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171 results on '"Rodriguez Flores, Juan L."'

1. Identification and characterization of human GDF15 knockouts

Author

Gurtan, Allan M., Khalid, Shareef, Koch, Christopher, Khan, Maleeha Zaman, Lamarche, Lindsey B., Splawski, Igor, Dolan, Elizabeth, Carrion, Ana M., Zessis, Richard, Clement, Matthew E., Chen, Zhiping, Lindsley, Loren D., Chiu, Yu-Hsin, Streeper, Ryan S., Denning, Daniel P., Goldfine, Allison B., Doyon, Brian, Abbasi, Ali, Harrow, Jennifer L., Tsunoyama, Kazuhisa, Asaumi, Makoto, Kou, Ikuyo, Shuldiner, Alan R., Rodriguez-Flores, Juan L., Rasheed, Asif, Jahanzaib, Muhammad, Mian, Muhammad Rehan, Liaqat, Muhammad Bilal, Raza, Syed Shahzaib, Sultana, Riffat, Jalal, Anjum, Saeed, Muhammad Hamid, Abbas, Shahid, Memon, Fazal Rehman, Ishaq, Mohammad, Dominy, John E., and Saleheen, Danish

Published
2024
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2. The Qatar Genome: A Population-Specific Tool for Precision Medicine in the Middle East

Author

Fakhro, Khalid A., Staudt, Michelle R., Ramstetter, Monica Denise, Robay, Amal, Malek, Joel A., Badii, Ramin, Al-Marri, Ajayeb Al-Nabet, Khalil, Charbel Abi, Al-Shakaki, Alya, Chidiac, Omar, Stadler, Dora, Zirie, Mahmoud, Jayyousi, Amin, Salit, Jacqueline, Mezey, Jason G., Crystal, Ronald G., and Rodriguez-Flores, Juan L.

Subjects
Quantitative Biology - Genomics
Abstract

Reaching the full potential of precision medicine depends on the quality of personalized genome interpretation. In order to facilitate precision medicine in regions of the Middle East and North Africa (MENA), a population-specific reference genome for the indigenous Arab popula-tion of Qatar (QTRG) was constructed by incorporating allele frequency data from sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million SNP and 3.1 million indels were observed in Qatar, including an average of 1.79% novel variants per individual ge-nome. Replacement of the GRCh37 standard reference with QTRG in a best practices genome analysis workflow resulted in an average of 7* deeper coverage depth (an improvement of 23%), and 756,671 fewer variants on average, a reduction of 16% that is attributed to common Qatari alleles being present in the QTRG reference. The benefit for using QTRG varies across ances-tries, a factor that should be taken into consideration when selecting an appropriate reference for analysis., Comment: Includes supplementary figures missing from publisher website

Published
2018
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3. Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation.

Author

Kolchanova, Sofiia, Kliver, Sergei, Komissarov, Aleksei, Dobrinin, Pavel, Tamazian, Gaik, Grigorev, Kirill, Wolfsberger, Walter W, Majeske, Audrey J, Velez-Valentin, Jafet, Valentin de la Rosa, Ricardo, Paul-Murphy, Joanne R, Guzman, David Sanchez-Migallon, Court, Michael H, Rodriguez-Flores, Juan L, Martínez-Cruzado, Juan Carlos, and Oleksyk, Taras K

Subjects
Animals, Parrots, Genome, Endangered Species, Transcriptome, Islands, Cuba, Hispaniola, Puerto Rican parrot, birds, conservation, demography, genomics, heterozygosity, parrots, Genetics
Abstract

Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.

Published
2019

4. The QChip1 knowledgebase and microarray for precision medicine in Qatar

Author

Rodriguez-Flores, Juan L., Messai-Badji, Radja, Robay, Amal, Temanni, Ramzi, Syed, Najeeb, Markovic, Monika, Al-khayat, Eiman, Qafoud, Fatima, Nawaz, Zafar, Badii, Ramin, Al-Sarraj, Yasser, Mbarek, Hamdi, Al-Muftah, Wadha, Alvi, Muhammad, Rostami, Mahboubeh R., Cruzado, Juan Carlos Martinez, Mezey, Jason G., Shakaki, Alya Al, Malek, Joel A., Greenblatt, Matthew B., Fakhro, Khalid A., Machaca, Khaled, Al-Nabet, Ajayeb, Afifi, Nahla, Brooks, Andrew, Ismail, Said I., Althani, Asmaa, and Crystal, Ronald G.

Published
2022
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5. Identification and characterization of human GDF15 knockouts

Author

Gurtan, Allan M, primary, Khalid, Shareef, additional, Koch, Christopher, additional, Khan, Maleeha Z, additional, Lamarche, Lindsey B, additional, Dolan, Elizabeth, additional, Carrion, Ana M, additional, Zessis, Richard, additional, Clement, Matthew E, additional, Chen, Zhiping, additional, Lindsley, Loren D, additional, Chiu, Yu-Hsin, additional, Streeper, Ryan S, additional, Denning, Daniel P, additional, Goldfine, Allison B, additional, Doyon, Brian, additional, Abbasi, Ali, additional, Harrow, Jennifer L, additional, Tsunoyama, Kazuhisa, additional, Asaumi, Makoto, additional, Kou, Ikuyo, additional, Shuldiner, Alan R, additional, Rodriguez-Flores, Juan L, additional, Rasheed, Asif, additional, Jahanzaib, Muhammad, additional, Mian, Muhammad Rehan, additional, Liaqat, Muhammad Bilal, additional, Raza, Syed Shahzaib, additional, Sultana, Riffat, additional, Jalal, Anjum, additional, Saeed, Muhammad Hamid, additional, Abbas, Shahid, additional, Memon, Fazal Rehman, additional, Ishaq, Muhammad, additional, Dominy, John E, additional, and Saleheen, Danish, additional

Published
2024
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6. Genetic Evaluation of Male Infertility

Author

Fakhro, Khalid A., Robay, Amal, Rodriguez-Flores, Juan L., Crystal, Ronald G., Arafa, Mohamed, editor, Elbardisi, Haitham, editor, Majzoub, Ahmad, editor, and Agarwal, Ashok, editor

Published
2020
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7. Rare Synaptogenesis-Impairing Mutations in SLITRK5 Are Associated with Obsessive Compulsive Disorder

Author

Song, Minseok, Mathews, Carol A, Stewart, S Evelyn, Shmelkov, Sergey V, Mezey, Jason G, Rodriguez-Flores, Juan L, Rasmussen, Steven A, Britton, Jennifer C, Oh, Yong-Seok, Walkup, John T, Lee, Francis S, and Glatt, Charles E

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Neurosciences, Clinical Research, Human Genome, Anxiety Disorders, Brain Disorders, Mental Health, Serious Mental Illness, Biotechnology, Aetiology, 2.1 Biological and endogenous factors, Mental health, Amino Acid Sequence, Animals, Female, Humans, Membrane Proteins, Mice, Mutation, Nerve Tissue Proteins, Obsessive-Compulsive Disorder, Sequence Homology, Amino Acid, Synapses, Synaptic Transmission, General Science & Technology
Abstract

Obsessive compulsive disorder (OCD) is substantially heritable, but few molecular genetic risk factors have been identified. Knockout mice lacking SLIT and NTRK-Like Family, Member 5 (SLITRK5) display OCD-like phenotypes including serotonin reuptake inhibitor-sensitive pathologic grooming, and corticostriatal dysfunction. Thus, mutations that impair SLITRK5 function may contribute to the genetic risk for OCD. We re-sequenced the protein-coding sequence of the human SLITRK5 gene (SLITRK5) in three hundred and seventy seven OCD subjects and compared rare non-synonymous mutations (RNMs) in that sample with similar mutations in the 1000 Genomes database. We also performed in silico assessments and in vitro functional synaptogenesis assays on the Slitrk5 mutations identified. We identified four RNM's among these OCD subjects. There were no significant differences in the prevalence or in silico effects of rare non-synonymous mutations in the OCD sample versus controls. Direct functional testing of recombinant SLITRK5 proteins found that all mutations identified in OCD subjects impaired synaptogenic activity whereas none of the pseudo-matched mutations identified in 1000 Genomes controls had significant effects on SLITRK5 function (Fisher's exact test P = 0.028). These results demonstrate that rare functional mutations in SLITRK5 contribute to the genetic risk for OCD in human populations. They also highlight the importance of biological characterization of allelic effects in understanding genotype-phenotype relationships as there were no statistical differences in overall prevalence or bioinformatically predicted effects of OCD case versus control mutations. Finally, these results converge with others to highlight the role of aberrant synaptic function in corticostriatal neurons in the pathophysiology of OCD.

Published
2017

8. False Negatives Are a Significant Feature of Next Generation Sequencing Callsets

Author

Bobo, Dean, Lipatov, Mikhail, Rodriguez-Flores, Juan L, Auton, Adam, and Henn, Brenna M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Aetiology
Abstract

Short-read, next-generation sequencing (NGS) is now broadly used to identify rare or de novo mutations in population samples and disease cohorts. However, NGS data is known to be error-prone and post-processing pipelines have primarily focused on the removal of spurious mutations or “false positives” for downstream genome datasets. Less attention has been paid to characterizing the fraction of missing mutations or “false negatives” (FN). Here we interrogate several publically available human NGS autosomal variant datasets using corresponding Sanger sequencing as a truth-set. We examine both low-coverage Illumina and high-coverage Complete Genomics genomes. We show that the FN rate varies between 3%-18% and that false-positive rates are considerably lower (

Published
2016

10. Reconstructing Native American Migrations from Whole-genome and Whole-exome Data

Author

Gravel, Simon, Zakharia, Fouad, Moreno-Estrada, Andres, Byrnes, Jake K, Muzzio, Marina, Rodriguez-Flores, Juan L., Kenny, Eimear E., Gignoux, Christopher R., Maples, Brian K., Guiblet, Wilfried, Dutil, Julie, Via, Marc, Sandoval, Karla, Bedoya, Gabriel, Oleksyk, Taras K, Ruiz-Linares, Andres, Burchard, Esteban G, Martinez-Cruzado, Juan Carlos, Bustamante, Carlos D., and Project, The 1000 Genomes

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics, 92D25
Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Ta\'ino people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent and ancestry tract length, we show that post-contact populations differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe., Comment: 30 pages, inludes supplement. v2 contains clarifications, extra analyses, and a change in the language classification scheme used

Published
2013

11. NOTCH3p.Arg1231Cys is Markedly Enriched in South Asians and Associated with Stroke

Author

Rodriguez-Flores, Juan L., primary, Khalid, Shareef, additional, Parikshak, Neelroop, additional, Rasheed, Asif, additional, Ye, Bin, additional, Kapoor, Manav, additional, Backman, Joshua, additional, Sepehrband, Farshid, additional, DiGioia, Silvio Alessandro, additional, Gelfman, Sahar, additional, De, Tanima, additional, Banerjee, Nilanjana, additional, Sharma, Deepika, additional, Martinez, Hector, additional, Castaneda, Sofia, additional, D’Ambrosio, David, additional, Zhang, Xingmin A., additional, Xun, Pengcheng, additional, Tsai, Ellen, additional, Tsai, I-Chun, additional, Center, Regeneron Genetics, additional, Jahanzaib, Muhammad, additional, Khan, Maleeha Zaman, additional, Mian, Muhammad Rehan, additional, Liaqat, Muhammad Bilal, additional, Mahmood, Khalid, additional, Salam, Tanvir Us, additional, Hussain, Muhammad, additional, Iqbal, Javed, additional, Aslam, Faizan, additional, Cantor, Michael N., additional, Tzoneva, Gannie, additional, Overton, John, additional, Marchini, Jonathan, additional, Reid, Jeff, additional, Baras, Aris, additional, Verweij, Niek, additional, Lotta, Luca A., additional, Coppola, Giovanni, additional, Karalis, Katia, additional, Economides, Aris, additional, Fazio, Sergio, additional, Liedtke, Wolfgang, additional, Danesh, John, additional, Kamal, Ayeesha, additional, Frossard, Philippe, additional, Coleman, Thomas, additional, Shuldiner, Alan R., additional, and Saleheen, Danish, additional

Published
2023
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13. Supplementary Table S2 from Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers

Author

Feusier, Julie E., primary, Arunachalam, Sasi, primary, Tashi, Tsewang, primary, Baker, Monika J., primary, VanSant-Webb, Chad, primary, Ferdig, Amber, primary, Welm, Bryan E., primary, Rodriguez-Flores, Juan L., primary, Ours, Christopher, primary, Jorde, Lynn B., primary, Prchal, Josef T., primary, and Mason, Clinton C., primary

Published
2023
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15. Supplementary Information from Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers

Author

Feusier, Julie E., primary, Arunachalam, Sasi, primary, Tashi, Tsewang, primary, Baker, Monika J., primary, VanSant-Webb, Chad, primary, Ferdig, Amber, primary, Welm, Bryan E., primary, Rodriguez-Flores, Juan L., primary, Ours, Christopher, primary, Jorde, Lynn B., primary, Prchal, Josef T., primary, and Mason, Clinton C., primary

Published
2023
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16. Cysteine-Altering NOTCH3 Variants Are Associated with an Increased Risk of Autoimmune Diseases.

Author

Rieder, Emily, Li, Jiang, Rodriguez-Flores, Juan L., Taimur Malik, Muhammad, Abedi, Vida, and Zand, Ramin

Subjects
AUTOIMMUNE diseases, MULTIPLE sclerosis, MEDICAL records, CONTROL groups, TESTING laboratories, PUBLIC health
Abstract

Autoimmune conditions have been reported among patients with cysteine-altering NOTCH3 variants and CADASIL. This study aimed to investigate the occurrence of autoimmune illnesses and markers of inflammation in such populations. Cases were identified who had a NOTCH3 cysteine-altering variant from the Geisinger MyCode® Community Health Initiative (MyCode®). We further performed external validation using the UK Biobank cohort. A cohort of 121 individuals with a NOTCH3 cysteine-altering variant from MyCode® was compared to a control group with no non-synonymous variation in NOTCH3 (n = 184). Medical records were evaluated for inflammatory markers and autoimmune conditions, which were grouped by the organ systems involved. A similar analysis was conducted using data from the UK Biobank (n~450,000). An overall increase in inflammatory markers among participants with a NOTCH3 cysteine-altering variant was observed when compared to an age- and sex-matched MyCode® control group (out of participants with laboratory testing: 50.9% versus 26.7%; p = 0.0047; out of total participants: 23.1% versus 10.9%; p = 0.004). Analysis of UK Biobank data indicated any autoimmune diagnosis (1.63 [1.14, 2.09], p= 2.665 × 10−3) and multiple sclerosis (3.42 [1.67, 6.02], p = 9.681 × 10−4) are associated with a NOTCH3 cysteine-altering variant in any domain. Our findings suggest a possible association between NOTCH3 cysteine-altering variants and autoimmune conditions. [ABSTRACT FROM AUTHOR]

Published
2023
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18. A global reference for human genetic variation

Author

Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming

Published
2015
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19. Naturally Occurring Human Genetic Variation in the 3′-Untranslated Region of the Secretory Protein Chromogranin A Is Associated With Autonomic Blood Pressure Regulation and Hypertension in a Sex-Dependent Fashion

Author

Chen, Yuqing, Rao, Fangwen, Rodriguez-Flores, Juan L., Mahata, Manjula, Fung, Maple M., Stridsberg, Mats, Vaingankar, Sucheta M., Wen, Gen, Salem, Rany M., Das, Madhusudan, Cockburn, Myles G., Schork, Nicholas J., Ziegler, Michael G., Hamilton, Bruce A., Mahata, Sushil K., Taupenot, Laurent, and O'Connor, Daniel T.

Published
2008
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22. Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers

Author

Feusier, Julie E., primary, Arunachalam, Sasi, additional, Tashi, Tsewang, additional, Baker, Monika J., additional, VanSant-Webb, Chad, additional, Ferdig, Amber, additional, Welm, Bryan E., additional, Rodriguez-Flores, Juan L., additional, Ours, Christopher, additional, Jorde, Lynn B., additional, Prchal, Josef T., additional, and Mason, Clinton C., additional

Published
2021
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23. Genome diversity in Ukraine

Author

Oleksyk, Taras K, primary, Wolfsberger, Walter W, additional, Weber, Alexandra M, additional, Shchubelka, Khrystyna, additional, Oleksyk, Olga T, additional, Levchuk, Olga, additional, Patrus, Alla, additional, Lazar, Nelya, additional, Castro-Marquez, Stephanie O, additional, Hasynets, Yaroslava, additional, Boldyzhar, Patricia, additional, Neymet, Mikhailo, additional, Urbanovych, Alina, additional, Stakhovska, Viktoriya, additional, Malyar, Kateryna, additional, Chervyakova, Svitlana, additional, Podoroha, Olena, additional, Kovalchuk, Natalia, additional, Rodriguez-Flores, Juan L, additional, Zhou, Weichen, additional, Medley, Sarah, additional, Battistuzzi, Fabia, additional, Liu, Ryan, additional, Hou, Yong, additional, Chen, Siru, additional, Yang, Huanming, additional, Yeager, Meredith, additional, Dean, Michael, additional, Mills, Ryan E, additional, and Smolanka, Volodymyr, additional

Published
2021
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24. An integrated map of genetic variation from 1,092 human genomes

Author

McVean, Gil A., Altshuler, David M., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Donnelly, Peter, Eichler, Evan E., Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Green, Eric D., Hurles, Matthew E., Knoppers, Bartha M., Korbel, Jan O., Lander, Eric S., Lee, Charles, Lehrach, Hans, Mardis, Elaine R., Marth, Gabor T., Nickerson, Deborah A., Schmidt, Jeanette P., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Dinh, Huyen, Kovar, Christie, Lee, Sandra, Lewis, Lora, Muzny, Donna, Reid, Jeff, Wang, Min, Wang, Jun, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Li, Zhuo, Liu, Xiao, Lu, Yao, Ma, Xuedi, Su, Zhe, Tai, Shuaishuai, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Yin, Ye, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Zhou, Yan, Lander, Eric S., Gabriel, Stacey B., Gupta, Namrata, Flicek, Paul, Clarke, Laura, Leinonen, Rasko, Smith, Richard E., Zheng-Bradley, Xiangqun, Bentley, David R., Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, Sudbrak, Ralf, Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Sherry, Stephen T., McVean, Gil A., Mardis, Elaine R., Wilson, Richard K., Fulton, Lucinda, Fulton, Robert, Weinstock, George M., Durbin, Richard M., Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, Yu, Fuli, Bainbridge, Matthew, Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Sabo, Aniko, Wang, Yi, Yu, Jin, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Qin, Nan, Shao, Haojing, Wang, Bingqiang, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Garrison, Erik P., Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Lee, Charles, Griffin, Lauren, Hsieh, Chih-Heng, Mills, Ryan E., Shi, Xinghua, von Grotthuss, Marcin, Zhang, Chengsheng, Daly, Mark J., DePristo, Mark A., Banks, Eric, Bhatia, Gaurav, Carneiro, Mauricio O., del Angel, Guillermo, Genovese, Giulio, Handsaker, Robert E., Hartl, Chris, McCarroll, Steven A., Nemesh, James C., Poplin, Ryan E., Schaffner, Stephen F., Shakir, Khalid, Yoon, Seungtai C., Lihm, Jayon, Makarov, Vladimir, Jin, Hanjun, Kim, Wook, Cheol Kim, Ki, Korbel, Jan O., Rausch, Tobias, Beal, Kathryn, Cunningham, Fiona, Herrero, Javier, McLaren, William M., Ritchie, Graham R. S., Clark, Andrew G., Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Sabeti, Pardis C., Grossman, Sharon R., Tabrizi, Shervin, Tariyal, Ridhi, Cooper, David N., Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Keira Cheetham, R., Cox, Tony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Ye, Kai, Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., Lek, Monkol, Sudbrak, Herwig, Ralf, Shriver, Mark D., Bustamante, Carlos D., Byrnes, Jake K., De La Vega, Francisco M., Gravel, Simon, Kenny, Eimear E., Kidd, Jeffrey M., Lacroute, Phil, Maples, Brian K., Moreno-Estrada, Andres, Zakharia, Fouad, Halperin, Eran, Baran, Yael, Craig, David W., Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, Bafna, Vineet, Ye, Kenny, Burchard, Esteban G., Hernandez, Ryan D., Gignoux, Christopher R., Haussler, David, Katzman, Sol J., James Kent, W., Howie, Bryan, Ruiz-Linares, Andres, Dermitzakis, Emmanouil T., Lappalainen, Tuuli, Devine, Scott E., Liu, Xinyue, Maroo, Ankit, Tallon, Luke J., Rosenfeld, Jeffrey A., Min Kang, Hyun, Anderson, Paul, Angius, Andrea, Bigham, Abigail, Blackwell, Tom, Busonero, Fabio, Cucca, Francesco, Fuchsberger, Christian, Jones, Chris, Jun, Goo, Li, Yun, Lyons, Robert, Maschio, Andrea, Porcu, Eleonora, Reinier, Fred, Sanna, Serena, Schlessinger, David, Sidore, Carlo, Tan, Adrian, Kate Trost, Mary, Awadalla, Philip, Hodgkinson, Alan, Lunter, Gerton, McVean, Gil A., Marchini, Jonathan L., Myers, Simon, Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Iqbal, Zamin, Mathieson, Iain, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., Fu, Yunxin, Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, Witherspoon, David, Xing, Jinchuan, Eichler, Evan E., Browning, Brian L., Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Ko, Arthur, Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Dooling, David, Koboldt, Daniel C., McLellan, Michael D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Hurles, Matthew E., Tyler-Smith, Chris, Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Coffey, Alison J., Colonna, Vincenza, Huang, Ni, Jostins, Luke, Li, Heng, Scally, Aylwyn, Walter, Klaudia, Xue, Yali, Zhang, Yujun, Gerstein, Mark B., Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Habegger, Lukas, Harmanci, Arif O., Jin, Mike, Khurana, Ekta, Jasmine Mu, Xinmeng, Sisu, Cristina, Lee, Charles, McCarroll, Steven A., Degenhardt, Jeremiah, Korbel, Jan O., Stütz, Adrian M., Church, Deanna, Michaelson, Jacob J., Eichler, Evan E., Hurles, Matthew E., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, DePristo, Mark A., Min Kang, Hyun, Mardis, Elaine R., Yu, Fuli, Michelson, Leslie P., Tyler-Smith, Chris, Frankish, Adam, Harrow, Jennifer, Fowler, Gerald, Hale, Walker, Kalra, Divya, Flicek, Paul, Clarke, Laura, Barker, Jonathan, Kelman, Gavin, Kulesha, Eugene, Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Streeter, Ian, Toneva, Iliana, Vaughan, Brendan, Sherry, Stephen T., Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, OʼSullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Chakravarti, Aravinda, Knoppers, Bartha M., Barnes, Kathleen C., Beiswanger, Christine, Burchard, Esteban G., Bustamante, Carlos D., Cai, Hongyu, Cao, Hongzhi, Durbin, Richard M., Gharani, Neda, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Reich, David, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H., Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Ruiz-Linares, Andres, Zhi Ming, Cai, Yang, Gao, Jia You, Chu, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Oleksyk, Taras K., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Clemm, Nicholas C., Duncanson, Audrey, Dunn, Michael, Guyer, Mark S., Peterson, Jane L., Abecasis, Goncalo R., and Auton, Adam

Published
2012
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25. Genome Diversity in Ukraine

Author

Oleksyk, Taras K., primary, Wolfsberger, Walter W., additional, Weber, Alexandra, additional, Shchubelka, Khrystyna, additional, Oleksyk, Olga T., additional, Levchuk, Olga, additional, Patrus, Alla, additional, Lazar, Nelya, additional, Castro-Marquez, Stephanie O., additional, Boldyzhar, Patricia, additional, Urbanovych, Alina, additional, Stakhovska, Viktoriya, additional, Malyar, Kateryna, additional, Chervyakova, Svitlana, additional, Podoroha, Olena, additional, Kovalchuk, Natalia, additional, Hasynets, Yaroslava, additional, Rodriguez-Flores, Juan L., additional, Medley, Sarah, additional, Battistuzzi, Fabia, additional, Liu, Ryan, additional, Hou, Yong, additional, Chen, Siru, additional, Yang, Huanming, additional, Yeager, Meredith, additional, Dean, Michael, additional, Mills, Ryan E., additional, and Smolanka, Volodymyr, additional

Published
2020
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27. Adrenergic Polymorphism and the Human Stress Response

Author

Rao, Fangwen, Zhang, Lian, Wessel, Jennifer, Zhang, Kuixing, Wen, Gen, Kennedy, Brian P., Rana, Brinda K., Das, Madhusudan, Rodriguez-Flores, Juan L., Smith, Douglas W., Cadman, Peter E., Salem, Rany M., Mahata, Sushil K., Schork, Nicholas J., Taupenot, Laurent, Ziegler, Michael G., and OʼConnor, Daniel T.

Published
2008
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29. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

Author

Omberg Larsson, Salit Jacqueline, Hackett Neil, Fuller Jennifer, Matthew Rebecca, Chouchane Lotfi, Rodriguez-Flores Juan L, Bustamante Carlos, Crystal Ronald G, and Mezey Jason G

Subjects
Human migration, Admixture, Arabian Peninsula, Qatar, Support vector machines, Genetics, QH426-470
Abstract

Abstract Background Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Results Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. Conclusions By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

Published
2012
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30. RNA-Seq quantification of the human small airway epithelium transcriptome

Author

Hackett Neil R, Butler Marcus W, Shaykhiev Renat, Salit Jacqueline, Omberg Larsson, Rodriguez-Flores Juan L, Mezey Jason G, Strulovici-Barel Yael, Wang Guoqing, Didon Lukas, and Crystal Ronald G

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The small airway epithelium (SAE), the cell population that covers the human airway surface from the 6th generation of airway branching to the alveoli, is the major site of lung disease caused by smoking. The focus of this study is to provide quantitative assessment of the SAE transcriptome in the resting state and in response to chronic cigarette smoking using massive parallel mRNA sequencing (RNA-Seq). Results The data demonstrate that 48% of SAE expressed genes are ubiquitous, shared with many tissues, with 52% enriched in this cell population. The most highly expressed gene, SCGB1A1, is characteristic of Clara cells, the cell type unique to the human SAE. Among other genes expressed by the SAE are those related to Clara cell differentiation, secretory mucosal defense, and mucociliary differentiation. The high sensitivity of RNA-Seq permitted quantification of gene expression related to infrequent cell populations such as neuroendocrine cells and epithelial stem/progenitor cells. Quantification of the absolute smoking-induced changes in SAE gene expression revealed that, compared to ubiquitous genes, more SAE-enriched genes responded to smoking with up-regulation, and those with the highest basal expression levels showed most dramatic changes. Smoking had no effect on SAE gene splicing, but was associated with a shift in molecular pattern from Clara cell-associated towards the mucus-secreting cell differentiation pathway with multiple features of cancer-associated molecular phenotype. Conclusions These observations provide insights into the unique biology of human SAE by providing quantit-ative assessment of the global transcriptome under physiological conditions and in response to the stress of chronic cigarette smoking.

Published
2012
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31. Point of Care Exome Sequencing Reveals Allelic and Phenotypic Heterogeneity Underlying Mendelian disease in Qatar.

Author

Fakhro, Khalid A., Robay, Amal, Rodriguez-Flores, Juan L., Mezey, Jason G., Al-Shakaki, Alya A., Chidiac, Omar, Stadler, Dora J., Malek, Joel A., Imam, Abu Bakr, Sheikh, Arwa, Azzam, Asmaa, Janahi, Ibrahim, Khanjar, Izzat, Osman, Kamal, Ziki, Maen Abou, Mahmah, Mohamed Adnan, Selim, Mohamed, Nimeri, Nuha, Ali, Rehab, and Lakhani, Shenela

Published
2019
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32. Exome sequencing-based identification of novel type 2 diabetes risk allele loci in the Qatari population

Author

O’Beirne, Sarah L., primary, Salit, Jacqueline, additional, Rodriguez-Flores, Juan L., additional, Staudt, Michelle R., additional, Abi Khalil, Charbel, additional, Fakhro, Khalid A., additional, Robay, Amal, additional, Ramstetter, Monica D., additional, Malek, Joel A., additional, Zirie, Mahmoud, additional, Jayyousi, Amin, additional, Badii, Ramin, additional, Al-Nabet Al-Marri, Ajayeb, additional, Bener, Abdulbari, additional, Mahmoud, Mai, additional, Chiuchiolo, Maria J., additional, Al-Shakaki, Alya, additional, Chidiac, Omar, additional, Stadler, Dora, additional, Mezey, Jason G., additional, and Crystal, Ronald G., additional

Published
2018
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33. Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population

Author

Yousri, Noha A., primary, Fakhro, Khalid A., additional, Robay, Amal, additional, Rodriguez-Flores, Juan L., additional, Mohney, Robert P., additional, Zeriri, Hassina, additional, Odeh, Tala, additional, Kader, Sara Abdul, additional, Aldous, Eman K., additional, Thareja, Gaurav, additional, Kumar, Manish, additional, Al-Shakaki, Alya, additional, Chidiac, Omar M., additional, Mohamoud, Yasmin A., additional, Mezey, Jason G., additional, Malek, Joel A., additional, Crystal, Ronald G., additional, and Suhre, Karsten, additional

Published
2018
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34. Correction: Type 2 Diabetes Risk Allele Loci in the Qatari Population

Author

O’Beirne, Sarah L., primary, Salit, Jacqueline, additional, Rodriguez-Flores, Juan L., additional, Staudt, Michelle R., additional, Abi Khalil, Charbel, additional, Fakhro, Khalid A., additional, Robay, Amal, additional, Ramstetter, Monica D., additional, Al-Azwani, Iman K., additional, Malek, Joel A., additional, Zirie, Mahmoud, additional, Jayyousi, Amin, additional, Badii, Ramin, additional, Al-Nabet Al-Marri, Ajayeb, additional, Chiuchiolo, Maria J., additional, Al-Shakaki, Alya, additional, Chidiac, Omar, additional, Gharbiah, Maey, additional, Bener, Abdulbari, additional, Stadler, Dora, additional, Hackett, Neil R., additional, Mezey, Jason G., additional, and Crystal, Ronald G., additional

Published
2016
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36. Type 2 Diabetes Risk Allele Loci in the Qatari Population

Author

O’Beirne, Sarah L., primary, Salit, Jacqueline, additional, Rodriguez-Flores, Juan L., additional, Staudt, Michelle R., additional, Abi Khalil, Charbel, additional, Fakhro, Khalid A., additional, Robay, Amal, additional, Ramstetter, Monica D., additional, Al-Azwani, Iman K., additional, Malek, Joel A., additional, Zirie, Mahmoud, additional, Jayyousi, Amin, additional, Badii, Ramin, additional, Al-Nabet Al-Marri, Ajayeb, additional, Chiuchiolo, Maria J., additional, Al-Shakaki, Alya, additional, Chidiac, Omar, additional, Gharbiah, Maey, additional, Bener, Abdulbari, additional, Stadler, Dora, additional, Hackett, Neil R., additional, Mezey, Jason G., additional, and Crystal, Ronald G., additional

Published
2016
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37. The Qatar genome: a population-specific tool for precision medicine in the Middle East

Author

Fakhro, Khalid A, primary, Staudt, Michelle R, additional, Ramstetter, Monica Denise, additional, Robay, Amal, additional, Malek, Joel A, additional, Badii, Ramin, additional, Al-Marri, Ajayeb Al-Nabet, additional, Khalil, Charbel Abi, additional, Al-Shakaki, Alya, additional, Chidiac, Omar, additional, Stadler, Dora, additional, Zirie, Mahmoud, additional, Jayyousi, Amin, additional, Salit, Jacqueline, additional, Mezey, Jason G, additional, Crystal, Ronald G, additional, and Rodriguez-Flores, Juan L, additional

Published
2016
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38. Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

Author

Rodriguez-Flores, Juan L., primary, Fakhro, Khalid, additional, Agosto-Perez, Francisco, additional, Ramstetter, Monica D., additional, Arbiza, Leonardo, additional, Vincent, Thomas L., additional, Robay, Amal, additional, Malek, Joel A., additional, Suhre, Karsten, additional, Chouchane, Lotfi, additional, Badii, Ramin, additional, Al-Nabet Al-Marri, Ajayeb, additional, Abi Khalil, Charbel, additional, Zirie, Mahmoud, additional, Jayyousi, Amin, additional, Salit, Jacqueline, additional, Keinan, Alon, additional, Clark, Andrew G., additional, Crystal, Ronald G., additional, and Mezey, Jason G., additional

Published
2016
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39. Prevalence of the ApoE Arg145Cys Dyslipidemia At-risk Polymorphism in African-derived Populations

Author

Abou Ziki, Maen D., Strulovici-Barel, Yael, Hackett, Neil R., Rodriguez-Flores, Juan L., Mezey, Jason G., Salit, Jacqueline, Radisch, Sharon, Hollmann, Charleen, Chouchane, Lotfi, Malek, Joel, Zirie, Mahmoud A., Jayyuosi, Amin, Gotto, Antonio M., and Crystal, Ronald G.

Subjects
Polymorphism, Genetic, Genotype, New York, DNA, Polymerase Chain Reaction, Article, Black or African American, Apolipoproteins E, Risk Factors, Prevalence, Humans, Genetic Predisposition to Disease, Alleles, Dyslipidemias
Abstract

Apolipoprotein E, a protein component of blood lipid particles, plays an important role in lipid transport. Different mutations in the apolipoprotein E gene have been associated with various clinical phenotypes. In an initiated study of Qataris, we observed that 17% of the African-derived genetic subgroup were heterozygotes for a rare Arg145Cys (R145C) variant that functions as a dominant trait with incomplete penetrance associated with type III hyperlipoproteinemia. On the basis of this observation, we hypothesized that the R145C polymorphism might be common in African-derived populations. The prevalence of the R145C variant was assessed worldwide in the "1000 Genomes Project" and in 1,012 whites and 1,226 African-Americans in New York, New York. The 1000 Genomes Project data demonstrated that the R145C polymorphism is rare in non-African-derived populations but present in 5% to 12% of Sub-Saharan African-derived populations. The R145C polymorphism was also rare in New York whites (1 of 1,012, 0.1%); however, strikingly, 53 of the 1,226 New York African-Americans (4.3%) were R145C heterozygotes. The lipid profiles of the Qatari and New York R145C heterozygotes were compared with those of controls. The Qatari R145C subjects had higher triglyceride levels than the Qatari controls (p0.007) and the New York African-American R145C subjects had an average of 52% greater fasting triglyceride levels than the New York African-American controls (p0.002). From these observations, likely millions of people worldwide derived from Sub-Saharan Africans are apolipoprotein E R145C. In conclusion, although larger epidemiologic studies are necessary to determine the long-term consequences of this polymorphism, the available evidence suggests it is a common cause of a mild triglyceride dyslipidemia.

Published
2013

40. Copy number variations in the genome of the Qatari population

Author

Fakhro, Khalid A., primary, Yousri, Noha A., additional, Rodriguez-Flores, Juan L., additional, Robay, Amal, additional, Staudt, Michelle R., additional, Agosto-Perez, Francisco, additional, Salit, Jacqueline, additional, Malek, Joel A., additional, Suhre, Karsten, additional, Jayyousi, Amin, additional, Zirie, Mahmoud, additional, Stadler, Dora, additional, Mezey, Jason G., additional, and Crystal, Ronald G., additional

Published
2015
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41. Neuropeptide Y1 receptor NPY1R: Discovery of naturally occurring human genetic variants governing gene expression in cella as well as pleiotropic effects on autonomic activity and blood pressure in vivo

Author

Wang, Lei, Rao, Fangwen, Zhang, Kuixing, Mahata, Manjula, Rodriguez-Flores, Juan L., Fung, Maple M., Waalen, Jill, Cockburn, Myles G., Hamilton, Bruce A., Mahata, Sushil K., and O'Connor, Daniel T.

Subjects
Adult, Male, Adolescent, Blood Pressure, Autonomic Nervous System, Transfection, Polymorphism, Single Nucleotide, Article, Linkage Disequilibrium, Young Adult, Stress, Physiological, Escherichia coli, Humans, genetics, Neuropeptide Y, Luciferases, Promoter Regions, Genetic, neuropeptide, Aged, Aged, 80 and over, Polymorphism, Genetic, Baroreflex, Middle Aged, beta-Galactosidase, Receptors, Neuropeptide Y, Cold Temperature, Phenotype, Gene Expression Regulation, Haplotypes, Hypertension, Female
Abstract

ObjectivesWe asked whether naturally occurring genetic variation at the human NPY1Rlocus alters autonomic traits that might predispose individuals to cardiovascular disease.BackgroundNeuropeptide Y (NPY) interacts with the Y1receptor, NPY1R, to control adrenergic activity and blood pressure (BP).MethodsWe searched for polymorphism at NPY1Rby systematic resequencing in ethnically diverse people. There were 376 twins/siblings who were evaluated for heritable autonomic traits: baroreflex function and pressor response to environmental stress.ResultsThe common NPY1Rvariant A+1050G in the 3′-untranslated region (3′-UTR) predicted baroreceptor slope (p = 0.014–0.047) and BP change to cold stress (p = 0.0091–0.016), with minor allele homozygotes displaying blunted slope and exaggerated pressor response. In 936 individuals with the most extreme BPs in the population, not only 3′-UTR A+1050G (p = 1.2 × 10−4) but also promoter A-585T (p = 0.001) affected both systolic BP and diastolic BP, in interactive fashion (p = 0.007), with combined homozygotes showing the highest diastolic BP (>20 mm Hg). The 3′-UTR variant +1050G decreased expression of a transfected luciferase reporter/NPY1R3′-UTR plasmid; promoter variant A-585 also decreased expression of an NPY1Rpromoter/luciferase reporter. Thus, alleles that increased BP in vivo (3′-UTR +1050G, promoter A-585) also decreased NPY1R expression in cella. Computational alignment showed that A+1050G disrupted a microRNA motif.ConclusionsOur results indicate that naturally occurring genetic variation at the NPY1Rlocus has implications for heritable autonomic control of the circulation, and ultimately, for systemic hypertension. The findings suggest novel pathophysiological links between the NPY1Rlocus, autonomic activity, and blood pressure, and suggest new strategies to approach the mechanism, diagnosis, and treatment of systemic hypertension.

Published
2009

42. Autonomic function in hypertension; role of genetic variation at the catecholamine storage vesicle protein chromogranin B

Author

Zhang, Kuixing, Rao, Fangwen, Rana, Brinda K., Gayen, Jiaur R., Calegari, Federico, King, Angus, Rosa, Patrizia, Huttner, Wieland B., Stridsberg, Mats, Mahata, Manjula, Vaingankar, Sucheta, Mahboubi, Vafa, Salem, Rany M., Rodriguez-Flores, Juan L., Fung, Maple M., Smith, Douglas W., Schork, Nicholas J., Ziegler, Michael G., Taupenot, Laurent, Mahata, Sushil K., OConnor, Daniel T., Zhang, Kuixing, Rao, Fangwen, Rana, Brinda K., Gayen, Jiaur R., Calegari, Federico, King, Angus, Rosa, Patrizia, Huttner, Wieland B., Stridsberg, Mats, Mahata, Manjula, Vaingankar, Sucheta, Mahboubi, Vafa, Salem, Rany M., Rodriguez-Flores, Juan L., Fung, Maple M., Smith, Douglas W., Schork, Nicholas J., Ziegler, Michael G., Taupenot, Laurent, Mahata, Sushil K., and OConnor, Daniel T.

Abstract

Background: Hypertension is a complex trait, with deranged autonomic control of circulation. Chromogranin B (CHGB) is the most abundant core protein in human catecholamine secretory vesicles, playing an important role in their biogenesis. Does common interindividual variation at the CHGB locus contribute to phenotypic variation in CHGB and catecholamine secretion, autonomic stability of circulation, or blood pressure (BP) in the population? Methods and Results: To probe interindividual variability in CHGB, we systematically studied polymorphism across the locus by resequencing CHGB (≈6 kbp footprint spanning the promoter, 5 exons, exon/intron borders, untranslated regions) in 160 subjects (2n=320 chromosomes) of diverse biogeographic ancestries. We identified 53 single-nucleotide polymorphisms, of which 22 were common. We then studied 1182 subjects drawn from the most extreme BP values in the population (highest and lowest 5th percentiles), typing 4 common polymorphisms spanning the ≈14 kbp locus. Sliding-window haplotype analysis indicated BP associations peaking in the 5'/promoter region, most prominent in men, and a peak effect in the proximal promoter at variant A-261T (A>T), accounting for ≈8/≈6 mm Hg BP in males. The promoter allele (A-261) that was a predictor of higher diastolic BP and systolic BP was also associated with lower circulating/plasma CHGB concentration (CHGB439to451 epitope) in twin pairs. In twins, the same CHGB variants that were predictors of lower basal CHGB secretion were also associated with exaggerated catecholamine secretion and BP response to environmental (cold) stress; likewise, women displayed increased plasma CHGB439to451 but decreased catecholamine secretion as well as BP response to environmental stress. The effect of A-261T on CHGB expression was confirmed in chromaffin cells by site-directed mutagenesis on transfected CHGB promoter/luciferase reporter activity, and the allelic effects of A-261T on gene expression were directi

Published
2009
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43. Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar

Author

Rodriguez-Flores, Juan L., primary, Fakhro, Khalid, additional, Hackett, Neil R., additional, Salit, Jacqueline, additional, Fuller, Jennifer, additional, Agosto-Perez, Francisco, additional, Gharbiah, Maey, additional, Malek, Joel A., additional, Zirie, Mahmoud, additional, Jayyousi, Amin, additional, Badii, Ramin, additional, Al-Nabet Al-Marri, Ajayeb, additional, Chouchane, Lotfi, additional, Stadler, Dora J., additional, Mezey, Jason G., additional, and Crystal, Ronald G., additional

Published
2013
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44. Exome Sequencing of Only Seven Qataris Identifies Potentially Deleterious Variants in the Qatari Population

Author

Rodriguez-Flores, Juan L., primary, Fuller, Jennifer, additional, Hackett, Neil R., additional, Salit, Jacqueline, additional, Malek, Joel A., additional, Al-Dous, Eman, additional, Chouchane, Lotfi, additional, Zirie, Mahmoud, additional, Jayoussi, Amin, additional, Mahmoud, Mai A., additional, Crystal, Ronald G., additional, and Mezey, Jason G., additional

Published
2012
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45. High prevalence of the ApoE Arg145Cys dyslipidemia at-risk polymorphism in African-derived populations

Author

Abou Ziki, Maen D., primary, Strulovici-Barel, Yael, additional, Hackett, Neil R., additional, Rodriguez-Flores, Juan L., additional, Mezey, Jason G., additional, Salit, Jacqueline, additional, Radisch, Sharon, additional, Hollmann, Charleen, additional, Chouchane, Lotfi, additional, Malek, Joel, additional, Zirie, Mahmoud A., additional, Jayyuosi, Amin, additional, Gotto, Antonio M., additional, and Crystal, Ronald G., additional

Published
2012
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46. Common Functional Genetic Variants in Catecholamine Storage Vesicle Protein Promoter Motifs Interact to Trigger Systemic Hypertension

Author

Zhang, Kuixing, primary, Rao, Fangwen, additional, Wang, Lei, additional, Rana, Brinda K., additional, Ghosh, Sajalendu, additional, Mahata, Manjula, additional, Salem, Rany M., additional, Rodriguez-Flores, Juan L., additional, Fung, Maple M., additional, Waalen, Jill, additional, Tayo, Bamidele, additional, Taupenot, Laurent, additional, Mahata, Sushil K., additional, and O'Connor, Daniel T., additional

Published
2010
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49. Human dopamine beta-hydroxylase (DBH) regulatory polymorphism that influences enzymatic activity, autonomic function, and blood pressure

Author

Chen, Yuqing, primary, Wen, Gen, additional, Rao, Fangwen, additional, Zhang, Kuixing, additional, Wang, Lei, additional, Rodriguez-Flores, Juan L, additional, Sanchez, Amber P, additional, Mahata, Manjula, additional, Taupenot, Laurent, additional, Sun, Ping, additional, Mahata, Sushil K, additional, Tayo, Bamidele, additional, Schork, Nicholas J, additional, Ziegler, Michael G, additional, Hamilton, Bruce A, additional, and O'Connor, Daniel T, additional

Published
2010
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50. Neuropeptide Y1Receptor NPY1R

Author

Wang, Lei, primary, Rao, Fangwen, additional, Zhang, Kuixing, additional, Mahata, Manjula, additional, Rodriguez-Flores, Juan L., additional, Fung, Maple M., additional, Waalen, Jill, additional, Cockburn, Myles G., additional, Hamilton, Bruce A., additional, Mahata, Sushil K., additional, and O'Connor, Daniel T., additional

Published
2009
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