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Charles OJ, Venturini C, Goldstein RA, Breuer J. HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping. BMC Bioinformatics 2024; 25:279. [PMID: 39192205 DOI: 10.1186/s12859-024-05885-5] [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: 04/14/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
The prevention and treatment of many herpesvirus associated diseases is based on the utilization of antiviral therapies, however therapeutic success is limited by the development of drug resistance. Currently no single database cataloguing resistance mutations exists, which hampers the use of sequence data for patient management. We therefore developed HerpesDRG, a drug resistance mutation database that incorporates all the known resistance genes and current treatment options, built from a systematic review of available genotype to phenotype literature. The database is released along with an R package that provides a simple approach to resistance variant annotation and clinical implication analysis from common sanger and next generation sequencing data. This represents the first openly available and community maintainable database of drug resistance mutations for the human herpesviruses (HHV), developed for the community of researchers and clinicians tackling HHV drug resistance.
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Affiliation(s)
- O J Charles
- Department of Infection, Immunity and Inflammation, University College London, Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK.
| | - C Venturini
- Department of Infection, Immunity and Inflammation, University College London, Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - R A Goldstein
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - J Breuer
- Department of Infection, Immunity and Inflammation, University College London, Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, WC1N 1LE, UK
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2
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Walker R, Clendenning M, Joo JE, Xue J, Mahmood K, Georgeson P, Como J, Joseland S, Preston SG, Chan JM, Jenkins MA, Rosty C, Macrae FA, Di Palma S, Campbell A, Winship IM, Buchanan DD. A mosaic pathogenic variant in MSH6 causes MSH6-deficient colorectal and endometrial cancer in a patient classified as suspected Lynch syndrome: a case report. Fam Cancer 2023; 22:423-428. [PMID: 37318702 PMCID: PMC10541337 DOI: 10.1007/s10689-023-00337-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/23/2023] [Indexed: 06/16/2023]
Abstract
Germline pathogenic variants in the DNA mismatch repair (MMR) genes (Lynch syndrome) predispose to colorectal (CRC) and endometrial (EC) cancer. However, mosaic variants in the MMR genes have been rarely described. We identified a likely de novo mosaic MSH6:c.1135_1139del p.Arg379* pathogenic variant in a patient diagnosed with suspected Lynch syndrome/Lynch-like syndrome. The patient developed MSH6-deficient EC and CRC at 54 and 58 years of age, respectively, without a detectable germline MMR pathogenic variant. Multigene panel sequencing of tumor and blood-derived DNA identified an MSH6 somatic mutation (MSH6:c.1135_1139del p.Arg379*) common to both the EC and CRC, raising suspicion of mosaicism. A droplet digital polymerase chain reaction (ddPCR) assay detected the MSH6 variant at 5.34% frequency in normal colonic tissue, 3.49% in saliva and 1.64% in blood DNA, demonstrating the presence of the MSH6 variant in all three germ layers. This study highlights the utility of tumor sequencing to guide sensitive ddPCR testing to detect low-level mosaicism in the MMR genes. Further investigation of the prevalence of MMR mosaicism is needed to inform routine diagnostic approaches and genetic counselling.
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Affiliation(s)
- Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia.
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia.
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
| | - Jessie Xue
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
| | - Susan G Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
| | - James M Chan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
| | - Mark A Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Envoi Specialist Pathologists, Brisbane, QLD, 4059, Australia
- University of Queensland, Brisbane, QLD, 4072, Australia
| | - Finlay A Macrae
- Genomic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Department of Medicine, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | | | - Ainsley Campbell
- Clinical Genetics Unit, Austin Health, Melbourne, VIC, 3084, Australia
| | - Ingrid M Winship
- Genomic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
- Department of Medicine, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3010, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Parkville, VIC, 3010, Australia
- Genomic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC, 3000, Australia
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3
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Pfrieger FW. The Niemann-Pick type diseases – A synopsis of inborn errors in sphingolipid and cholesterol metabolism. Prog Lipid Res 2023; 90:101225. [PMID: 37003582 DOI: 10.1016/j.plipres.2023.101225] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Disturbances of lipid homeostasis in cells provoke human diseases. The elucidation of the underlying mechanisms and the development of efficient therapies represent formidable challenges for biomedical research. Exemplary cases are two rare, autosomal recessive, and ultimately fatal lysosomal diseases historically named "Niemann-Pick" honoring the physicians, whose pioneering observations led to their discovery. Acid sphingomyelinase deficiency (ASMD) and Niemann-Pick type C disease (NPCD) are caused by specific variants of the sphingomyelin phosphodiesterase 1 (SMPD1) and NPC intracellular cholesterol transporter 1 (NPC1) or NPC intracellular cholesterol transporter 2 (NPC2) genes that perturb homeostasis of two key membrane components, sphingomyelin and cholesterol, respectively. Patients with severe forms of these diseases present visceral and neurologic symptoms and succumb to premature death. This synopsis traces the tortuous discovery of the Niemann-Pick diseases, highlights important advances with respect to genetic culprits and cellular mechanisms, and exposes efforts to improve diagnosis and to explore new therapeutic approaches.
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Cadena-Ullauri S, Paz-Cruz E, Tamayo-Trujillo R, Guevara-Ramírez P, Ruiz-Pozo V, Solis-Pazmino P, Garcia C, Godoy R, Lincango-Naranjo E, Zambrano AK. Identification of KIT and BRAF mutations in thyroid tissue using next-generation sequencing in an Ecuadorian patient: A case report. Front Oncol 2023; 12:1101530. [PMID: 36733350 PMCID: PMC9887188 DOI: 10.3389/fonc.2022.1101530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Background The incidence of thyroid cancer has increased worldwide. Ecuador presents the highest incidence among Latin American countries and the second around the world. Genetic alteration is the driving force for thyroid tumorigenesis and progression. The change from valine (V) to glutamic acid (E) at codon 600 of the BRAF gene (BRAFVal600Glu) is the most commonly reported mutation in thyroid cancer. Moreover, the BRAF mutation is not the only mutation that has been correlated with TC. For instance, mutations and overexpression of the KIT gene has been associated with different types of cancer, including lung and colon cancer, and neuroblastoma. Case presentation A woman in her early fifties, self-identified as mestizo, from Otavalo, Imbabura-Ecuador had no systemic diseases and denied allergies, but she had a family history of a benign thyroid nodule. Physical examination revealed a thyroid gland enlargement. The fine-needle aspiration biopsy indicated papillary thyroid cancer. The patient underwent a successful total thyroidectomy with an excellent recovery and no additional treatments after surgery. Using Next-Generation sequencing a heterozygous mutation in the BRAF gene, causing an amino acid change Val600Glu was identified. Similarly, in the KIT gene, a heterozygous mutation resulting in an amino acid change Leu678Phe was detected. Moreover, an ancestry analysis was performed, and the results showed 3.1% African, 20.9% European, and 76% Native American ancestry. Conclusions This report represents the genetic characteristics of papillary thyroid cancer in an Ecuadorian woman with a mainly Native American ethnic component. Further studies of pathological variants are needed to determine if the combined demographic and molecular profiles are useful to develop targeted treatments focused on the Ecuadorian population.
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Affiliation(s)
- Santiago Cadena-Ullauri
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Elius Paz-Cruz
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rafael Tamayo-Trujillo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Viviana Ruiz-Pozo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Paola Solis-Pazmino
- Surgery Group of Los Angeles, Department of Colorectal Surgery, Los Angeles, CA, United States,Instituto de la Tiroides y Enfermedades de Cabeza y Cuello (ITECC), Department of Head and Neck Surgery, Quito, Ecuador
| | - Cristhian Garcia
- Instituto de la Tiroides y Enfermedades de Cabeza y Cuello (ITECC), Department of Head and Neck Surgery, Quito, Ecuador
| | - Richard Godoy
- Instituto de la Tiroides y Enfermedades de Cabeza y Cuello (ITECC), Department of Head and Neck Surgery, Quito, Ecuador
| | - Eddy Lincango-Naranjo
- Instituto de la Tiroides y Enfermedades de Cabeza y Cuello (ITECC), Department of Head and Neck Surgery, Quito, Ecuador,Department of Teaching and Research, Hospital Vozandes, Quito, Ecuador,CaTaLiNA Research Initiative (Cáncer de tiroides en Latinoamérica), Quito, Ecuador
| | - Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador,*Correspondence: Ana Karina Zambrano,
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5
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Zhang ZY, Ding Y, Ezhilarasan R, Lhakhang T, Wang Q, Yang J, Modrek AS, Zhang H, Tsirigos A, Futreal A, Draetta GF, Verhaak RGW, Sulman EP. Lineage-coupled clonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAF V600E inhibition resistance in melanoma. Cell Discov 2022; 8:102. [PMID: 36202798 PMCID: PMC9537441 DOI: 10.1038/s41421-022-00462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Targeted cancer therapies have revolutionized treatment but their efficacies are limited by the development of resistance driven by clonal evolution within tumors. We developed "CAPTURE", a single-cell barcoding approach to comprehensively trace clonal dynamics and capture live lineage-coupled resistant cells for in-depth multi-omics analysis and functional exploration. We demonstrate that heterogeneous clones, either preexisting or emerging from drug-tolerant persister cells, dominated resistance to vemurafenib in BRAFV600E melanoma. Further integrative studies uncovered diverse resistance mechanisms. This includes a previously unrecognized and clinically relevant mechanism, chromosome 18q21 gain, which leads to vulnerability of the cells to BCL2 inhibitor. We also identified targetable common dependencies of captured resistant clones, such as oxidative phosphorylation and E2F pathways. Our study provides new therapeutic insights into overcoming therapy resistance in BRAFV600E melanoma and presents a platform for exploring clonal evolution dynamics and vulnerabilities that can be applied to study treatment resistance in other cancers.
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Affiliation(s)
- Ze-Yan Zhang
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA.
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Yingwen Ding
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ravesanker Ezhilarasan
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Tenzin Lhakhang
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA
| | - Qianghu Wang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing, Jiangsu, China
| | - Jie Yang
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aram S Modrek
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Hua Zhang
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roel G W Verhaak
- Department of Computational Biology, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Erik P Sulman
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA.
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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6
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Sharma V, Kumar D, Kumar S, Singh H, Sharma N, Gupta S. Impact of tobacco smoking on oral cancer genetics-A next-generation sequencing perspective. IMETA 2022; 1:e44. [PMID: 38868711 PMCID: PMC10989814 DOI: 10.1002/imt2.44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/22/2022] [Accepted: 07/16/2022] [Indexed: 06/14/2024]
Abstract
This study identified a total of 28 genetic loci (comprising 31 genes), which were found to be altered in oral cancer patients having a habit of tobacco smoking. Three loci, that is, 17p13.1 (TP53), 9p21.3 (CDKN2A), and 9q34.3 (NOTCH1) were found to be modified and common in three records whereas one locus, that is, 3q26.32 (PIK3CA) was found to be modified and common in two records. This study suggests that oral cancer patients should be categorized into different subgroups based on (i) genetic signatures, and (ii) smoking status, then the treatment strategies for each group should be precisely defined.
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Affiliation(s)
- Vishwas Sharma
- Division of CytopathologyICMR—National Institute of Cancer Prevention and ResearchNoidaUttar PradeshIndia
| | - Dinesh Kumar
- WHO FCTC Global Knowledge Hub on Smokeless TobaccoICMR‐ National Institute of Cancer Prevention and ResearchNoidaUttar PradeshIndia
| | - Shravan Kumar
- WHO FCTC Global Knowledge Hub on Smokeless TobaccoICMR‐ National Institute of Cancer Prevention and ResearchNoidaUttar PradeshIndia
| | - Harpreet Singh
- Indian Council of Medical ResearchInformatics, Systems & Research Management (ISRM)New DelhiIndia
| | - Naveen Sharma
- Biomedical Informatics DivisionIndian Council of Medical ResearchNew DelhiIndia
| | - Sanjay Gupta
- Division of CytopathologyICMR—National Institute of Cancer Prevention and ResearchNoidaUttar PradeshIndia
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Hulten KG, Genta RM, Kalfus IN, Zhou Y, Zhang H, Graham DY. Comparison of Culture With Antibiogram to Next-Generation Sequencing Using Bacterial Isolates and Formalin-Fixed, Paraffin-Embedded Gastric Biopsies. Gastroenterology 2021; 161:1433-1442.e2. [PMID: 34293298 PMCID: PMC9047521 DOI: 10.1053/j.gastro.2021.07.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The decline in Helicobacter pylori cure rates emphasizes the need for readily available methods to determine antimicrobial susceptibility. Our aim was to compare targeted next-generation sequencing (NGS) and culture-based H pylori susceptibility testing using clinical isolates and paired formalin-fixed, paraffin-embedded (FFPE) gastric biopsies. METHODS H pylori isolates and FFPE tissues were tested for susceptibility to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and rifabutin using agar dilution and NGS targeted to 23S rRNA, gyrA, 16S rRNA, pbp1, rpoB and rdxA. Agreement was quantified using κ statistics. RESULTS Paired comparisons included 170 isolates and FFPE tissue for amoxicillin, clarithromycin, metronidazole, and rifabutin and 57 isolates and FFPE tissue for levofloxacin and tetracycline. Agreement between agar dilution and NGS from culture isolates was very good for clarithromycin (κ = 0.90012), good for levofloxacin (κ = 0.78161) and fair for metronidazole (κ = 0.55880), and amoxicillin (κ = 0.21400). Only 1 isolate was resistant to tetracycline (culture) and 1 to rifabutin (NGS). Comparison of NGS from tissue blocks and agar dilution from isolates from the same stomachs demonstrated good accuracy to predict resistance for clarithromycin (94.1%), amoxicillin (95.9%), metronidazole (77%), levofloxacin (87.7%), and tetracycline (98.2%). Lack of resistance precluded comparisons for tetracycline and rifabutin. CONCLUSIONS Compared with agar dilution, NGS reliably determined resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline from clinical isolates and formalin-fixed gastric tissue. Consistency was fair for metronidazole and amoxicillin. Culture-based testing can predict treatment outcomes with clarithromycin and levofloxacin. Studies are needed to compare the relative ability of both methods to predict treatment outcomes for other antibiotics.
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Affiliation(s)
| | - Robert M. Genta
- Inform Diagnostics, Irving, Texas,Department of Pathology, Baylor College of Medicine, Houston, Texas
| | | | - Yi Zhou
- American Molecular Laboratories, Vernon Hills, Illinois
| | - Hongjun Zhang
- American Molecular Laboratories, Vernon Hills, Illinois
| | - David Y. Graham
- Department of Medicine, Michael E. DeBakey VA Medical Center and Baylor College of Medicine, Houston, Texas
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8
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Berisha SZ, Shetty S, Prior TW, Mitchell AL. Cytogenetic and molecular diagnostic testing associated with prenatal and postnatal birth defects. Birth Defects Res 2021; 112:293-306. [PMID: 32115903 PMCID: PMC9290954 DOI: 10.1002/bdr2.1648] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 11/23/2022]
Abstract
Genetic testing is beneficial for patients and providers when in search of answers to medical problems related to the prenatal or early postnatal period. It can help to identify the cause or confirm a diagnosis associated with developmental delay, intellectual disability, dysmorphic features, heart defects, multiple malformations, short stature, stillbirth, neonatal death, or fertility problems. Genetic testing can be used to rule out single‐gene or chromosome abnormalities. Different diagnostic cytogenetic and molecular genetic techniques are applied in clinical genetics laboratories, from conventional ones to the state of the art chromosomal microarrays and next‐generation sequencing. Each of the genetic techniques or methods has its strengths and limitations, however different methods complement each‐other in trying to identify the genetic variation(s) responsible for a medical condition, especially the ones related to birth defects.
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Affiliation(s)
- Stela Z Berisha
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Shashi Shetty
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Pathology, Case Western Reserve University, University Hospitals, Cleveland, Ohio
| | - Thomas W Prior
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Pathology, Case Western Reserve University, University Hospitals, Cleveland, Ohio
| | - Anna L Mitchell
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Genetics and Genome Sciences, Case Western Reserve University, University Hospitals, Cleveland, Ohio
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9
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Bidshahri R, Fakhfakh K, McNeil K, Won JR, Wolber R, Hughesman C, Haynes C. Analysis of
KRAS
G12
/
G13
in colorectal cancer using an economical digital
PCR
assay that unequivocally differentiates missense and synonymous alleles. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Roza Bidshahri
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
| | - Kareem Fakhfakh
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
| | - Kelly McNeil
- Department of Genetics and Molecular Diagnostics British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Jennifer R. Won
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
| | - Robert Wolber
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
- Department of Pathology Lion's Gate Hospital North Vancouver British Columbia Canada
| | - Curtis Hughesman
- Cancer Genetics and Genomics Lab British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Charles Haynes
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
- Genome Sciences and Technology Program Vancouver British Columbia Canada
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10
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Mn W, L J, Jw H, Ks R, J T, At H, Cf W. Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation. BMJ 2021; 372:n214. [PMID: 33589468 PMCID: PMC7879796 DOI: 10.1136/bmj.n214] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To determine whether the sensitivity and specificity of SNP chips are adequate for detecting rare pathogenic variants in a clinically unselected population. DESIGN Retrospective, population based diagnostic evaluation. PARTICIPANTS 49 908 people recruited to the UK Biobank with SNP chip and next generation sequencing data, and an additional 21 people who purchased consumer genetic tests and shared their data online via the Personal Genome Project. MAIN OUTCOME MEASURES Genotyping (that is, identification of the correct DNA base at a specific genomic location) using SNP chips versus sequencing, with results split by frequency of that genotype in the population. Rare pathogenic variants in the BRCA1 and BRCA2 genes were selected as an exemplar for detailed analysis of clinically actionable variants in the UK Biobank, and BRCA related cancers (breast, ovarian, prostate, and pancreatic) were assessed in participants through use of cancer registry data. RESULTS Overall, genotyping using SNP chips performed well compared with sequencing; sensitivity, specificity, positive predictive value, and negative predictive value were all above 99% for 108 574 common variants directly genotyped on the SNP chips and sequenced in the UK Biobank. However, the likelihood of a true positive result decreased dramatically with decreasing variant frequency; for variants that are very rare in the population, with a frequency below 0.001% in UK Biobank, the positive predictive value was very low and only 16% of 4757 heterozygous genotypes from the SNP chips were confirmed with sequencing data. Results were similar for SNP chip data from the Personal Genome Project, and 20/21 individuals analysed had at least one false positive rare pathogenic variant that had been incorrectly genotyped. For pathogenic variants in the BRCA1 and BRCA2 genes, which are individually very rare, the overall performance metrics for the SNP chips versus sequencing in the UK Biobank were: sensitivity 34.6%, specificity 98.3%, positive predictive value 4.2%, and negative predictive value 99.9%. Rates of BRCA related cancers in UK Biobank participants with a positive SNP chip result were similar to those for age matched controls (odds ratio 1.31, 95% confidence interval 0.99 to 1.71) because the vast majority of variants were false positives, whereas sequence positive participants had a significantly increased risk (odds ratio 4.05, 2.72 to 6.03). CONCLUSIONS SNP chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.
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Affiliation(s)
- Weedon Mn
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Jackson L
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Harrison Jw
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Ruth Ks
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Tyrrell J
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Hattersley At
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Wright Cf
- Institute of Biomedical and Clinical Science, University of Exeter College of Medicine and Health, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
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11
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Kim J, Cho H, Kim J, Park JS, Han KH. A disposable smart microfluidic platform integrated with on-chip flow sensors. Biosens Bioelectron 2020; 176:112897. [PMID: 33342692 DOI: 10.1016/j.bios.2020.112897] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 01/27/2023]
Abstract
Microfluidic devices are powerful tools for biological, biomedical, chemical, and pharmaceutical applications, but their commercialization is still hindered by the lack of methods to automatically control fluid flow in a low-cost, simple, accurate, and safe manner. This study introduces a disposable smart microfluidic platform (DIS-μChip), which can be fully automated and utilized for a wide range of applications. On-chip microfluidic flow sensors are integrated with the platform and placed at all inlet and outlet channels, thereby allowing the DIS-μChip to be fully automated with a pressure control system. Furthermore, these confer a self-diagnosis function through monitoring of all the input and output flow rates. The DIS-μChip consists of a disposable polymeric microchannel superstrate and a permanent multifunctional substrate, which could be assembled and disassembled using only vacuum pressure. The superstrate was fabricated by combining a polydimethylsiloxane microchannel structure with a polyethylene terephthalate (PET) thin film. The substrate contains sense electrodes for the on-chip-integrated flow sensors and functional components for creating an energy field, which can penetrate the PET thin film and manipulate the fluid in the microchannels of the superstrate. Owing to the film-chip technique, the superstrate was disposable and could prevent biological cross-contamination, which cannot be realized with conventional flow sensors. The usefulness of the DIS-μChip was demonstrated by using it to isolate circulating tumor cells from the blood of patients with pancreatic cancer and to obtain cancer-specific genetic information from them with droplet digital PCR.
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Affiliation(s)
- Jinho Kim
- Department of Nanoscience and Engineering, Center for Nano Manufacturing, Inje University, Gimhae-si, 50834, South Korea
| | - Hyungseok Cho
- Department of Nanoscience and Engineering, Center for Nano Manufacturing, Inje University, Gimhae-si, 50834, South Korea
| | - Junhyeong Kim
- Department of Nanoscience and Engineering, Center for Nano Manufacturing, Inje University, Gimhae-si, 50834, South Korea
| | - Joon Seong Park
- Pancreatobiliary Cancer Clinic, Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06229, South Korea
| | - Ki-Ho Han
- Department of Nanoscience and Engineering, Center for Nano Manufacturing, Inje University, Gimhae-si, 50834, South Korea.
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12
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Cho H, Chung JI, Kim J, Seo WI, Lee CH, Morgan TM, Byun SS, Chung JS, Han KH. Multigene model for predicting metastatic prostate cancer using circulating tumor cells by microfluidic magnetophoresis. Cancer Sci 2020; 112:859-870. [PMID: 33232539 PMCID: PMC7893993 DOI: 10.1111/cas.14745] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 11/19/2020] [Indexed: 12/24/2022] Open
Abstract
We aimed to isolate circulating tumor cells (CTCs) using a microfluidic technique with a novel lateral magnetophoretic microseparator. Prostate cancer–specific gene expressions were evaluated using mRNA from the isolated CTCs. A CTC‐based multigene model was then developed for identifying advanced prostate cancer. Peripheral blood samples were obtained from five healthy donors and patients with localized prostate cancer (26 cases), metastatic hormone‐sensitive prostate cancer (mHSPC, 10 cases), and metastatic castration‐resistant prostate cancer (mCRPC, 28 cases). CTC recovery rate and purity (enriched CTCs/total cells) were evaluated according to cancer stage. The areas under the curves of the six gene expressions were used to evaluate whether multigene models could identify mHSPC or mCRPC. The number of CTCs and their purity increased at more advanced cancer stages. In mHSPC/mCRPC cases, the specimens had an average of 27.5 CTCs/mL blood, which was 4.2 × higher than the isolation rate for localized disease. The CTC purity increased from 2.1% for localized disease to 3.8% for mHSPC and 6.7% for mCRPC, with increased CTC expression of the genes encoding prostate‐specific antigen (PSA), prostate‐specific membrane antigen (PSMA), and cytokeratin 19 (KRT19). All disease stages exhibited expression of the genes encoding androgen receptor (AR) and epithelial cell adhesion molecule (EpCAM), although expression of the AR‐V7 variant was relatively rare. Relative to each gene alone, the multigene model had better accuracy for predicting advanced prostate cancer. Our lateral magnetophoretic microseparator can be used for identifying prostate cancer biomarkers. In addition, CTC‐based genetic signatures may guide the early diagnosis of advanced prostate cancer.
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Affiliation(s)
- Hyungseok Cho
- Department of Nanoscience and Engineering Center for Nano Manufacturing, Inje University, Gimhae, South Korea
| | - Jae Il Chung
- Department of Urology, Busan Paik Hospital, Inje University, Gimhae, South Korea
| | - Jinho Kim
- Department of Nanoscience and Engineering Center for Nano Manufacturing, Inje University, Gimhae, South Korea
| | - Won Ik Seo
- Department of Urology, Busan Paik Hospital, Inje University, Gimhae, South Korea
| | - Chan Ho Lee
- Department of Urology, Busan Paik Hospital, Inje University, Gimhae, South Korea
| | - Todd M Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Seok-Soo Byun
- Department of Urology, Seoul National University Bundang Hospital, Seongnamߚsi, South Korea
| | - Jae-Seung Chung
- Department of Urology, Haeundae Paik Hospital, Inje University, Busan, South Korea
| | - Ki-Ho Han
- Department of Nanoscience and Engineering Center for Nano Manufacturing, Inje University, Gimhae, South Korea
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13
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Al Hashmi M, Sastry KS, Silcock L, Chouchane L, Mattei V, James N, Mathew R, Bedognetti D, De Giorgi V, Murtas D, Liu W, Chouchane A, Temanni R, Seliger B, Wang E, Marincola FM, Tomei S. Differential responsiveness to BRAF inhibitors of melanoma cell lines BRAF V600E-mutated. J Transl Med 2020; 18:192. [PMID: 32393282 PMCID: PMC7216681 DOI: 10.1186/s12967-020-02350-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
Background Most mutations in melanoma affect one critical amino acid on BRAF gene, resulting in the V600E substitution. Patient management is often based on the use of specific inhibitors targeting this mutation. Methods DNA and RNA mutation status was assessed in 15 melanoma cell lines by Sanger sequencing and RNA-seq. We tested the cell lines responsiveness to BRAF inhibitors (vemurafenib and PLX4720, BRAF-specific and sorafenib, BRAF non-specific). Cell proliferation was assessed by MTT colorimetric assay. BRAF V600E RNA expression was assessed by qPCR. Expression level of phosphorylated-ERK protein was assessed by Western Blotting as marker of BRAF activation. Results Three cell lines were discordant in the mutation detection (BRAF V600E at DNA level/Sanger sequencing and BRAF WT on RNA-seq). We initially postulated that those cell lines may express only the WT allele at the RNA level although mutated at the DNA level. A more careful analysis showed that they express low level of BRAF RNA and the expression may be in favor of the WT allele. We tested whether the discordant cell lines responded differently to BRAF-specific inhibitors. Their proliferation rate decreased after treatment with vemurafenib and PLX4720 but was not affected by sorafenib, suggesting a BRAF V600E biological behavior. Yet, responsiveness to the BRAF specific inhibitors was lower as compared to the control. Western Blot analysis revealed a decreased expression of p-ERK protein in the BRAF V600E control cell line and in the discordant cell lines upon treatment with BRAF-specific inhibitors. The discordant cell lines showed a lower responsiveness to BRAF inhibitors when compared to the BRAF V600E control cell line. The results obtained from the inhibition experiment and molecular analyses were also confirmed in three additional cell lines. Conclusion Cell lines carrying V600E mutation at the DNA level may respond differently to BRAF targeted treatment potentially due to a lower V600E RNA expression.
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Affiliation(s)
- Muna Al Hashmi
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Konduru S Sastry
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Lee Silcock
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Valentina Mattei
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Nicola James
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Rebecca Mathew
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Davide Bedognetti
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Valeria De Giorgi
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, USA
| | - Daniela Murtas
- Department of Biomedical Sciences, Section of Cytomorphology, University of Cagliari, Cagliari, Italy
| | - Wei Liu
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Aouatef Chouchane
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Ramzi Temanni
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Ena Wang
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Francesco M Marincola
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar.,Refuge Biotechnologies, Menlo Park, CA, USA
| | - Sara Tomei
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar.
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14
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Browne DJ, Brady JL, Waardenberg AJ, Loiseau C, Doolan DL. An Analytically and Diagnostically Sensitive RNA Extraction and RT-qPCR Protocol for Peripheral Blood Mononuclear Cells. Front Immunol 2020; 11:402. [PMID: 32265908 PMCID: PMC7098950 DOI: 10.3389/fimmu.2020.00402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Reliable extraction and sensitive detection of RNA from human peripheral blood mononuclear cells (PBMCs) is critical for a broad spectrum of immunology research and clinical diagnostics. RNA analysis platforms are dependent upon high-quality and high-quantity RNA; however, sensitive detection of specific responses associated with high-quality RNA extractions from human samples with limited PBMCs can be challenging. Furthermore, the comparative sensitivity between RNA quantification and best-practice protein quantification is poorly defined. Therefore, we provide herein a critical evaluation of the wide variety of current generation of RNA-based kits for PBMCs, representative of several strategies designed to maximize sensitivity. We assess these kits with a reverse transcription quantitative PCR (RT-qPCR) assay optimized for both analytically and diagnostically sensitive cell-based RNA-based applications. Specifically, three RNA extraction kits, one post-extraction RNA purification/concentration kit, four SYBR master-mix kits, and four reverse transcription kits were tested. RNA extraction and RT-qPCR reaction efficiency were evaluated with commonly used reference and cytokine genes. Significant variation in RNA expression of reference genes was apparent, and absolute quantification based on cell number was established as an effective RT-qPCR normalization strategy. We defined an optimized RNA extraction and RT-qPCR protocol with an analytical sensitivity capable of single cell RNA detection. The diagnostic sensitivity of this assay was sufficient to show a CD8+ T cell peptide epitope hierarchy with as few as 1 × 104 cells. Finally, we compared our optimized RNA extraction and RT-qPCR protocol with current best-practice immune assays and demonstrated that our assay is a sensitive alternative to protein-based assays for peptide-specific responses, especially with limited PBMCs number. This protocol with high analytical and diagnostic sensitivity has broad applicability for both primary research and clinical practice.
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Affiliation(s)
- Daniel J Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Jamie L Brady
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Ashley J Waardenberg
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
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15
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Rosas-Vara D, Molina-Contreras JR, Villalobos-Piña F, Zenteno JC, Buentello-Volante B, Chacon-Camacho OF, Ayala-Ramírez R, Frausto-Reyes C, Hernández-Martínez R, Ríos-Corripio MA. Point mutation in the TGFBI gene: surface-enhanced infrared absorption spectroscopy (SEIRAS) as an analytical method. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-019-00948-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Bevilacqua JA, Guecaimburu Ehuletche MDR, Perna A, Dubrovsky A, Franca MC, Vargas S, Hegde M, Claeys KG, Straub V, Daba N, Faria R, Periquet M, Sparks S, Thibault N, Araujo R. The Latin American experience with a next generation sequencing genetic panel for recessive limb-girdle muscular weakness and Pompe disease. Orphanet J Rare Dis 2020; 15:11. [PMID: 31931849 PMCID: PMC6958675 DOI: 10.1186/s13023-019-1291-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/27/2019] [Indexed: 02/08/2023] Open
Abstract
Background Limb-girdle muscular dystrophy (LGMD) is a group of neuromuscular disorders of heterogeneous genetic etiology with more than 30 directly related genes. LGMD is characterized by progressive muscle weakness involving the shoulder and pelvic girdles. An important differential diagnosis among patients presenting with proximal muscle weakness (PMW) is late-onset Pompe disease (LOPD), a rare neuromuscular glycogen storage disorder, which often presents with early respiratory insufficiency in addition to PMW. Patients with PMW, with or without respiratory symptoms, were included in this study of Latin American patients to evaluate the profile of variants for the included genes related to LGMD recessive (R) and LOPD and the frequency of variants in each gene among this patient population. Results Over 20 institutions across Latin America (Brazil, Argentina, Peru, Ecuador, Mexico, and Chile) enrolled 2103 individuals during 2016 and 2017. Nine autosomal recessive LGMDs and Pompe disease were investigated in a 10-gene panel (ANO5, CAPN3, DYSF, FKRP, GAA, SGCA, SGCB, SGCD, SGCG, TCAP) based on reported disease frequency in Latin America. Sequencing was performed with Illumina’s NextSeq500 and variants were classified according to ACMG guidelines; pathogenic and likely pathogenic were treated as one category (P) and variants of unknown significance (VUS) are described. Genetic variants were identified in 55.8% of patients, with 16% receiving a definitive molecular diagnosis; 39.8% had VUS. Nine patients were identified with Pompe disease. Conclusions The results demonstrate the effectiveness of this targeted genetic panel and the importance of including Pompe disease in the differential diagnosis for patients presenting with PMW.
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Affiliation(s)
- Jorge A Bevilacqua
- Departamento de Neurología y Neurocirugía, Hospital Clínico, Universidad de Chile, Santiago, Chile.,Departamento de Anatomía y Medicina Legal, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Departamento de Neurología y Neurocirugía, Clínica Dávila, Santiago, Chile
| | | | - Abayuba Perna
- Institute of Neurology, Hospital de Clínicas, School of Medicine, UDELAR, Montevideo, Uruguay
| | - Alberto Dubrovsky
- Institute of Neuroscience, Favaloro Foundation, Buenos Aires, Argentina
| | - Marcondes C Franca
- Department of Neurology, University of Campinas-UNICAMP, Campinas, Sao Paulo, Brazil
| | - Steven Vargas
- Center of Neurology and Neurosurgery, Mexico City, Mexico
| | - Madhuri Hegde
- Global Laboratory Services, Diagnostics, PerkinElmer, Waltham, MA, USA
| | - Kristl G Claeys
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium.,Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Centre for Life, Newcastle, United Kingdom
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17
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Zelli V, Compagnoni C, Cannita K, Capelli R, Capalbo C, Di Vito Nolfi M, Alesse E, Zazzeroni F, Tessitore A. Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer. High Throughput 2020; 9:ht9010001. [PMID: 31936873 PMCID: PMC7151204 DOI: 10.3390/ht9010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Katia Cannita
- Medical Oncology Unit, St Salvatore Hospital, Via L. Natali 1, 67100 L’Aquila, Italy;
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Rome “La Sapienza”, Viale Regina Elena 324, 00161 Rome, Italy;
| | - Mauro Di Vito Nolfi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence:
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18
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Detecting TP53 mutations in diagnostic and archival liquid-based Pap samples from ovarian cancer patients using an ultra-sensitive ddPCR method. Sci Rep 2019; 9:15506. [PMID: 31664085 PMCID: PMC6820715 DOI: 10.1038/s41598-019-51697-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 10/07/2019] [Indexed: 12/14/2022] Open
Abstract
High-grade serous ovarian cancer (HGSOC) is the most common subtype of epithelial ovarian cancer and early detection is challenging. TP53 mutations are a hallmark of HGSOC and detection of these mutations in liquid-based Pap samples could provide a method for early diagnosis. Here we evaluate the use of IBSAFE, an ultra-sensitive droplet digital PCR (ddPCR) method, for detecting TP53 mutations in liquid-based Pap samples collected from fifteen women at the time of diagnosis (diagnostic samples) and/or up to seven years prior to diagnosis (archival samples). We analysed tumours for somatic TP53 mutations with next generation sequencing and were able to detect the corresponding mutations in diagnostic samples from six of eight women, while one patient harboured a germline mutation. We further detected a mutation in an archival sample obtained 20 months prior to the ovarian cancer diagnosis. The custom designed IBSAFE assays detected minor allele frequencies (MAFs) with very high assay sensitivity (MAF = 0.0068%) and were successful despite low DNA abundance (0.17–206.14 ng, median: 17.27 ng). These results provide support for further evaluation of archival liquid-based Pap samples for diagnostic purposes and demonstrate that ultra-sensitive ddPCR should be evaluated for ovarian cancer screening in high-risk groups or in the recurrent setting.
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19
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Evaluation of Positive and Negative Methods for Isolation of Circulating Tumor Cells by Lateral Magnetophoresis. MICROMACHINES 2019; 10:mi10060386. [PMID: 31181790 PMCID: PMC6631028 DOI: 10.3390/mi10060386] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 01/12/2023]
Abstract
We developed an epithelial cell adhesion molecule (EpCAM)-based positive method and CD45/CD66b-based negative method for isolating circulating tumor cells (CTCs) by lateral magnetophoresis. The CTC recovery rate, white blood cell depletion rate, and purity of CTCs isolated using the positive and negative methods were analyzed using blood samples spiked with cancer cells with different expression levels of EpCAM. The aim was to assess the strengths and weaknesses of the positive and negative isolation methods for CTC-based diagnostics, prognostics, and therapeutics for cancer. The EpCAM-based positive method yielded CTCs of high purity, while the CD45/CD66b-based negative method yielded a large number of CTCs. In conclusion, the positive method shows promise for detecting somatic oncogenic mutations and the negative method shows promise for discovery of cellular and transcriptomic biomarkers of cancer.
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20
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Mercier-Darty M, Boutolleau D, Rodriguez C, Burrel S. Added value of ultra-deep sequencing (UDS) approach for detection of genotypic antiviral resistance of herpes simplex virus (HSV). Antiviral Res 2019; 168:128-133. [PMID: 31158412 DOI: 10.1016/j.antiviral.2019.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/03/2019] [Accepted: 05/30/2019] [Indexed: 11/16/2022]
Abstract
Classically, Sanger sequencing is considered the gold standard for detection of HSV drug resistance mutations (DRMs). As a complementary method, ultra-deep sequencing (UDS) has an improved ability to detect minor variants and mixed populations. The aim of this work was to apply UDS performed on MiSeq® Illumina platform to the detection of HSV DRMs and to the evaluation of the subpopulation diversity in clinical samples in comparison with Sanger sequencing. A total of 59 HSV-positive clinical samples (31 HSV-1 and 28 HSV-2) recovered from 50 patients mainly immunocompromised (70%) were retrospectively analyzed. Remarkably, UDS analysis revealed significant differences of relative abundance according to the type of DRMs within TK and Pol: natural polymorphisms and amino acid changes associated with resistance to antivirals were identified as high-abundant mutations (>96%), whereas TK frameshifts conferring resistance to ACV were systematically detected at lower abundance (≈80%). This work also revealed that UDS can detect low-frequency DRMs and provides extensive information on viral population composition.
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Affiliation(s)
- Mélanie Mercier-Darty
- INSERM U955 Eq18, IMRB, UPEC, AP-HP, Virology Department, Hospital Henri Mondor, Créteil, France
| | - David Boutolleau
- Sorbonne Université, INSERM, Institut Pierre Louis D'Epidémiologie et de Santé Publique (iPLESP), AP-HP, University Hospital Pitié-Salpêtrière - Charles Foix, National Reference Center for Herpesviruses, Virology Department, Paris, France
| | - Christophe Rodriguez
- INSERM U955 Eq18, IMRB, UPEC, AP-HP, Virology Department, Hospital Henri Mondor, Créteil, France
| | - Sonia Burrel
- Sorbonne Université, INSERM, Institut Pierre Louis D'Epidémiologie et de Santé Publique (iPLESP), AP-HP, University Hospital Pitié-Salpêtrière - Charles Foix, National Reference Center for Herpesviruses, Virology Department, Paris, France.
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Campo E, Cymbalista F, Ghia P, Jäger U, Pospisilova S, Rosenquist R, Schuh A, Stilgenbauer S. TP53 aberrations in chronic lymphocytic leukemia: an overview of the clinical implications of improved diagnostics. Haematologica 2018; 103:1956-1968. [PMID: 30442727 PMCID: PMC6269313 DOI: 10.3324/haematol.2018.187583] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/26/2018] [Indexed: 12/19/2022] Open
Abstract
Chronic lymphocytic leukemia is associated with a highly heterogeneous disease course in terms of clinical outcomes and responses to chemoimmunotherapy. This heterogeneity is partly due to genetic aberrations identified in chronic lymphocytic leukemia cells such as mutations of TP53 and/or deletions in chromosome 17p [del(17p)], resulting in loss of one TP53 allele. These aberrations are associated with markedly decreased survival and predict impaired response to chemoimmunotherapy thus being among the strongest predictive markers guiding treatment decisions in chronic lymphocytic leukemia. Clinical trials demonstrate the importance of accurately testing for TP53 aberrations [both del(17p) and TP53 mutations] before each line of treatment to allow for appropriate treatment decisions that can optimize patients' outcomes. The current report reviews the diagnostic methods to detect TP53 disruption better, the role of TP53 aberrations in treatment decisions and current therapies available for patients with chronic lymphocytic leukemia carrying these abnormalities. The standardization in sequencing technologies for accurate identification of TP53 mutations and the importance of continued evaluation of TP53 aberrations throughout initial and subsequent lines of therapy remain unmet clinical needs as new therapeutic alternatives become available.
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Affiliation(s)
- Elias Campo
- Hospital Clinic of Barcelona, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, and CIBERONC, Spain
| | - Florence Cymbalista
- Hôpital Avicenne, AP-HP, UMR INSERMU978/Paris 13 University, Bobigny, France
| | - Paolo Ghia
- Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Stephan Stilgenbauer
- Internal Medicine III, Ulm University, Germany and Innere Medizin I, Universitätsklinikum des Saarlandes, Homburg, Germany
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Development of an evidence-based algorithm that optimizes sensitivity and specificity in ES-based diagnostics of a clinically heterogeneous patient population. Genet Med 2018; 21:53-61. [PMID: 30100613 PMCID: PMC6752300 DOI: 10.1038/s41436-018-0016-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/20/2018] [Indexed: 11/29/2022] Open
Abstract
Purpose Next-generation sequencing (NGS) is rapidly replacing Sanger sequencing in genetic diagnostics. Sensitivity and specificity of NGS approaches are not well-defined, but can be estimated from applying NGS and Sanger sequencing in parallel. Utilizing this strategy, we aimed at optimizing exome sequencing (ES)–based diagnostics of a clinically diverse patient population. Methods Consecutive DNA samples from unrelated patients with suspected genetic disease were exome-sequenced; comparatively nonstringent criteria were applied in variant calling. One thousand forty-eight variants in genes compatible with the clinical diagnosis were followed up by Sanger sequencing. Based on a set of variant-specific features, predictors for true positives and true negatives were developed. Results Sanger sequencing confirmed 81.9% of ES-derived variants. Calls from the lower end of stringency accounted for the majority of the false positives, but also contained ~5% of the true positives. A predictor incorporating three variant-specific features classified 91.7% of variants with 100% specificity and 99.75% sensitivity. Confirmation status of the remaining variants (8.3%) was not predictable. Conclusions Criteria for variant calling in ES-based diagnostics impact on specificity and sensitivity. Confirmatory sequencing for a proportion of variants, therefore, remains a necessity. Our study exemplifies how these variants can be defined on an empirical basis.
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Kalcioglu MT, Guldemir D, Unaldi O, Egilmez OK, Celebi B, Durmaz R. Metagenomics Analysis of Bacterial Population of Tympanosclerotic Plaques and Cholesteatomas. Otolaryngol Head Neck Surg 2018; 159:724-732. [PMID: 29688828 DOI: 10.1177/0194599818772039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Objective Chronic otitis media can cause cholesteatomas or tympanosclerosis; however, the pathophysiology of such conditions is not completely known. The aim was to identify a bacterial genome that might be present in tympanosclerotic plaques and cholesteatomas using sequence analysis of the gene responsible for the transcription of 16 ribosomal RNA (rRNA). Study Design Metagenomics analysis of the samples. Setting Samples were collected and evaluated at tertiary care centers. Subjects and Methods Sixty-five tympanosclerotic plaques and 37 cholesteatomas were evaluated. The polymerase chain reaction (PCR) was performed using primers designed for the amplification of the gene responsible for the transcription of bacterial 16 rRNA. The PCR-positive samples were sequenced via Sanger method, and 46 selected samples were analyzed with next-generation sequencing (NGS). Results Sanger sequencing revealed the presence of bacterial genomes in a total of 18 of the 102 samples tested. Sequencing of these genomes indicated the presence of Alloiococcus otitis, Staphylococcus aureus, Achromobacter xylosoxidans, Escherichia coli, Staphylococcus sciuri, Staphylococcus caprae, Parvimonas spp., and Bacillus sp. in the tested samples. The NGS showed 1 or more different bacterial genomes in 44 (95.7%) of the 46 samples tested. Predominately, genome of Clostridiales (27 samples), Staphylococcaceae (24 samples), Peptoniphilaceae (12 samples), and Turicella otitidis (9 samples) were identified. Conclusion The middle ear is inhabited by a diverse microbial community than that previously known. With the use of molecular biology, it has become easier to identify the bacterial genomes and improve our understanding of the role of middle ear microbiota in the pathogenesis of chronic inflammatory ear diseases.
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Affiliation(s)
- M Tayyar Kalcioglu
- 1 Istanbul Medeniyet University, Goztepe Training and Research Hospital, Department of Otorhinolaryngology-Head and Neck Surgery Istanbul, Turkey
| | - Dilek Guldemir
- 2 National Public Health Agency, Department of Microbiology, Ankara, Turkey
| | - Ozlem Unaldi
- 2 National Public Health Agency, Department of Microbiology, Ankara, Turkey
| | - Oguz Kadir Egilmez
- 1 Istanbul Medeniyet University, Goztepe Training and Research Hospital, Department of Otorhinolaryngology-Head and Neck Surgery Istanbul, Turkey
| | - Bekir Celebi
- 2 National Public Health Agency, Department of Microbiology, Ankara, Turkey
| | - Riza Durmaz
- 2 National Public Health Agency, Department of Microbiology, Ankara, Turkey.,3 Yıldırım Beyazıt University, Faculty of Medicine, Department of Clinical Microbiology, Ankara, Turkey
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Domínguez-Vigil IG, Moreno-Martínez AK, Wang JY, Roehrl MH, Barrera-Saldaña HA. The dawn of the liquid biopsy in the fight against cancer. Oncotarget 2018; 9:2912-2922. [PMID: 29416824 PMCID: PMC5788692 DOI: 10.18632/oncotarget.23131] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/10/2017] [Indexed: 01/06/2023] Open
Abstract
Cancer is a molecular disease associated with alterations in the genome, which, thanks to the highly improved sensitivity of mutation detection techniques, can be identified in cell-free DNA (cfDNA) circulating in blood, a method also called liquid biopsy. This is a non-invasive alternative to surgical biopsy and has the potential of revealing the molecular signature of tumors to aid in the individualization of treatments. In this review, we focus on cfDNA analysis, its advantages, and clinical applications employing genomic tools (NGS and dPCR) particularly in the field of oncology, and highlight its valuable contributions to early detection, prognosis, and prediction of treatment response.
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Affiliation(s)
- Irma G. Domínguez-Vigil
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Ana K. Moreno-Martínez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
- Genetics Laboratory, Vitagénesis, Monterrey, Nuevo León, México
| | | | - Michael H.A. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hugo A. Barrera-Saldaña
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina de la Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
- TecSalud, Tecnológico de Monterrey, San Pedro Garza García, Nuevo León, México
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25
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Fang M, Zhu L, Li H, Li X, Wu Y, Wu K, Lin J, Sheng Y, Yu Y. Characterization of mutations in BRCA1/2 and the relationship with clinic-pathological features of breast cancer in a hereditarily high-risk sample of chinese population. Oncol Lett 2017; 15:3068-3074. [PMID: 29435039 PMCID: PMC5778890 DOI: 10.3892/ol.2017.7717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 12/14/2017] [Indexed: 12/16/2022] Open
Abstract
The database of BRCA1/2 mutations in Chinese population remains incomplete at present. Therefore, the present study aimed to report specific harmful BRCA1/2 mutations in the Chinese population and discuss the clinicopathological features in mutation carriers. BRCA1/2 germline mutation tests for 71 patients with breast cancer from a hereditarily high-risk Chinese population were performed using next-generation sequencing for identification of deleterious mutations. Furthermore, the clinicopathological features between BRCA1/2 mutation carriers and non-carriers were compared. A total of 13/71 (18.3%) patients carried a BRCA1 or BRCA2 mutation (7 BRCA1 and 6 BRCA2). The incidence of BRCA1/2 mutation in patients with bilateral breast cancer and patients with family history were 25, and 32.2%, respectively. Eleven pathogenic or likely pathogenic mutations were identified in 13 patients, among the mutation sites 7 were never reported before in Asian populations. The age at diagnosis of BRCA1/2 mutation carriers was older compared with non-mutation carriers (44.73 vs. 35.39 years; P=0.001) in this cohort. BRCA1/2 deleterious mutation carriers had a significantly lower chance of human epidermal growth factor receptor-2 (Her-2) positive status (P=0.010), higher tumor grade at diagnosis (P=0.009), higher probability to have a family history (P=0.016) and older age at diagnosis. Estrogen receptor (ER) and progesterone receptor (PR) status were significantly different between BRCA1, and BRCA2 mutation carriers (P=0.007). The current interpretation of BRCA1/2 status can only explain a small part of hereditary high-risk breast cancer. However, BRCA1/2 gene testing should still be recommended for women with a family history of breast cancer, as well as patients with breast cancer with specific pathologic types, which may be useful to make appropriate clinical decisions for treatment and prevention.
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Affiliation(s)
- Min Fang
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Li Zhu
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Hengyu Li
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Xizhou Li
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Yanmei Wu
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Kainan Wu
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Jian Lin
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Yuan Sheng
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
| | - Yue Yu
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Second Military Medical University, Shanghai 200433, P.R. China
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Siqueira ECD, de Sousa SF, França JA, Diniz MG, Pereira TDSF, Moreira RG, Vargas PA, Gomez RS, Gomes CC. Targeted next-generation sequencing of glandular odontogenic cyst: a preliminary study. Oral Surg Oral Med Oral Pathol Oral Radiol 2017; 124:490-494. [DOI: 10.1016/j.oooo.2017.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/05/2017] [Accepted: 07/13/2017] [Indexed: 02/04/2023]
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Kassem HS, Walsh R, Barton PJ, Abdelghany BS, Azer RS, Buchan R, John S, Elguindy A, Moharem-ElGamal S, Badran HM, Shehata H, Cook SA, Yacoub MH. A comparative study of mutation screening of sarcomeric genes ( MYBPC3 , MYH7 , TNNT2 ) using single gene approach versus targeted gene panel next generation sequencing in a cohort of HCM patients in Egypt. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2017. [DOI: 10.1016/j.ejmhg.2017.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Analytical evaluation for somatic mutation detection in circulating tumor cells isolated using a lateral magnetophoretic microseparator. Biomed Microdevices 2017; 18:91. [PMID: 27628059 DOI: 10.1007/s10544-016-0116-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CTCs are currently in the spotlight because provide comprehensive genetic information that enables monitoring of the evolution of cancer and selection of appropriate therapeutic strategies that cannot be obtained from a single-site tumor biopsy. Despite their importance, current techniques for isolating CTCs are limited in terms of their ability to yield high-quality CTCs from peripheral blood for use in profiling cancer genetic mutations by DNA sequencing technologies. This paper introduces a lateral magnetophoretic microseparator (the 'CTC-μChip') for isolating highly pure CTCs from blood, which facilitates the detection of somatic mutations in isolated CTCs. To isolate CTCs from peripheral blood, nucleated cells were first prepared by red blood cell lysis. Then, CTCs were isolated from nucleated cells within 30 min using the CTC-μChip. Analytical evaluation using 5 mL blood samples spiked with 5-50 MCF7 breast cancer cells demonstrated that the average recovery rate of the CTC-μChip was 99.08 %. The average number of residual white blood cells (WBCs) in isolated samples was 53, meaning that the WBC depletion rate is 472,000-fold (5.67 log), assuming that blood contains 5 × 10(6) WBCs per milliliter. The isolated MCF7 cells had a purity of 6.9 - 67.9 %, depending on the spiked MCF7 concentration. Using next-generation sequencing technology, heterozygous somatic mutations (PIK3CA and APC) of MCF7 cells were evaluated in the isolated samples. The results showed that somatic mutations could be detected in as few as two MCF7 cells per milliliter of blood, indicating that the CTC-μChip facilitates the detection of somatic variants in CTCs.
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29
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Omoyinmi E, Standing A, Keylock A, Price-Kuehne F, Melo Gomes S, Rowczenio D, Nanthapisal S, Cullup T, Nyanhete R, Ashton E, Murphy C, Clarke M, Ahlfors H, Jenkins L, Gilmour K, Eleftheriou D, Lachmann HJ, Hawkins PN, Klein N, Brogan PA. Clinical impact of a targeted next-generation sequencing gene panel for autoinflammation and vasculitis. PLoS One 2017; 12:e0181874. [PMID: 28750028 PMCID: PMC5531484 DOI: 10.1371/journal.pone.0181874] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/07/2017] [Indexed: 12/27/2022] Open
Abstract
Background Monogenic autoinflammatory diseases (AID) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity. They cause significant morbidity, mortality and economic burden. Here, we aimed to develop and evaluate the clinical impact of a NGS targeted gene panel, the “Vasculitis and Inflammation Panel” (VIP) for AID and vasculitis. Methods The Agilent SureDesign tool was used to design 2 versions of VIP; VIP1 targeting 113 genes, and a later version, VIP2, targeting 166 genes. Captured and indexed libraries (QXT Target Enrichment System) prepared for 72 patients were sequenced as a multiplex of 16 samples on an Illumina MiSeq sequencer in 150bp paired-end mode. The cohort comprised 22 positive control DNA samples from patients with previously validated mutations in a variety of the genes; and 50 prospective samples from patients with suspected AID in whom previous Sanger based genetic screening had been non-diagnostic. Results VIP was sensitive and specific at detecting all the different types of known mutations in 22 positive controls, including gene deletion, small INDELS, and somatic mosaicism with allele fraction as low as 3%. Six/50 patients (12%) with unclassified AID had at least one class 5 (clearly pathogenic) variant; and 11/50 (22%) had at least one likely pathogenic variant (class 4). Overall, testing with VIP resulted in a firm or strongly suspected molecular diagnosis in 16/50 patients (32%). Conclusions The high diagnostic yield and accuracy of this comprehensive targeted gene panel validate the use of broad NGS-based testing for patients with suspected AID.
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Affiliation(s)
- Ebun Omoyinmi
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
- * E-mail:
| | - Ariane Standing
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
| | - Annette Keylock
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
| | - Fiona Price-Kuehne
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
| | - Sonia Melo Gomes
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
| | - Dorota Rowczenio
- National Amyloidosis Centre (NAC), UCL, Royal Free Campus, London, United Kingdom
| | - Sira Nanthapisal
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
| | - Thomas Cullup
- NE Thames Regional Genetics laboratory, GOSH NHS Foundation Trust, London, United Kingdom
| | - Rodney Nyanhete
- NE Thames Regional Genetics laboratory, GOSH NHS Foundation Trust, London, United Kingdom
| | - Emma Ashton
- NE Thames Regional Genetics laboratory, GOSH NHS Foundation Trust, London, United Kingdom
| | - Claire Murphy
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
| | - Megan Clarke
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
| | - Helena Ahlfors
- NE Thames Regional Genetics laboratory, GOSH NHS Foundation Trust, London, United Kingdom
| | - Lucy Jenkins
- NE Thames Regional Genetics laboratory, GOSH NHS Foundation Trust, London, United Kingdom
| | - Kimberly Gilmour
- Immunology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Despina Eleftheriou
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
- Arthritis Research UK Centre for Adolescent Rheumatology, UCL, UCLH and GOSH, London, United Kingdom
| | - Helen J. Lachmann
- National Amyloidosis Centre (NAC), UCL, Royal Free Campus, London, United Kingdom
| | - Philip N. Hawkins
- National Amyloidosis Centre (NAC), UCL, Royal Free Campus, London, United Kingdom
| | - Nigel Klein
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
| | - Paul A. Brogan
- UCL Great Ormond Street Institute of Child Health (ICH), London, United Kingdom
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Nallamilli BRR, Hegde M. Genetic Testing for Hereditary Nonpolyposis Colorectal Cancer (HNPCC). ACTA ACUST UNITED AC 2017; 94:10.12.1-10.12.23. [PMID: 28696559 DOI: 10.1002/cphg.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hereditary nonpolyposis colorectal cancer (HNPCC), also called Lynch syndrome, is an autosomal dominant cancer syndrome that confers an elevated risk of early-onset colorectal cancer (CRC) and increased lifetime risk for other cancers of the endometrium, stomach, small intestine, hepatobiliary system, kidney, ureter, and ovary. Lynch syndrome accounts for up to 3% of all CRC, making it the most common hereditary colorectal cancer syndrome. Germline mutations in methyl-directed mismatch repair (MMR) genes give rise to microsatellite instability (MSI) in tumor DNA. Lynch syndrome is most frequently caused by pathogrenic variants in the mismatch repair genes MLH1, MSH2, MSH6, and PMS2. Germline mutations in MLH1 and MSH2 account for approximately 90% of detected mutations in families with Lynch syndrome. Pathogenic vatiants in MSH6 have been reported in approximately 7-10% of families with Lynch syndrome. Pathogenic variants in PMS2 account for fewer than 5% of mutations in families with Lynch syndrome. This unit presents a comprehensive molecular genetic testing strategy for Lynch syndrome including MSI analysis, next generation sequencing (NGS)-based targeted sequence analysis, PCR-based Sanger sequencing and microarray-based comparative genomic hybridization (array-CGH). © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
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Kim J, Park WY, Kim NKD, Jang SJ, Chun SM, Sung CO, Choi J, Ko YH, Choi YL, Shim HS, Won JK. Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests. J Pathol Transl Med 2017; 51:191-204. [PMID: 28535585 PMCID: PMC5445206 DOI: 10.4132/jptm.2017.03.14] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/14/2017] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing (NGS) has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS. This consensus standard proposal consists of two parts: laboratory guidelines and requirements for clinical NGS laboratories. The laboratory guidelines part addressed several important issues across multistep NGS cancer panel tests including choice of gene panel and platform, sample handling, nucleic acid management, sample identity tracking, library preparation, sequencing, analysis and reporting. Requirements for clinical NGS tests were summarized in terms of documentation, validation, quality management, and other required written policies. Together with appropriate pathologist training and international laboratory standards, these laboratory standards would help molecular pathology laboratories to successfully implement NGS cancer panel tests in clinic. In this way, the oncology community would be able to help patients to benefit more from personalized cancer medicine.
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Affiliation(s)
- Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nayoung K. D. Kim
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Sung-Min Chun
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Chang-Ohk Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Jene Choi
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young-Hyeh Ko
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - The Molecular Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
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Jenkins S, Yang JCH, Ramalingam SS, Yu K, Patel S, Weston S, Hodge R, Cantarini M, Jänne PA, Mitsudomi T, Goss GD. Plasma ctDNA Analysis for Detection of the EGFR T790M Mutation in Patients with Advanced Non-Small Cell Lung Cancer. J Thorac Oncol 2017; 12:1061-1070. [PMID: 28428148 DOI: 10.1016/j.jtho.2017.04.003] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/08/2017] [Accepted: 04/06/2017] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Tumor biopsies for detecting EGFR mutations in advanced NSCLC are invasive, costly, and not always feasible for patients with late-stage disease. The clinical utility of the cobas EGFR Mutation Test v2 (Roche Molecular Systems, Inc., Pleasanton, CA) with plasma samples from patients with NSCLC at disease progression after previous EGFR tyrosine kinase inhibitor therapy was investigated to determine eligibility for osimertinib treatment. METHODS Matched tumor tissue and plasma samples from patients screened for the AURA extension and AURA2 phase II studies were tested for EGFR mutations by using tissue- and plasma-based cobas EGFR mutation tests. Plasma test performance was assessed by using the cobas tissue test and a next-generation sequencing method (MiSeq [Illumina Inc., San Diego, CA]) as references. The objective response rate, measured by blinded independent central review, was assessed in patients receiving osimertinib with a plasma T790M mutation-positive status. RESULTS During screening, 551 patients provided matched tumor tissue and plasma samples. Pooled analysis of the positive and negative percent agreements between the cobas plasma and tissue tests for detection of T790M mutation were 61% and 79%, respectively. Comparing cobas plasma test with next-generation sequencing demonstrated positive and negative percent agreements of 90% or higher. The objective response rate was 64% (95% confidence interval: 57-70) in T790M mutation-positive patients by both cobas tissue and plasma tests (evaluable for response). CONCLUSIONS The cobas plasma test detected the T790M mutation in 61% of tumor tissue T790M mutation-positive patients. To mitigate the risk of false-negative plasma results, patients with a negative plasma result should undergo a tissue test where feasible.
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Affiliation(s)
| | - James C-H Yang
- National Taiwan University Hospital, Taipei, Republic of China
| | | | - Karen Yu
- Roche Molecular Systems, Inc., Pleasanton, California
| | | | | | | | | | - Pasi A Jänne
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Glenwood D Goss
- Ottawa Hospital Research Institute, Centre for Cancer Therapeutics, Ottawa, Canada
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33
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Sandmann S, de Graaf AO, van der Reijden BA, Jansen JH, Dugas M. GLM-based optimization of NGS data analysis: A case study of Roche 454, Ion Torrent PGM and Illumina NextSeq sequencing data. PLoS One 2017; 12:e0171983. [PMID: 28222155 PMCID: PMC5319672 DOI: 10.1371/journal.pone.0171983] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/30/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND There are various next-generation sequencing techniques, all of them striving to replace Sanger sequencing as the gold standard. However, false positive calls of single nucleotide variants and especially indels are a widely known problem of basically all sequencing platforms. METHODS We considered three common next-generation sequencers-Roche 454, Ion Torrent PGM and Illumina NextSeq-and applied standard as well as optimized variant calling pipelines. Optimization was achieved by combining information of 23 diverse parameters characterizing the reported variants and generating individually calibrated generalized linear models. Models were calibrated using amplicon-based targeted sequencing data (19 genes, 28,775 bp) from seven to 12 myelodysplastic syndrome patients. Evaluation of the optimized pipelines and platforms was performed using sequencing data from three additional myelodysplastic syndrome patients. RESULTS Using standard analysis methods, true mutations were missed and the obtained results contained many artifacts-no matter which platform was considered. Analysis of the parameters characterizing the true and false positive calls revealed significant platform- and variant specific differences. Application of optimized variant calling pipelines considerably improved results. 76% of all false positive single nucleotide variants and 97% of all false positive indels could be filtered out. Positive predictive values could be increased by factors of 1.07 to 1.27 in case of single nucleotide variant calling and by factors of 3.33 to 53.87 in case of indel calling. Application of the optimized variant calling pipelines leads to comparable results for all next-generation sequencing platforms analyzed. However, regarding clinical diagnostics it needs to be considered that even the optimized results still contained false positive as well as false negative calls.
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Affiliation(s)
- Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | | | | | - Joop H. Jansen
- Laboratory Hematology, RadboudUMC, Nijmegen, Netherlands
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
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Nallamilli BRR, Hegde M. Detecting APC Gene Mutations in Familial Adenomatous Polyposis (FAP). ACTA ACUST UNITED AC 2017; 92:10.8.1-10.8.16. [PMID: 28075483 DOI: 10.1002/cphg.29] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hereditary forms of colorectal cancer (CRC) account for up to 5% of total cases. Familial adenomatous polyposis (FAP) is an autosomal dominant condition affecting nearly 1 in 5000 people and accounts for only about 1% of all CRCs. It is characterized by the progressive development of hundreds to thousands of adenomatous colon polyps. The gene associated with FAP (APC) contains 15 coding exons. The mutation spectrum of the APC gene is broad in that 87% of causative mutations are point mutations (including other sequence variants) and around 10% to 15% are intragenic deletions and duplications. The strategy for molecular diagnostic testing for FAP involves initial full sequence analysis of APC for sequence variants followed by screening for deletion/duplications using microarray-based comparative genomic hybridization (array CGH) or Multiplex Ligation-dependent Probe Amplification (MLPA). Recently, next generation sequencing (NGS)-based targeted gene analysis has become clinically available for detection of point mutations and other sequence variants. This unit discusses detailed protocols for an NGS-based sequencing assay, PCR-based Sanger sequencing, and array CGH. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
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35
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Regulating whole exome sequencing as a diagnostic test. Hum Genet 2016; 135:655-73. [PMID: 27167135 DOI: 10.1007/s00439-016-1677-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/26/2016] [Indexed: 10/21/2022]
Abstract
In the last decade, there has been a flood of new technology in the sequencing arena. The onset of next-generation sequencing (NGS) technology has resulted in the vast increase in genetic diagnostic testing available to the ordering physician. Whole exome sequencing (WES) has become available as a diagnostic test performed in certified clinical laboratories. This has led to increased presence in the diagnostic marketplace, increased consumer awareness, and the question has been raised by various stakeholders to whether there is sufficient stringent regulation of WES and other NGS-based tests. We discuss the various WES services currently available in the marketplace, current regulation of WES as a laboratory developed test, the proposed FDA involvement in its oversight as well as the response of various laboratory groups that provide these diagnostic services. Overall, a rigorous process oversight and assessment of inter-lab reproducibility is strongly warranted for WES as it is used as a diagnostic test, but regulation should be mindful of the excessive administrative burden on academic and smaller diagnostic laboratories.
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Vosberg S, Herold T, Hartmann L, Neumann M, Opatz S, Metzeler KH, Schneider S, Graf A, Krebs S, Blum H, Baldus CD, Hiddemann W, Spiekermann K, Bohlander SK, Mansmann U, Greif PA. Close correlation of copy number aberrations detected by next-generation sequencing with results from routine cytogenetics in acute myeloid leukemia. Genes Chromosomes Cancer 2016; 55:553-67. [PMID: 27015608 DOI: 10.1002/gcc.22359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022] Open
Abstract
High throughput sequencing approaches, including the analysis of exomes or gene panels, are widely used and established to detect tumor-specific sequence variants such as point mutations or small insertions/deletions. Beyond single nucleotide resolution, sequencing data also contain information on changes in sequence coverage between samples and thus allow the detection of somatic copy number alterations (CNAs) representing gain or loss of genomic material in tumor cells arising from aneuploidy, amplifications, or deletions. To test the feasibility of CNA detection in sequencing data we analyzed the exomes of 25 paired leukemia/remission samples from acute myeloid leukemia (AML) patients with well-defined chromosomal aberrations, detected by conventional chromosomal analysis and/or molecular cytogenetics assays. Thereby, we were able to confirm chromosomal aberrations including trisomies, monosomies, and partial chromosomal deletions in 20 out of 25 samples. Comparison of CNA detection using exome, custom gene panel, and SNP array analysis showed equivalent results in five patients with variable clone size. Gene panel analysis of AML samples without matched germline control samples resulted in confirmation of cytogenetic findings in 18 out of 22 cases. In all cases with discordant findings, small clone size (<33%) was limiting for CNA detection. We detected CNAs consistent with cytogenetics in 83% of AML samples including highly correlated clone size estimation (R = 0.85), while six out of 65 cytogenetically normal AML samples exhibited CNAs apparently missed by routine cytogenetics. Overall, our results show that high throughput targeted sequencing data can be reliably used to detect copy number changes in the dominant AML clone. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sebastian Vosberg
- Experimental Leukemia and Lymphoma Research (ELLF), Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Tobias Herold
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Laboratory for Leukemia Diagnostics, Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Luise Hartmann
- Experimental Leukemia and Lymphoma Research (ELLF), Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Martin Neumann
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Hematology and Oncology, Charité University Hospital, Berlin, Germany
| | - Sabrina Opatz
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Laboratory for Leukemia Diagnostics, Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Klaus H Metzeler
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Laboratory for Leukemia Diagnostics, Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Stephanie Schneider
- Laboratory for Leukemia Diagnostics, Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Claudia D Baldus
- Department of Hematology and Oncology, Charité University Hospital, Berlin, Germany
| | - Wolfgang Hiddemann
- Experimental Leukemia and Lymphoma Research (ELLF), Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Karsten Spiekermann
- Experimental Leukemia and Lymphoma Research (ELLF), Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Stefan K Bohlander
- Molecular Medicine and Pathology, the University of Auckland, New Zealand
| | - Ulrich Mansmann
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Philipp A Greif
- Experimental Leukemia and Lymphoma Research (ELLF), Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-Universität (LMU) München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
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McGann P, Bunin JL, Snesrud E, Singh S, Maybank R, Ong AC, Kwak YI, Seronello S, Clifford RJ, Hinkle M, Yamada S, Barnhill J, Lesho E. Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time? Diagn Microbiol Infect Dis 2016; 85:277-282. [PMID: 27185645 DOI: 10.1016/j.diagmicrobio.2016.04.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/30/2016] [Accepted: 04/27/2016] [Indexed: 12/20/2022]
Abstract
Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations.
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Affiliation(s)
- Patrick McGann
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Jessica L Bunin
- Department of Critical Care, Tripler Army Medical Center, Honolulu, HI, USA
| | - Erik Snesrud
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Seema Singh
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Rosslyn Maybank
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ana C Ong
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Yoon I Kwak
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Scott Seronello
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Robert J Clifford
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mary Hinkle
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Stephen Yamada
- Infectious Diseases Service, Tripler Army Medical Center, Honolulu, HI, USA
| | - Jason Barnhill
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Emil Lesho
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Doo JW, Jang JH, Cho EH, Kim JK, Cho SC. Identification of a Novel Nonsense Mutation in the ARSE Gene of a Patient with X-Linked Recessive Chondrodysplasia Punctata. NEONATAL MEDICINE 2016. [DOI: 10.5385/nm.2016.23.3.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Affiliation(s)
- Jin Woong Doo
- Department of Pediatrics, Chonbuk National University Hospital, Jeonju, Korea
| | - Ja-Hyun Jang
- Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Korea
| | - Eun Hae Cho
- Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Korea
| | - Jin Kyu Kim
- Department of Pediatrics, Chonbuk National University Hospital, Jeonju, Korea
- Green Cross Genome, Yongin, Korea
| | - Soo Chul Cho
- Department of Pediatrics, Chonbuk National University Hospital, Jeonju, Korea
- Green Cross Genome, Yongin, Korea
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Arsenic R, Treue D, Lehmann A, Hummel M, Dietel M, Denkert C, Budczies J. Comparison of targeted next-generation sequencing and Sanger sequencing for the detection of PIK3CA mutations in breast cancer. BMC Clin Pathol 2015; 15:20. [PMID: 26587011 PMCID: PMC4652376 DOI: 10.1186/s12907-015-0020-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/12/2015] [Indexed: 01/04/2023] Open
Abstract
Background Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha, PIK3CA, is one of the most frequently mutated genes in breast cancer, and the mutation status of PIK3CA has clinical relevance related to response to therapy. The aim of our study was to investigate the mutation status of PIK3CA gene and to evaluate the concordance between NGS and SGS for the most important hotspot regions in exon 9 and 20, to investigate additional hotspots outside of these exons using NGS, and to correlate the PIK3CA mutation status with the clinicopathological characteristics of the cohort. Methods In the current study, next-generation sequencing (NGS) and Sanger Sequencing (SGS) was used for the mutational analysis of PIK3CA in 186 breast carcinomas. Results Altogether, 64 tumors had PIK3CA mutations, 55 of these mutations occurred in exons 9 and 20. Out of these 55 mutations, 52 could also be detected by Sanger sequencing resulting in a concordance of 98.4 % between the two sequencing methods. The three mutations missed by SGS had low variant frequencies below 10 %. Additionally, 4.8 % of the tumors had mutations in exons 1, 4, 7, and 13 of PIK3CA that were not detected by SGS. PIK3CA mutation status was significantly associated with hormone receptor-positivity, HER2-negativity, tumor grade, and lymph node involvement. However, there was no statistically significant association between the PIK3CA mutation status and overall survival. Conclusions Based on our study, NGS is recommended as follows: 1) for correctly assessing the mutation status of PIK3CA in breast cancer, especially for cases with low tumor content, 2) for the detection of subclonal mutations, and 3) for simultaneous mutation detection in multiple exons. Electronic supplementary material The online version of this article (doi:10.1186/s12907-015-0020-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruza Arsenic
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Denise Treue
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Annika Lehmann
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Manfred Dietel
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Jan Budczies
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
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Zhang G, Wang J, Yang J, Li W, Deng Y, Li J, Huang J, Hu S, Zhang B. Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling. BMC Genomics 2015; 16:581. [PMID: 26242175 PMCID: PMC4524363 DOI: 10.1186/s12864-015-1796-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 07/23/2015] [Indexed: 12/30/2022] Open
Abstract
Background To promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor-based sequencing instrument from Life Technologies, is designed to provide investigators with an inexpensive platform for human whole exome sequencing that achieves a rapid turnaround time. However, few studies have comprehensively compared and evaluated the accuracy of variant calling between Ion Proton and Illumina sequencing platforms such as HiSeq 2000, which is the most popular sequencing platform for the human genome. The Ion Proton sequencer combined with the Ion TargetSeq™ Exome Enrichment Kit together make up TargetSeq-Proton, whereas SureSelect-Hiseq is based on the Agilent SureSelect Human All Exon v4 Kit and the HiSeq 2000 sequencer. Results Here, we sequenced exonic DNA from four human blood samples using both TargetSeq-Proton and SureSelect-HiSeq. We then called variants in the exonic regions that overlapped between the two exome capture kits (33.6 Mb). The rates of shared variant loci called by two sequencing platforms were from 68.0 to 75.3 % in four samples, whereas the concordance of co-detected variant loci reached 99 %. Sanger sequencing validation revealed that the validated rate of concordant single nucleotide polymorphisms (SNPs) (91.5 %) was higher than the SNPs specific to TargetSeq-Proton (60.0 %) or specific to SureSelect-HiSeq (88.3 %). With regard to 1-bp small insertions and deletions (InDels), the Sanger sequencing validated rates of concordant variants (100.0 %) and SureSelect-HiSeq-specific (89.6 %) were higher than those of TargetSeq-Proton-specific (15.8 %). Conclusions In the sequencing of exonic regions, a combination of using of two sequencing strategies (SureSelect-HiSeq and TargetSeq-Proton) increased the variant calling specificity for concordant variant loci and the sensitivity for variant loci called by any one platform. However, for the sequencing of platform-specific variants, the accuracy of variant calling by HiSeq 2000 was higher than that of Ion Proton, specifically for the InDel detection. Moreover, the variant calling software also influences the detection of SNPs and, specifically, InDels in Ion Proton exome sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1796-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guoqiang Zhang
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jianfeng Wang
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jin Yang
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wenjie Li
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yutian Deng
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing Li
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jun Huang
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Songnian Hu
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Bing Zhang
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
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Van Giau V, An SSA, Bagyinszky E, Kim S. Gene panels and primers for next generation sequencing studies on neurodegenerative disorders. Mol Cell Toxicol 2015. [DOI: 10.1007/s13273-015-0011-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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42
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Millat G, Chanavat V, Rousson R. Evaluation of a new high-throughput next-generation sequencing method based on a custom AmpliSeq™ library and ion torrent PGM™ sequencing for the rapid detection of genetic variations in long QT syndrome. Mol Diagn Ther 2015; 18:533-9. [PMID: 24687331 DOI: 10.1007/s40291-014-0099-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND OBJECTIVE Inherited long QT syndrome (LQTS) is a cardiac channelopathy associated with a high risk of sudden death. The prevalence has been estimated at close to 1:2,000. Due to large cohorts to investigate and high rate of private mutations, mutational screening must be performed using an extremely sensitive and specific detection method. Mutational screening is crucial as this may have implications for therapy and management of LQTS patients. METHODS Next-generation sequencing (NGS) workflow based on a custom AmpliSeq™ panel was designed for sequencing the five most prevalent cardiomyopathy-causing genes (KCNQ1, KCNH2, SCN5A, KCNE1, KCNE2) on Ion PGM™ Sequencer. A cohort of 30 previously studied patients was screened to evaluate this strategy in terms of sensitivity, specificity, practicability, and cost. In silico analysis was performed using NextGENe(®) software. RESULTS Our AmpliSeq™ custom panel allowed us to explore 86 % of targeted sequences efficiently. Using adjusted alignment settings, all genetic variants (40 substitutions, 17 indels) present in covered regions and previously detected by high-resolution melt (HRM)/sequencing were readily identified. Uncovered targeted regions, which were mainly located in KCNH2, were further analyzed by HRM/sequencing strategy. Complete molecular investigation was performed faster and cheaper than with previously used mutation detection methods. CONCLUSION Finally, these results suggested that our new NGS approach based on AmpliSeq™ libraries and Ion PGM™ sequencing is a highly efficient, fast, and cheap high-throughput mutation detection method that is ready to be deployed in clinical laboratories. This method will allow fast identification of LQTS mutations that will have further implications for therapeutics.
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Affiliation(s)
- Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, 69677, Bron Cedex, France,
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Mitsumoto H, Nagy PL, Gennings C, Murphy J, Andrews H, Goetz R, Floeter MK, Hupf J, Singleton J, Barohn RJ, Nations S, Shoesmith C, Kasarskis E, Factor-Litvak P. Phenotypic and molecular analyses of primary lateral sclerosis. NEUROLOGY-GENETICS 2015; 1:e3. [PMID: 27066542 PMCID: PMC4821084 DOI: 10.1212/01.nxg.0000464294.88607.dd] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/17/2015] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To understand phenotypic and molecular characteristics of patients with clinically "definite" primary lateral sclerosis (PLS) in a prospective study. METHODS Six sites enrolled 41 patients who had pure upper motor neuron dysfunction, bulbar symptoms, a normal EMG done within 12 months of enrollment, and onset of symptoms ≥5 years before enrollment. For phenotypic analyses, 27 demographic, clinical, and cognitive variables were analyzed using the k-means clustering method. For molecular studies, 34 available DNA samples were tested for the C9ORF72 mutation, and exome sequencing was performed to exclude other neurologic diseases with known genetic cause. RESULTS K-means clustering using the 25 patients with complete datasets suggested that patients with PLS can be classified into 2 groups based on clinical variables, namely dysphagia, objective bulbar signs, and urinary urgency. Secondary analyses performed in all 41 patients and including only variables with complete data corroborated the results from the primary analysis. We found no evidence that neurocognitive variables are important in classifying patients with PLS. Molecular studies identified C9ORF72 expansion in one patient. Well-characterized pathogenic mutations were identified in SPG7, DCTN1, and PARK2. Most cases showed no known relevant mutations. CONCLUSIONS Cluster analyses based on clinical variables indicated at least 2 subgroups of clinically definite PLS. Molecular analyses further identified 4 cases with mutations associated with amyotrophic lateral sclerosis, Parkinson disease, and possibly hereditary spastic paraplegia. Phenotypic and molecular characterization is the first step in investigating biological clues toward the definition of PLS. Further studies with larger numbers of patients are essential.
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Affiliation(s)
- Hiroshi Mitsumoto
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Peter L Nagy
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Chris Gennings
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Jennifer Murphy
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Howard Andrews
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Raymond Goetz
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Mary Kay Floeter
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Jonathan Hupf
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Jessica Singleton
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Richard J Barohn
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Sharon Nations
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Christen Shoesmith
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Edward Kasarskis
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
| | - Pam Factor-Litvak
- Department of Neurology (H.M., J.H., J.S.), Eleanor and Lou Gehrig MDA/ALS Research Center, Columbia University Medical Center (CUMC), New York, NY; Department of Pathology and Cell Biology (P.L.N.), Personalized Genomic Medicine Laboratory, CUMC, New York, NY; Department of Biostatistics (C.G.), Virginia Commonwealth University, Richmond, VA; Department of Neurology (J.M.), University of California, San Francisco, CA; Departments of Biostatistics and Psychiatry (H.A., R.G.), Mailman School of Medicine, CUMC, New York, NY; Clinical Neuroscience Program (M.K.F.), NINDS, NIH, Bethesda, MD; Department of Neurology (R.J.B.), University of Kansas, Lawrence, KS; Department of Neurology (S.N.), University of Texas Southwestern Medical Center, Dallas, TX; Department of Neurology (C.S.), Western University, London, Ontario, Canada; Department of Neurology (E.K.), University of Kentucky, Lexington, KY; and Department of Epidemiology (P.F.-L), Mailman School of Public Health, CUMC, New York, NY
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Hokland P, Ommen HB, Mulé MP, Hourigan CS. Advancing the Minimal Residual Disease Concept in Acute Myeloid Leukemia. Semin Hematol 2015; 52:184-92. [PMID: 26111465 DOI: 10.1053/j.seminhematol.2015.04.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The criteria to evaluate response to treatment in acute myeloid leukemia (AML) have changed little in the past 60 years. It is now possible to use higher sensitivity tools to measure residual disease burden in AML. Such minimal or measurable residual disease (MRD) measurements provide a deeper understanding of current patient status and allow stratification for risk of subsequent clinical relapse. Despite these obvious advantages, and after over a decade of laboratory investigation and preclinical validation, MRD measurements are not currently routinely used for clinical decision-making or drug development in non-acute promyelocytic leukemia (non-APL) AML. We review here some potential constraints that may have delayed adoption, including a natural hesitancy of end users, economic impact concerns, misperceptions regarding the meaning of and need for assay sensitivity, the lack of one single MRD solution for all AML patients, and finally the need to involve patients in decision-making based on such correlates. It is our opinion that none of these issues represent insurmountable barriers and our hope is that by providing potential solutions we can help map a path forward to a future where our patients will be offered personalized treatment plans based on the amount of AML they have left remaining to treat.
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Affiliation(s)
- Peter Hokland
- Department of Hematology, Aarhus University Hospital, Denmark
| | - Hans B Ommen
- Department of Hematology, Aarhus University Hospital, Denmark
| | - Matthew P Mulé
- Myeloid Malignancies Section, Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Christopher S Hourigan
- Myeloid Malignancies Section, Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD.
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Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, Gibson JS, Grody WW, Hegde MR, Hoeltge GA, Leonard DGB, Merker JD, Nagarajan R, Palicki LA, Robetorye RS, Schrijver I, Weck KE, Voelkerding KV. College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests. Arch Pathol Lab Med 2015; 139:481-93. [DOI: 10.5858/arpa.2014-0250-cp] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ankala A, da Silva C, Gualandi F, Ferlini A, Bean LJH, Collins C, Tanner AK, Hegde MR. A comprehensive genomic approach for neuromuscular diseases gives a high diagnostic yield. Ann Neurol 2014; 77:206-14. [PMID: 25380242 DOI: 10.1002/ana.24303] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/31/2014] [Accepted: 11/02/2014] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Neuromuscular diseases (NMDs) are a group of >200 highly genetically as well as clinically heterogeneous inherited genetic disorders that affect the peripheral nervous and muscular systems, resulting in gross motor disability. The clinical and genetic heterogeneities of NMDs make disease diagnosis complicated and expensive, often involving multiple tests. METHODS To expedite the molecular diagnosis of NMDs, we designed and validated several next generation sequencing (NGS)-based comprehensive gene panel tests that include complementary deletion and duplication testing through comparative genomic hybridization arrays. Our validation established the targeted gene panel test to have 100% sensitivity and specificity for single nucleotide variant detection. To compare the clinical diagnostic yields of single gene (NMD-associated) tests with the various NMD NGS panel tests, we analyzed data from all clinical tests performed at the Emory Genetics Laboratory from October 2009 through May 2014. We further compared the clinical utility of the targeted NGS panel test with that of exome sequencing (ES). RESULTS We found that NMD comprehensive panel testing has a 3-fold greater diagnostic yield (46%) than single gene testing (15-19%). Sanger fill-in of low-coverage exons, copy number variation analysis, and thorough in-house validation of the assay all complement panel testing and allow the detection of all types of causative pathogenic variants, some of which (about 18%) may be missed by ES. INTERPRETATION Our results strongly indicate that for molecular diagnosis of heterogeneous disorders such as NMDs, targeted panel testing has the highest clinical yield and should therefore be the preferred first-tier approach.
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Affiliation(s)
- Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
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Park JY, Clark P, Londin E, Sponziello M, Kricka LJ, Fortina P. Clinical exome performance for reporting secondary genetic findings. Clin Chem 2014; 61:213-20. [PMID: 25414276 DOI: 10.1373/clinchem.2014.231456] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Reporting clinically actionable incidental genetic findings in the course of clinical exome testing is recommended by the American College of Medical Genetics and Genomics (ACMG). However, the performance of clinical exome methods for reporting small subsets of genes has not been previously reported. METHODS In this study, 57 exome data sets performed as clinical (n = 12) or research (n = 45) tests were retrospectively analyzed. Exome sequencing data was examined for adequacy in the detection of potentially pathogenic variant locations in the 56 genes described in the ACMG incidental findings recommendation. All exons of the 56 genes were examined for adequacy of sequencing coverage. In addition, nucleotide positions annotated in HGMD (Human Gene Mutation Database) were examined. RESULTS The 56 ACMG genes have 18 336 nucleotide variants annotated in HGMD. None of the 57 exome data sets possessed a HGMD variant. The clinical exome test had inadequate coverage for >50% of HGMD variant locations in 7 genes. Six exons from 6 different genes had consistent failure across all 3 test methods; these exons had high GC content (76%-84%). CONCLUSIONS The use of clinical exome sequencing for the interpretation and reporting of subsets of genes requires recognition of the substantial possibility of inadequate depth and breadth of sequencing coverage at clinically relevant locations. Inadequate depth of coverage may contribute to false-negative clinical exome results.
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Affiliation(s)
- Jason Y Park
- Department of Pathology and Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center and Children's Medical Center, Dallas, TX;
| | - Peter Clark
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Marialuisa Sponziello
- Department of Internal Medicine and Medical Specialties, University of Rome "Sapienza," Rome, Italy
| | - Larry J Kricka
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Philadelphia, PA
| | - Paolo Fortina
- Cancer Genomics Laboratory, Sidney Kimmel Cancer Center, Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Molecular Medicine, University of Rome "Sapienza," Rome, Italy
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48
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Exploring the Genomic Roadmap and Molecular Phylogenetics Associated with MODY Cascades Using Computational Biology. Cell Biochem Biophys 2014; 71:1491-502. [DOI: 10.1007/s12013-014-0372-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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49
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Esplin ED, Oei L, Snyder MP. Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease. Pharmacogenomics 2014; 15:1771-1790. [PMID: 25493570 DOI: 10.2217/pgs.14.117] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The potential for personalized sequencing to individually optimize medical treatment in diseases such as cancer and for pharmacogenomic application is just beginning to be realized, and the utility of sequencing healthy individuals for managing health is also being explored. The data produced requires additional advancements in interpretation of variants of unknown significance to maximize clinical benefit. Nevertheless, personalized sequencing, only recently applied to clinical medicine, has already been broadly applied to the discovery and study of disease. It is poised to enable the earlier and more accurate diagnosis of disease risk and occurrence, guide prevention and individualized intervention as well as facilitate monitoring of healthy and treated patients, and play a role in the prevention and recurrence of future disease. This article documents the advancing capacity of personalized sequencing, reviews its impact on disease-oriented scientific discovery and anticipates its role in the future of medicine.
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Affiliation(s)
- Edward D Esplin
- 300 Pasteur Drive, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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Gréen A, Gréen H, Rehnberg M, Svensson A, Gunnarsson C, Jonasson J. Assessment of HaloPlex amplification for sequence capture and massively parallel sequencing of arrhythmogenic right ventricular cardiomyopathy-associated genes. J Mol Diagn 2014; 17:31-42. [PMID: 25445213 DOI: 10.1016/j.jmoldx.2014.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 08/12/2014] [Accepted: 09/03/2014] [Indexed: 12/30/2022] Open
Abstract
The genetic basis of arrhythmogenic right ventricular cardiomyopathy (ARVC) is complex. Mutations in genes encoding components of the cardiac desmosomes have been implicated as being causally related to ARVC. Next-generation sequencing allows parallel sequencing and duplication/deletion analysis of many genes simultaneously, which is appropriate for screening of mutations in disorders with heterogeneous genetic backgrounds. We designed and validated a next-generation sequencing test panel for ARVC using HaloPlex. We used SureDesign to prepare a HaloPlex enrichment system for sequencing of DES, DSC2, DSG2, DSP, JUP, PKP2, RYR2, TGFB3, TMEM43, and TTN from patients with ARVC using a MiSeq instrument. Performance characteristics were determined by comparison with Sanger, as the gold standard, and TruSeq Custom Amplicon sequencing of DSC2, DSG2, DSP, JUP, and PKP2. All the samples were successfully sequenced after HaloPlex capture, with >99% of targeted nucleotides covered by >20×. The sequences were of high quality, although one problematic area due to a presumptive context-specific sequencing error-causing motif located in exon 1 of the DSP gene was detected. The mutations found by Sanger sequencing were also found using the HaloPlex technique. Depending on the bioinformatics pipeline, sensitivity varied from 99.3% to 100%, and specificity varied from 99.9% to 100%. Three variant positions found by Sanger and HaloPlex sequencing were missed by TruSeq Custom Amplicon owing to loss of coverage.
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Affiliation(s)
- Anna Gréen
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Department of Clinical Genetics, County Council of Östergötland, Linköping, Sweden.
| | - Henrik Gréen
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Division of Drug Research, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden; Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
| | - Malin Rehnberg
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Department of Clinical Genetics, County Council of Östergötland, Linköping, Sweden
| | - Anneli Svensson
- Department of Medicine and Health Science, Linköping University, Linköping, Sweden; Department of Cardiology, County Council of Östergötland, Linköping, Sweden
| | - Cecilia Gunnarsson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Department of Clinical Genetics, County Council of Östergötland, Linköping, Sweden
| | - Jon Jonasson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Department of Clinical Genetics, County Council of Östergötland, Linköping, Sweden
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