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4 results on '"Schoenherr, Sebastian"'

1. South Asian medical cohorts reveal strong founder effects and high rates of homozygosity

Author

Wall, Jeffrey D, Sathirapongsasuti, J Fah, Gupta, Ravi, Rasheed, Asif, Venkatesan, Radha, Belsare, Saurabh, Menon, Ramesh, Phalke, Sameer, Mittal, Anuradha, Fang, John, Tanneeru, Deepak, Deshmukh, Manjari, Bassi, Akshi, Robinson, Jacqueline, Chaudhary, Ruchi, Murugan, Sakthivel, ul-Asar, Zameer, Saleem, Imran, Ishtiaq, Unzila, Fatima, Areej, Sheikh, Saqib Shafi, Hameed, Shahid, Ishaq, Mohammad, Rasheed, Syed Zahed, Memon, Fazal-ur-Rehman, Jalal, Anjum, Abbas, Shahid, Frossard, Philippe, Fuchsberger, Christian, Forer, Lukas, Schoenherr, Sebastian, Bei, Qixin, Bhangale, Tushar, Tom, Jennifer, Gadde, Santosh Gopi Krishna, B V, Priya, Naik, Naveen Kumar, Wang, Minxian, Kwok, Pui-Yan, Khera, Amit V, Lakshmi, BR, Butterworth, Adam S, Chowdhury, Rajiv, Danesh, John, di Angelantonio, Emanuele, Naheed, Aliya, Goyal, Vinay, Kandadai, Rukmini M, Kumar, Hrishikesh, Borgohain, Rupam, Mukherjee, Adreesh, Wadia, Pettarusp M, Yadav, Ravi, Desai, Soaham, Kumar, Niraj, Biswas, Atanu, Pal, Pramod Kumar, Muthane, Uday B, Das, Shymal K, Ramprasad, Vedam L, Kukkle, Prashanth L, Seshagiri, Somasekar, Kathiresan, Sekar, Ghosh, Arkasubhra, Mohan, V, Saleheen, Danish, Stawiski, Eric W, and Peterson, Andrew S

Subjects
Genetics, Biotechnology, Clinical Research, Human Genome, Generic health relevance, Good Health and Well Being, Humans, Asian People, Bangladesh, Founder Effect, Homozygote, India, Pakistan, South Asian People
Abstract

The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.

Published
2023

2. South Asian Patient Population Genetics Reveal Strong Founder Effects and High Rates of Homozygosity – New Resources for Precision Medicine

Author

Wall, Jeffrey D, Sathirapongsasuti, J Fah, Gupta, Ravi, Barik, Anamitra, Rai, Rajesh Kumar, Rasheed, Asif, Radha, Venkatesan, Belsare, Saurabh, Menon, Ramesh, Phalke, Sameer, Mittal, Anuradha, Fang, John, Tanneeru, Deepak, Robinson, Jacqueline, Chaudhary, Ruchi, Fuchsberger, Christian, Forer, Lukas, Schoenherr, Sebastian, Bei, Qixin, Bhangale, Tushar, Tom, Jennifer, Gadde, Santosh Gopi Krishna, Priya, BV, Naik, Naveen Kumar, Wang, Minxian, Kwok, Pui-Yan, Khera, Amit V, Lakshmi, BR, Butterworth, Adam, Danesh, John, Seshagiri, Sekar, Kathiresan, Sekar, Ghosh, Arkasubhra, Mohan, V, Chowdhury, Abhijit, Saleheen, Danish, Stawiski, Eric, and Peterson, Andrew S

Subjects
Genetics, Biotechnology, Human Genome, Clinical Research, Generic health relevance, Good Health and Well Being
Abstract

AbstractPopulation-scale genetic studies can identify drug targets and allow disease risk to be predicted with resulting benefit for management of individual health risks and system-wide allocation of health care delivery resources. Although population-scale projects are underway in many parts of the world, genetic variation between population groups means that additional projects are warranted. South Asia has a population whose genetics is the least characterized of any of the world’s major populations. Here we describe GenomeAsia studies that characterize population structure in South Asia and that create tools for economical and accurate genotyping at population-scale. Prior work on population structure characterized isolated population groups, the relevance of which to large-scale studies of disease genetics is unclear. For our studies we used whole genome sequence information from 4,807 individuals recruited in the health care delivery systems of Pakistan, India and Bangladesh to ensure relevance to population-scale studies of disease genetics. We combined this with WGS data from 927 individuals from isolated South Asian population groups, and developed a custom SNP array (called SARGAM) that is optimized for future human genetic studies in South Asia. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of homozygosity that approach 100 times that seen in outbred populations. We describe founder effects that increase the power to associate functional variants with disease processes and that make South Asia a uniquely powerful place for population-scale genetic studies.

Published
2020

3. Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease

Author

Nielsen, Jonas B, Rom, Oren, Surakka, Ida, Graham, Sarah E, Zhou, Wei, Roychowdhury, Tanmoy, Fritsche, Lars G, Gagliano Taliun, Sarah A, Sidore, Carlo, Liu, Yuhao, Gabrielsen, Maiken E, Skogholt, Anne Heidi, Wolford, Brooke, Overton, William, Zhao, Ying, Chen, Jin, Zhang, He, Hornsby, Whitney E, Acheampong, Akua, Grooms, Austen, Schaefer, Amanda, Zajac, Gregory JM, Villacorta, Luis, Zhang, Jifeng, Brumpton, Ben, Løset, Mari, Rai, Vivek, Lundegaard, Pia R, Olesen, Morten S, Taylor, Kent D, Palmer, Nicholette D, Chen, Yii-Der, Choi, Seung H, Lubitz, Steven A, Ellinor, Patrick T, Barnes, Kathleen C, Daya, Michelle, Rafaels, Nicholas, Weiss, Scott T, Lasky-Su, Jessica, Tracy, Russell P, Vasan, Ramachandran S, Cupples, L Adrienne, Mathias, Rasika A, Yanek, Lisa R, Becker, Lewis C, Peyser, Patricia A, Bielak, Lawrence F, Smith, Jennifer A, Aslibekyan, Stella, Hidalgo, Bertha A, Arnett, Donna K, Irvin, Marguerite R, Wilson, James G, Musani, Solomon K, Correa, Adolfo, Rich, Stephen S, Guo, Xiuqing, Rotter, Jerome I, Konkle, Barbara A, Johnsen, Jill M, Ashley-Koch, Allison E, Telen, Marilyn J, Sheehan, Vivien A, Blangero, John, Curran, Joanne E, Peralta, Juan M, Montgomery, Courtney, Sheu, Wayne H-H, Chung, Ren-Hua, Schwander, Karen, Nouraie, Seyed M, Gordeuk, Victor R, Zhang, Yingze, Kooperberg, Charles, Reiner, Alexander P, Jackson, Rebecca D, Bleecker, Eugene R, Meyers, Deborah A, Li, Xingnan, Das, Sayantan, Yu, Ketian, LeFaive, Jonathon, Smith, Albert, Blackwell, Tom, Taliun, Daniel, Zollner, Sebastian, Forer, Lukas, Schoenherr, Sebastian, Fuchsberger, Christian, Pandit, Anita, Zawistowski, Matthew, Kheterpal, Sachin, Brummett, Chad M, Natarajan, Pradeep, Schlessinger, David, Lee, Seunggeun, Kang, Hyun Min, Cucca, Francesco, and Holmen, Oddgeir L

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Heart Disease, Human Genome, Prevention, Biotechnology, Digestive Diseases, Aging, Cardiovascular, Liver Disease, Atherosclerosis, Aetiology, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, 2.1 Biological and endogenous factors, Good Health and Well Being, Biological Specimen Banks, Cardiovascular Diseases, Gene Silencing, Gene Targeting, Genome, Human, Genome-Wide Association Study, Humans, Lipids, Liver, Loss of Function Mutation, Molecular Targeted Therapy, Phenomics, Receptors, LDL, United Kingdom
Abstract

Pharmaceutical drugs targeting dyslipidemia and cardiovascular disease (CVD) may increase the risk of fatty liver disease and other metabolic disorders. To identify potential novel CVD drug targets without these adverse effects, we perform genome-wide analyses of participants in the HUNT Study in Norway (n = 69,479) to search for protein-altering variants with beneficial impact on quantitative blood traits related to cardiovascular disease, but without detrimental impact on liver function. We identify 76 (11 previously unreported) presumed causal protein-altering variants associated with one or more CVD- or liver-related blood traits. Nine of the variants are predicted to result in loss-of-function of the protein. This includes ZNF529:p.K405X, which is associated with decreased low-density-lipoprotein (LDL) cholesterol (P = 1.3 × 10-8) without being associated with liver enzymes or non-fasting blood glucose. Silencing of ZNF529 in human hepatoma cells results in upregulation of LDL receptor and increased LDL uptake in the cells. This suggests that inhibition of ZNF529 or its gene product should be prioritized as a novel candidate drug target for treating dyslipidemia and associated CVD.

Published
2020

4. The GenomeAsia 100K Project enables genetic discoveries across Asia

Author

Wall, Jeffrey D, Stawiski, Eric W, Ratan, Aakrosh, Kim, Hie Lim, Kim, Changhoon, Gupta, Ravi, Suryamohan, Kushal, Gusareva, Elena S, Purbojati, Rikky Wenang, Bhangale, Tushar, Stepanov, Vadim, Kharkov, Vladimir, Schroeder, Markus S, Ramprasad, Vedam, Tom, Jennifer, Durinck, Steffen, Bei, Qixin, Li, Jiani, Guillory, Joseph, Phalke, Sameer, Basu, Analabha, Stinson, Jeremy, Nair, Sandhya, Malaichamy, Sivasankar, Biswas, Nidhan K, Chambers, John C, Cheng, Keith C, George, Joyner T, Khor, Seik Soon, Kim, Jong-Il, Cho, Belong, Menon, Ramesh, Sattibabu, Thiramsetti, Bassi, Akshi, Deshmukh, Manjari, Verma, Anjali, Gopalan, Vivek, Shin, Jong-Yeon, Pratapneni, Mahesh, Santhosh, Sam, Tokunaga, Katsushi, Md-Zain, Badrul M, Chan, Kok Gan, Parani, Madasamy, Natarajan, Purushothaman, Hauser, Michael, Allingham, R Rand, Santiago-Turla, Cecilia, Ghosh, Arkasubhra, Gadde, Santosh Gopi Krishna, Fuchsberger, Christian, Forer, Lukas, Schoenherr, Sebastian, Sudoyo, Herawati, Lansing, J Stephen, Friedlaender, Jonathan, Koki, George, Cox, Murray P, Hammer, Michael, Karafet, Tatiana, Ang, Khai C, Mehdi, Syed Q, Radha, Venkatesan, Mohan, Viswanathan, Majumder, Partha P, Seshagiri, Somasekar, Seo, Jeong-Sun, Schuster, Stephan C, and Peterson, Andrew S

Subjects
Human Genome, Genetics, Biotechnology, Alleles, Asian People, Datasets as Topic, Genome, Human, Genome-Wide Association Study, Genotype, Humans, GenomeAsia100K Consortium, General Science & Technology
Abstract

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world's population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide.

Published
2019

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