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Article ; Online: Researching COVID to enhance recovery (RECOVER) tissue pathology study protocol: Rationale, objectives, and design.

Troxel, Andrea B / Bind, Marie-Abele C / Flotte, Thomas J / Cordon-Cardo, Carlos / Decker, Lauren A / Finn, Aloke V / Padera, Robert F / Reichard, R Ross / Stone, James R / Adolphi, Natalie L / Casimero, Faye Victoria C / Crary, John F / Elifritz, Jamie / Faustin, Arline / Ghosh, Saikat Kumar B / Krausert, Amanda / Martinez-Lage, Maria / Melamed, Jonathan / Mitchell, Roger A /

Sampson, Barbara A / Seifert, Alan C / Simsir, Aylin / Adams, Cheryle / Haasnoot, Stephanie / Hafner, Stephanie / Siciliano, Michelle A / Vallejos, Brittany B / Del Boccio, Phoebe / Lamendola-Essel, Michelle F / Young, Chloe E / Kewlani, Deepshikha / Akinbo, Precious A / Parent, Brendan / Chung, Alicia / Cato, Teresa C / Mudumbi, Praveen C / Esquenazi-Karonika, Shari / Wood, Marion J / Chan, James / Monteiro, Jonathan / Shinnick, Daniel J / Thaweethai, Tanayott / Nguyen, Amber N / Fitzgerald, Megan L / Perlowski, Alice A / Stiles, Lauren E / Paskett, Moira L / Katz, Stuart D / Foulkes, Andrea S

PloS one

2024 Volume 19, Issue 1, Page(s) e0285645

Abstract: Importance: SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or organ dysfunction after the acute phase of infection, termed Post-Acute Sequelae of SARS-CoV-2 (PASC), or long COVID. The characteristics, prevalence, trajectory and ... ...

Abstract	Importance: SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or organ dysfunction after the acute phase of infection, termed Post-Acute Sequelae of SARS-CoV-2 (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are poorly understood. The objectives of the Researching COVID to Enhance Recovery (RECOVER) tissue pathology study (RECOVER-Pathology) are to: (1) characterize prevalence and types of organ injury/disease and pathology occurring with PASC; (2) characterize the association of pathologic findings with clinical and other characteristics; (3) define the pathophysiology and mechanisms of PASC, and possible mediation via viral persistence; and (4) establish a post-mortem tissue biobank and post-mortem brain imaging biorepository. Methods: RECOVER-Pathology is a cross-sectional study of decedents dying at least 15 days following initial SARS-CoV-2 infection. Eligible decedents must meet WHO criteria for suspected, probable, or confirmed infection and must be aged 18 years or more at the time of death. Enrollment occurs at 7 sites in four U.S. states and Washington, DC. Comprehensive autopsies are conducted according to a standardized protocol within 24 hours of death; tissue samples are sent to the PASC Biorepository for later analyses. Data on clinical history are collected from the medical records and/or next of kin. The primary study outcomes include an array of pathologic features organized by organ system. Causal inference methods will be employed to investigate associations between risk factors and pathologic outcomes. Discussion: RECOVER-Pathology is the largest autopsy study addressing PASC among US adults. Results of this study are intended to elucidate mechanisms of organ injury and disease and enhance our understanding of the pathophysiology of PASC.
MeSH term(s)	Adult ; Humans ; COVID-19 ; SARS-CoV-2 ; Cross-Sectional Studies ; Post-Acute COVID-19 Syndrome ; Disease Progression ; Risk Factors
Language	English
Publishing date	2024-01-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0285645
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: PD-1 Blockade in Solid Tumors with Defects in Polymerase Epsilon.

Rousseau, Benoit / Bieche, Ivan / Pasmant, Eric / Hamzaoui, Nadim / Leulliot, Nicolas / Michon, Lucas / de Reynies, Aurelien / Attignon, Valerie / Foote, Michael B / Masliah-Planchon, Julien / Svrcek, Magali / Cohen, Romain / Simmet, Victor / Augereau, Paule / Malka, David / Hollebecque, Antoine / Pouessel, Damien / Gomez-Roca, Carlos / Guimbaud, Rosine /

Bruyas, Amandine / Guillet, Marielle / Grob, Jean-Jacques / Duluc, Muriel / Cousin, Sophie / de la Fouchardiere, Christelle / Flechon, Aude / Rolland, Frederic / Hiret, Sandrine / Saada-Bouzid, Esma / Bouche, Olivier / Andre, Thierry / Pannier, Diane / El Hajbi, Farid / Oudard, Stephane / Tournigand, Christophe / Soria, Jean-Charles / Champiat, Stephane / Gerber, Drew G / Stephens, Dennis / Lamendola-Essel, Michelle F / Maron, Steven B / Diplas, Bill H / Argiles, Guillem / Krishnan, Asha R / Tabone-Eglinger, Severine / Ferrari, Anthony / Segal, Neil H / Cercek, Andrea / Hoog-Labouret, Natalie / Legrand, Frederic / Simon, Clotilde / Lamrani-Ghaouti, Assia / Diaz, Luis A / Saintigny, Pierre / Chevret, Sylvie / Marabelle, Aurelien

Cancer discovery

2022 Volume 12, Issue 6, Page(s) 1435–1448

Abstract: Missense mutations in the polymerase epsilon (POLE) gene have been reported to generate proofreading defects resulting in an ultramutated genome and to sensitize tumors to checkpoint blockade immunotherapy. However, many POLE-mutated tumors do not ... ...

Abstract	Missense mutations in the polymerase epsilon (POLE) gene have been reported to generate proofreading defects resulting in an ultramutated genome and to sensitize tumors to checkpoint blockade immunotherapy. However, many POLE-mutated tumors do not respond to such treatment. To better understand the link between POLE mutation variants and response to immunotherapy, we prospectively assessed the efficacy of nivolumab in a multicenter clinical trial in patients bearing advanced mismatch repair-proficient POLE-mutated solid tumors. We found that only tumors harboring selective POLE pathogenic mutations in the DNA binding or catalytic site of the exonuclease domain presented high mutational burden with a specific single-base substitution signature, high T-cell infiltrates, and a high response rate to anti-PD-1 monotherapy. This study illustrates how specific DNA repair defects sensitize to immunotherapy. POLE proofreading deficiency represents a novel agnostic biomarker for response to PD-1 checkpoint blockade therapy. Significance: POLE proofreading deficiency leads to high tumor mutational burden with high tumor-infiltrating lymphocytes and predicts anti-PD-1 efficacy in mismatch repair-proficient tumors. Conversely, tumors harboring POLE mutations not affecting proofreading derived no benefit from PD-1 blockade. POLE proofreading deficiency is a new tissue-agnostic biomarker for cancer immunotherapy. This article is highlighted in the In This Issue feature, p. 1397.
MeSH term(s)	DNA Polymerase II/genetics ; Humans ; Immunotherapy ; Mutation, Missense ; Neoplasms/drug therapy ; Neoplasms/enzymology ; Neoplasms/genetics ; Poly-ADP-Ribose Binding Proteins/genetics ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Programmed Cell Death 1 Receptor/genetics
Chemical Substances	PDCD1 protein, human ; Poly-ADP-Ribose Binding Proteins ; Programmed Cell Death 1 Receptor ; DNA Polymerase II (EC 2.7.7.7) ; POLE protein, human (EC 2.7.7.7)
Language	English
Publishing date	2022-04-11
Publishing country	United States
Document type	Journal Article ; Multicenter Study
ZDB-ID	2625242-9
ISSN	2159-8290 ; 2159-8274
ISSN (online)	2159-8290
ISSN	2159-8274
DOI	10.1158/2159-8290.CD-21-0521
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Article ; Online: Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer.

The Journal of molecular diagnostics : JMD

2018 Volume 20, Issue 6, Page(s) 822–835

Abstract: We developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay that provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to ... ...

Abstract	We developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay that provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, insertions/deletions, copy number variants, structural variants, and RNA gene fusions was analyzed. New York State's Department of Health next-generation DNA sequencing guidelines were expanded for establishing performance validation applicable to whole-genome and transcriptome sequencing. Whole-genome sequencing laboratory protocols were validated for the Illumina HiSeq X Ten platform and RNA sequencing for Illumina HiSeq2500 platform for fresh or frozen and formalin-fixed, paraffin-embedded tumor samples. Various bioinformatics tools were also tested, and CIs for sensitivity and specificity thresholds in calling clinically significant somatic aberrations were determined. The validation was performed on a set of 125 tumor normal pairs. RNA sequencing was performed to call fusions and to confirm the DNA variants or exonic alterations. Here, we present our results and WGTS standards for variant allele frequency, reproducibility, analytical sensitivity, and present limit of detection analysis for single nucleotide variant calling, copy number identification, and structural variants. We show that The New York Genome Center WGTS clinical assay can provide a comprehensive patient variant discovery approach suitable for directed oncologic therapeutic applications.
MeSH term(s)	DNA Copy Number Variations/genetics ; Gene Frequency/genetics ; Genetic Variation ; Humans ; Limit of Detection ; Neoplasms/genetics ; Reproducibility of Results ; Research Report ; Transcriptome/genetics ; Whole Genome Sequencing/methods
Language	English
Publishing date	2018-08-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Validation Study
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2018.06.007
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Article ; Online: Researching COVID to enhance recovery (RECOVER) autopsy tissue pathology study protocol: Rationale, objectives, and design

Troxel, Andrea B. / Bind, Marie-Abele C. / Flotte, Thomas J. / Cordon-Cardo, Carlos / Decker, Lauren A. / Finn, Aloke V. / Padera, Robert F. / Reichard, R. Ross / Stone, James R. / Adolphi, Natalie L. / Casimero, Faye Victoria C. / Crary, John F. / Elifritz, Jamie / Faustin, Arline / Ghosh, Saikat Kumar B. / Krausert, Amanda / Martinez-Lage, Maria / Melamed, Jonathan / Mitchell, Roger A. /

Sampson, Barbara A. / Seifert, Alan C. / Simsir, Aylin / Adams, Cheryle / Haasnoot, Stephanie / Hafner, Stephanie / Siciliano, Michelle A. / Vallejos, Brittany B. / Boccio, Phoebe Del / Lamendola-Essel, Michelle F. / Young, Chloe E. / Kewlani, Deepshikha / Akinbo, Precious A. / Parent, Brendan / Chung, Alicia / Cato, Teresa C. / Mudumbi, Praveen C. / Esquenazi-Karonika, Shari / Wood, Marion J. / Chan, James / Monteiro, Jonathan / Shinnick, Daniel J. / Thaweethai, Tanayott / Nguyen, Amber N. / Fitzgerald, Megan L. / Perlowski, Alice A. / Stiles, Lauren E. / Paskett, Moira L. / Katz, Stuart D. / Foulkes, Andrea S.

medRxiv

Abstract	Importance: SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or organ dysfunction after the acute phase of infection, termed Post-Acute Sequelae of SARS-CoV-2 (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are poorly understood. The objectives of the Researching COVID to Enhance Recovery (RECOVER) Tissue Pathology Study (RECOVER-Pathology) are to: (1) characterize prevalence and types of organ injury/disease and pathology occurring with PASC; (2) characterize the association of pathologic findings with clinical and other characteristics; (3) define the pathophysiology and mechanisms of PASC, and possible mediation via viral persistence; and (4) establish a post-mortem tissue biobank and post-mortem brain imaging biorepository. Methods: RECOVER-Pathology is a cross-sectional study of decedents dying at least 15 days following initial SARS-CoV-2 infection. Eligible decedents must meet WHO criteria for suspected, probable, or confirmed infection and must be aged 18 years or more at the time of death. Enrollment occurs at 7 sites in four U.S. states and Washington, DC. Comprehensive autopsies are conducted according to a standardized protocol within 24 hours of death; tissue samples are sent to the PASC Biorepository for later analyses. Data on clinical history are collected from the medical records and/or next of kin. The primary study outcomes include an array of pathologic features organized by organ system. Casual inference methods will be employed to investigate associations between risk factors and pathologic outcomes. Discussion: RECOVER-Pathology is the largest autopsy study addressing PASC among US adults. Results of this study are intended to elucidate mechanisms of organ injury and disease and enhance our understanding of the pathophysiology of PASC.
Keywords	covid19
Language	English
Publishing date	2023-05-04
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.04.27.23289234
Database	COVID19

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Article ; Online: Researching COVID to enhance recovery (RECOVER) autopsy study protocol: Rationale, objectives, and design

Sampson, Barbara A. / Seifert, Alan C. / Simsir, Aylin / Adams, Cheryle / Haasnoot, Stephanie / Hafner, Stephanie / Siciliano, Michelle A. / Vallejos, Brittany / Del Boccio, Phoebe / Lamendola-Essel, Michelle F. / Young, Chloe E. / Kewlani, Deepshikha / Akinbo, Precious A. / Parent, Brendan / Chung, Alicia / Cato, Teresa C. / Mudumbi, Praveen C. / Esquenazi-Karonika, Shari / Wood, Marion J. / Chan, James / Monteiro, Jonathan / Shinnick, Daniel J. / Thaweethai, Tanayott / Nguyen, Amber N. / Fitzgerald, Megan L. / Perlowski, Alice A. / Stiles, Lauren E. / Paskett, Moira L. / Katz, Stuart D. / Foulkes, Andrea S. / RECOVER Initiative

medRxiv

Abstract	Importance: SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or organ dysfunction after the acute phase of infection, termed Post-Acute Sequelae of SARS-CoV-2 (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are poorly understood. The objectives of the Researching COVID to Enhance Recovery (RECOVER) Tissue Pathology Study (RECOVER-Pathology) are to: (1) characterize prevalence and types of organ injury/disease and pathology occurring with PASC; (2) characterize the association of pathologic findings with clinical and other characteristics; (3) define the pathophysiology and mechanisms of PASC, and possible mediation via viral persistence; and (4) establish a post-mortem tissue biobank and post-mortem brain imaging biorepository. Methods: RECOVER-Pathology is a cross-sectional study of decedents dying at least 15 days following initial SARS-CoV-2 infection. Eligible decedents must meet WHO criteria for suspected, probable, or confirmed infection and must be aged 18 years or more at the time of death. Enrollment occurs at 7 sites in four U.S. states and Washington, DC. Comprehensive autopsies are conducted according to a standardized protocol within 24 hours of death; tissue samples are sent to the PASC Biorepository for later analyses. Data on clinical history are collected from the medical records and/or next of kin. The primary study outcomes include an array of pathologic features organized by organ system. Casual inference methods will be employed to investigate associations between risk factors and pathologic outcomes. Discussion: RECOVER-Pathology is the largest autopsy study addressing PASC among US adults. Results of this study are intended to elucidate mechanisms of organ injury and disease and enhance our understanding of the pathophysiology of PASC.
Keywords	covid19
Language	English
Publishing date	2023-05-04
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.04.27.23289234
Database	COVID19

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Article ; Online: DRUL for school: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2.

Frank, Mayu O / Blachere, Nathalie E / Parveen, Salina / Hacisuleyman, Ezgi / Fak, John / Luna, Joseph M / Michailidis, Eleftherios / Wright, Samara / Stark, Pamela / Campbell, Ann / Foo, Ashley / Sakmar, Thomas P / Huffman, Virginia / Bergh, Marissa / Goldfarb, Audrey / Mansisidor, Andres / Patriotis, Agata L / Palmquist, Karl H / Poulton, Nicolas /

Leicher, Rachel / Vargas, César D M / Duba, Irene / Hurley, Arlene / Colagreco, Joseph / Pagane, Nicole / Orange, Dana E / Mora, Kevin / Rakeman, Jennifer L / Fowler, Randal C / Fernandes, Helen / Lamendola-Essel, Michelle F / Didkovsky, Nicholas / Silvera, Leopolda / Masci, Joseph / Allen, Machelle / Rice, Charles M / Darnell, Robert B

PloS one

2021 Volume 16, Issue 6, Page(s) e0252949

Abstract: To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 μl saliva in vials containing Darnell Rockefeller ... ...

Abstract	To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 μl saliva in vials containing Darnell Rockefeller University Laboratory (DRUL) buffer and extracted RNA was assayed by RT-PCR (the DRUL saliva assay). The limit of detection was confirmed to be 1 viral copy/μl in 20 of 20 replicate extractions. Viral RNA was stable in DRUL buffer at room temperature up to seven days after sample collection, and safety studies demonstrated that DRUL buffer immediately inactivated virus at concentrations up to 2.75x106 PFU/ml. Results from SARS-CoV-2 positive nasopharyngeal (NP) swab samples collected in viral transport media and assayed with a standard FDA Emergency Use Authorization (EUA) test were highly correlated with samples placed in DRUL buffer. Direct comparison of results from 162 individuals tested by FDA EUA oropharyngeal (OP) or NP swabs with co-collected saliva samples identified four otherwise unidentified positive cases in DRUL buffer. Over six months, we collected 3,724 samples from individuals ranging from 3 months to 92 years of age. This included collecting weekly samples over 10 weeks from teachers, children, and parents from a pre-school program, which allowed its safe reopening while at-risk pods were quarantined. In sum, we validated a simple, sensitive, stable, and safe PCR-based test using a self-collected saliva sample as a valuable tool for clinical diagnosis and screening at workplaces and schools.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/genetics ; COVID-19 Nucleic Acid Testing ; Child ; Female ; Humans ; Male ; SARS-CoV-2 ; Saliva/virology ; Schools ; Specimen Handling
Language	English
Publishing date	2021-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0252949
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sequencing and curation strategies for identifying candidate glioblastoma treatments.

Frank, Mayu O / Koyama, Takahiko / Rhrissorrakrai, Kahn / Robine, Nicolas / Utro, Filippo / Emde, Anne-Katrin / Chen, Bo-Juen / Arora, Kanika / Shah, Minita / Geiger, Heather / Felice, Vanessa / Dikoglu, Esra / Rahman, Sadia / Fang, Alice / Vacic, Vladimir / Bergmann, Ewa A / Vogel, Julia L Moore / Reeves, Catherine / Khaira, Depinder /

Calabro, Anthony / Kim, Duyang / Lamendola-Essel, Michelle F / Esteves, Cecilia / Agius, Phaedra / Stolte, Christian / Boockvar, John / Demopoulos, Alexis / Placantonakis, Dimitris G / Golfinos, John G / Brennan, Cameron / Bruce, Jeffrey / Lassman, Andrew B / Canoll, Peter / Grommes, Christian / Daras, Mariza / Diamond, Eli / Omuro, Antonio / Pentsova, Elena / Orange, Dana E / Harvey, Stephen J / Posner, Jerome B / Michelini, Vanessa V / Jobanputra, Vaidehi / Zody, Michael C / Kelly, John / Parida, Laxmi / Wrzeszczynski, Kazimierz O / Royyuru, Ajay K / Darnell, Robert B

BMC medical genomics

2019 Volume 12, Issue 1, Page(s) 56

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Female ; Glioblastoma/drug therapy ; Glioblastoma/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Molecular Targeted Therapy ; Ploidies ; Reproducibility of Results ; Whole Genome Sequencing
Language	English
Publishing date	2019-04-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1755-8794
ISSN (online)	1755-8794
DOI	10.1186/s12920-019-0500-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Correction to: Sequencing and curation strategies for identifying candidate glioblastoma treatments.

Frank, Mayu O / Koyama, Takahiko / Rhrissorrakrai, Kahn / Robine, Nicolas / Utro, Filippo / Emde, Anne-Katrin / Chen, Bo-Juen / Arora, Kanika / Shah, Minita / Geiger, Heather / Felice, Vanessa / Dikoglu, Esra / Rahman, Sadia / Fang, Xiaolan / Vacic, Vladimir / Bergmann, Ewa A / Moore Vogel, Julia L / Reeves, Catherine / Khaira, Depinder /

BMC medical genomics

2019 Volume 12, Issue 1, Page(s) 114

Abstract: Following publication of the original article [1], it was reported that the given name of the fourteenth author was incorrectly published. The incorrect and the correct names are given below. ...

Abstract	Following publication of the original article [1], it was reported that the given name of the fourteenth author was incorrectly published. The incorrect and the correct names are given below.
Language	English
Publishing date	2019-08-02
Publishing country	England
Document type	Published Erratum
ISSN	1755-8794
ISSN (online)	1755-8794
DOI	10.1186/s12920-019-0563-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Researching COVID to enhance recovery (RECOVER) pediatric study protocol: Rationale, objectives and design.

Gross, Rachel S / Thaweethai, Tanayott / Rosenzweig, Erika B / Chan, James / Chibnik, Lori B / Cicek, Mine S / Elliott, Amy J / Flaherman, Valerie J / Foulkes, Andrea S / Gage Witvliet, Margot / Gallagher, Richard / Gennaro, Maria Laura / Jernigan, Terry L / Karlson, Elizabeth W / Katz, Stuart D / Kinser, Patricia A / Kleinman, Lawrence C / Lamendola-Essel, Michelle F / Milner, Joshua D /

Mohandas, Sindhu / Mudumbi, Praveen C / Newburger, Jane W / Rhee, Kyung E / Salisbury, Amy L / Snowden, Jessica N / Stein, Cheryl R / Stockwell, Melissa S / Tantisira, Kelan G / Thomason, Moriah E / Truong, Dongngan T / Warburton, David / Wood, John C / Ahmed, Shifa / Akerlundh, Almary / Alshawabkeh, Akram N / Anderson, Brett R / Aschner, Judy L / Atz, Andrew M / Aupperle, Robin L / Baker, Fiona C / Balaraman, Venkataraman / Banerjee, Dithi / Barch, Deanna M / Baskin-Sommers, Arielle / Bhuiyan, Sultana / Bind, Marie-Abele C / Bogie, Amanda L / Bradford, Tamara / Buchbinder, Natalie C / Bueler, Elliott / Bükülmez, Hülya / Casey, B J / Chang, Linda / Chrisant, Maryanne / Clark, Duncan B / Clifton, Rebecca G / Clouser, Katharine N / Cottrell, Lesley / Cowan, Kelly / D'Sa, Viren / Dapretto, Mirella / Dasgupta, Soham / Dehority, Walter / Dionne, Audrey / Dummer, Kirsten B / Elias, Matthew D / Esquenazi-Karonika, Shari / Evans, Danielle N / Faustino, E Vincent S / Fiks, Alexander G / Forsha, Daniel / Foxe, John J / Friedman, Naomi P / Fry, Greta / Gaur, Sunanda / Gee, Dylan G / Gray, Kevin M / Handler, Stephanie / Harahsheh, Ashraf S / Hasbani, Keren / Heath, Andrew C / Hebson, Camden / Heitzeg, Mary M / Hester, Christina M / Hill, Sophia / Hobart-Porter, Laura / Hong, Travis K F / Horowitz, Carol R / Hsia, Daniel S / Huentelman, Matthew / Hummel, Kathy D / Irby, Katherine / Jacobus, Joanna / Jacoby, Vanessa L / Jone, Pei-Ni / Kaelber, David C / Kasmarcak, Tyler J / Kluko, Matthew J / Kosut, Jessica S / Laird, Angela R / Landeo-Gutierrez, Jeremy / Lang, Sean M / Larson, Christine L / Lim, Peter Paul C / Lisdahl, Krista M / McCrindle, Brian W / McCulloh, Russell J / McHugh, Kimberly / Mendelsohn, Alan L / Metz, Torri D / Miller, Julie / Mitchell, Elizabeth C / Morgan, Lerraughn M / Müller-Oehring, Eva M / Nahin, Erica R / Neale, Michael C / Ness-Cochinwala, Manette / Nolan, Sheila M / Oliveira, Carlos R / Osakwe, Onyekachukwu / Oster, Matthew E / Payne, R Mark / Portman, Michael A / Raissy, Hengameh / Randall, Isabelle G / Rao, Suchitra / Reeder, Harrison T / Rosas, Johana M / Russell, Mark W / Sabati, Arash A / Sanil, Yamuna / Sato, Alice I / Schechter, Michael S / Selvarangan, Rangaraj / Sexson Tejtel, S Kristen / Shakti, Divya / Sharma, Kavita / Squeglia, Lindsay M / Srivastava, Shubika / Stevenson, Michelle D / Szmuszkovicz, Jacqueline / Talavera-Barber, Maria M / Teufel, Ronald J / Thacker, Deepika / Trachtenberg, Felicia / Udosen, Mmekom M / Warner, Megan R / Watson, Sara E / Werzberger, Alan / Weyer, Jordan C / Wood, Marion J / Yin, H Shonna / Zempsky, William T / Zimmerman, Emily / Dreyer, Benard P

PloS one

2024 Volume 19, Issue 5, Page(s) e0285635

Abstract: Importance: The prevalence, pathophysiology, and long-term outcomes of COVID-19 (post-acute sequelae of SARS-CoV-2 [PASC] or "Long COVID") in children and young adults remain unknown. Studies must address the urgent need to define PASC, its mechanisms, ... ...

Abstract	Importance: The prevalence, pathophysiology, and long-term outcomes of COVID-19 (post-acute sequelae of SARS-CoV-2 [PASC] or "Long COVID") in children and young adults remain unknown. Studies must address the urgent need to define PASC, its mechanisms, and potential treatment targets in children and young adults. Observations: We describe the protocol for the Pediatric Observational Cohort Study of the NIH's REsearching COVID to Enhance Recovery (RECOVER) Initiative. RECOVER-Pediatrics is an observational meta-cohort study of caregiver-child pairs (birth through 17 years) and young adults (18 through 25 years), recruited from more than 100 sites across the US. This report focuses on two of four cohorts that comprise RECOVER-Pediatrics: 1) a de novo RECOVER prospective cohort of children and young adults with and without previous or current infection; and 2) an extant cohort derived from the Adolescent Brain Cognitive Development (ABCD) study (n = 10,000). The de novo cohort incorporates three tiers of data collection: 1) remote baseline assessments (Tier 1, n = 6000); 2) longitudinal follow-up for up to 4 years (Tier 2, n = 6000); and 3) a subset of participants, primarily the most severely affected by PASC, who will undergo deep phenotyping to explore PASC pathophysiology (Tier 3, n = 600). Youth enrolled in the ABCD study participate in Tier 1. The pediatric protocol was developed as a collaborative partnership of investigators, patients, researchers, clinicians, community partners, and federal partners, intentionally promoting inclusivity and diversity. The protocol is adaptive to facilitate responses to emerging science. Conclusions and relevance: RECOVER-Pediatrics seeks to characterize the clinical course, underlying mechanisms, and long-term effects of PASC from birth through 25 years old. RECOVER-Pediatrics is designed to elucidate the epidemiology, four-year clinical course, and sociodemographic correlates of pediatric PASC. The data and biosamples will allow examination of mechanistic hypotheses and biomarkers, thus providing insights into potential therapeutic interventions. Clinical trials.gov identifier: Clinical Trial Registration: http://www.clinicaltrials.gov. Unique identifier: NCT05172011.
MeSH term(s)	Humans ; COVID-19/epidemiology ; COVID-19/virology ; Adolescent ; Child ; Child, Preschool ; Female ; Young Adult ; Adult ; Male ; Infant ; SARS-CoV-2/isolation & purification ; Infant, Newborn ; Prospective Studies ; Research Design ; Cohort Studies ; Post-Acute COVID-19 Syndrome
Language	English
Publishing date	2024-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Observational Study
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0285635
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: DRUL for School: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2

Frank, Mayu / Blachere, Nathalie E / Parveen, Salina / Hacisuleyman, Ezgi / Fak, John / Luna, Joseph M / Michailidis, Eleftherios / Wright, Samara / Stark, Pamela / Campbell, Ann H / Foo, Ashley / Sakmar, Thomas P / Huffman, Virginia / Bergh, Marissa / Goldfarb, Audrey / Mansisidor, Andrew / Patriotis, Agata L / Palmquist, Karl H / Poulton, Nicolas /

Leicher, Rachel / Vargas, Cesar D / Duba, Irene / Hurley, Arlene / Colagreco, Joseph P / Pagane, Nicole / Orange, Dana E / Mora, Kevin / Rakeman, Jennifer L / Fowler, Randal C / Fernandes, Helen / Lamendola-Essel, Michelle F / Didkovsky, Nick / Silvera, Leopolda / Masci, Joseph / Allen, Machelle / Rice, Charles M / Darnell, Robert B

medRxiv

Abstract: To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 ul saliva in vials containing Darnell Rockefeller ... ...

Abstract	To address the need for simple, safe, sensitive, and scalable SARS-CoV-2 tests, we validated and implemented a PCR test that uses a saliva collection kit use at home. Individuals self-collected 300 ul saliva in vials containing Darnell Rockefeller University Laboratory (DRUL) buffer and extracted RNA was assayed by RT-PCR (the DRUL saliva assay). The limit of detection was confirmed to be 1 viral copy/ul in 20 of 20 replicate extractions. Viral RNA was stable in DRUL buffer at room temperature up to seven days after sample collection, and safety studies demonstrated that DRUL buffer immediately inactivated virus at concentrations up to 2.75x106 PFU/ml. Results from SARS-CoV-2 positive nasopharyngeal (NP) swab samples collected in viral transport media and assayed with a standard FDA Emergency Use Authorization (EUA) test were highly correlated with samples placed in DRUL buffer. Direct comparison of results from 162 individuals tested by FDA EUA oropharyngeal (OP) or NP swabs with co-collected saliva samples identified four otherwise unidentified positive cases in DRUL buffer. Over six months, we collected 3,724 samples from individuals ranging from 3 months to 92 years of age. This included collecting weekly samples over 10 weeks from teachers, children, and parents from a pre-school program, which allowed its safe reopening while at-risk pods were quarantined. In sum, we validated a simple, sensitive, stable, and safe PCR-based test using a self-collected saliva sample as a valuable tool for clinical diagnosis and screening at workplaces and schools.
Keywords	covid19
Language	English
Publishing date	2021-04-06
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.04.03.21254873
Database	COVID19

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