immunology, Allergology, Pulmonology Program, Corporate Fund "University Medical Center" of Nazarbayev University, Astana, Kazakhstan
| | - Lucia Andries
- Laboratory of Clinical Immunology and Allergology, Nicolae Testemitanu State University of Medicine and Pharmacy of the Republic of Moldova, Chișinău, Moldova
| | - Dmitry Anatolyevich Kudlay
- The Department of Pharmacology, Faculty of Medicine, I.M. Sechenov First Moscow State Medical University, Pogodinskaya St. 1, Moscow 119991, Russia
| | - Maxim Leonidovich Filipenko
- Laboratory of Pharmacogenomics, The Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia
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3
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Możdżan M, Węgiel A, Biskup L, Brzezińska O, Makowska J. Anti-Th/To Antibodies in Scleroderma: Good Prognosis or Serious Concern? J Clin Med 2024; 13:3022. [PMID: 38892733 PMCID: PMC11172938 DOI: 10.3390/jcm13113022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Systemic sclerosis (SSc) represents a rare and intricate autoimmune connective tissue disease, the pathophysiology of which has not been fully understood. Its key features include progressive fibrosis of the skin and internal organs, vasculopathy and aberrant immune activation. While various anti-nuclear antibodies can serve as biomarkers for the classification and prognosis of SSc, their direct role in organ dysfunction remains unclear. Anti-Th/To antibodies are present in approximately 5% of SSc patients, and are particularly prevalent among those with the limited subtype of the disease. Although the presence of these autoantibodies is associated with a mild course of the disease, there is a strong connection between them and severe clinical manifestations of SSc, including interstitial lung disease, pulmonary arterial hypertension and gastrointestinal involvement. Also, the additional clinical correlations, particularly with malignancies, need further research. Moreover, the disease's course seems to be influenced by antibodies, specific serum cytokines and TLR signaling pathways. Understanding the relationships between presence of anti-Th/To, its molecular aspects and response to treatment options is crucial for the development of novel, personalized therapeutic techniques and should undergo profound analysis in future studies.
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Affiliation(s)
- Maria Możdżan
- Department of Rheumatology, Medical University of Lodz, 90-549 Lodz, Poland; (A.W.); (L.B.); (O.B.)
| | | | | | | | - Joanna Makowska
- Department of Rheumatology, Medical University of Lodz, 90-549 Lodz, Poland; (A.W.); (L.B.); (O.B.)
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Lake KE, Colonnetta MM, Smith CA, Saunders K, Martinez-Algarin K, Mohta S, Pena J, McArthur HL, Reddy SM, Roussos Torres ET, Chen EH, Chan IS. Digital droplet PCR analysis of organoids generated from mouse mammary tumors demonstrates proof-of-concept capture of tumor heterogeneity. Front Cell Dev Biol 2024; 12:1358583. [PMID: 38827528 PMCID: PMC11140600 DOI: 10.3389/fcell.2024.1358583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/19/2024] [Indexed: 06/04/2024] Open
Abstract
Breast cancer metastases exhibit many different genetic alterations, including copy number amplifications (CNA). CNA are genetic alterations that are increasingly becoming relevant to breast oncology clinical practice. Here we identify CNA in metastatic breast tumor samples using publicly available datasets and characterize their expression and function using a metastatic mouse model of breast cancer. Our findings demonstrate that our organoid generation can be implemented to study clinically relevant features that reflect the genetic heterogeneity of individual tumors.
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Affiliation(s)
- Katherine E. Lake
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Megan M. Colonnetta
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Clayton A. Smith
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Kaitlyn Saunders
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Kenneth Martinez-Algarin
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Sakshi Mohta
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jacob Pena
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Heather L. McArthur
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Sangeetha M. Reddy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Evanthia T. Roussos Torres
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Elizabeth H. Chen
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Isaac S. Chan
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern, Dallas, TX, United States
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
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5
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Barbieri G, Cassioli G, Kura A, Orsi R, Magi A, Berteotti M, Scaturro GM, Lotti E, Gori AM, Marcucci R, Giusti B, Sticchi E. Digital droplet PCR versus quantitative PCR for lipoprotein (a) kringle IV type 2 repeat polymorphism genetic characterization. J Clin Lab Anal 2024; 38:e24998. [PMID: 38444303 PMCID: PMC10959181 DOI: 10.1002/jcla.24998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 12/01/2023] [Accepted: 12/17/2023] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Lipoprotein(a) [Lp(a)] level variability, related to atherothrombotic risk increase, is mainly attributed to LPA gene, encoding apolipoprotein(a), with kringle IV type 2 (KIV2) copy number variation (CNV) acting as the primary genetic determinant. Genetic characterization of Lp(a) is in continuous growth; nevertheless, the peculiar structural characteristics of this variant constitute a significant challenge to the development of effective detection methods. The aim of the study was to compare quantitative real-time PCR (qPCR) and digital droplet PCR (ddPCR) in the evaluation of KIV2 repeat polymorphism. METHODS We analysed 100 subjects tested for cardiovascular risk in which Lp(a) plasma levels were assessed. RESULTS Correlation analysis between CNV values obtained with the two methods was slightly significant (R = 0.413, p = 0.00002), because of the wider data dispersion in qPCR compared with ddPCR. Internal controls C1, C2 and C3 measurements throughout different experimental sessions revealed the superior stability of ddPCR, which was supported by a reduced intra/inter-assay coefficient of variation determined in this method compared to qPCR. A significant inverse correlation between Lp(a) levels and CNV values was confirmed for both techniques, but it was higher when evaluated by ddPCR than qPCR (R = -0.393, p = 0.000053 vs R = -0.220, p = 0.028, respectively). When dividing subjects into two groups according to 500 mg/L Lp(a) cut-off value, a significantly lower number of KIV2 repeats emerged among subjects with greater Lp(a) levels, with stronger evidence in ddPCR than in qPCR (p = 0.000013 and p = 0.001, respectively). CONCLUSIONS Data obtained support a better performance of ddPCR in the evaluation of KIV2 repeat polymorphism.
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Affiliation(s)
- Giulia Barbieri
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
| | - Giulia Cassioli
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
| | - Ada Kura
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
| | - Rebecca Orsi
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
| | - Alberto Magi
- Department of Information EngineeringUniversity of FlorenceFlorenceItaly
| | - Martina Berteotti
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
- Atherothrombotic Diseases CenterCareggi University HospitalFlorenceItaly
| | - Giusi Maria Scaturro
- Metabolic Diseases UnitA. Meyer Children's Hospital, University of FlorenceFlorenceItaly
| | - Elena Lotti
- Atherothrombotic Diseases CenterCareggi University HospitalFlorenceItaly
| | - Anna Maria Gori
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
- Atherothrombotic Diseases CenterCareggi University HospitalFlorenceItaly
| | - Rossella Marcucci
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
- Atherothrombotic Diseases CenterCareggi University HospitalFlorenceItaly
| | - Betti Giusti
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
- Atherothrombotic Diseases CenterCareggi University HospitalFlorenceItaly
| | - Elena Sticchi
- Department of Experimental and Clinical MedicineUniversity of FlorenceFlorenceItaly
- Atherothrombotic Diseases CenterCareggi University HospitalFlorenceItaly
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6
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Zhang X, Van Treeck B, Horton CA, McIntyre JJR, Palm SM, Shumate JL, Collins K. Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci. Nat Biotechnol 2024:10.1038/s41587-024-02137-y. [PMID: 38379101 PMCID: PMC11371274 DOI: 10.1038/s41587-024-02137-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Current approaches for inserting autonomous transgenes into the genome, such as CRISPR-Cas9 or virus-based strategies, have limitations including low efficiency and high risk of untargeted genome mutagenesis. Here, we describe precise RNA-mediated insertion of transgenes (PRINT), an approach for site-specifically primed reverse transcription that directs transgene synthesis directly into the genome at a multicopy safe-harbor locus. PRINT uses delivery of two in vitro transcribed RNAs: messenger RNA encoding avian R2 retroelement-protein and template RNA encoding a transgene of length validated up to 4 kb. The R2 protein coordinately recognizes the target site, nicks one strand at a precise location and primes complementary DNA synthesis for stable transgene insertion. With a cultured human primary cell line, over 50% of cells can gain several 2 kb transgenes, of which more than 50% are full-length. PRINT advantages include no extragenomic DNA, limiting risk of deleterious mutagenesis and innate immune responses, and the relatively low cost, rapid production and scalability of RNA-only delivery.
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Affiliation(s)
- Xiaozhu Zhang
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Briana Van Treeck
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Connor A Horton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jeremy J R McIntyre
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Sarah M Palm
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Justin L Shumate
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
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7
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Li O, Hackney JA, Choy DF, Chang D, Nersesian R, Staton TL, Cai F, Toghi Eshghi S. A targeted amplicon next-generation sequencing assay for tryptase genotyping to support personalized therapy in mast cell-related disorders. PLoS One 2024; 19:e0291947. [PMID: 38335181 PMCID: PMC10857577 DOI: 10.1371/journal.pone.0291947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/09/2023] [Indexed: 02/12/2024] Open
Abstract
Tryptase, the most abundant mast cell granule protein, is elevated in severe asthma patients independent of type 2 inflammation status. Higher active β tryptase allele counts are associated with higher levels of peripheral tryptase and lower clinical benefit from anti-IgE therapies. Tryptase is a therapeutic target of interest in severe asthma and chronic spontaneous urticaria. Active and inactive allele counts may enable stratification to assess response to therapies in asthmatic patient subpopulations. Tryptase gene loci TPSAB1 and TPSB2 have high levels of sequence identity, which makes genotyping a challenging task. Here, we report a targeted next-generation sequencing (NGS) assay and downstream bioinformatics analysis for determining polymorphisms at tryptase TPSAB1 and TPSB2 loci. Machine learning modeling using multiple polymorphisms in the tryptase loci was used to improve the accuracy of genotyping calls. The assay was tested and qualified on DNA extracted from whole blood of healthy donors and asthma patients, achieving accuracy of 96%, 96% and 94% for estimation of inactive α and βΙΙΙFS tryptase alleles and α duplication on TPSAB1, respectively. The reported NGS assay is a cost-effective method that is more efficient than Sanger sequencing and provides coverage to evaluate known as well as unreported tryptase polymorphisms.
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Affiliation(s)
- Olga Li
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Jason A. Hackney
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - David F. Choy
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Diana Chang
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Rhea Nersesian
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Tracy L. Staton
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Fang Cai
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Shadi Toghi Eshghi
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
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Giunta EF, Malapelle U, Russo A, De Giorgi U. Blood-based liquid biopsy in advanced prostate cancer. Crit Rev Oncol Hematol 2024; 194:104241. [PMID: 38122919 DOI: 10.1016/j.critrevonc.2023.104241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/25/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Prostate cancer is characterized by several genetic alterations which could impact prognosis and therapeutic decisions in the advanced disease. Tissue biopsy is still considered the gold standard approach for molecular characterization in prostate cancer, but it has several limitations, including the possibility of insufficient/inadequate tumor tissue to be analyzed. Blood-based liquid biopsy is a non-invasive method to investigate tumor cell derivatives in the bloodstream, being a valid alternative to tissue biopsy for molecular characterization but also for predictive and/or prognostic purposes. In this review, we analyze the most relevant evidence in this field, focusing on clinically relevant targets such as HRD genetic alterations and also focusing on the differences between tissue and liquid biopsy in light of the data from the latest clinical trials.
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Affiliation(s)
- Emilio Francesco Giunta
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, FC, Italy.
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Ugo De Giorgi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, FC, Italy
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9
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Roemen GMJM, Theunissen TEJ, Hoezen WWJ, Steyls ARM, Paulussen ADC, Mosterd K, Rahikkala E, zur Hausen A, Speel EJM, van Geel M. Detection of PTCH1 Copy-Number Variants in Mosaic Basal Cell Nevus Syndrome. Biomedicines 2024; 12:330. [PMID: 38397932 PMCID: PMC10886644 DOI: 10.3390/biomedicines12020330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Basal cell nevus syndrome (BCNS) is an inherited disorder characterized mainly by the development of basal cell carcinomas (BCCs) at an early age. BCNS is caused by heterozygous small-nucleotide variants (SNVs) and copy-number variants (CNVs) in the Patched1 (PTCH1) gene. Genetic diagnosis may be complicated in mosaic BCNS patients, as accurate SNV and CNV analysis requires high-sensitivity methods due to possible low variant allele frequencies. We compared test outcomes for PTCH1 CNV detection using multiplex ligation-probe amplification (MLPA) and digital droplet PCR (ddPCR) with samples from a BCNS patient heterozygous for a PTCH1 CNV duplication and the patient's father, suspected to have a mosaic form of BCNS. ddPCR detected a significantly increased PTCH1 copy-number ratio in the index patient's blood, and the father's blood and tissues, indicating that the father was postzygotic mosaic and the index patient inherited the CNV from him. MLPA only detected the PTCH1 duplication in the index patient's blood and in hair and saliva from the mosaic father. Our data indicate that ddPCR more accurately detects CNVs, even in low-grade mosaic BCNS patients, which may be missed by MLPA. In general, quantitative ddPCR can be of added value in the genetic diagnosis of mosaic BCNS patients and in estimating the recurrence risk for offspring.
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Affiliation(s)
- Guido M. J. M. Roemen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Tom E. J. Theunissen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Ward W. J. Hoezen
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Anja R. M. Steyls
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
| | - Aimee D. C. Paulussen
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
| | - Klara Mosterd
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Elisa Rahikkala
- Research Unit of Clinical Medicine, Department of Clinical Genetics, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, 90570 Oulu, Finland
| | - Axel zur Hausen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Ernst Jan M. Speel
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Michel van Geel
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
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10
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Wainman LM, Sathyanarayana SH, Lefferts JA. Applications of Digital Polymerase Chain Reaction (dPCR) in Molecular and Clinical Testing. J Appl Lab Med 2024; 9:124-137. [PMID: 38167753 DOI: 10.1093/jalm/jfad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/15/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Digital polymerase chain reaction (dPCR) is an accurate and sensitive molecular method that can be used in clinical diagnostic, prognostic, and predictive tests. The key component of the dPCR method is the partitioning of a single reaction into many thousands of droplets, nanochannels or other nano- or picoliter-sized reactions. This results in high enough sensitivity to detect rare nucleic acid targets and provides an absolute quantification of target sequences or alleles compared to other PCR-based methods. CONTENT An increasing number of dPCR platforms have been introduced commercially in recent years and more are being developed. These platforms differ in the method of partitioning, degree of automation, and multiplexing capabilities but all can be used in similar ways for sensitive and highly accurate quantification of a variety of nucleic acid targets. Currently, clinical applications of dPCR include oncology, microbiology and infectious disease, genetics, and prenatal/newborn screening. Commercially available tests for clinical applications are being developed for variants with diagnostic, prognostic, and therapeutic significance in specific disease types. SUMMARY The power of dPCR technology relies on the partitioning of the reactions and results in increased sensitivity and accuracy compared to qPCR. More recently, the sensitivity of dPCR has been applied to the detection of known variants in cell-free DNA and circulating tumor DNA. Future clinical applications of dPCR include liquid biopsy, treatment resistance detection, screening for minimal residual disease, and monitoring allograft engraftment in transplanted patients.
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Affiliation(s)
- Lauren M Wainman
- Laboratory for Clinical Genomics and Advanced Technology (CGAT), Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Shivaprasad H Sathyanarayana
- Laboratory for Clinical Genomics and Advanced Technology (CGAT), Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Joel A Lefferts
- Laboratory for Clinical Genomics and Advanced Technology (CGAT), Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
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11
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Kechin A, Boyarskikh U, Borobova V, Khrapov E, Subbotin S, Filipenko M. BRACNAC: A BRCA1 and BRCA2 Copy Number Alteration Caller from Next-Generation Sequencing Data. Int J Mol Sci 2023; 24:16630. [PMID: 38068953 PMCID: PMC10706169 DOI: 10.3390/ijms242316630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Detecting copy number variations (CNVs) and alterations (CNAs) in the BRCA1 and BRCA2 genes is essential for testing patients for targeted therapy applicability. However, the available bioinformatics tools were initially designed for identifying CNVs/CNAs in whole-genome or -exome (WES) NGS data or targeted NGS data without adaptation to the BRCA1/2 genes. Most of these tools were tested on sample cohorts of limited size, with their use restricted to specific library preparation kits or sequencing platforms. We developed BRACNAC, a new tool for detecting CNVs and CNAs in the BRCA1 and BRCA2 genes in NGS data of different origin. The underlying mechanism of this tool involves various coverage normalization steps complemented by CNV probability evaluation. We estimated the sensitivity and specificity of our tool to be 100% and 94%, respectively, with an area under the curve (AUC) of 94%. The estimation was performed using the NGS data obtained from 213 ovarian and prostate cancer samples tested with in-house and commercially available library preparation kits and additionally using multiplex ligation-dependent probe amplification (MLPA) (12 CNV-positive samples). Using freely available WES and targeted NGS data from other research groups, we demonstrated that BRACNAC could also be used for these two types of data, with an AUC of up to 99.9%. In addition, we determined the limitations of the tool in terms of the minimum number of samples per NGS run (≥20 samples) and the minimum expected percentage of CNV-negative samples (≥80%). We expect that our findings will improve the efficacy of BRCA1/2 diagnostics. BRACNAC is freely available at the GitHub server.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ulyana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Viktoriya Borobova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Sergey Subbotin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
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12
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Lee WS, Lockhart PJ. Utility of droplet digital polymerase chain reaction for studying somatic mosaicism: brain malformations and beyond. Neural Regen Res 2023; 18:2389-2390. [PMID: 37282462 PMCID: PMC10360090 DOI: 10.4103/1673-5374.371356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Affiliation(s)
- Wei Shern Lee
- Bruce Lefroy Centre, Murdoch Children's Research Institute; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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13
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Glaser V, Flugel C, Kath J, Du W, Drosdek V, Franke C, Stein M, Pruß A, Schmueck-Henneresse M, Volk HD, Reinke P, Wagner DL. Combining different CRISPR nucleases for simultaneous knock-in and base editing prevents translocations in multiplex-edited CAR T cells. Genome Biol 2023; 24:89. [PMID: 37095570 PMCID: PMC10123993 DOI: 10.1186/s13059-023-02928-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Multiple genetic modifications may be required to develop potent off-the-shelf chimeric antigen receptor (CAR) T cell therapies. Conventional CRISPR-Cas nucleases install sequence-specific DNA double-strand breaks (DSBs), enabling gene knock-out or targeted transgene knock-in. However, simultaneous DSBs provoke a high rate of genomic rearrangements which may impede the safety of the edited cells. RESULTS Here, we combine a non-viral CRISPR-Cas9 nuclease-assisted knock-in and Cas9-derived base editing technology for DSB free knock-outs within a single intervention. We demonstrate efficient insertion of a CAR into the T cell receptor alpha constant (TRAC) gene, along with two knock-outs that silence major histocompatibility complexes (MHC) class I and II expression. This approach reduces translocations to 1.4% of edited cells. Small insertions and deletions at the base editing target sites indicate guide RNA exchange between the editors. This is overcome by using CRISPR enzymes of distinct evolutionary origins. Combining Cas12a Ultra for CAR knock-in and a Cas9-derived base editor enables the efficient generation of triple-edited CAR T cells with a translocation frequency comparable to unedited T cells. Resulting TCR- and MHC-negative CAR T cells resist allogeneic T cell targeting in vitro. CONCLUSIONS We outline a solution for non-viral CAR gene transfer and efficient gene silencing using different CRISPR enzymes for knock-in and base editing to prevent translocations. This single-step procedure may enable safer multiplex-edited cell products and demonstrates a path towards off-the-shelf CAR therapeutics.
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Affiliation(s)
- Viktor Glaser
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Christian Flugel
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jonas Kath
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Weijie Du
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Vanessa Drosdek
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Clemens Franke
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Maik Stein
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Axel Pruß
- Institute of Transfusion Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Charité Mitte, Charitéplatz 1, 10117, Berlin, Germany
| | - Michael Schmueck-Henneresse
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Hans-Dieter Volk
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- CheckImmune GmbH, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Petra Reinke
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Dimitrios L Wagner
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.
- Institute of Transfusion Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Charité Mitte, Charitéplatz 1, 10117, Berlin, Germany.
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.
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14
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van Zogchel LMJ, Lak NSM, Gelineau NU, Sergeeva I, Stelloo E, Swennenhuis J, Feitsma H, van Min M, Splinter E, Bleijs M, Groot Koerkamp M, Breunis W, Meister MT, Kholossy WH, Holstege FCP, Molenaar JJ, de Leng WWJ, Stutterheim J, van der Schoot CE, Tytgat GAM. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors. Front Oncol 2023; 13:1124737. [PMID: 37152023 PMCID: PMC10157037 DOI: 10.3389/fonc.2023.1124737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Background Liquid biopsies combine minimally invasive sample collection with sensitive detection of residual disease. Pediatric malignancies harbor tumor-driving copy number alterations or fusion genes, rather than recurrent point mutations. These regions contain tumor-specific DNA breakpoint sequences. We investigated the feasibility to use these breakpoints to design patient-specific markers to detect tumor-derived cell-free DNA (cfDNA) in plasma from patients with pediatric solid tumors. Materials and methods Regions of interest (ROI) were identified through standard clinical diagnostic pipelines, using SNP array for CNAs, and FISH or RT-qPCR for fusion genes. Using targeted locus amplification (TLA) on tumor organoids grown from tumor material or targeted locus capture (TLC) on FFPE material, ROI-specific primers and probes were designed, which were used to design droplet digital PCR (ddPCR) assays. cfDNA from patient plasma at diagnosis and during therapy was analyzed. Results TLA was performed on material from 2 rhabdomyosarcoma, 1 Ewing sarcoma and 3 neuroblastoma. FFPE-TLC was performed on 8 neuroblastoma tumors. For all patients, at least one patient-specific ddPCR was successfully designed and in all diagnostic plasma samples the patient-specific markers were detected. In the rhabdomyosarcoma and Ewing sarcoma patients, all samples after start of therapy were negative. In neuroblastoma patients, presence of patient-specific markers in cfDNA tracked tumor burden, decreasing during induction therapy, disappearing at complete remission and re-appearing at relapse. Conclusion We demonstrate the feasibility to determine tumor-specific breakpoints using TLA/TLC in different pediatric solid tumors and use these for analysis of cfDNA from plasma. Considering the high prevalence of CNAs and fusion genes in pediatric solid tumors, this approach holds great promise and deserves further study in a larger cohort with standardized plasma sampling protocols.
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Affiliation(s)
- Lieke M. J. van Zogchel
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Nathalie S. M. Lak
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Nina U. Gelineau
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | | | | | | | | | | | | | - Margit Bleijs
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Willemijn Breunis
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- University Children’s Hospital Zürich, Zürich, Switzerland
| | - Michael Torsten Meister
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Frank C. P. Holstege
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center (UMC) Utrecht and Utrecht University, Utrecht, Netherlands
| | - Jan J. Molenaar
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Wendy W. J. de Leng
- Department of Pathology, University Medical Center (UMC) Utrecht, Utrecht, Netherlands
| | - Janine Stutterheim
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - C. Ellen van der Schoot
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Godelieve A. M. Tytgat
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- *Correspondence: Godelieve A. M. Tytgat,
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15
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Hou Y, Chen S, Zheng Y, Zheng X, Lin JM. Droplet-based digital PCR (ddPCR) and its applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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16
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Wu J, Yu S, Wang Y, Zhu J, Zhang Z. New insights into the role of ribonuclease P protein subunit p30 from tumor to internal reference. Front Oncol 2022; 12:1018279. [PMID: 36313673 PMCID: PMC9606464 DOI: 10.3389/fonc.2022.1018279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease P protein subunit p30 (RPP30) is a highly conserved housekeeping gene that exists in many species and tissues throughout the three life kingdoms (archaea, bacteria, and eukaryotes). RPP30 is closely related to a few types of tumors in human diseases but has a very stable transcription level in most cases. Based on this feature, increasing number of studies have used RPP30 as an internal reference gene. Here, the structure and basic functions of RPP30 are summarized and the likely relationship between RPP30 and various diseases in plants and human is outlined. Finally, the current application of RPP30 as an internal reference gene and its advantages over traditional internal reference genes are reviewed. RPP30 characteristics suggest that it has a good prospect of being selected as an internal reference; more work is needed to develop this research avenue.
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Affiliation(s)
- Junchao Wu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Sijie Yu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yalan Wang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,Department of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China,*Correspondence: Zhenhua Zhang,
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17
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Wu J, Tang B, Qiu Y, Tan R, Liu J, Xia J, Zhang J, Huang J, Qu J, Sun J, Wang X, Qu H. Clinical validation of a multiplex droplet digital PCR for diagnosing suspected bloodstream infections in ICU practice: a promising diagnostic tool. Crit Care 2022; 26:243. [PMID: 35941654 PMCID: PMC9358819 DOI: 10.1186/s13054-022-04116-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/31/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Droplet digital PCR (ddPCR) has emerged as a promising tool of pathogen detection in bloodstream infections (BSIs) in critical care medicine. However, different ddPCR platforms have variable sensitivity and specificity for diverse microorganisms at various infection sites. There is still a lack of prospective clinical studies aimed at validating and interpreting the discrepant ddPCR results for diagnosing BSI in intensive care unit (ICU) practice.
Methods
A prospective diagnostic study of multiplex ddPCR panels was conducted in a general ICU from May 21, 2021, to December 22, 2021. Paired blood cultures (BCs) and ddPCRs (2.5 h) were obtained synchronously to detect the 12 most common BSI pathogens and three antimicrobial resistance (AMR) genes. Firstly, ddPCR performance was compared to definite BSI. Secondly, clinical validation of ddPCR was compared to composite clinical diagnosis. Sensitivity, specificity, and positive and negative predictive values were calculated. Thirdly, the positive rate of AMR genes and related analysis was presented.
Results
A total of 438 episodes of suspected BSIs occurring in 150 critical patients were enrolled. BC and ddPCR were positive for targeted bacteria in 40 (9.1%) and 180 (41.1%) cases, respectively. There were 280 concordant and 158 discordant. In comparison with BCs, the sensitivity of ddPCR ranged from 58.8 to 86.7% with an aggregate of 72.5% in different species, with corresponding specificity ranging from 73.5 to 92.2% with an aggregate of 63.1%. Furthermore, the rate of ddPCR+/BC− results was 33.6% (147/438) with 87.1% (128 of 147) cases was associated with probable (n = 108) or possible (n = 20) BSIs. When clinically diagnosed BSI was used as true positive, the final sensitivity and specificity of ddPCR increased to 84.9% and 92.5%, respectively. In addition, 40 blaKPC, 3blaNDM, and 38 mecA genes were detected, among which 90.5% were definitely positive for blaKPC. Further, 65.8% specimens were predicted to be mecA-positive in Staphylococcus sp. according to all microbiological analysis.
Conclusions
The multiplexed ddPCR is a flexible and universal platform, which can be used as an add-on complementary to conventional BC. When combined with clinical infection evidence, ddPCR shows potential advantages for rapidly diagnosing suspected BSIs and AMR genes in ICU practice.
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18
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Wang K, Liu L, Wang J, Sun X, Han Q, Zhou C, Xu X, Wang J. Quantification of hepatitis E virus in raw pork livers using droplet digital RT-PCR. Food Microbiol 2022; 109:104114. [DOI: 10.1016/j.fm.2022.104114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 10/14/2022]
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19
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Kim KB, Park S, Ha JS, Ryoo N, Kim DH. Three Cases of False-positive Multiplex Ligation-dependent Probe Amplification of BRCA1. Ann Lab Med 2022; 42:497-499. [PMID: 35177575 PMCID: PMC8859565 DOI: 10.3343/alm.2022.42.4.497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/17/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Kyoung Bo Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Sunggyun Park
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Jung Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Namhee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Do-Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
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20
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Han Y, Wang J, Zhang S, Yang S, Wang X, Han Y, Shen Z, Xu X. Simultaneous quantification of hepatitis A virus and norovirus genogroup I and II by triplex droplet digital PCR. Food Microbiol 2022; 103:103933. [DOI: 10.1016/j.fm.2021.103933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 11/04/2022]
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21
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Lavoro A, Scalisi A, Candido S, Zanghì GN, Rizzo R, Gattuso G, Caruso G, Libra M, Falzone L. Identification of the most common BRCA alterations through analysis of germline mutation databases: Is droplet digital PCR an additional strategy for the assessment of such alterations in breast and ovarian cancer families? Int J Oncol 2022; 60:58. [PMID: 35383859 PMCID: PMC8997337 DOI: 10.3892/ijo.2022.5349] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Abstract
Breast and ovarian cancer represent two of the most common tumor types in females worldwide. Over the years, several non‑modifiable and modifiable risk factors have been associated with the onset and progression of these tumors, including age, reproductive factors, ethnicity, socioeconomic status and lifestyle factors, as well as family history and genetic factors. Of note, BRCA1 and BRCA2 are two tumor suppressor genes with a key role in DNA repair processes, whose mutations may induce genomic instability and increase the risk of cancer development. Specifically, females with a family history of breast or ovarian cancer harboring BRCA1/2 germline mutations have a 60‑70% increased risk of developing breast cancer and a 15‑40% increased risk for ovarian cancer. Different databases have collected the most frequent germline mutations affecting BRCA1/2. Through the analysis of such databases, it is possible to identify frequent hotspot mutations that may be analyzed with next‑generation sequencing (NGS) and novel innovative strategies. In this context, NGS remains the gold standard method for the assessment of BRCA1/2 mutations, while novel techniques, including droplet digital PCR (ddPCR), may improve the sensitivity to identify such mutations in the hereditary forms of breast and ovarian cancer. On these bases, the present study aimed to provide an update of the current knowledge on the frequency of BRCA1/2 mutations and cancer susceptibility, focusing on the diagnostic potential of the most recent methods, such as ddPCR.
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Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Aurora Scalisi
- Italian League Against Cancer, Section of Catania, I‑95122 Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Guido Nicola Zanghì
- Department of General Surgery and Medical‑Surgical Specialties, Policlinico‑Vittorio Emanuele Hospital, University of Catania, I‑95123 Catania, Italy
| | - Roberta Rizzo
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Caruso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Luca Falzone
- Epidemiology and Biostatistics Unit, National Cancer Institute IRCCS Fondazione 'G. Pascale', I‑80131 Naples, Italy
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22
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Oscorbin IP, Smertina MA, Pronyaeva KA, Voskoboev ME, Boyarskikh UA, Kechin AA, Demidova IA, Filipenko ML. Multiplex Droplet Digital PCR Assay for Detection of MET and HER2 Genes Amplification in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14061458. [PMID: 35326608 PMCID: PMC8945941 DOI: 10.3390/cancers14061458] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC), a subtype of lung cancer, remains one of the most common tumors with a high mortality and morbidity rate. Numerous targeted drugs were implemented or are now developed for the treatment of NSCLC. Two genes, HER2 and MET, are among targets for these specific therapeutic agents. Alterations in HER2 and MET could lead to primary or acquired resistance to commonly used anti-EGFR drugs. Using current methods for detecting HER2 and MET amplifications is time and labor-consuming; alternative methods are required for HER2 and MET testing. We developed the first multiplex droplet digital PCR assay for the simultaneous detection of MET and HER2 amplification in NSCLC samples. The suitability of qPCR was assessed for the optimization of multiplex ddPCR. The optimal elongation temperature, reference genes for DNA quantification, and amplicon length were selected. The developed ddPCR was validated on control samples with various DNA concentrations and ratios of MET and HER2 genes. Using ddPCR, 436 EGFR-negative NSCLC samples were analyzed. Among the tested samples, five specimens (1.15%) showed a higher ratio of MET, and six samples (1.38%) showed a higher ratio of HER2. The reported multiplex ddPCR assay could be used for the routine screening of MET and HER2 amplification in NSCLC samples.
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Affiliation(s)
- Igor P. Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
- Correspondence: ; Tel.: +7-9137061694
| | - Maria A. Smertina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
| | - Ksenia A. Pronyaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Mikhail E. Voskoboev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ulyana A. Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
| | - Andrey A. Kechin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
| | | | - Maxim L. Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
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Abstract
While conventional PCR applications typically focus on a single PCR assay per reaction, multiplex PCR applications are a convenient and scalable solution becoming more routine. Multiplex methods can be applied to virtually any DNA template source (e.g., plant or human DNA, FFPE DNA isolated from clinical samples, bisulfite-converted DNA for DNA methylation analysis), and offers a cheap, convenient, and scalable solution for experiments that require characterization and analysis of multiple genomic regions.This method will detail the procedures to successfully design, screen, and prepare multiplex amplicon libraries; as well as supporting instructions on how to prepare these libraries for sequencing on Illumina, Ion Torrent, and Oxford Nanopore platforms. The flexibility of assay design allows means that custom multiplex panels can range in size from two assays up to a few hundred amplicons or more. Notably, the method described here is also amenable to whatever PCR buffer system the user prefers to use, making the system globally adaptable to the needs and preferences of the end user.
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Affiliation(s)
- Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia.
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
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24
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Multiplexed analysis of small extracellular vesicle-derived mRNAs by droplet digital PCR and machine learning improves breast cancer diagnosis. Biosens Bioelectron 2021; 194:113615. [PMID: 34507095 DOI: 10.1016/j.bios.2021.113615] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 12/29/2022]
Abstract
Breast cancer has become the leading cause of global cancer incidence and a serious threat to women's health. Accurate diagnosis and early treatment are of great importance to prognosis. Although clinically used diagnostic approaches can be used for cancer screening, accurate diagnosis of breast cancer is still a critical unmet need. Here, we report a 4-plex droplet digital PCR technology for simultaneous detection of four small extracellular vesicle (sEV)-derived mRNAs (PGR, ESR1, ERBB2 and GAPDH) in combination with machine learning (ML) algorithms to improve breast cancer diagnosis. We evaluate the diagnsotic results with and without the assistance of the ML models. The results indicate that ML-assisted analysis exhibits higher diagnostic performance even using a single marker for breast cancer diagnosis, and demonstrate improved diagnostic performance under the best combination of biomarkers and suitable ML diagnostic model. Therefore, multiple sEV-derived mRNAs analysis coupled with ML not only provides the best combination of markers for breast cancer diagnosis, but also significantly improves the diagnostic efficiency of breast cancer.
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Wen T, Zhang X, Lippuner C, Schiff M, Stuber F. Development and Evaluation of a Droplet Digital PCR Assay for 8p23 β-Defensin Cluster Copy Number Determination. Mol Diagn Ther 2021; 25:607-615. [PMID: 34327613 PMCID: PMC8320422 DOI: 10.1007/s40291-021-00546-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2021] [Indexed: 12/01/2022]
Abstract
Introduction It has been proposed that the copy number (CN) variation (CNV) in β-defensin genes (DEFB) on human chromosome 8p23 determines phenotypic differences in inflammatory diseases. However, no method for accurate and easy DEFB CN quantification is yet available. Objective Droplet digital polymerase chain reaction (ddPCR) is a novel method for CNV quantification and has been used for genes such as CCL4L, CCL3L1, AMY1, and HER2. However, to date, no ddPCR assay has been available for DEFB CN determination. In the present study, we aimed to develop and evaluate such a ddPCR assay. Methods The assay was designed using DEFB4 and RPP30 as the target and the reference gene, respectively. To evaluate the assay, 283 DNA samples with known CNs previously determined using the multiple ligation-dependent probe amplification (MLPA) method, the current gold standard, were used as standards. To discover the optimal DNA template amount, we tested 80 to 2.5 ng DNA by a serial of one to two dilutions of eight samples. To evaluate the reproducibility of the assay, 31 samples were repeated to calculate the intra- and inter-assay variations. To further validate the reliability of the assay, the CNs of all 283 samples were determined using ddPCR. To compare results with those using quantitative PCR (qPCR), DEFB CNs for 48 samples were determined using qPCR with the same primers and probes. Results In a one-dimensional plot, the positive and negative droplets were clearly separated in both DEFB4 and RPP30 detection channels. In a two-dimensional plot, four populations of droplets were observed. The 20 ng template DNA proved optimal, with either high (80 ng) or low (10, 5, 2.5 ng) template input leading to ambiguous or inaccurate results. For the 31 standard samples, DEFB CNs were accurately determined with small intra- and inter-assay variations (coefficient of variation < 0.04 for both). In the validation cohort, ddPCR provided the correct CN for all 283 samples with high confidence. qPCR measurements for the 48 samples produced noisy data with high uncertainty and low accuracy. Conclusions ddPCR is an accurate, reproducible, easy-to-use, cheap, high-throughput method for DEFB CN determination. ddPCR could be applied to DEFB CN quantification in large-scale case–control studies. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-021-00546-2.
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Affiliation(s)
- Tingting Wen
- Department of Anesthesiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xianghong Zhang
- Department of Cardiac Intensive Care Unit, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Heath, Hangzhou, Zhejiang, China.
| | - Christoph Lippuner
- Department of Anesthesiology and Pain Medicine, Bern University Hospital, Inselspital, Bern, Switzerland
| | - Marcel Schiff
- Department of Anesthesiology and Pain Medicine, Bern University Hospital, Inselspital, Bern, Switzerland
| | - Frank Stuber
- Department of Anesthesiology and Pain Medicine, Bern University Hospital, Inselspital, Bern, Switzerland
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26
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Palacín-Aliana I, García-Romero N, Asensi-Puig A, Carrión-Navarro J, González-Rumayor V, Ayuso-Sacido Á. Clinical Utility of Liquid Biopsy-Based Actionable Mutations Detected via ddPCR. Biomedicines 2021; 9:906. [PMID: 34440110 PMCID: PMC8389639 DOI: 10.3390/biomedicines9080906] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/10/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and remains a major public health challenge. The introduction of more sensitive and powerful technologies has permitted the appearance of new tumor-specific molecular aberrations with a significant cancer management improvement. Therefore, molecular pathology profiling has become fundamental not only to guide tumor diagnosis and prognosis but also to assist with therapeutic decisions in daily practice. Although tumor biopsies continue to be mandatory in cancer diagnosis and classification, several studies have demonstrated that liquid biopsies could be used as a potential tool for the detection of cancer-specific biomarkers. One of the main advantages is that circulating free DNA (cfDNA) provides information about intra-tumoral heterogeneity, reflecting dynamic changes in tumor burden. This minimally invasive tool has become an accurate and reliable instrument for monitoring cancer genetics. However, implementing liquid biopsies across the clinical practice is still ongoing. The main challenge is to detect genomic alterations at low allele fractions. Droplet digital PCR (ddPCR) is a powerful approach that can overcome this issue due to its high sensitivity and specificity. Here we explore the real-world clinical utility of the liquid biopsy ddPCR assays in the most diagnosed cancer subtypes.
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Affiliation(s)
- Irina Palacín-Aliana
- Atrys Health, 08025 Barcelona, Spain; (I.P.-A.); (A.A.-P.); (V.G.-R.)
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain
- Faculty of Science, Universidad de Alcalá, 28801 Madrid, Spain
| | - Noemí García-Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | - Adrià Asensi-Puig
- Atrys Health, 08025 Barcelona, Spain; (I.P.-A.); (A.A.-P.); (V.G.-R.)
| | - Josefa Carrión-Navarro
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | | | - Ángel Ayuso-Sacido
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, 28223 Madrid, Spain
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27
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Schlenker F, Kipf E, Borst N, Hutzenlaub T, Zengerle R, von Stetten F, Juelg P. Virtual Fluorescence Color Channels by Selective Photobleaching in Digital PCR Applied to the Quantification of KRAS Point Mutations. Anal Chem 2021; 93:10538-10545. [PMID: 34279918 DOI: 10.1021/acs.analchem.1c01488] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Multiplexing of analyses is essential to reduce sample and reagent consumption in applications with large target panels. In applications such as cancer diagnostics, the required degree of multiplexing often exceeds the number of available fluorescence channels in polymerase chain reaction (PCR) devices. The combination of photobleaching-sensitive and photobleaching-resistant fluorophores of the same color can boost the degree of multiplexing by a factor of 2 per channel. The only additional hardware required to create virtual fluorescence color channels is a low-cost light-emitting diode (LED) setup for selective photobleaching. Here, we present an assay concept for fluorescence color multiplexing in up to 10 channels (five standard channels plus five virtual channels) using the mediator probe PCR with universal reporter (UR) fluorogenic oligonucleotides. We evaluate the photobleaching characteristic of 21 URs, which cover the whole spectral range from blue to crimson. This comprehensive UR data set is employed to demonstrate the use of three virtual channels in addition to the three standard channels of a commercial dPCR device (blue, green, and red) targeting cancer-associated point mutations (KRAS G12D and G12V). Moreover, a LOD (limit of detection) analysis of this assay confirms the high sensitivity of the multiplexing method (KRAS G12D: 16 DNA copies/reaction in the standard red channel and KRAS G12V: nine DNA copies/reaction in the virtual red channel). Based on the presented data set, optimal fluorogenic reporter combinations can be easily selected for the application-specific creation of virtual channels, enabling a high degree of multiplexing at low optical and technical effort.
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Affiliation(s)
| | - Elena Kipf
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nadine Borst
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Tobias Hutzenlaub
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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28
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Kao YF, Peake B, Madden R, Cowan SR, Scimeca RC, Thomas JE, Reichard MV, Ramachandran A, Miller CA. A probe-based droplet digital polymerase chain reaction assay for early detection of feline acute cytauxzoonosis. Vet Parasitol 2021; 292:109413. [PMID: 33765571 DOI: 10.1016/j.vetpar.2021.109413] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/14/2022]
Abstract
Cytauxzoonosis is a tick-borne disease of domestic cats with high mortality and narrow therapeutic window, particularly in the southcentral and southeastern United States. The causative agent is the apicomplexan protozoal parasite Cytauxzoon felis and is primarily transmitted by Amblyomma americanum, the lone star tick. Currently there is no vaccine available to prevent cytauxzoonosis and treatment is often ineffective if not initiated early enough in the course of disease. Early diagnosis and therapeutic intervention are therefore crucial for the survival of infected cats. Several methods are available for diagnosis of cytauxzoonosis, with PCR being the most sensitive. However, current PCR assays, which employ double-stranded DNA intercalating dyes to detect C. felis infection, have inherent limitations such as the potential for false positive detection of non-specific amplification products and inability to provide absolute quantification of parasite load. The objective of this study was to develop a probe-based droplet digital PCR (ddPCR) assay capable of detection and quantification of C. felis load over time and during treatment. The C. felis ddPCR assay was able to (i) reliably detect and quantify C. felis DNA in clinical blood samples from cats with acute cytauxzoonosis and (ii) monitor clinical parasite load in response to anti-protozoal treatment through absolute quantification of C. felis DNA over time. When tested on blood samples from cats with experimental C. felis infection, the assay was able to detect infection in cats as early as 24 h prior to the development of clinical signs. In addition, we demonstrate that this probe-based design can be utilized in traditional real-time PCR systems, with similar detection capabilities as compared to ddPCR. The C. felis probe-based ddPCR was also able to detect infection in samples with lower parasite loads when compared to existing nested PCR assays, although these results were not significant due to small sample size. To the author's knowledge, this is the first reported probe-based ddPCR assay to detect Cytauxzoon felis infection in domestic cats.
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Affiliation(s)
- Yun-Fan Kao
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA
| | - Brittanie Peake
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, 1950 W Farm Rd, Stillwater, OK, 74078, USA
| | - Robin Madden
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, 1950 W Farm Rd, Stillwater, OK, 74078, USA
| | - Shannon R Cowan
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA
| | - Ruth C Scimeca
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, 1950 W Farm Rd, Stillwater, OK, 74078, USA
| | - Jennifer E Thomas
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA
| | - Mason V Reichard
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, 1950 W Farm Rd, Stillwater, OK, 74078, USA
| | - Craig A Miller
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA.
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Srisutham S, Suwannasin K, Sugaram R, Dondorp AM, Imwong M. Measurement of gene amplifications related to drug resistance in Plasmodium falciparum using droplet digital PCR. Malar J 2021; 20:120. [PMID: 33639924 PMCID: PMC7916280 DOI: 10.1186/s12936-021-03659-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) of the Plasmodium falciparum multidrug resistance 1 (pfmdr1), P. falciparum plasmepsin2 (pfplasmepsin2) and P. falciparum GTP cyclohydrolase 1 (pfgch1) genes are associated with anti-malarial drug resistance in P. falciparum malaria. Droplet digital PCR (ddPCR) assays have been developed for accurate assessment of CNVs in several human genes. The aim of the present study was to develop and validate ddPCR assays for detection of the CNVs of P. falciparum genes associated with resistance to anti-malarial drugs. METHODS A multiplex ddPCR assay was developed to detect the CNVs in the pfmdr1 and pfplasmepsin2 genes, while a duplex ddPCR assay was developed to detect CNV in the pfgch1 gene. The gene copy number (GCN) quantification limit, as well as the accuracy and precision of the ddPCR assays were determined and compared to conventional quantitative PCR (qPCR). In order to reduce the cost of testing, a multiplex ddPCR assay of two target genes, pfmdr1 and pfplasmepsin2, was validated. In addition, the CNVs of genes of field samples collected from Thailand from 2015 to 2019 (n = 84) were assessed by ddPCR and results were compared to qPCR as the reference assay. RESULTS There were no significant differences between the GCN results obtained from uniplex and multiplex ddPCR assays for detection of CNVs in the pfmdr1 and pfplasmepsin2 genes (p = 0.363 and 0.330, respectively). Based on the obtained gene copy number quantification limit, the accuracy and percent relative standard deviation (%RSD) value of the multiplex ddPCR assay were 95% and 5%, respectively, for detection of the CNV of the pfmdr1 gene, and 91% and 5% for detection of the CNV of the pfplasmepsin2 gene. There was no significant difference in gene copy numbers assessed by uniplex or duplex ddPCR assays regarding CNV in the pfgch1 gene (p = 0.276). The accuracy and %RSD value of the duplex ddPCR assay were 95% and 4%, respectively, regarding pfgch1 GCN. In the P. falciparum field samples, pfmdr1 and pfplasmepsin2 GCNs were amplified in 15% and 27% of samples from Ubon Ratchathani, Thailand, while pfgch1 GCN was amplified in 50% of samples from Yala, Thailand. There was 100% agreement between the GCN results obtained from the ddPCR and qPCR assays (κ = 1.00). The results suggested that multiplex ddPCR assay is the optional assay for the accurate detection of gene copy number without requiring calibration standards, while the cost and required time are reduced. Based on the results of this study, criteria for GCN detection by ddPCR analysis were generated. CONCLUSIONS The developed ddPCR assays are simple, accurate, precise and cost-effective tools for detection of the CNVs in the pfmdr1, pfplasmepsin2 and pfgch1 genes of P. falciparum. The ddPCR assay is a useful additional tool for the surveillance of anti-malarial drug resistance.
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Affiliation(s)
- Suttipat Srisutham
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanokon Suwannasin
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungniran Sugaram
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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30
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Strati A, Zavridou M, Economopoulou P, Gkolfinopoulos S, Psyrri A, Lianidou E. Development and Analytical Validation of a Reverse Transcription Droplet Digital PCR (RT-ddPCR) Assay for PD-L1 Transcripts in Circulating Tumor Cells. Clin Chem 2021; 67:642-652. [PMID: 33421061 DOI: 10.1093/clinchem/hvaa321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/09/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND PD-L1, an immune checkpoint protein, is an important biomarker for monitoring cancer patients during the administration of cancer immunotherapy. Droplet digital PCR (ddPCR), is a highly sensitive and accurate tool for the quantification of cancer biomarkers in liquid biopsy. We report the development and analytical validation of a novel duplex RT-ddPCR assay for the simultaneous quantification of PD-L1 and hypoxanthine phosphoribosyltransferase (HPRT) (used as reference gene) transcripts in circulating tumor cells (CTCs). METHODS RT-ddPCR experimental conditions were first optimized and the assay was analytically validated using synthetic standards and the BB49 and SCC47 cancer cell lines. The developed assay was further applied in 71 peripheral blood (PB) samples from head and neck squamous cell carcinoma (HNSCC) patients and 20 PB samples from healthy donors. PD-L1 and HPRT transcripts were quantified in cDNAs derived from CTCs isolated by a size-dependent microfluidic device. The developed RT-ddPCR assay was directly compared to RT-qPCR using 71 identical patient cDNA samples. RESULTS Analytical sensitivity was 0.64 copies/μL, while estimation of intra- and interassay variation revealed a high reproducibility (within-run CV%:4.7-23%; between-run CV%:13%). Using the developed RT-ddPCR assay 33/71(46.5%) HNSCC patients' samples were found positive for PD-L1 expression in CTCs, while by using RT-qPCR fewer samples (23/71, 32.4%) were positive (concordance: 55/71, 77.5%). CONCLUSIONS The developed RT-ddPCR assay for PD-L1 in CTCs is highly sensitive, specific, and reproducible; additionally, it offers improved diagnostic sensitivity over RT-qPCR. The clinical utility of the assay should be prospectively evaluated for the real-time monitoring of CTCs of cancer patients under immunotherapy.
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Affiliation(s)
- Areti Strati
- Department of Chemistry, Analysis of Circulating Tumor Cells Lab, National and Kapodistrian University of Athens, Athens, Greece
| | - Martha Zavridou
- Department of Chemistry, Analysis of Circulating Tumor Cells Lab, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiota Economopoulou
- Oncology Unit, 2nd Department of Internal Medicine-Propaedeutic, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Stavros Gkolfinopoulos
- Oncology Unit, 2nd Department of Internal Medicine-Propaedeutic, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Amanda Psyrri
- Oncology Unit, 2nd Department of Internal Medicine-Propaedeutic, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells Lab, National and Kapodistrian University of Athens, Athens, Greece
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31
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The carriage rates of ααα anti3.7, ααα anti4.2, and HKαα in the population of Guangxi, China measured using a rapid detection qPCR system to determine CNV in the α-globin gene cluster. Gene 2020; 768:145296. [PMID: 33181251 DOI: 10.1016/j.gene.2020.145296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/20/2020] [Accepted: 11/04/2020] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Our study group encountered a pregnant woman whose gene analysis of thalassemia was β41-42/βN; however, the patient was severely anemic and had a history of multiple blood transfusions. Further analysis showed that the individual carried the αααanti4.2. Our research group occasionally detected individuals with copy number variations of the α gene, including αααanti3.7, αααanti4.2, and HKαα, but these variations are not within the detection range of conventional gene detection for thalassemia. The purpose of this study was to determine the carriage rate of these α gene copy number variants in the population of southern Guangxi. RESULTS We used the method of relative quantitative homologous fragments to analyze α1 and α2 genes. 23,900 samples were analyzed. A total of 201 individuals with αααanti3.7, αααanti4.2, and HKαα genes were identified. The carriage rates of these genes in southern Guangxi were 0.39%, 0.29% and 0.16%, respectively. We also collected positive samples from 18 families, and hematology data analysis confirmed that if these individuals carried the β-thalassemia allele at the same time, would lead to further imbalance of the ratio of α-chain to β-chain, and then produce varying degrees of anemia. CONCLUSIONS The individuals carrying αααanti3.7, αααanti4.2, and HKαα genes suffer harms related to β0 thalassemia, and these variations are not included in the detection range of conventional gene analysis reagents; therefore, these individuals are at risk. Prenatal diagnosis institutions could pay more attention to carriage of copy number variations of α-globin, so as to give more accurate prenatal advice to patients.
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Liu X, Tao T, Zhao L, Li G, Yang L. Molecular diagnosis based on comprehensive genetic testing in 800 Chinese families with non-syndromic inherited retinal dystrophies. Clin Exp Ophthalmol 2020; 49:46-59. [PMID: 33090715 DOI: 10.1111/ceo.13875] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022]
Abstract
IMPORTANCE Inherited retinal dystrophies (IRDs) are a group of monogenic diseases, one of the leading causes of blindness. BACKGROUND Introducing a comprehensive genetic testing strategy by combining single gene Sanger sequencing, next-generation sequencing (NGS) including whole exome sequencing (WES), and a specific hereditary eye disease enrichment panel (HEDEP) sequencing, to identify the disease-causing variants of 800 Chinese probands affected with non-syndromic IRDs. DESIGN Retrospective analysis. PARTICIPANTS Eight hundred Chinese non-syndromic IRDs probands and their families. METHODS A total of 149 patients were subjected to Sanger sequencing. Of the 651 patients subjected to NGS, 86 patients underwent WES and 565 underwent HEDEP. Patients that likely carried copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA) or quantitative fluorescence PCR (QF-PCR). MAIN OUTCOME MEASURES The diagnostic rate. RESULTS (Likely) pathogenic variants were determined in 481 cases (60.13% detection rate). The detection rates of single gene Sanger sequencing, WES and HEDEP were 86.58%, 31.40% and 56.99%, respectively. Approximately 11.64% of 481 cases carried autosomal dominant variants, 72.97% carried AR variants and 15.39% were found to be X-linked. CNVs were confirmed by MLPA or QF-PCR in 17 families. Fourteen genes that each caused disease in 1% or more of the cohort were detected, and these genes were collectively responsible for disease in almost one half (46.38%) of the families. CONCLUSIONS AND RELEVANCE Sanger sequencing is ideal to detect pathogenic variants of clinical homogeneous diseases, whereas NGS is more appropriate for patients without an explicit clinical diagnosis.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Tianchang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Lin Zhao
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
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Dutra L, Franz O, Puupponen VM, Tiirola M. DNA recovery from Droplet Digital™ PCR emulsions using liquid nitrogen. Biotechniques 2020; 69:450-454. [PMID: 33103914 DOI: 10.2144/btn-2020-0076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Droplet microfluidics is a technology that enables the production and manipulation of small volumes. In biosciences, the most popular application of this technology is Droplet Digital™ PCR (ddPCR™), where parallel nanoliter-scale PCR assays are used to provide a high sensitivity and specificity for DNA detection. However, the recovery of PCR products for downstream applications such as sequencing can be challenging due to the droplets' stability. Here we compared five methods for disrupting the droplets to recover DNA. We found that rapid freezing in liquid nitrogen results in a clear phase separation and recovery of up to 70% of the DNA content. Liquid nitrogen freezing can thus offer a simple and environmentally friendly protocol for recovering DNA from ddPCR.
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Affiliation(s)
- Lara Dutra
- Department of Biological & Environmental Science, Nanoscience Center, University of Jyväskylä, Finland
| | - Ole Franz
- Department of Biological & Environmental Science, Nanoscience Center, University of Jyväskylä, Finland
| | - Veli-Mikko Puupponen
- Department of Biological & Environmental Science, Nanoscience Center, University of Jyväskylä, Finland
| | - Marja Tiirola
- Department of Biological & Environmental Science, Nanoscience Center, University of Jyväskylä, Finland
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Yang SR, Bouhlal Y, De La Vega FM, Ballard M, Kuo CJ, Vilborg A, Jensen G, Allison K. Integrated genomic characterization of ERBB2/HER2 alterations in invasive breast carcinoma: a focus on unusual FISH groups. Mod Pathol 2020; 33:1546-1556. [PMID: 32161378 DOI: 10.1038/s41379-020-0504-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/11/2020] [Accepted: 01/30/2020] [Indexed: 01/29/2023]
Abstract
In patients with invasive breast cancer, fluorescence in situ hybridization (FISH) testing for HER2 typically demonstrates the clear presence or lack of ERBB2 (HER2) amplification (i.e., groups 1 or 5). However, a small subset of patients can present with unusual HER2 FISH patterns (groups 2-4), resulting in diagnostic confusion. To provide clarity, the 2018 CAP/ASCO HER2 testing guideline recommends additional testing using HER2 immunohistochemistry (IHC) for determining the final HER2 status. Despite this effort, the genomic correlates of unusual HER2 FISH groups remain poorly understood. Here, we used droplet digital PCR (ddPCR) and targeted next-generation sequencing (NGS) to characterize the genomic features of both usual and unusual HER2 FISH groups. In this study, 51 clinical samples were selected to represent FISH groups 1-5. Furthermore, group 1 was subdivided into two groups, with groups 1A and 1B corresponding to cases with HER2 signals/cell ≥6.0 and 4-6, respectively. Overall, our findings revealed a wide range of copy number alterations in HER2 across the different FISH groups. As expected, groups 1A and 5 showed the clear presence and lack of HER2 copy number gain, respectively, as measured by ddPCR and NGS. In contrast, group 1B and other uncommon FISH groups (groups 2-4) were characterized by a broader range of HER2 copy levels with only a few select cases showing high-level gain. Notably, these cases with increased HER2 copy levels also showed HER2 overexpression by IHC, thus highlighting the correlation between HER2 copy number and HER2 protein expression. Given the concordance between the genomic and protein results, our findings suggest that HER2 IHC may inform HER2 copy number status in patients with unusual FISH patterns. Hence, our results support the current recommendation for using IHC to resolve HER2 status in FISH groups 2-4.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Francisco M De La Vega
- TOMA Biosciences, Holland, MI, USA.,Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA
| | - Morgan Ballard
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Calvin J Kuo
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Kimberly Allison
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
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Li G, Zhai Y, Liu H, Wang Z, Huang R, Jiang H, Feng Y, Chang Y, Wu F, Zeng F, Jiang T, Zhang W. RPP30, a transcriptional regulator, is a potential pathogenic factor in glioblastoma. Aging (Albany NY) 2020; 12:16155-16171. [PMID: 32702667 PMCID: PMC7485703 DOI: 10.18632/aging.103596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022]
Abstract
Background: Old age has been demonstrated to be a risk factor for GBM, but the underlying biological mechanism is still unclear. We designed this study intending to determine a mechanistic explanation for the link between age and pathogenesis in GBM. Results: The expression of RPP30, an independent prognostic factor in GBM, was negatively correlated with age in both tumor and non-tumor brain samples. However, the post-transcriptional modifications carried out by RPP30 were different in primary GBM and non-tumor brain samples. RPP30 affected protein expression of cancer pathways by performing RNA modifications. Further, we found that RPP30 was related to drug metabolism pathways important in GBM. The decreased expression of RPP30 in older patients might be a pathogenic factor for GBM. Conclusion: This study revealed the role of RPP30 in gliomagenesis and provided the theoretical foundation for targeted therapy. Methods: In total, 616 primary GBM samples and 41 non-tumor brain samples were enrolled in this study. Transcriptome data and clinical information were obtained from the CGGA, TCGA, and GSE53890 databases. Gene Set Variation Analysis and Gene Ontology analyses were the primary analytical methods used in this study. All statistical analyses were performed using R.
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Affiliation(s)
- Guanzhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - You Zhai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Hanjie Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhiliang Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Ruoyu Huang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Haoyu Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuemei Feng
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yuanhao Chang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Fan Zeng
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA)
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Boone EC, Wang WY, Gaedigk R, Cherner M, Bérard A, Leeder JS, Miller NA, Gaedigk A. Long-Distance Phasing of a Tentative "Enhancer" Single-Nucleotide Polymorphism With CYP2D6 Star Allele Definitions. Front Pharmacol 2020; 11:486. [PMID: 32457600 PMCID: PMC7226225 DOI: 10.3389/fphar.2020.00486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The CYP2D6 gene locus has been extensively studied over decades, yet a portion of variability in CYP2D6 activity cannot be explained by known sequence variations within the gene, copy number variation, or structural rearrangements. It was proposed that rs5758550, located 116 kb downstream of the CYP2D6 gene locus, increases gene expression and thus contributes to variability in CYP2D6 activity. This finding has, however, not been validated. The purpose of the study was to address a major technological barrier, i.e., experimentally linking rs5758550, also referred to as the "enhancer" single-nucleotide polymorphism (SNP), to CYP2D6 haplotypes >100 kb away. To overcome this challenge is essential to ultimately determine the contribution of the "enhancer" SNP to interindividual variability in CYP2D6 activity. METHODS A large ethnically mixed population sample (n=3,162) was computationally phased to determine linkage between the "enhancer" SNP and CYP2D6 haplotypes (or star alleles). To experimentally validate predicted linkages, DropPhase2D6, a digital droplet PCR (ddPCR)-based method was developed. 10X Genomics Linked-Reads were utilized as a proof of concept. RESULTS Phasing predicted that the "enhancer" SNP can occur on numerous CYP2D6 haplotypes including CYP2D6*1, *2, *5, and *41 and suggested that linkage is incomplete, i.e., a portion of these alleles do not have the "enhancer" SNP. Phasing also revealed differences among the European and African ancestry data sets regarding the proportion of alleles with and without the "enhancer" SNP. DropPhase2D6 was utilized to confirm or refute the predicted "enhancer" SNP location for individual samples, e.g., of n=3 samples genotyped as *1/*41, rs5758550 was on the *41 allele of two samples and on the *1 allele of one sample. Our findings highlight that the location of the "enhancer" SNP must not be assigned by "default." Furthermore, linkage between the "enhancer" SNP and CYP2D6 star allele haplotypes was confirmed with 10X Genomics technology. CONCLUSIONS Since the "enhancer" SNP can be present on a portion of normal, decreased, or no function alleles, the phase of the "enhancer" SNP must be considered when investigating the impact of the "enhancer" SNP on CYP2D6 activity.
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Affiliation(s)
- Erin C. Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
| | - Wendy Y. Wang
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
| | - Roger Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Mariana Cherner
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Anick Bérard
- Faculty of Pharmacy, University of Montreal, Montreal, QC, Canada
- Research Center, CHU Sainte-Justine, Montreal, QC, Canada
| | - J. Steven Leeder
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Neil A. Miller
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
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