8 results on '"Khalid, Shareef"'
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2. Thrombotic risk determined by rare and common SERPINA1variants in a population‐based cohort study
- Author
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Manderstedt, Eric, Halldén, Christer, Lind‐Halldén, Christina, Elf, Johan, Svensson, Peter J., Engström, Gunnar, Melander, Olle, Baras, Aris, Lotta, Luca A., Zöller, Bengt, Abecasis, Goncalo, Cantor, Michael, Coppola, Giovanni, Economides, Aris, Overton, John D., Reid, Jeffrey G., Shuldiner, Alan, Beechert, Christina, Forsythe, Caitlin, Fuller, Erin D., Gu, Zhenhua, Lattari, Michael, Lopez, Alexander, Manoochehri, Kia, Overton, John D., Padilla, Maria Sotiropoulos, Pradhan, Manasi, Schleicher, Thomas D., Ulloa, Ricardo H., Widom, Louis, Wolf, Sarah E., Bai, Xiaodong, Balasubramanian, Suganthi, Blumenfeld, Andrew, Boutkov, Boris, Eom, Gisu, Habegger, Lukas, Hawes, Alicia, Khalid, Shareef, Krasheninina, Olga, Lanche, Rouel, Mansfield, Adam J., Maxwell, Evan K., Nafde, Mrunali, O’Keeffe, Sean, Orelus, Max, Panea, Razvan, Polanco, Tommy, Rasool, Ayesha, Reid, Jeffrey G., Salerno, William, Staples, Jeffrey C., Jones, Marcus B., Mighty, Jason, and Mitnaul, Lyndon J.
- Abstract
Severe alpha‐1‐antitrypsin deficiency (AATD), phenotype PiZZ, was associated with venous thromboembolism (VTE) in a case‐control study.
- Published
- 2022
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3. Thrombotic risk determined by rare and common SERPINA1variants in a population‐based cohort study
- Author
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Manderstedt, Eric, Halldén, Christer, Lind‐Halldén, Christina, Elf, Johan, Svensson, Peter J., Engström, Gunnar, Melander, Olle, Baras, Aris, Lotta, Luca A., Zöller, Bengt, Abecasis, Goncalo, Cantor, Michael, Coppola, Giovanni, Economides, Aris, Overton, John D., Reid, Jeffrey G., Shuldiner, Alan, Beechert, Christina, Forsythe, Caitlin, Fuller, Erin D., Gu, Zhenhua, Lattari, Michael, Lopez, Alexander, Manoochehri, Kia, Overton, John D., Padilla, Maria Sotiropoulos, Pradhan, Manasi, Schleicher, Thomas D., Ulloa, Ricardo H., Widom, Louis, Wolf, Sarah E., Bai, Xiaodong, Balasubramanian, Suganthi, Blumenfeld, Andrew, Boutkov, Boris, Eom, Gisu, Habegger, Lukas, Hawes, Alicia, Khalid, Shareef, Krasheninina, Olga, Lanche, Rouel, Mansfield, Adam J., Maxwell, Evan K., Nafde, Mrunali, O’Keeffe, Sean, Orelus, Max, Panea, Razvan, Polanco, Tommy, Rasool, Ayesha, Reid, Jeffrey G., Salerno, William, Staples, Jeffrey C., Jones, Marcus B., Mighty, Jason, and Mitnaul, Lyndon J.
- Abstract
Severe alpha‐1‐antitrypsin deficiency (AATD), phenotype PiZZ, was associated with venous thromboembolism (VTE) in a case‐control study. This study aimed to determine the genetic variation in the SERPINA1gene and a possible thrombotic risk of these variants in a population‐based cohort study. The coding sequence of SERPINA1was analyzed for the Z (rs28929474), S (rs17580), and other qualifying variants in 28,794 subjects without previous VTE (born 1923–1950, 60% women), who participated in the Malmö Diet and Cancer study (1991–1996). Individuals were followed from baseline until the first event of VTE, death, or 2018. Resequencing the coding sequence of SERPINA1identified 84 variants in the total study population, 21 synonymous, 62 missense, and 1 loss‐of‐function variant. Kaplan‐Meier analysis showed that homozygosity for the Z allele increased the risk of VTE whereas heterozygosity showed no effect. The S (rs17580) variant was not associated with VTE. Thirty‐one rare variants were qualifying and included in collapsing analysis using the following selection criteria, loss of function, in frame deletion or non‐benign (PolyPhen‐2) missense variants with minor allele frequency (MAF) <0.1%. Combining the rare qualifying variants with the Z variant showed that carrying two alleles (ZZ or compound heterozygotes) showed increased risk. Cox regression analysis revealed an adjusted hazard ratio of 4.5 (95% confidence interval 2.0–10.0) for combinations of the Z variant and rare qualifying variants. One other variant (rs141620200; MAF = 0.002) showed an increased risk of VTE. The SERPINA1ZZ genotype and compound heterozygotes for severe AATD are rare but associated with VTE in a population‐based Swedish study.
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- 2022
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4. Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank
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Wang, Louise, Desai, Heena, Verma, Shefali S., Le, Anh, Hausler, Ryan, Verma, Anurag, Judy, Renae, Doucette, Abigail, Gabriel, Peter E., Abecasis, Goncalo, Bai, Xiaodong, Balasubramanian, Suganthi, Baras, Aris, Blumenfeld, Andrew, Boutkov, Boris, Cantor, Michael, Coppola, Giovanni, Economides, Aris, Eom, Gisu, Habegger, Lukas, Hawes, Alicia, Jones, Marcus B., Khalid, Shareef, Krasheninina, Olga, Lanche, Rouel, Lotta, Luca A., Mansfield, Adam J., Maxwell, Evan K., Mighty, Jason, Mitnaul, Lyndon J., Nafde, Mrunali, O’Keeffe, Sean, Orelus, Max, Overton, John D., Panea, Razvan, Polanco, Tommy, Rasool, Ayesha, Reid, Jeffrey G., Salerno, William, Staples, Jeffrey C., Shuldiner, Alan, Beechert, Christina, Forsythe, Caitlin, Fuller, Erin D., Gu, Zhenhua, Lattari, Michael, Lopez, Alexander, Manoochehri, Kia, Overton, John D., Pradhan, Manasi, Schleicher, Thomas D., Padilla, Maria Sotiropoulos, Ulloa, Ricardo H., Widom, Louis, Wolf, Sarah E., Nathanson, Katherine L., Damrauer, Scott M., Mowery, Danielle L., Ritchie, Marylyn D., Kember, Rachel L., and Maxwell, Kara N.
- Abstract
Genome-wide association studies have identified hundreds of single nucleotide variations (formerly single nucleotide polymorphisms) associated with several cancers, but the predictive ability of polygenic risk scores (PRSs) is unclear, especially among non-Whites.
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- 2022
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5. Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank
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Szustakowski, Joseph D., Balasubramanian, Suganthi, Kvikstad, Erika, Khalid, Shareef, Bronson, Paola G., Sasson, Ariella, Wong, Emily, Liu, Daren, Wade Davis, J., Haefliger, Carolina, Katrina Loomis, A., Mikkilineni, Rajesh, Noh, Hyun Ji, Wadhawan, Samir, Bai, Xiaodong, Hawes, Alicia, Krasheninina, Olga, Ulloa, Ricardo, Lopez, Alex E., Smith, Erin N., Waring, Jeffrey F., Whelan, Christopher D., Tsai, Ellen A., Overton, John D., Salerno, William J., Jacob, Howard, Szalma, Sandor, Runz, Heiko, Hinkle, Gregory, Nioi, Paul, Petrovski, Slavé, Miller, Melissa R., Baras, Aris, Mitnaul, Lyndon J., and Reid, Jeffrey G.
- Abstract
The UK Biobank Exome Sequencing Consortium (UKB-ESC) is a private–public partnership between the UK Biobank (UKB) and eight biopharmaceutical companies that will complete the sequencing of exomes for all ~500,000 UKB participants. Here, we describe the early results from ~200,000 UKB participants and the features of this project that enabled its success. The biopharmaceutical industry has increasingly used human genetics to improve success in drug discovery. Recognizing the need for large-scale human genetics data, as well as the unique value of the data access and contribution terms of the UKB, the UKB-ESC was formed. As a result, exome data from 200,643 UKB enrollees are now available. These data include ~10 million exonic variants—a rich resource of rare coding variation that is particularly valuable for drug discovery. The UKB-ESC precompetitive collaboration has further strengthened academic and industry ties and has provided teams with an opportunity to interact with and learn from the wider research community.
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- 2021
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6. Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline
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Gorski, Mathias, Jung, Bettina, Li, Yong, Matias-Garcia, Pamela R., Wuttke, Matthias, Coassin, Stefan, Thio, Chris H.L., Kleber, Marcus E., Winkler, Thomas W., Wanner, Veronika, Chai, Jin-Fang, Chu, Audrey Y., Cocca, Massimiliano, Feitosa, Mary F., Ghasemi, Sahar, Hoppmann, Anselm, Horn, Katrin, Li, Man, Nutile, Teresa, Scholz, Markus, Sieber, Karsten B., Teumer, Alexander, Tin, Adrienne, Wang, Judy, Tayo, Bamidele O., Ahluwalia, Tarunveer S., Almgren, Peter, Bakker, Stephan J.L., Banas, Bernhard, Bansal, Nisha, Biggs, Mary L., Boerwinkle, Eric, Bottinger, Erwin P., Brenner, Hermann, Carroll, Robert J., Chalmers, John, Chee, Miao-Li, Chee, Miao-Ling, Cheng, Ching-Yu, Coresh, Josef, de Borst, Martin H., Degenhardt, Frauke, Eckardt, Kai-Uwe, Endlich, Karlhans, Franke, Andre, Freitag-Wolf, Sandra, Gampawar, Piyush, Gansevoort, Ron T., Ghanbari, Mohsen, Gieger, Christian, Hamet, Pavel, Ho, Kevin, Hofer, Edith, Holleczek, Bernd, Xian Foo, Valencia Hui, Hutri-Kähönen, Nina, Hwang, Shih-Jen, Ikram, M. Arfan, Josyula, Navya Shilpa, Kähönen, Mika, Khor, Chiea-Chuen, Koenig, Wolfgang, Kramer, Holly, Krämer, Bernhard K., Kühnel, Brigitte, Lange, Leslie A., Lehtimäki, Terho, Lieb, Wolfgang, Alizadeh, Behrooz Z., Boezen, H. Marike, Franke, Lude, van der Harst, Pim, Navis, Gerjan, Rots, Marianne, Snieder, Harold, Swertz, Morris, Wolffenbuttel, Bruce H.R., Wijmenga, Cisca, Abecasis, Goncalo, Baras, Aris, Cantor, Michael, Coppola, Giovanni, Economides, Aris, Lotta, Luca A., Overton, John D., Reid, Jeffrey G., Shuldiner, Alan, Beechert, Christina, Forsythe, Caitlin, Fuller, Erin D., Gu, Zhenhua, Lattari, Michael, Lopez, Alexander, Overton, John D., Schleicher, Thomas D., Padilla, Maria Sotiropoulos, Toledo, Karina, Widom, Louis, Wolf, Sarah E., Pradhan, Manasi, Manoochehri, Kia, Ulloa, Ricardo H., Bai, Xiaodong, Balasubramanian, Suganthi, Barnard, Leland, Blumenfeld, Andrew, Eom, Gisu, Habegger, Lukas, Hawes, Alicia, Khalid, Shareef, Reid, Jeffrey G., Maxwell, Evan K., Salerno, William, Staples, Jeffrey C., Jones, Marcus B., Mitnaul, Lyndon J., Loos, Ruth J.F., Lukas, Mary Ann, Lyytikäinen, Leo-Pekka, Meisinger, Christa, Meitinger, Thomas, Melander, Olle, Milaneschi, Yuri, Mishra, Pashupati P., Mononen, Nina, Mychaleckyj, Josyf C., Nadkarni, Girish N., Nauck, Matthias, Nikus, Kjell, Ning, Boting, Nolte, Ilja M., O’Donoghue, Michelle L., Orho-Melander, Marju, Pendergrass, Sarah A., Penninx, Brenda W.J.H., Preuss, Michael H., Psaty, Bruce M., Raffield, Laura M., Raitakari, Olli T., Rettig, Rainer, Rheinberger, Myriam, Rice, Kenneth M., Rosenkranz, Alexander R., Rossing, Peter, Rotter, Jerome I., Sabanayagam, Charumathi, Schmidt, Helena, Schmidt, Reinhold, Schöttker, Ben, Schulz, Christina-Alexandra, Sedaghat, Sanaz, Shaffer, Christian M., Strauch, Konstantin, Szymczak, Silke, Taylor, Kent D., Tremblay, Johanne, Chaker, Layal, van der Harst, Pim, van der Most, Peter J., Verweij, Niek, Völker, Uwe, Waldenberger, Melanie, Wallentin, Lars, Waterworth, Dawn M., White, Harvey D., Wilson, James G., Wong, Tien-Yin, Woodward, Mark, Yang, Qiong, Yasuda, Masayuki, Yerges-Armstrong, Laura M., Zhang, Yan, Snieder, Harold, Wanner, Christoph, Böger, Carsten A., Köttgen, Anna, Kronenberg, Florian, Pattaro, Cristian, and Heid, Iris M.
- Abstract
Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m2/year or more (“Rapid3”; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m2at follow-up among those with eGFRcrea 60 mL/min/1.73m2or more at baseline (“CKDi25”; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT(2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATMor LARP4B. Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.
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- 2021
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7. Exome sequencing and characterization of 49,960 individuals in the UK Biobank
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Van Hout, Cristopher V., Tachmazidou, Ioanna, Backman, Joshua D., Hoffman, Joshua D., Liu, Daren, Pandey, Ashutosh K., Gonzaga-Jauregui, Claudia, Khalid, Shareef, Ye, Bin, Banerjee, Nilanjana, Li, Alexander H., O’Dushlaine, Colm, Marcketta, Anthony, Staples, Jeffrey, Schurmann, Claudia, Hawes, Alicia, Maxwell, Evan, Barnard, Leland, Lopez, Alexander, Penn, John, Habegger, Lukas, Blumenfeld, Andrew L., Bai, Xiaodong, O’Keeffe, Sean, Yadav, Ashish, Praveen, Kavita, Jones, Marcus, Salerno, William J., Chung, Wendy K., Surakka, Ida, Willer, Cristen J., Hveem, Kristian, Leader, Joseph B., Carey, David J., Ledbetter, David H., Cardon, Lon, Yancopoulos, George D., Economides, Aris, Coppola, Giovanni, Shuldiner, Alan R., Balasubramanian, Suganthi, Cantor, Michael, Nelson, Matthew R., Whittaker, John, Reid, Jeffrey G., Marchini, Jonathan, Overton, John D., Scott, Robert A., Abecasis, Gonçalo R., Yerges-Armstrong, Laura, and Baras, Aris
- Abstract
The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1. Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, including PIEZO1on varicose veins, COL6A1on corneal resistance, MEPEon bone density, and IQGAP2and GMPRon blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenic BRCA1and BRCA2variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.
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- 2020
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8. Abstract 14556: Deep Phenotyping APOC3 Knockouts in a Population With High Consanguinity
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Khalid, Shareef, Khan, Maleeha Z, Wu, Liya, Jahanzaib, Muhammad, Saeed, Subhan, Mian, M. Rehan, Liaqat, Muhammad Bilal, Rasheed, Asif, Millar, John S, Rader, Daniel J, and Saleheen, Danish
- Abstract
Apolipoprotein C-III (APOC3) plays an integral role in the regulation of triglyceride-rich lipoproteins, by inhibiting the clearance of triglycerides carried by VLDL and chylomicron remnants in the blood. Prior work has shown that heterozygous loss of function (LOF) carriers of APOC3 have lower triglyceride levels and a lower risk of coronary artery disease (CAD). The quantitative impact of disease risk remains unknown in complete knockouts (KOs). Additionally, the effects and safety implications of complete APOC3 LOF have not been characterized. APOC3 inhibition is an active therapeutic strategy to lower CAD risk; hence these questions have therapeutic relevance. Among 37,244 unrelated sequenced individuals, including 19,681 cases of myocardial infarction (MI), in the Pakistan Genomic Resource - a biobank with high levels of consanguinity - we identified 207 heterozygous LOF carriers and 14 KOs. As expected, the KOs had undetectable APOC3 levels. We also observed a decrease in plasma triglycerides (P = 9E-85), VLDL-C levels (P = 2E-73), APOE levels (P = 5.4E-9) and an increase in HDL-C levels (P = 1E-34) and APOA1 levels (P = 6E-5) consistent with a gene-dosage effect. We observed a significant decrease in the risk of MI among heterozygous carriers (P = 0.01); however, we did not observe any protection from MI risk in complete KOs. Conversely, we observed a non-significant increase in the risk of MI in complete KOs compared to non-carriers; of the 14 knockouts identified, 9 were found to have MI. The loss of protection against MI could not be explained by the genetic background or by the increase in levels of homozygosity of the KOs. By recalling complete KOs and their family members, we were able to identify and phenotype an additional 33 complete KOs and 152 heterozygotes and assess other safety concerns related to complete APOC3 inhibition (i.e., glucose intolerance, fat content in the liver, etc.). In conclusion, by leveraging a highly consanguineous cohort, we have identified and phenotyped APOC3 KOs that have, hitherto, not been identified elsewhere. We did not observe APOC3 LOF to confer protection in complete KOs and observed other biomarker and phenotypic associations; these findings should inform existing therapeutic programs targeting APOC3.
- Published
- 2022
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