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236 results on '"Boardman L"'

9. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Author

Gong, B, Li, D, Kusko, R, Novoradovskaya, N, Zhang, Y, Wang, S, Pabón-Peña, C, Zhang, Z, Lai, K, Cai, W, LoCoco, JS, Lader, E, Richmond, TA, Mittal, VK, Liu, LC, Johann, DJ, Willey, JC, Bushel, PR, Yu, Y, Xu, C, Chen, G, Burgess, D, Cawley, S, Giorda, K, Haseley, N, Qiu, F, Wilkins, K, Arib, H, Attwooll, C, Babson, K, Bao, L, Bao, W, Lucas, AB, Best, H, Bhandari, A, Bisgin, H, Blackburn, J, Blomquist, TM, Boardman, L, Burgher, B, Butler, DJ, Chang, CJ, Chaubey, A, Chen, T, Chierici, M, Chin, CR, Close, D, Conroy, J, Coleman, JC, Craig, DJ, Crawford, E, del Pozo, A, Deveson, IW, Duncan, D, Eterovic, AK, Fan, X, Foox, J, Furlanello, C, Ghosal, A, Glenn, S, Guan, M, Haag, C, Hang, X, Happe, S, Hennigan, B, Hipp, J, Hong, H, Horvath, K, Hu, J, Hung, LY, Jarosz, M, Kerkhof, J, Kipp, B, Kreil, DP, Łabaj, P, Lapunzina, P, Li, P, Li, QZ, Li, W, Li, Z, Liang, Y, Liu, S, Liu, Z, Ma, C, Marella, N, Martín-Arenas, R, Megherbi, DB, Meng, Q, Mieczkowski, PA, Morrison, T, Muzny, D, Ning, B, Parsons, BL, Paweletz, CP, Pirooznia, M, Qu, W, Raymond, A, Rindler, P, Ringler, R, Sadikovic, B, Gong, B, Li, D, Kusko, R, Novoradovskaya, N, Zhang, Y, Wang, S, Pabón-Peña, C, Zhang, Z, Lai, K, Cai, W, LoCoco, JS, Lader, E, Richmond, TA, Mittal, VK, Liu, LC, Johann, DJ, Willey, JC, Bushel, PR, Yu, Y, Xu, C, Chen, G, Burgess, D, Cawley, S, Giorda, K, Haseley, N, Qiu, F, Wilkins, K, Arib, H, Attwooll, C, Babson, K, Bao, L, Bao, W, Lucas, AB, Best, H, Bhandari, A, Bisgin, H, Blackburn, J, Blomquist, TM, Boardman, L, Burgher, B, Butler, DJ, Chang, CJ, Chaubey, A, Chen, T, Chierici, M, Chin, CR, Close, D, Conroy, J, Coleman, JC, Craig, DJ, Crawford, E, del Pozo, A, Deveson, IW, Duncan, D, Eterovic, AK, Fan, X, Foox, J, Furlanello, C, Ghosal, A, Glenn, S, Guan, M, Haag, C, Hang, X, Happe, S, Hennigan, B, Hipp, J, Hong, H, Horvath, K, Hu, J, Hung, LY, Jarosz, M, Kerkhof, J, Kipp, B, Kreil, DP, Łabaj, P, Lapunzina, P, Li, P, Li, QZ, Li, W, Li, Z, Liang, Y, Liu, S, Liu, Z, Ma, C, Marella, N, Martín-Arenas, R, Megherbi, DB, Meng, Q, Mieczkowski, PA, Morrison, T, Muzny, D, Ning, B, Parsons, BL, Paweletz, CP, Pirooznia, M, Qu, W, Raymond, A, Rindler, P, Ringler, R, and Sadikovic, B

Abstract

Background: Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing. Results: All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5–20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden. Conclusion: This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.

Published
2021

12. 'n Multinavorsingsmodel toegerus met sagteware-instrumente vir die afstandanalisering van rotskunsdata: Bosworth-plaas gevallestudie.

Author

Boardman, L. and de Klerk, T. C.

Abstract

The global distribution of rock art complicates the research thereof and has forced researchers to rely on its online availability. Should some of the elements in such an artwork appear to be unclear, online applications that could lead to its possible enhancement must be sought on an individual basis. The aim of this study was to attempt to fill this need by, firstly, creating an interactive multi-research model, and secondly, to determine the research value of such a model. Petroglyphs of the Bosworth rock art site have been documented and presented for this purpose in the context of their immediate surroundings, namely the relevant rocks and site. To make this data available online, a web application has been created offering analytical capabilities with regards to the magnification, manipulation of the viewing angle, allocation of new colour combinations, as well as the casting of digital shadows over the artworks. A combination of these built-in manipulation options was then made available for application to both 2D and 3D depictions of each artwork, in colour as well as in monochrome. Researchers are thus given the opportunity to virtually visit the rock art site and enhance the visibility of the petroglyphs by means of integrated software tools. These digital archaeological techniques can be applied in the same way to other rock art sites for the analysis and study of rock art. [ABSTRACT FROM AUTHOR]

Published
2022
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13. STK11 status and intussusception risk in Peutz-Jeghers syndrome

Author

Hearle, N, Schumacher, V, Menko, F H, Olschwang, S, Boardman, L A, Gille, J J P, Keller, J J, Westerman, A M, Scott, R J, Lim, W, Trimbath, J D, Giardiello, F M, Gruber, S B, Offerhaus, G J A, Rooij, F W M D E, Wilson, J H P, Hansmann, A, Möslein, G, Royer-Pokora, B, Vogel, T, Phillips, R K S, Spigelman, A D, and Houlston, R S

Published
2006

16. The Burden of Specific Symptoms Reported by Survivors after Critical Illness

Author

Griffith, David M., primary, Salisbury, Lisa G., additional, Lee, Robert J., additional, Lone, Nazir, additional, Merriweather, Judith L., additional, Walsh, Timothy S., additional, Walsh, T. S., additional, Salisbury, L. G., additional, Merriweather, J. L., additional, Boyd, J. A., additional, Griffith, D. M., additional, Huby, G., additional, Kean, S., additional, Mackenzie, S. J., additional, Krishan, A., additional, Lewis, S. C., additional, Murray, G. D., additional, Forbes, J. F., additional, Smith, J., additional, Rattray, J. E., additional, Hull, A. M., additional, Ramsay, P., additional, Wallis, C., additional, Stewart, J., additional, Bateman, A., additional, Wilson, E., additional, Gillies, M., additional, Hope, D., additional, Dawson, H., additional, McCulloch, C., additional, Antonelli, J., additional, Boardman, L., additional, Dow, L., additional, Williams, W., additional, McCann, A., additional, Alexander, S., additional, Norrie, J., additional, Dennis, M., additional, Waldmann, C., additional, and Brett, S., additional

Published
2018
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24. DNA damage-induced ephrin-B2 reverse signaling promotes chemoresistance and drives EMT in colorectal carcinoma harboring mutant p53

Author

Alam, S K, primary, Yadav, V K, additional, Bajaj, S, additional, Datta, A, additional, Dutta, S K, additional, Bhattacharyya, M, additional, Bhattacharya, S, additional, Debnath, S, additional, Roy, S, additional, Boardman, L A, additional, Smyrk, T C, additional, Molina, J R, additional, Chakrabarti, S, additional, Chowdhury, S, additional, Mukhopadhyay, D, additional, and Roychoudhury, S, additional

Published
2015
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25. Effects of temperature on heat-shock responses and survival of two species of marine invertebrates from sub-Antarctic Marion Island

Author

Clusella-Trullas, S., Boardman, L., Faulkner, K.T., Peck, L.S., Chown, S.L., Clusella-Trullas, S., Boardman, L., Faulkner, K.T., Peck, L.S., and Chown, S.L.

Abstract

This study examined high temperature survival and heat shock protein 70 (Hsp70) responses to temperature variation for two marine invertebrate species on sub-Antarctic Marion Island. The isopod Exosphaeroma gigas Leach and the amphipod Hyale hirtipalma Dana had the same tolerance to high temperature. The mean upper temperature which was lethal for 50% of the population (upper lethal temperature, ULT50) was 26.4°C for both species. However, the isopod E. gigas showed significant plasticity of ULT50, with a positive response to acclimation. In addition, the isopod had a heat shock response of Hsp70 at all acclimations, and the amount of Hsp70 protein increased significantly from basal levels upon an acute warm exposure after a cold acclimation. By contrast, the amphipod H. hirtipalma showed limited plasticity of ULT50 and no evidence for a heat shock response (failure of three different Hsp70 antibodies to bind to the extracted 70kDa proteins). Overall, these results reflect different flexibility of thermal tolerance of intertidal invertebrate species on Marion Island, with possible variation in the underlying cellular mechanisms, suggesting that warming associated with climate change may result in changes in species assemblage structure in sub-polar environments.

Published
2014

26. HDAC8 and STAT3 repress BMF gene activity in colon cancer cells

Author

Kang, Y, primary, Nian, H, additional, Rajendran, P, additional, Kim, E, additional, Dashwood, W M, additional, Pinto, J T, additional, Boardman, L A, additional, Thibodeau, S N, additional, Limburg, P J, additional, Löhr, C V, additional, Bisson, W H, additional, Williams, D E, additional, Ho, E, additional, and Dashwood, R H, additional

Published
2014
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40. DNA damage-induced ephrin-B2 reverse signaling promotes chemoresistance and drives EMT in colorectal carcinoma harboring mutant p53

Author

Alam, S K, Yadav, V K, Bajaj, S, Datta, A, Dutta, S K, Bhattacharyya, M, Bhattacharya, S, Debnath, S, Roy, S, Boardman, L A, Smyrk, T C, Molina, J R, Chakrabarti, S, Chowdhury, S, Mukhopadhyay, D, and Roychoudhury, S

Abstract

Mutation in the TP53 gene positively correlates with increased incidence of chemoresistance in different cancers. In this study, we investigated the mechanism of chemoresistance and epithelial-to-mesenchymal transition (EMT) in colorectal cancer involving the gain-of-function (GOF) mutant p53/ephrin-B2 signaling axis. Bioinformatic analysis of the NCI-60 data set and subsequent hub prediction identified EFNB2 as a possible GOF mutant p53 target gene, responsible for chemoresistance. We show that the mutant p53-NF-Y complex transcriptionally upregulates EFNB2 expression in response to DNA damage. Moreover, the acetylated form of mutant p53 protein is recruited on the EFNB2 promoter and positively regulates its expression in conjunction with coactivator p300. In vitro cell line and in vivo nude mice data show that EFNB2 silencing restores chemosensitivity in mutant p53-harboring tumors. In addition, we observed high expression of EFNB2 in patients having neoadjuvant non-responder colorectal carcinoma compared with those having responder version of the disease. In the course of deciphering the drug resistance mechanism, we also show that ephrin-B2 reverse signaling induces ABCG2 expression after drug treatment that involves JNK-c-Jun signaling in mutant p53 cells. Moreover, 5-fluorouracil-induced ephrin-B2 reverse signaling promotes tumorigenesis through the Src-ERK pathway, and drives EMT via the Src-FAK pathway. We thus conclude that targeting ephrin-B2 might enhance the therapeutic potential of DNA-damaging chemotherapeutic agents in mutant p53-bearing human tumors.

Published
2016
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47. Positive cone biopsy specimen margins in women infected with the human immunodeficiency virus.

Author

Boardman, Lori A., Peipert, Jeffrey F., Boardman, L A, Peipert, J F, Hogan, J W, and Cooper, A S

Subjects
CERVIX uteri diseases, HIV-positive women, DISEASES, CERVIX uteri surgery, CERVIX uteri, COMPARATIVE studies, RESEARCH methodology, MEDICAL cooperation, RESEARCH, CERVIX uteri tumors, EVALUATION research, PREDICTIVE tests, CROSS-sectional method, HIV seroconversion, DISEASE progression, CERVICAL intraepithelial neoplasia, CONIZATION, DISEASE complications
Abstract

Objectives: The purpose of this study was to compare the positive margin rate associated with cervical conization among women who are seropositive for human immunodeficiency virus with that among women who are seronegative.Study Design: This was a cross-sectional study of 245 women who underwent cervical conization for the following indications: biopsy-proven cervical intraepithelial neoplasia grade 2 or 3, abnormal endocervical curettage specimen, cytologic-histologic examination discrepancy, persistent cervical intraepithelial neoplasia grade 1, or abnormal cytologic characteristics with inadequate colposcopic examination.Results: Twenty-two (47.8%) of 46 women who were seropositive for human immunodeficiency virus and 65 (32.7%) of 199 women who were seronegative had positive cone biopsy specimen margins. In a multivariable logistic regression the human immunodeficiency virus-seropositive women had a 2-fold increased risk of having a positive cone biopsy margin (odds ratio, 2.25; 95% confidence interval, 1.07-4.76).Conclusion: If the presence of positive cone biopsy specimen margins represents the potential for disease progression, then our findings of a positive margin rate of nearly 50% in a human immunodeficiency virus-positive population may argue against the kind of conservative management of colposcopic follow-up that has been proposed for immunocompetent women. [ABSTRACT FROM AUTHOR]

Published
1999
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48. Increased risk for cancer in patients with the Peutz-Jeghers syndrome.

Author

Boardman, Lisa A., Thibodeau, Stephen N., Schaid, Daniel J., Lindor, Noralane M., McDonnell, Shannon K., Burgart, Lawrence J., Ahlquist, David A., Podratz, Karl C., Pittelkow, Mark, Hartmann, Lynn C., Boardman, L A, Thibodeau, S N, Schaid, D J, Lindor, N M, McDonnell, S K, Burgart, L J, Ahlquist, D A, Podratz, K C, Pittelkow, M, and Hartmann, L C

Subjects
PEUTZ-Jeghers syndrome, CANCER
Abstract

Background: Some reports describe an increased risk for cancer in patients with the Peutz-Jeghers syndrome.Objective: To characterize occurrences of cancer in a large cohort of patients with the Peutz-Jeghers syndrome.Design: Retrospective cohort study.Setting: Tertiary care center.Patients: 34 patients with the Peutz-Jeghers syndrome identified from Mayo Clinic records from 1945 to 1996.Measurements: Cases of cancer documented by chart review and telephone follow-up.Results: 26 cases of noncutaneous cancer developed in 18 of the 34 patients: 10 cases of gastrointestinal cancer and 16 cases of extraintestinal cancer. With the use of SEER (Surveillance, Epidemiology, and End Results) data for comparison, the relative risk for cancer was 18.5 (95% CI, 8.5 to 35.2) in women with the Peutz-Jeghers syndrome and 6.2 (CI, 2.5 to 12.8) in men with the syndrome (P = 0.001). In women, the relative risk for breast and gynecologic cancer was 20.3 (CI, 7.4 to 44.2).Conclusions: The Peutz-Jeghers syndrome is associated with an increased risk for cancer. The relative risk for breast and gynecologic cancers is particularly high. [ABSTRACT FROM AUTHOR]

Published
1998
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