المؤلفون: Chang, Ellen T.^{Aff1, IDs10552023018424_cor1}, Clarke, Christina A., Colditz, Graham A., Kurian, Allison W., Hubbell, Earl

المصدر: Cancer Causes & Control: An International Journal of Studies of Cancer in Human Populations. 35(5):849-864

المؤلفون: McGuire, Valerie^{Aff1, IDs10552023018362_cor1}, Lichtensztajn, Daphne Y.^{Aff1, Aff2}, Tao, Li, Yang, Juan^{Aff1, Aff2}, Clarke, Christina A., Wu, Anna H., Wilkens, Lynne, Glaser, Sally L., Park, Sungshim Lani, Cheng, Iona^{Aff1, Aff2}

المصدر: Cancer Causes & Control: An International Journal of Studies of Cancer in Human Populations. 35(5):799-815

المؤلفون: Boggs, Jennifer M.^{Aff1, IDs11121024016416_cor1}, Quintana, LeeAnn M., Beck, Arne, Clarke, Christina L., Richardson, Laura, Conley, Amy, Buckingham, Edward T.^{Aff2, Aff3}, Richards, Julie E., Betz, Marian E.

المصدر: Prevention Science: Official Journal of the Society for Prevention Research. 25(2):358-368

المؤلفون: Ramchandar, Nanda, Coufal, Nicole G, Warden, Anna S, Briggs, Benjamin, Schwarz, Toni, Stinnett, Rita, Xie, Heng, Schlaberg, Robert, Foley, Jennifer, Clarke, Christina, Waldeman, Bryce, Enriquez, Claudia, Osborne, Stephanie, Arrieta, Antonio, Salyakina, Daria, Janvier, Michelin, Sendi, Prithvi, Totapally, Balagangadhar R, Dimmock, David, Farnaes, Lauge

المصدر: Open Forum Infectious Diseases. 8(6)

مصطلحات موضوعية: Biomedical and Clinical Sciences, Clinical Sciences, Genetics, Neurosciences, Pediatric, Clinical Research, Infectious Diseases, Brain Disorders, Infection, Good Health and Well Being, encephalitis, meningitis, metagenomics, next-generation sequencing, pediatric, Clinical sciences, Medical microbiology

الوصف: BackgroundPediatric central nervous system (CNS) infections are potentially life-threatening and may incur significant morbidity. Identifying a pathogen is important, both in terms of guiding therapeutic management and in characterizing prognosis. Usual care testing by culture and polymerase chain reaction is often unable to identify a pathogen. We examined the systematic application of metagenomic next-generation sequencing (mNGS) for detecting organisms and transcriptomic analysis of cerebrospinal fluid (CSF) in children with central nervous system (CNS) infections.MethodsWe conducted a prospective multisite study that aimed to enroll all children with a CSF pleocytosis and suspected CNS infection admitted to 1 of 3 tertiary pediatric hospitals during the study timeframe. After usual care testing had been performed, the remaining CSF was sent for mNGS and transcriptomic analysis.ResultsWe screened 221 and enrolled 70 subjects over a 12-month recruitment period. A putative organism was isolated from CSF in 25 (35.7%) subjects by any diagnostic modality. Metagenomic next-generation sequencing of the CSF samples identified a pathogen in 20 (28.6%) subjects, which were also all identified by usual care testing. The median time to result was 38 hours.ConclusionsMetagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections.

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URL الوصول: https://escholarship.org/uc/item/54n897tj

المؤلفون: Cakici, Julie A., Dimmock, David, Caylor, Sara, Gaughran, Mary, Clarke, Christina, Triplett, Cynthia, Clark, Michelle M., Kingsmore, Stephen F., Bloss, Cinnamon S.

المصدر: In Clinical Therapeutics August 2023 45(8):736-744

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المؤلفون: Dimmock, David P, Clark, Michelle M, Gaughran, Mary, Cakici, Julie A, Caylor, Sara A, Clarke, Christina, Feddock, Michele, Chowdhury, Shimul, Salz, Lisa, Cheung, Cynthia, Bird, Lynne M, Hobbs, Charlotte, Wigby, Kristen, Farnaes, Lauge, Bloss, Cinnamon S, Kingsmore, Stephen F, Investigators, the RCIGM, Bainbridge, Matthew N, Barea, Jaime, Batalov, Sergey, Bezares, Zaira, Braun, Joshua JA, Del Campo, Miguel, Carroll, Jeanne, Cohenmeyer, Casey, Coufal, Nicole G, Diaz, Carlos, Ding, Yan, Ellsworth, Katarzyna, Evans, Marva, Feigenbaum, Annette, Friedman, Jennifer, Gleeson, Joe, Hansen, Christian, Honold, Jose, James, Kiely, Jones, Marilyn C, Kimball, Amy, Knight, Gail, Van Der Kraan, Lucitia, Lane, Brian, Le, Jennie, Leibel, Sandra, Lenberg, Jerica, Mashburn, Dana, Moyer, Laurel, Mulrooney, Patrick, Nahas, Shareef, Oh, Daeheon, Orendain, Daniken, Oriol, Albert, Ortiz-Arechiga, Maria, Prince, Lance, Rego, Seema, Reyes, Iris, Sanford, Erica, Sauer, Charles, Schwanemann, Leila, Speziale, Mark, Suttner, Denise, Sweeney, Nathaly, Song, Richard, Tokita, Mari, Veeraraghavan, Narayanan, Watkins, Kelly, Wong, Terence, Wright, Meredith S, Yamada, Catherine

المصدر: American Journal of Human Genetics. 107(5)

مصطلحات موضوعية: Biological Sciences, Biomedical and Clinical Sciences, Health Sciences, Genetics, Clinical Trials and Supportive Activities, Clinical Research, Biotechnology, Infectious Diseases, Pediatric, Human Genome, Good Health and Well Being, Chromosome Mapping, Clinical Decision-Making, Critical Illness, Disease Management, Female, Genetic Diseases, Inborn, Genetic Testing, Genome, Human, Humans, Infant, Infant, Newborn, Intensive Care Units, Neonatal, Logistic Models, Male, Prospective Studies, Time Factors, Whole Genome Sequencing, RCIGM Investigators, NSIGHT2, clinical utility, diagnostic testing outcomes, healthcare cost-benefit analysis, neonatal intensive care unit, pediatric intensive care unit, rapid whole-exome sequencing, rapid whole-genome sequencing, ultra-rapid whole-genome sequencing, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences

الوصف: The second Newborn Sequencing in Genomic Medicine and Public Health (NSIGHT2) study was a randomized, controlled trial of rapid whole-genome sequencing (rWGS) or rapid whole-exome sequencing (rWES) in infants with diseases of unknown etiology in intensive care units (ICUs). Gravely ill infants were not randomized and received ultra-rapid whole-genome sequencing (urWGS). Herein we report results of clinician surveys of the clinical utility of rapid genomic sequencing (RGS). The primary end-point-clinician perception that RGS was useful- was met for 154 (77%) of 201 infants. Both positive and negative tests were rated as having clinical utility (42 of 45 [93%] and 112 of 156 [72%], respectively). Physicians reported that RGS changed clinical management in 57 (28%) infants, particularly in those receiving urWGS (p = 0.0001) and positive tests (p < 0.00001). Outcomes of 32 (15%) infants were perceived to be changed by RGS. Positive tests changed outcomes more frequently than negative tests (p < 0.00001). In logistic regression models, the likelihood that RGS was perceived as useful increased 6.7-fold when associated with changes in management (95% CI 1.8-43.3). Changes in management were 10.1-fold more likely when results were positive (95% CI 4.7-22.4) and turnaround time was shorter (odds ratio 0.92, 95% CI 0.85-0.99). RGS seldom led to clinician-perceived confusion or distress among families (6 of 207 [3%]). In summary, clinicians perceived high clinical utility and low likelihood of harm with first-tier RGS of infants in ICUs with diseases of unknown etiology. RGS was perceived as beneficial irrespective of whether results were positive or negative.

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URL الوصول: https://escholarship.org/uc/item/289757jt
https://escholarship.org/content/qt289757jt/qt289757jt.pdf

المؤلفون: Raoof, Sana, Clarke, Christina A., Hubbell, Earl, Chang, Ellen T., Cusack, James

المصدر: In Cancer Epidemiology June 2023 84

المؤلفون: Kingsmore, Stephen F, Cakici, Julie A, Clark, Michelle M, Gaughran, Mary, Feddock, Michele, Batalov, Sergey, Bainbridge, Matthew N, Carroll, Jeanne, Caylor, Sara A, Clarke, Christina, Ding, Yan, Ellsworth, Katarzyna, Farnaes, Lauge, Hildreth, Amber, Hobbs, Charlotte, James, Kiely, Kint, Cyrielle I, Lenberg, Jerica, Nahas, Shareef, Prince, Lance, Reyes, Iris, Salz, Lisa, Sanford, Erica, Schols, Peter, Sweeney, Nathaly, Tokita, Mari, Veeraraghavan, Narayanan, Watkins, Kelly, Wigby, Kristen, Wong, Terence, Chowdhury, Shimul, Wright, Meredith S, Dimmock, David, Investigators, the RCIGM, Bezares, Zaira, Bloss, Cinnamon, Braun, Joshua JA, Diaz, Carlos, Mashburn, Dana, Tamang, Dorjee, Orendain, Daniken, Friedman, Jenni, Gleeson, Joe, Barea, Jaime, Chiang, George, Cohenmeyer, Casey, Coufal, Nicole G, Evans, Marva, Honold, Jose, Hovey, Raymond L, Kimball, Amy, Lane, Brian, Le, Crystal, Le, Jennie, Leibel, Sandra, Moyer, Laurel, Mulrooney, Patrick, Oh, Daeheon, Ordonez, Paulina, Oriol, Albert, Ortiz-Arechiga, Maria, Puckett, Laura, Speziale, Mark, Suttner, Denise, Van Der Kraan, Lucitia, Knight, Gail, Sauer, Charles, Song, Richard, White, Sarah, Wise, Audra, Yamada, Catherine

المصدر: American Journal of Human Genetics. 105(4)

مصطلحات موضوعية: Human Genome, Pediatric, Clinical Research, Genetics, Clinical Trials and Supportive Activities, Good Health and Well Being, Genetic Testing, Humans, Infant, Infant, Newborn, Exome Sequencing, Whole Genome Sequencing, RCIGM Investigators, diagnosis, genetic disease, genomic medicine, infant, intensive care unit, precision medicine, ultra-rapid whole-genome sequencing, whole-exome sequencing, whole-genome sequencing, Biological Sciences, Medical and Health Sciences, Genetics & Heredity

الوصف: The second Newborn Sequencing in Genomic Medicine and Public Health study was a randomized, controlled trial of the effectiveness of rapid whole-genome or -exome sequencing (rWGS or rWES, respectively) in seriously ill infants with diseases of unknown etiology. Here we report comparisons of analytic and diagnostic performance. Of 1,248 ill inpatient infants, 578 (46%) had diseases of unknown etiology. 213 infants (37% of those eligible) were enrolled within 96 h of admission. 24 infants (11%) were very ill and received ultra-rapid whole-genome sequencing (urWGS). The remaining infants were randomized, 95 to rWES and 94 to rWGS. The analytic performance of rWGS was superior to rWES, including variants likely to affect protein function, and ClinVar pathogenic/likely pathogenic variants (p < 0.0001). The diagnostic performance of rWGS and rWES were similar (18 diagnoses in 94 infants [19%] versus 19 diagnoses in 95 infants [20%], respectively), as was time to result (median 11.0 versus 11.2 days, respectively). However, the proportion diagnosed by urWGS (11 of 24 [46%]) was higher than rWES/rWGS (p = 0.004) and time to result was less (median 4.6 days, p < 0.0001). The incremental diagnostic yield of reflexing to trio after negative proband analysis was 0.7% (1 of 147). In conclusion, rapid genomic sequencing can be performed as a first-tier diagnostic test in inpatient infants. urWGS had the shortest time to result, which was important in unstable infants, and those in whom a genetic diagnosis was likely to impact immediate management. Further comparison of urWGS and rWES is warranted because genomic technologies and knowledge of variant pathogenicity are evolving rapidly.

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URL الوصول: https://escholarship.org/uc/item/9h05k7vh

المؤلفون: Hausauer, Amelia K, Keegan, Theresa HM, Chang, Ellen T, Clarke, Christina A

المصدر: Hausauer, Amelia K and Keegan, Theresa HM and Chang, Ellen T and Clarke, Christina A (2007) Recent breast cancer trends among Asian/Pacific Islander, Hispanic, and African-American women in the US: changes by tumor subtype. Breast Cancer Research, 9 (6). R90. ISSN 1465-5411

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Relation: http://health-equity.pitt.edu/3802/