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1. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia

Author

Kebede, Alebachew Messele, Sutanto, Edwin, Trimarsanto, Hidayat, Benavente, Ernest Diez, Barnes, Mariana, Pearson, Richard D., Siegel, Sasha V., Erko, Berhanu, Assefa, Ashenafi, Getachew, Sisay, Aseffa, Abraham, Petros, Beyene, Lo, Eugenia, Mohammed, Rezika, Yilma, Daniel, Rumaseb, Angela, Nosten, Francois, Noviyanti, Rintis, Rayner, Julian C., Kwiatkowski, Dominic P., Price, Ric N., Golassa, Lemu, and Auburn, Sarah

Published
2023
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2. Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas

Author

Sutanto, Edwin, Pava, Zuleima, Echeverry, Diego F., Lopera-Mesa, Tatiana M., Montenegro, Lidia Madeline, Yasnot-Acosta, Maria F., Benavente, Ernest Diez, Pearson, Richard D., Herrera, Sócrates, Arévalo-Herrera, Myriam, Trimarsanto, Hidayat, Rumaseb, Angela, Noviyanti, Rintis, Kwiatkowski, Dominic P., Price, Ric N., and Auburn, Sarah

Published
2023
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3. Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites

Author

Siegel, Sasha V., Trimarsanto, Hidayat, Amato, Roberto, Murie, Kathryn, Taylor, Aimee R., Sutanto, Edwin, Kleinecke, Mariana, Whitton, Georgia, Watson, James A., Imwong, Mallika, Assefa, Ashenafi, Rahim, Awab Ghulam, Nguyen, Hoang Chau, Tran, Tinh Hien, Green, Justin A., Koh, Gavin C. K. W., White, Nicholas J., Day, Nicholas, Kwiatkowski, Dominic P., Rayner, Julian C., Price, Ric N., and Auburn, Sarah

Published
2024
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4. A description of Lineage 1 Mycobacterium tuberculosis from Papua, Indonesia

Author

Djunaedy, Hanif Ahmad Kautsar, primary, Febinia, Clarissa A., additional, Hamers, Raph L., additional, Baird, Kevin, additional, Elyazar, Iqbal, additional, Thuong, Nguyen Thuy Thuong, additional, Trimarsanto, Hidayat, additional, Malik, Safarina G., additional, Thwaites, Guy, additional, van Crevel, Reinout, additional, Alisjahbana, Bachti, additional, Chaidir, Lidya, additional, and Ashton, Philip M., additional

Published
2024
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5. Genomic epidemiology of Plasmodium knowlesi reveals putative genetic drivers of adaptation in Malaysia.

Author

Westaway, Jacob, primary, Diez Benavente, Ernest, additional, Auburn, Sarah, additional, Kucharski, Michal, additional, Aranciaga, Nicolas, additional, Nayak, Sourav, additional, William, Timothy, additional, Rajahram, Giri S, additional, Piera, Kim A, additional, Braima, Kamil, additional, Tan, Angelica F, additional, Alaza, Danshy, additional, Barber, Bridget E, additional, Drakeley, Chris, additional, Amato, Roberto, additional, Sutanto, Edwin, additional, Trimarsanto, Hidayat, additional, Anstey, Nicholas M, additional, Bozdech, Zbynek, additional, Field, Matthew, additional, and Grigg, Matthew J, additional

Published
2024
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6. Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia

Author

Oktavianthi, Sukma, primary, Lages, Aksar Chair, additional, Kusuma, Rinaldy, additional, Kurniasih, Tri Shinta, additional, Trimarsanto, Hidayat, additional, Andriani, Febi, additional, Rustandi, David, additional, Meriyanti, Tandry, additional, Yusuf, Irawan, additional, Malik, Safarina G., additional, Jo, Juandy, additional, and Suriapranata, Ivet, additional

Published
2024
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7. A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria

Author

Trimarsanto, Hidayat, Amato, Roberto, Pearson, Richard D., Sutanto, Edwin, Noviyanti, Rintis, Trianty, Leily, Marfurt, Jutta, Pava, Zuleima, Echeverry, Diego F., Lopera-Mesa, Tatiana M., Montenegro, Lidia M., Tobón-Castaño, Alberto, Grigg, Matthew J., Barber, Bridget, William, Timothy, Anstey, Nicholas M., Getachew, Sisay, Petros, Beyene, Aseffa, Abraham, Assefa, Ashenafi, Rahim, Awab G., Chau, Nguyen H., Hien, Tran T., Alam, Mohammad S., Khan, Wasif A., Ley, Benedikt, Thriemer, Kamala, Wangchuck, Sonam, Hamedi, Yaghoob, Adam, Ishag, Liu, Yaobao, Gao, Qi, Sriprawat, Kanlaya, Ferreira, Marcelo U., Laman, Moses, Barry, Alyssa, Mueller, Ivo, Lacerda, Marcus V. G., Llanos-Cuentas, Alejandro, Krudsood, Srivicha, Lon, Chanthap, Mohammed, Rezika, Yilma, Daniel, Pereira, Dhelio B., Espino, Fe E. J., Chu, Cindy S., Vélez, Iván D., Namaik-larp, Chayadol, Villegas, Maria F., Green, Justin A., Koh, Gavin, Rayner, Julian C., Drury, Eleanor, Gonçalves, Sónia, Simpson, Victoria, Miotto, Olivo, Miles, Alistair, White, Nicholas J., Nosten, Francois, Kwiatkowski, Dominic P., Price, Ric N., and Auburn, Sarah

Published
2022
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8. Genomic analysis of Plasmodium vivax identifies putative drivers of adaptation and connectivity across diverse districts in Ethiopia

Author

Kebede, Alebachew Messele, primary, Sutanto, Edwin, additional, Trimarsanto, Hidayat, additional, Benavente, Ernest Diez, additional, Barnes, Mariana, additional, Pearson, Richard, additional, Siegel, Sasha, additional, Erko, Berhanu, additional, Assefa, Ashenafi, additional, Getachew, Sisay, additional, Aseffa, Abraham, additional, Petros, Beyene, additional, Lo, Eugenia, additional, Mohammed, Rezika, additional, Yilma, Daniel, additional, Rumaseb, Angela, additional, Nosten, Francois, additional, Noviyanti, Rintis, additional, Rayner, Julian, additional, Kwiatkowski, Dominic, additional, Price, Ric, additional, Golassa, Lemu, additional, and Auburn, Sarah, additional

Published
2023
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10. Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites

Author

Siegel, Sasha V, primary, Amato, Roberto, additional, Trimarsanto, Hidayat, additional, Sutanto, Edwin, additional, Kleinecke, Mariana, additional, Murie, Kathryn, additional, Whitton, Georgia, additional, Taylor, Aimee R, additional, Watson, James A, additional, Imwong, Mallika, additional, Assefa, Ashenafi, additional, Rahim, Awab Ghulam, additional, Chao, Nguyen Hoang, additional, Hien, Tran Tinh, additional, Green, Justin A, additional, Koh, Gavin, additional, White, Nicholas J, additional, Kwiatkowski, Dominic P, additional, Rayner, Julian C, additional, Price, Ric N, additional, and Auburn, Sarah, additional

Published
2023
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11. Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia–Pacific region

Author

Noviyanti, Rintis, Miotto, Olivo, Barry, Alyssa, Marfurt, Jutta, Siegel, Sasha, Thuy-Nhien, Nguyen, Quang, Huynh Hong, Anggraeni, Nancy Dian, Laihad, Ferdinand, Liu, Yaobao, Sumiwi, Maria Endang, Trimarsanto, Hidayat, Coutrier, Farah, Fadila, Nadia, Ghanchi, Najia, Johora, Fatema Tuj, Puspitasari, Agatha Mia, Tavul, Livingstone, Trianty, Leily, Utami, Retno Ayu Setya, Wang, Duoquan, Wangchuck, Kesang, Price, Ric N., and Auburn, Sarah

Published
2020
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14. Genomic profiles of Indonesian colorectal cancer patients

Author

Abdullah, Murdani, primary, Meilany, Sofy, additional, Trimarsanto, Hidayat, additional, Malik, Safarina G., additional, Sukartini, Ninik, additional, Idrus, Firhat, additional, Nursyirwan, Saskia A., additional, Muzellina, Virly N., additional, Pribadi, Rabbinu R., additional, Utari, Amanda P., additional, Maulahela, Hasan, additional, and Syam, Ari F., additional

Published
2023
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15. Novel highly-multiplexed AmpliSeq targeted assay for Plasmodium vivax genetic surveillance use cases at multiple geographical scales

Author

Kattenberg, Johanna Helena, primary, Nguyen, Hong Van, additional, Nguyen, Hieu Luong, additional, Sauve, Erin, additional, Nguyen, Ngoc Thi Hong, additional, Chopo-Pizarro, Ana, additional, Trimarsanto, Hidayat, additional, Monsieurs, Pieter, additional, Guetens, Pieter, additional, Nguyen, Xa Xuan, additional, Esbroeck, Marjan Van, additional, Auburn, Sarah, additional, Nguyen, Binh Thi Huong, additional, and Rosanas-Urgell, Anna, additional

Published
2022
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16. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

Author

Adam, Ishag, Alam, Mohammad Shafiul, Alemu, Sisay, Amaratunga, Chanaki, Amato, Roberto, Andrianaranjaka, Voahangy, Anstey, Nicholas M, Aseffa, Abraham, Ashley, Elizabeth, Assefa, Ashenafi, Auburn, Sarah, Barber, Bridget E, Barry, Alyssa, Batista Pereira, Dhelio, Cao, Jun, Chau, Nguyen Hoang, Chotivanich, Kesinee, Chu, Cindy, Dondorp, Arjen M, Drury, Eleanor, Echeverry, Diego F, Erko, Berhanu, Espino, Fe, Fairhurst, Rick, Faiz, Abdul, Fernanda Villegas, María, Gao, Qi, Golassa, Lemu, Goncalves, Sonia, Grigg, Matthew J, Hamedi, Yaghoob, Hien, Tran Tinh, Htut, Ye, Johnson, Kimberly J, Karunaweera, Nadira, Khan, Wasif, Krudsood, Srivicha, Kwiatkowski, Dominic P, Lacerda, Marcus, Ley, Benedikt, Lim, Pharath, Liu, Yaobao, Llanos-Cuentas, Alejandro, Lon, Chanthap, Lopera-Mesa, Tatiana, Marfurt, Jutta, Michon, Pascal, Miotto, Olivo, Mohammed, Rezika, Mueller, Ivo, Namaik-Larp, Chayadol, Newton, Paul N, Nguyen, Thuy-Nhien, Nosten, Francois, Noviyanti, Rintis, Pava, Zuleima, Pearson, Richard D, Petros, Beyene, Phyo, Aung P, Price, Ric N, Pukrittayakamee, Sasithon, Rahim, Awab Ghulam, Randrianarivelojosia, Milijaona, Rayner, Julian C, Rumaseb, Angela, Siegel, Sasha V, Simpson, Victoria J, Thriemer, Kamala, Tobon-Castano, Alberto, Trimarsanto, Hidayat, Urbano Ferreira, Marcelo, Vélez, Ivan D, Wangchuk, Sonam, Wellems, Thomas E, White, Nicholas J, William, Timothy, Yasnot, Maria F, Yilma, Daniel, Alam, Mohammad Shafiul [0000-0001-8330-5499], Ashley, Elizabeth [0000-0002-7620-4822], Barber, Bridget E [0000-0003-1066-7960], Batista Pereira, Dhelio [0000-0002-7761-5498], Chu, Cindy [0000-0001-9465-8214], Dondorp, Arjen M [0000-0001-5190-2395], Echeverry, Diego F [0000-0003-0301-4478], Espino, Fe [0000-0003-1690-1711], Faiz, Abdul [0000-0002-3460-7535], Golassa, Lemu [0000-0002-1216-8711], Grigg, Matthew J [0000-0001-9914-8352], Karunaweera, Nadira [0000-0003-3985-1817], Kwiatkowski, Dominic P [0000-0002-5023-0176], Ley, Benedikt [0000-0002-5734-0845], Miotto, Olivo [0000-0001-8060-6771], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Pearson, Richard D [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Urbano Ferreira, Marcelo [0000-0002-5293-9090], Wellems, Thomas E [0000-0003-3899-8454], Yasnot, Maria F [0000-0001-8081-4212], Yilma, Daniel [0000-0001-6058-2696], and Apollo - University of Cambridge Repository

Subjects
parasitic diseases, Genomics, Genomic Epidemiology, Plasmodium vivax, Malaria, Data Resource
Abstract

This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

Published
2022

17. Genomic profiles of Indonesian colorectal cancer patients

Author

Abdullah, Murdani, primary, Meilany, Sofy, additional, Trimarsanto, Hidayat, additional, Malik, Safarina G., additional, Sukartini, Ninik, additional, Idrus, Firhat, additional, Nursyirwan, Saskia A., additional, Muzellina, Virly N., additional, Pribadi, Rabbinu R., additional, Utari, Amanda P., additional, Maulahela, Hasan, additional, and Syam, Ari F., additional

Published
2022
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18. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

Author

MalariaGEN, Adam, Ishag, Alam, Mohammad Shafiul, Alemu, Sisay, Amaratunga, Chanaki, Amato, Roberto, Andrianaranjaka, Voahangy, Anstey, Nicholas M, Aseffa, Abraham, Ashley, Elizabeth, Assefa, Ashenafi, Auburn, Sarah, Barber, Bridget E, Barry, Alyssa, Batista Pereira, Dhelio, Cao, Jun, Chau, Nguyen Hoang, Chotivanich, Kesinee, Chu, Cindy, Dondorp, Arjen M, Drury, Eleanor, Echeverry, Diego F, Erko, Berhanu, Espino, Fe, Fairhurst, Rick, Faiz, Abdul, Fernanda Villegas, María, Gao, Qi, Golassa, Lemu, Goncalves, Sonia, Grigg, Matthew J, Hamedi, Yaghoob, Hien, Tran Tinh, Htut, Ye, Johnson, Kimberly J, Karunaweera, Nadira, Khan, Wasif, Krudsood, Srivicha, Kwiatkowski, Dominic P, Lacerda, Marcus, Ley, Benedikt, Lim, Pharath, Liu, Yaobao, Llanos-Cuentas, Alejandro, Lon, Chanthap, Lopera-Mesa, Tatiana, Marfurt, Jutta, Michon, Pascal, Miotto, Olivo, Mohammed, Rezika, Mueller, Ivo, Namaik-Larp, Chayadol, Newton, Paul N, Nguyen, Thuy-Nhien, Nosten, Francois, Noviyanti, Rintis, Pava, Zuleima, Pearson, Richard D, Petros, Beyene, Phyo, Aung P, Price, Ric N, Pukrittayakamee, Sasithon, Rahim, Awab Ghulam, Randrianarivelojosia, Milijaona, Rayner, Julian C, Rumaseb, Angela, Siegel, Sasha V, Simpson, Victoria J, Thriemer, Kamala, Tobon-Castano, Alberto, Trimarsanto, Hidayat, Urbano Ferreira, Marcelo, Vélez, Ivan D, Wangchuk, Sonam, Wellems, Thomas E, White, Nicholas J, William, Timothy, Yasnot, Maria F, Yilma, Daniel, AII - Infectious diseases, Intensive Care Medicine, MalariaGEN, Alam, Mohammad Shafiul [0000-0001-8330-5499], Ashley, Elizabeth [0000-0002-7620-4822], Barber, Bridget E [0000-0003-1066-7960], Batista Pereira, Dhelio [0000-0002-7761-5498], Chu, Cindy [0000-0001-9465-8214], Dondorp, Arjen M [0000-0001-5190-2395], Echeverry, Diego F [0000-0003-0301-4478], Espino, Fe [0000-0003-1690-1711], Faiz, Abdul [0000-0002-3460-7535], Golassa, Lemu [0000-0002-1216-8711], Karunaweera, Nadira [0000-0003-3985-1817], Kwiatkowski, Dominic P [0000-0002-5023-0176], Ley, Benedikt [0000-0002-5734-0845], Miotto, Olivo [0000-0001-8060-6771], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Pearson, Richard D [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Urbano Ferreira, Marcelo [0000-0002-5293-9090], Wellems, Thomas E [0000-0003-3899-8454], Yasnot, Maria F [0000-0001-8081-4212], Yilma, Daniel [0000-0001-6058-2696], and Apollo - University of Cambridge Repository

Subjects
Data resource, parasitic diseases, Medicine (miscellaneous), Genomics, Genomic epidemiology, Plasmodium vivax, General Biochemistry, Genetics and Molecular Biology, Malaria
Abstract

This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

Published
2022

19. Genetic diversity and neutral selection in Plasmodium vivax erythrocyte binding protein correlates with patient antigenicity

Author

Han, Jin-Hee, primary, Cho, Jee-Sun, additional, Ong, Jessica J. Y., additional, Park, Ji-Hoon, additional, Nyunt, Myat Htut, additional, Sutanto, Edwin, additional, Trimarsanto, Hidayat, additional, Petros, Beyene, additional, Aseffa, Abraham, additional, Getachew, Sisay, additional, Sriprawat, Kanlaya, additional, Anstey, Nicholas M., additional, Grigg, Matthew J., additional, Barber, Bridget E., additional, William, Timothy, additional, Qi, Gao, additional, Liu, Yaobao, additional, Pearson, Richard D., additional, Auburn, Sarah, additional, Price, Ric N., additional, Nosten, Francois, additional, Rénia, Laurent, additional, Russell, Bruce, additional, and Han, Eun-Taek, additional

Published
2020
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20. Molecular surveillance over 14 years confirms reduction of Plasmodium vivax and falciparum transmission after implementation of Artemisinin-based combination therapy in Papua, Indonesia

Author

Pava, Zuleima, primary, Puspitasari, Agatha M., additional, Rumaseb, Angela, additional, Handayuni, Irene, additional, Trianty, Leily, additional, Utami, Retno A. S., additional, Tirta, Yusrifar K., additional, Burdam, Faustina, additional, Kenangalem, Enny, additional, Wirjanata, Grennady, additional, Kho, Steven, additional, Trimarsanto, Hidayat, additional, Anstey, Nicholas M., additional, Poespoprodjo, Jeanne Rini, additional, Noviyanti, Rintis, additional, Price, Ric N., additional, Marfurt, Jutta, additional, and Auburn, Sarah, additional

Published
2020
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21. A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax

Author

Trimarsanto, Hidayat, primary, Amato, Roberto, additional, Pearson, Richard D, additional, Sutanto, Edwin, additional, Noviyanti, Rintis, additional, Trianty, Leily, additional, Marfurt, Jutta, additional, Pava, Zuleima, additional, Echeverry, Diego F, additional, Lopera-Mesa, Tatiana M, additional, Montenegro, Lidia Madeline, additional, Tobón-Castaño, Alberto, additional, Grigg, Matthew J, additional, Barber, Bridget, additional, William, Timothy, additional, Anstey, Nicholas M, additional, Getachew, Sisay, additional, Petros, Beyene, additional, Aseffa, Abraham, additional, Assefa, Ashenafi, additional, Rahim, Awab Ghulam, additional, Chau, Nguyen Hoang, additional, Hien, Tran Tinh, additional, Alam, Mohammad Shafiul, additional, Khan, Wasif A, additional, Ley, Benedikt, additional, Thriemer, Kamala, additional, Wangchuck, Sonam, additional, Hamedi, Yaghoob, additional, Adam, Ishag, additional, Liu, Yaobao, additional, Gao, Qi, additional, Sriprawat, Kanlaya, additional, Ferreira, Marcelo U, additional, Barry, Alyssa, additional, Mueller, Ivo, additional, Drury, Eleanor, additional, Goncalves, Sonia, additional, Simpson, Victoria, additional, Miotto, Olivo, additional, Miles, Alistair, additional, White, Nicholas J, additional, Nosten, Francois, additional, Kwiatkowski, Dominic P, additional, Price, Ric N, additional, and Auburn, Sarah, additional

Published
2019
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22. Uncoupling protein 2 gene polymorphisms are associated with obesity

Author

Oktavianthi Sukma, Trimarsanto Hidayat, Febinia Clarissa A, Suastika Ketut, Saraswati Made R, Dwipayana Pande, Arindrarto Wibowo, Sudoyo Herawati, and Malik Safarina G

Subjects
UCP2, Ala55Val, G(−866)A, Obesity, Serum lipids, Type 2 diabetes mellitus, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Abstract Background Uncoupling protein 2 (UCP2) gene polymorphisms have been reported as genetic risk factors for obesity and type 2 diabetes mellitus (T2DM). We examined the association of commonly observed UCP2 G(−866)A (rs659366) and Ala55Val (C > T) (rs660339) single nucleotide polymorphisms (SNPs) with obesity, high fasting plasma glucose, and serum lipids in a Balinese population. Methods A total of 603 participants (278 urban and 325 rural subjects) were recruited from Bali Island, Indonesia. Fasting plasma glucose (FPG), triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) were measured. Obesity was determined based on WHO classifications for adult Asians. Participants were genotyped for G(−866)A and Ala55Val polymorphisms of the UCP2 gene. Results Obesity prevalence was higher in urban subjects (51%) as compared to rural subjects (23%). The genotype, minor allele (MAF), and heterozygosity frequencies were similar between urban and rural subjects for both SNPs. All genotype frequencies were in Hardy-Weinberg equilibrium. A combined analysis of genotypes and environment revealed that the urban subjects carrying the A/A genotype of the G(−866)A SNP have higher BMI than the rural subjects with the same genotype. Since the two SNPs showed strong linkage disequilibrium (D’ = 0.946, r2 = 0.657), a haplotype analysis was performed. We found that the AT haplotype was associated with high BMI only when the urban environment was taken into account. Conclusions We have demonstrated the importance of environmental settings in studying the influence of the common UCP2 gene polymorphisms in the development of obesity in a Balinese population.

Published
2012
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27. Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms

Author

Auburn, Sarah, primary, Getachew, Sisay, additional, Pearson, Richard D, additional, Amato, Roberto, additional, Miotto, Olivo, additional, Trimarsanto, Hidayat, additional, Zhu, Sha Joe, additional, Rumaseb, Angela, additional, Marfurt, Jutta, additional, Noviyanti, Rintis, additional, Grigg, Matthew J, additional, Barber, Bridget, additional, William, Timothy, additional, Goncalves, Sonia Morgado, additional, Drury, Eleanor, additional, Sriprawat, Kanlaya, additional, Anstey, Nicholas M, additional, Nosten, Francois, additional, Petros, Beyene, additional, Aseffa, Abraham, additional, McVean, Gil, additional, Kwiatkowski, Dominic P, additional, and Price, Ric N, additional

Published
2019
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28. Association of beta3-adrenergic receptor (ADRB3) Trp64Arg gene polymorphism with obesity and metabolic syndrome in the Balinese: a pilot study

Author

Trimarsanto Hidayat, Oktavianthi Sukma, Suastika Ketut, Saraswati Made R, Malik Safarina G, and Sudoyo Herawati

Subjects
Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background Prevalence of obesity is increasing all over the world. ADRB3 Trp64Arg gene polymorphism was proposed to be associated with obesity, although inconsistent findings and differences of the Arg64 allele frequency among various ethnics were reported. Westernization was reported to increase the prevalence of obesity in developing world. In this study we determined the prevalence of obesity and metabolic syndrome among urban and rural Balinese, and studied the association of ADRB3 Trp64Arg polymorphism with obesity and MetS. Findings A total of 528 Balinese (urban 282, rural 246) were recruited. Body mass index (BMI) and waist circumference (WC) were determined; high-density lipoprotein cholesterol (HDL-C), triglyceride (TG), systolic and diastolic blood pressure (SBP and DBP), and fasting plasma glucose (FPG) were measured using standard procedures. BMI and WC classifications were based on WHO classifications for Asian. Metabolic syndrome (MetS) was defined as described in the Joint Interim Statement. Chi-square test was employed to test the association between the ADRB3 Trp64Arg genotype and disease traits. Urban have higher BMI (p = 2.8 × 10-13), WC ( p < 2.2 × 10-16), TG (p = 0.0028), DBP (p = 1.8 × 10-5), and lower HDL-C (p = 0.0376) when compared to rural. Abdominal obesity and MetS prevalence were significantly higher in urban as compared to rural (both p < 0.001). The Arg64 allele frequency was similar between urban (0.06) and rural (0.05). The Arg64 rural female carriers have higher BMI and WC as compared to their Trp64 counterparts (p = 0.041 for BMI and p = 0.012 for WC), and consequently higher abdominal obesity prevalence (p = 0.007). Comparison between male and female, as well as urban and rural, showed different prevalence of MetS co-morbidities. Abdominal obesity and hypertriglyceridaemia were consistently appeared in all groups, suggesting to play a role as determinant of MetS in both urban and rural. Conclusions Prevalence of obesity and MetS in urban were two times higher when compared to rural. Abdominal obesity and hypertriglyceridaemia appears to be the key determinant of MetS in both urban and rural Balinese. Our results indicated an association of the ADRB3 Trp64Arg gene polymorphism with obesity in the rural female.

Published
2011
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30. Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics

Author

Auburn, Sarah, primary, Benavente, Ernest D., additional, Miotto, Olivo, additional, Pearson, Richard D., additional, Amato, Roberto, additional, Grigg, Matthew J., additional, Barber, Bridget E., additional, William, Timothy, additional, Handayuni, Irene, additional, Marfurt, Jutta, additional, Trimarsanto, Hidayat, additional, Noviyanti, Rintis, additional, Sriprawat, Kanlaya, additional, Nosten, Francois, additional, Campino, Susana, additional, Clark, Taane G., additional, Anstey, Nicholas M., additional, Kwiatkowski, Dominic P., additional, and Price, Ric N., additional

Published
2018
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31. Isolation and complete genome analysis of neurotropic dengue virus serotype 3 from the cerebrospinal fluid of an encephalitis patient

Author

Dhenni, Rama, primary, Karyanti, Mulya Rahma, additional, Putri, Nina Dwi, additional, Yohan, Benediktus, additional, Yudhaputri, Frilasita A., additional, Ma'roef, Chairin Nisa, additional, Fadhilah, Araniy, additional, Perkasa, Aditya, additional, Restuadi, Restuadi, additional, Trimarsanto, Hidayat, additional, Mangunatmadja, Irawan, additional, Ledermann, Jeremy P., additional, Rosenberg, Ronald, additional, Powers, Ann M., additional, Myint, Khin Saw Aye, additional, and Sasmono, R. Tedjo, additional

Published
2018
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32. Passively versus Actively Detected Malaria: Similar Genetic Diversity but Different Complexity of Infection

Author

Pava, Zuleima, primary, Handayuni, Irene, additional, Trianty, Leily, additional, Utami, Retno A. S., additional, Tirta, Yusrifar K., additional, Puspitasari, Agatha M., additional, Burdam, Faustina, additional, Kenangalem, Enny, additional, Wirjanata, Grennady, additional, Kho, Steven, additional, Trimarsanto, Hidayat, additional, Anstey, Nicholas, additional, Poespoprodjo, Jeanne Rini, additional, Noviyanti, Rintis, additional, Price, Ric N., additional, Marfurt, Jutta, additional, and Auburn, Sarah, additional

Published
2017
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33. Genomic characterization of Zika virus isolated from Indonesia

Author

Yudhaputri, Frilasita A., primary, Trimarsanto, Hidayat, additional, Perkasa, Aditya, additional, Yohan, Benediktus, additional, Haryanto, Sotianingsih, additional, Wiyatno, Ageng, additional, Soebandrio, Amin, additional, Myint, Khin Saw, additional, Ledermann, Jeremy P., additional, Rosenberg, Ronald, additional, Powers, Ann M., additional, and Sasmono, R. Tedjo, additional

Published
2017
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34. Genomic analysis of local variation and recent evolution in Plasmodium vivax

Author

Pearson, Richard D, Amato, Roberto, Auburn, Sarah, Miotto, Olivo, Almagro-Garcia, Jacob, Amaratunga, Chanaki, Suon, Seila, Mao, Sivanna, Noviyanti, Rintis, Trimarsanto, Hidayat, Marfurt, Jutta, Anstey, Nicholas M, William, Timothy, Boni, Maciej F, Dolecek, Christiane, Hien, Tinh Tran, White, Nicholas J, Michon, Pascal, Siba, Peter, Tavul, Livingstone, Harrison, Gabrielle, Barry, Alyssa, Mueller, Ivo, Ferreira, Marcelo U, Karunaweera, Nadira, Randrianarivelojosia, Milijaona, Gao, Qi, Hubbart, Christina, Hart, Lee, Jeffery, Ben, Drury, Eleanor, Mead, Daniel, Kekre, Mihir, Campino, Susana, Manske, Magnus, Cornelius, Victoria J, MacInnis, Bronwyn, Rockett, Kirk A, Miles, Alistair, Rayner, Julian C, Fairhurst, Rick M, Nosten, Francois, Price, Ric N, and Kwiatkowski, Dominic P

Abstract

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.

Published
2016

36. Chloroquine efficacy for Plasmodium vivax in Myanmar in populations with high genetic diversity and moderate parasite gene flow

Author

Htun, Myo Win, primary, Mon, Nan Cho Nwe, additional, Aye, Khin Myo, additional, Hlaing, Chan Myae, additional, Kyaw, Myat Phone, additional, Handayuni, Irene, additional, Trimarsanto, Hidayat, additional, Bustos, Dorina, additional, Ringwald, Pascal, additional, Price, Ric N., additional, Auburn, Sarah, additional, and Thriemer, Kamala, additional

Published
2017
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37. Clinical and virological characteristics of dengue in Surabaya, Indonesia

Author

Wardhani, Puspa, primary, Aryati, Aryati, additional, Yohan, Benediktus, additional, Trimarsanto, Hidayat, additional, Setianingsih, Tri Y., additional, Puspitasari, Dwiyanti, additional, Arfijanto, Muhammad Vitanata, additional, Bramantono, Bramantono, additional, Suharto, Suharto, additional, and Sasmono, R. Tedjo, additional

Published
2017
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38. Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections

Author

Pava, Zuleima, primary, Noviyanti, Rintis, additional, Handayuni, Irene, additional, Trimarsanto, Hidayat, additional, Trianty, Leily, additional, Burdam, Faustina H., additional, Kenangalem, Enny, additional, Utami, Retno A. S., additional, Tirta, Yusrifar K., additional, Coutrier, Farah, additional, Poespoprodjo, Jeanne R., additional, Price, Ric N., additional, Marfurt, Jutta, additional, and Auburn, Sarah, additional

Published
2017
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39. VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations

Author

Trimarsanto, Hidayat, primary, Benavente, Ernest D., additional, Noviyanti, Rintis, additional, Utami, Retno Ayu Setya, additional, Trianty, Leily, additional, Pava, Zuleima, additional, Getachew, Sisay, additional, Kim, Jung-Yeon, additional, Goo, Youn-Kyoung, additional, Wangchuck, Sonam, additional, Liu, Yaobao, additional, Gao, Qi, additional, Dowd, Simone, additional, Cheng, Qin, additional, Clark, Taane G., additional, Price, Ric N., additional, and Auburn, Sarah, additional

Published
2017
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40. A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Author

Auburn, Sarah, primary, Böhme, Ulrike, additional, Steinbiss, Sascha, additional, Trimarsanto, Hidayat, additional, Hostetler, Jessica, additional, Sanders, Mandy, additional, Gao, Qi, additional, Nosten, François, additional, Newbold, Chris I., additional, Berriman, Matthew, additional, Price, Ric N., additional, and Otto, Thomas D., additional

Published
2016
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43. Where chloroquine still works: the genetic make-up and susceptibility of Plasmodium vivax to chloroquine plus primaquine in Bhutan

Author

Wangchuk, Sonam, primary, Drukpa, Tobgyel, additional, Penjor, Kinley, additional, Peldon, Tashi, additional, Dorjey, Yeshey, additional, Dorji, Kunzang, additional, Chhetri, Vishal, additional, Trimarsanto, Hidayat, additional, To, Sheren, additional, Murphy, Amanda, additional, von Seidlein, Lorenz, additional, Price, Ric N., additional, Thriemer, Kamala, additional, and Auburn, Sarah, additional

Published
2016
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47. Genomic analysis and growth characteristic of dengue viruses from Makassar, Indonesia

Author

Sasmono, R. Tedjo, primary, Wahid, Isra, additional, Trimarsanto, Hidayat, additional, Yohan, Benediktus, additional, Wahyuni, Sitti, additional, Hertanto, Martin, additional, Yusuf, Irawan, additional, Mubin, Halim, additional, Ganda, Idham J., additional, Latief, Rachmat, additional, Bifani, Pablo J., additional, Shi, Pei-Yong, additional, and Schreiber, Mark J., additional

Published
2015
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48. Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination

Author

Noviyanti, Rintis, primary, Coutrier, Farah, additional, Utami, Retno A. S., additional, Trimarsanto, Hidayat, additional, Tirta, Yusrifar K., additional, Trianty, Leily, additional, Kusuma, Andreas, additional, Sutanto, Inge, additional, Kosasih, Ayleen, additional, Kusriastuti, Rita, additional, Hawley, William A., additional, Laihad, Ferdinand, additional, Lobo, Neil, additional, Marfurt, Jutta, additional, Clark, Taane G., additional, Price, Ric N., additional, and Auburn, Sarah, additional

Published
2015
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49. Exceptional Complex Chromosomal Rearrangements in Three Generations

Author

Kartapradja, Hannie, primary, Marzuki, Nanis Sacharina, additional, Pertile, Mark D., additional, Francis, David, additional, Suciati, Lita Putri, additional, Anggaratri, Helena Woro, additional, Ambarwati, Debby Dwi, additional, Idris, Firman Prathama, additional, Lesmana, Harry, additional, Trimarsanto, Hidayat, additional, Paramayuda, Chrysantine, additional, and Harahap, Alida Roswita, additional

Published
2015
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50. Chloroquine efficacy for Plasmodium vivax in Myanmar in populations with high genetic diversity and moderate parasite gene flow.

Author

Myo Win Htun, Nan Cho Nwe Mon, Khin Myo Aye, Chan Myae Hlaing, Myat Phone Kyaw, Handayuni, Irene, Trimarsanto, Hidayat, Bustos, Dorina, Ringwald, Pascal, Price, Ric N., Auburn, Sarah, and Thriemer, Kamala

Subjects
PLASMODIUM vivax, MALARIA, CHLOROQUINE, PUBLIC health, DRUG resistance, DIAGNOSIS
Abstract

Background: Plasmodium vivax malaria remains a major public health burden in Myanmar. Resistance to chloroquine (CQ), the first-line treatment for P. vivax, has been reported in the country and has potential to undermine local control efforts. Methods: Patients over 6 years of age with uncomplicated P. vivax mono-infection were enrolled into clinical efficacy studies in Myawaddy in 2014 and Kawthoung in 2012. Study participants received a standard dose of CQ (25 mg/ kg over 3 days) followed by weekly review until day 28. Pvmdr1 copy number (CN) and microsatellite diversity were assessed on samples from the patients enrolled in the clinical study and additional cross-sectional surveys undertaken in Myawaddy and Shwegyin in 2012. Results: A total of 85 patients were enrolled in the CQ clinical studies, 25 in Myawaddy and 60 in Kawthoung. One patient in Myawaddy (1.2%) had an early treatment failure and two patients (2.3%) in Kawthoung presented with late treatment failures on day 28. The day 28 efficacy was 92.0% (95% CI 71.6-97.9) in Myawaddy and 98.3% (95% CI 88.7-99.8) in Kawthoung. By day 2, 92.2% (23/25) in Myawaddy and 85.0% (51/60) in Kawthoung were aparasitaemic. Genotyping and pvmdr1 CN assessment was undertaken on 43, 52 and 46 clinical isolates from Myawaddy, Kawthoung and Shwegyin respectively. Pvmdr1 amplification was observed in 3.2% (1/31) of isolates in Myawaddy, 0% (0/49) in Kawthoung and 2.5% (1/40) in Shwegyin. Diversity was high in all sites (HE 0.855-0.876), with low inter-population differentiation (FST 0.016-0.026, P < 0.05). Conclusions: Treatment failures after chloroquine were observed following chloroquine monotherapy, with pvmdr1 amplification present in both Myawaddy and Shwegyin. The results emphasize the importance of ongoing P. vivax drug resistance surveillance in Myanmar, particularly given the potential connectivity between parasite population at different sites. [ABSTRACT FROM AUTHOR]

Published
2017
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