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6 results on '"Heyderman, R"'

1. Direct inference and control of genetic population structure from RNA sequencing data

Author

Fachrul, M, Karkey, AM, Shakya, M, Judd, L, Harshegyi, T, Sim, KS, Tonks, S, Dongol, S, Shrestha, R, Salim, A, Adhikari, A, Banda, HCC, Blohmke, C, Darton, T, Farooq, Y, Ghimire, M, Hill, J, Hoang, NT, Jere, TM, Kamzati, M, Kao, Y-H, Masesa, C, Mbewe, M, Msuku, H, Munthali, P, Nga, TVTJ, Nkhata, R, Saad, N, Tan, TV, Thindwa, D, Khanam, FD, Meiring, J, Clemens, JE, Dougan, G, Pitzer, VS, Qadri, FA, Heyderman, R, Gordon, M, Voysey, MJ, Baker, S, Pollard, A, Khor, CC, Dolecek, CJ, Basnyat, BE, Dunstan, S, Holt, K, Inouye, M, Fachrul, M, Karkey, AM, Shakya, M, Judd, L, Harshegyi, T, Sim, KS, Tonks, S, Dongol, S, Shrestha, R, Salim, A, Adhikari, A, Banda, HCC, Blohmke, C, Darton, T, Farooq, Y, Ghimire, M, Hill, J, Hoang, NT, Jere, TM, Kamzati, M, Kao, Y-H, Masesa, C, Mbewe, M, Msuku, H, Munthali, P, Nga, TVTJ, Nkhata, R, Saad, N, Tan, TV, Thindwa, D, Khanam, FD, Meiring, J, Clemens, JE, Dougan, G, Pitzer, VS, Qadri, FA, Heyderman, R, Gordon, M, Voysey, MJ, Baker, S, Pollard, A, Khor, CC, Dolecek, CJ, Basnyat, BE, Dunstan, S, Holt, K, and Inouye, M

Abstract

RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data.

Published
2023

2. Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification

Author

Gliddon, HD, Kaforou, M, Alikian, M, Habgood-Coote, D, Zhou, C, Oni, T, Anderson, ST, Brent, AJ, Crampin, AC, Eley, B, Heyderman, R, Kern, F, Langford, PR, Ottenhoff, THM, Hibberd, ML, French, N, Wright, VJ, Dockrell, HM, Coin, LJ, Wilkinson, RJ, Levin, M, Gliddon, HD, Kaforou, M, Alikian, M, Habgood-Coote, D, Zhou, C, Oni, T, Anderson, ST, Brent, AJ, Crampin, AC, Eley, B, Heyderman, R, Kern, F, Langford, PR, Ottenhoff, THM, Hibberd, ML, French, N, Wright, VJ, Dockrell, HM, Coin, LJ, Wilkinson, RJ, and Levin, M

Abstract

Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Signatures were further investigated using reverse transcriptase (RT)-digital PCR (dPCR). A four-transcript signature (GBP6, TMCC1, PRDM1, and ARG1) measured using RT-dPCR distinguished TB patients from those with OD (area under the curve (AUC) 93.8% (CI95% 82.2-100%). A three-transcript signature (FCGR1A, ZNF296, and C1QB) differentiated TB from LTBI (AUC 97.3%, CI95%: 93.3-100%), regardless of HIV. These signatures have been validated across platforms and across samples offering strong, quantitative support for their use as diagnostic biomarkers for TB.

Published
2021

3. Adjunctive Dexamethasone in HIV-Associated Cryptococcal Meningitis.

Author

Beardsley, J., Wolbers, M., Kibengo, F.M., Ggayi, A.B., Kamali, A., Cuc, N.T., Binh, T.Q., Chau, N.V., Farrar, J., Merson, L., Phuong, L., Thwaites, G., Kinh, N. Van, Thuy, P.T., Chierakul, W., Siriboon, S., Thiansukhon, E., Onsanit, S., Supphamongkholchaikul, W., Chan, A.K., Heyderman, R., Mwinjiwa, E., Oosterhout, J.J. van, Imran, D., Basri, H., Mayxay, M., Dance, D., Phimmasone, P., Rattanavong, S., Lalloo, D.G., Day, J.N., Wertheim, H.F.L., et al., Beardsley, J., Wolbers, M., Kibengo, F.M., Ggayi, A.B., Kamali, A., Cuc, N.T., Binh, T.Q., Chau, N.V., Farrar, J., Merson, L., Phuong, L., Thwaites, G., Kinh, N. Van, Thuy, P.T., Chierakul, W., Siriboon, S., Thiansukhon, E., Onsanit, S., Supphamongkholchaikul, W., Chan, A.K., Heyderman, R., Mwinjiwa, E., Oosterhout, J.J. van, Imran, D., Basri, H., Mayxay, M., Dance, D., Phimmasone, P., Rattanavong, S., Lalloo, D.G., Day, J.N., Wertheim, H.F.L., and et al.

Abstract

Item does not contain fulltext

Published
2016

4. Adjunctive Dexamethasone in HIV-Associated Cryptococcal Meningitis.

Author

Beardsley, J., Wolbers, M., Kibengo, F.M., Ggayi, A.B., Kamali, A., Cuc, N.T., Binh, T.Q., Chau, N.V., Farrar, J., Merson, L., Phuong, L., Thwaites, G., Kinh, N. Van, Thuy, P.T., Chierakul, W., Siriboon, S., Thiansukhon, E., Onsanit, S., Supphamongkholchaikul, W., Chan, A.K., Heyderman, R., Mwinjiwa, E., Oosterhout, J.J. van, Imran, D., Basri, H., Mayxay, M., Dance, D., Phimmasone, P., Rattanavong, S., Lalloo, D.G., Day, J.N., Wertheim, H.F.L., et al., Beardsley, J., Wolbers, M., Kibengo, F.M., Ggayi, A.B., Kamali, A., Cuc, N.T., Binh, T.Q., Chau, N.V., Farrar, J., Merson, L., Phuong, L., Thwaites, G., Kinh, N. Van, Thuy, P.T., Chierakul, W., Siriboon, S., Thiansukhon, E., Onsanit, S., Supphamongkholchaikul, W., Chan, A.K., Heyderman, R., Mwinjiwa, E., Oosterhout, J.J. van, Imran, D., Basri, H., Mayxay, M., Dance, D., Phimmasone, P., Rattanavong, S., Lalloo, D.G., Day, J.N., Wertheim, H.F.L., and et al.

Abstract

Item does not contain fulltext

Published
2016

5. Adjunctive Dexamethasone in HIV-Associated Cryptococcal Meningitis.

Author

Beardsley, J., Wolbers, M., Kibengo, F.M., Ggayi, A.B., Kamali, A., Cuc, N.T., Binh, T.Q., Chau, N.V., Farrar, J., Merson, L., Phuong, L., Thwaites, G., Kinh, N. Van, Thuy, P.T., Chierakul, W., Siriboon, S., Thiansukhon, E., Onsanit, S., Supphamongkholchaikul, W., Chan, A.K., Heyderman, R., Mwinjiwa, E., Oosterhout, J.J. van, Imran, D., Basri, H., Mayxay, M., Dance, D., Phimmasone, P., Rattanavong, S., Lalloo, D.G., Day, J.N., Wertheim, H.F.L., et al., Beardsley, J., Wolbers, M., Kibengo, F.M., Ggayi, A.B., Kamali, A., Cuc, N.T., Binh, T.Q., Chau, N.V., Farrar, J., Merson, L., Phuong, L., Thwaites, G., Kinh, N. Van, Thuy, P.T., Chierakul, W., Siriboon, S., Thiansukhon, E., Onsanit, S., Supphamongkholchaikul, W., Chan, A.K., Heyderman, R., Mwinjiwa, E., Oosterhout, J.J. van, Imran, D., Basri, H., Mayxay, M., Dance, D., Phimmasone, P., Rattanavong, S., Lalloo, D.G., Day, J.N., Wertheim, H.F.L., and et al.

Abstract

Item does not contain fulltext

Published
2016

6. Adjunctive Dexamethasone in HIV-Associated Cryptococcal Meningitis.

Author

Beardsley, J., Wolbers, M., Kibengo, F.M., Ggayi, A.B., Kamali, A., Cuc, N.T., Binh, T.Q., Chau, N.V., Farrar, J., Merson, L., Phuong, L., Thwaites, G., Kinh, N. Van, Thuy, P.T., Chierakul, W., Siriboon, S., Thiansukhon, E., Onsanit, S., Supphamongkholchaikul, W., Chan, A.K., Heyderman, R., Mwinjiwa, E., Oosterhout, J.J. van, Imran, D., Basri, H., Mayxay, M., Dance, D., Phimmasone, P., Rattanavong, S., Lalloo, D.G., Day, J.N., Wertheim, H.F.L., et al., Beardsley, J., Wolbers, M., Kibengo, F.M., Ggayi, A.B., Kamali, A., Cuc, N.T., Binh, T.Q., Chau, N.V., Farrar, J., Merson, L., Phuong, L., Thwaites, G., Kinh, N. Van, Thuy, P.T., Chierakul, W., Siriboon, S., Thiansukhon, E., Onsanit, S., Supphamongkholchaikul, W., Chan, A.K., Heyderman, R., Mwinjiwa, E., Oosterhout, J.J. van, Imran, D., Basri, H., Mayxay, M., Dance, D., Phimmasone, P., Rattanavong, S., Lalloo, D.G., Day, J.N., Wertheim, H.F.L., and et al.

Abstract

Item does not contain fulltext

Published
2016

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