دورية أكاديمية
أعرض في EDS

Sequencing and curation strategies for identifying candidate glioblastoma treatments.

التفاصيل البيبلوغرافية
العنوان: Sequencing and curation strategies for identifying candidate glioblastoma treatments.
المؤلفون: Frank MO; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA., Koyama T; IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA., Rhrissorrakrai K; IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA., Robine N; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Utro F; IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA., Emde AK; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Chen BJ; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Present address: Google, 76 9th Avenue, New York, NY, 10011, USA., Arora K; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Shah M; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Geiger H; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Felice V; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Dikoglu E; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Present address: Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA., Rahman S; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Fang A; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Vacic V; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Present address: 23&Me, 899 W Evelyn Ave, Mountain View, CA, 94041, USA., Bergmann EA; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Present address: Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51 D-79108, Freiburg, Germany., Vogel JLM; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.; Present address: The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA., Reeves C; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Khaira D; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Calabro A; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Present address: The Tisch Cancer Institute, 1470 Madison Avenue, New York, NY, 10029, USA., Kim D; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Lamendola-Essel MF; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Present address: Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Esteves C; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Present address: Harvard Medical School, 10 Shattuck Street, Boston, MA, 02115, USA., Agius P; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Stolte C; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Boockvar J; Northwell Health, Lenox Hill Hospital, 100 E. 77th Street, New York, NY, 10075, USA., Demopoulos A; Northwell Health, The Brain Tumor Center, 450 Lakeville Road, Lake Success, Lakeville, NY, 11042, USA., Placantonakis DG; New York University, School of Medicine, 550 First Avenue, New York, NY, 10016, USA., Golfinos JG; New York University, School of Medicine, 550 First Avenue, New York, NY, 10016, USA., Brennan C; Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Bruce J; Columbia University Medical Center, 710 West 168th Street, New York, NY, 10032, USA., Lassman AB; Columbia University Medical Center, 710 West 168th Street, New York, NY, 10032, USA., Canoll P; Columbia University Medical Center, 710 West 168th Street, New York, NY, 10032, USA., Grommes C; Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Daras M; Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Diamond E; Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Omuro A; Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.; Present address: Yale School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA., Pentsova E; Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Orange DE; Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.; Hospital for Special Surgery, 535 E. 70th Street, New York, NY, 10021, USA., Harvey SJ; IBM Watson Health, NW Broken Sound Bkwy, Boca Raton, FL, 33487, USA., Posner JB; Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA., Michelini VV; IBM Watson Health, NW Broken Sound Bkwy, Boca Raton, FL, 33487, USA., Jobanputra V; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.; Columbia University Medical Center, 710 West 168th Street, New York, NY, 10032, USA., Zody MC; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Kelly J; IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA., Parida L; IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA., Wrzeszczynski KO; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA., Royyuru AK; IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA., Darnell RB; New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA. darnelr@rockefeller.edu.; Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA. darnelr@rockefeller.edu.; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA. darnelr@rockefeller.edu.
المصدر: BMC medical genomics [BMC Med Genomics] 2019 Apr 25; Vol. 12 (1), pp. 56. Date of Electronic Publication: 2019 Apr 25.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 101319628 Publication Model: Electronic Cited Medium: Internet ISSN: 1755-8794 (Electronic) Linking ISSN: 17558794 NLM ISO Abbreviation: BMC Med Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central
مواضيع طبية MeSH: Whole Genome Sequencing*, Glioblastoma/*drug therapy , Glioblastoma/*genetics, Adult ; Aged ; Aged, 80 and over ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Molecular Targeted Therapy ; Ploidies ; Reproducibility of Results
مستخلص: Background: Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and analysis methods to analyze glioblastoma tumors and generate real-time potential treatment options for physicians.
Methods: A consortium of seven institutions in New York City enrolled 30 patients with glioblastoma and performed tumor whole genome sequencing (WGS) and RNA sequencing (RNA-seq; collectively WGS/RNA-seq); 20 of these patients were also analyzed with independent targeted panel sequencing. We also compared results of expert manual annotations with those from an automated annotation system, Watson Genomic Analysis (WGA), to assess the reliability and time required to identify potentially relevant pharmacologic interventions.
Results: WGS/RNAseq identified more potentially actionable clinical results than targeted panels in 90% of cases, with an average of 16-fold more unique potentially actionable variants identified per individual; 84 clinically actionable calls were made using WGS/RNA-seq that were not identified by panels. Expert annotation and WGA had good agreement on identifying variants [mean sensitivity = 0.71, SD = 0.18 and positive predictive value (PPV) = 0.80, SD = 0.20] and drug targets when the same variants were called (mean sensitivity = 0.74, SD = 0.34 and PPV = 0.79, SD = 0.23) across patients. Clinicians used the information to modify their treatment plan 10% of the time.
Conclusion: These results present the first comprehensive comparison of technical and machine augmented analysis of targeted panel and WGS/RNA-seq to identify potential cancer treatments.
التعليقات: Erratum in: BMC Med Genomics. 2019 Aug 2;12(1):114. (PMID: 31375115)
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معلومات مُعتمدة: UL1 TR000043 United States TR NCATS NIH HHS; UL1 TR001863 United States TR NCATS NIH HHS; United States HHMI Howard Hughes Medical Institute; P30 CA008748 United States CA NCI NIH HHS; R01 NS102665 United States NS NINDS NIH HHS; R21 NS088775 United States NS NINDS NIH HHS; R21 NS087241 United States NS NINDS NIH HHS; R03 NS087349 United States NS NINDS NIH HHS
تواريخ الأحداث: Date Created: 20190427 Date Completed: 20191230 Latest Revision: 20200729
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC6485090
DOI: 10.1186/s12920-019-0500-0
PMID: 31023376
قاعدة البيانات: MEDLINE
الوصف
تدمد:1755-8794
DOI:10.1186/s12920-019-0500-0