Exome sequencing and characterization of 49,960 individuals in the UK Biobank
The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world 1 . Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million...
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| Published in | Nature (London) Vol. 586; no. 7831; pp. 749 - 756 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
29.10.2020
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0028-0836 1476-4687 1476-4687 |
| DOI | 10.1038/s41586-020-2853-0 |
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| 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 world
1
. 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
PIEZO1
on varicose veins,
COL6A1
on corneal resistance,
MEPE
on bone density, and
IQGAP2
and
GMPR
on 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
BRCA1
and
BRCA2
variants. 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.
Exome sequences from the first 49,960 participants in the UK Biobank highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community. |
|---|---|
| AbstractList | The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world.sup.1. 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 PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on 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 BRCA1 and BRCA2 variants. 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. The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world . 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 PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on 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 BRCA1 and BRCA2 variants. 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. The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world 1 . 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 PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on 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 BRCA1 and BRCA2 variants. 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. The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world.sup.1. 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 PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on 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 BRCA1 and BRCA2 variants. 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. Exome sequences from the first 49,960 participants in the UK Biobank highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community. 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 PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on 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 BRCA1 and BRCA2 variants. 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. The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world 1 . 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 PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on 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 BRCA1 and BRCA2 variants. 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. Exome sequences from the first 49,960 participants in the UK Biobank highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community. 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 PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on 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 BRCA1 and BRCA2 variants. 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.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 PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on 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 BRCA1 and BRCA2 variants. 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. |
| Audience | Academic |
| Author | Khalid, Shareef Jones, Marcus Whittaker, John Van Hout, Cristopher V. Abecasis, Gonçalo R. Scott, Robert A. Overton, John D. Banerjee, Nilanjana Hoffman, Joshua D. Liu, Daren Leader, Joseph B. Backman, Joshua D. Ye, Bin Schurmann, Claudia Hveem, Kristian Praveen, Kavita O’Dushlaine, Colm Hawes, Alicia Lopez, Alexander Pandey, Ashutosh K. Salerno, William J. Blumenfeld, Andrew L. Cardon, Lon Baras, Aris Marcketta, Anthony Habegger, Lukas Yadav, Ashish Reid, Jeffrey G. Gonzaga-Jauregui, Claudia Ledbetter, David H. Tachmazidou, Ioanna Nelson, Matthew R. Carey, David J. Li, Alexander H. Shuldiner, Alan R. O’Keeffe, Sean Chung, Wendy K. Willer, Cristen J. Coppola, Giovanni Cantor, Michael Staples, Jeffrey Bai, Xiaodong Barnard, Leland Yerges-Armstrong, Laura Balasubramanian, Suganthi Yancopoulos, George D. Penn, John Maxwell, Evan Economides, Aris Marchini, Jonathan Surakka, Ida |
| Author_xml | – sequence: 1 givenname: Cristopher V. orcidid: 0000-0001-9689-5344 surname: Van Hout fullname: Van Hout, Cristopher V. email: cristopher.vanhout@regeneron.com organization: Regeneron Genetics Center – sequence: 2 givenname: Ioanna surname: Tachmazidou fullname: Tachmazidou, Ioanna organization: GlaxoSmithKline, AstraZeneca – sequence: 3 givenname: Joshua D. surname: Backman fullname: Backman, Joshua D. organization: Regeneron Genetics Center – sequence: 4 givenname: Joshua D. surname: Hoffman fullname: Hoffman, Joshua D. organization: GlaxoSmithKline, Foresite Labs – sequence: 5 givenname: Daren surname: Liu fullname: Liu, Daren organization: Regeneron Genetics Center – sequence: 6 givenname: Ashutosh K. surname: Pandey fullname: Pandey, Ashutosh K. organization: GlaxoSmithKline – sequence: 7 givenname: Claudia surname: Gonzaga-Jauregui fullname: Gonzaga-Jauregui, Claudia organization: Regeneron Genetics Center – sequence: 8 givenname: Shareef surname: Khalid fullname: Khalid, Shareef organization: Regeneron Genetics Center – sequence: 9 givenname: Bin surname: Ye fullname: Ye, Bin organization: Regeneron Genetics Center – sequence: 10 givenname: Nilanjana surname: Banerjee fullname: Banerjee, Nilanjana organization: Regeneron Genetics Center – sequence: 11 givenname: Alexander H. surname: Li fullname: Li, Alexander H. organization: Regeneron Genetics Center – sequence: 12 givenname: Colm surname: O’Dushlaine fullname: O’Dushlaine, Colm organization: Regeneron Genetics Center – sequence: 13 givenname: Anthony surname: Marcketta fullname: Marcketta, Anthony organization: Regeneron Genetics Center – sequence: 14 givenname: Jeffrey surname: Staples fullname: Staples, Jeffrey organization: Regeneron Genetics Center – sequence: 15 givenname: Claudia surname: Schurmann fullname: Schurmann, Claudia organization: Regeneron Genetics Center, Digital Health Center, Hasso Plattner Institute, University of Potsdam, Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai – sequence: 16 givenname: Alicia surname: Hawes fullname: Hawes, Alicia organization: Regeneron Genetics Center – sequence: 17 givenname: Evan surname: Maxwell fullname: Maxwell, Evan organization: Regeneron Genetics Center – sequence: 18 givenname: Leland surname: Barnard fullname: Barnard, Leland organization: Regeneron Genetics Center – sequence: 19 givenname: Alexander surname: Lopez fullname: Lopez, Alexander organization: Regeneron Genetics Center – sequence: 20 givenname: John surname: Penn fullname: Penn, John organization: Regeneron Genetics Center, DNANexus – sequence: 21 givenname: Lukas surname: Habegger fullname: Habegger, Lukas organization: Regeneron Genetics Center – sequence: 22 givenname: Andrew L. surname: Blumenfeld fullname: Blumenfeld, Andrew L. organization: Regeneron Genetics Center – sequence: 23 givenname: Xiaodong surname: Bai fullname: Bai, Xiaodong organization: Regeneron Genetics Center – sequence: 24 givenname: Sean surname: O’Keeffe fullname: O’Keeffe, Sean organization: Regeneron Genetics Center – sequence: 25 givenname: Ashish surname: Yadav fullname: Yadav, Ashish organization: Regeneron Genetics Center – sequence: 26 givenname: Kavita surname: Praveen fullname: Praveen, Kavita organization: Regeneron Genetics Center – sequence: 27 givenname: Marcus surname: Jones fullname: Jones, Marcus organization: Regeneron Pharmaceuticals – sequence: 28 givenname: William J. surname: Salerno fullname: Salerno, William J. organization: Regeneron Genetics Center – sequence: 29 givenname: Wendy K. surname: Chung fullname: Chung, Wendy K. organization: Department of Pediatrics, Columbia University Irving Medical Center, Department of Medicine, Columbia University Irving Medical Center – sequence: 30 givenname: Ida surname: Surakka fullname: Surakka, Ida organization: University of Michigan – sequence: 31 givenname: Cristen J. orcidid: 0000-0001-5645-4966 surname: Willer fullname: Willer, Cristen J. organization: University of Michigan – sequence: 32 givenname: Kristian surname: Hveem fullname: Hveem, Kristian organization: Norwegian University of Science and Technology – sequence: 33 givenname: Joseph B. orcidid: 0000-0002-4101-5423 surname: Leader fullname: Leader, Joseph B. organization: Geisinger – sequence: 34 givenname: David J. surname: Carey fullname: Carey, David J. organization: Geisinger – sequence: 35 givenname: David H. orcidid: 0000-0001-8934-4210 surname: Ledbetter fullname: Ledbetter, David H. organization: Geisinger – sequence: 37 givenname: Lon surname: Cardon fullname: Cardon, Lon organization: GlaxoSmithKline – sequence: 38 givenname: George D. surname: Yancopoulos fullname: Yancopoulos, George D. organization: Regeneron Pharmaceuticals – sequence: 39 givenname: Aris orcidid: 0000-0002-6508-8942 surname: Economides fullname: Economides, Aris organization: Regeneron Pharmaceuticals – sequence: 40 givenname: Giovanni surname: Coppola fullname: Coppola, Giovanni organization: Regeneron Genetics Center – sequence: 41 givenname: Alan R. surname: Shuldiner fullname: Shuldiner, Alan R. organization: Regeneron Genetics Center – sequence: 42 givenname: Suganthi surname: Balasubramanian fullname: Balasubramanian, Suganthi organization: Regeneron Genetics Center – sequence: 43 givenname: Michael surname: Cantor fullname: Cantor, Michael organization: Regeneron Genetics Center – sequence: 45 givenname: Matthew R. surname: Nelson fullname: Nelson, Matthew R. organization: GlaxoSmithKline, Deerfield – sequence: 46 givenname: John surname: Whittaker fullname: Whittaker, John organization: GlaxoSmithKline – sequence: 47 givenname: Jeffrey G. orcidid: 0000-0001-8645-4713 surname: Reid fullname: Reid, Jeffrey G. organization: Regeneron Genetics Center – sequence: 48 givenname: Jonathan surname: Marchini fullname: Marchini, Jonathan organization: Regeneron Genetics Center – sequence: 49 givenname: John D. surname: Overton fullname: Overton, John D. organization: Regeneron Genetics Center – sequence: 50 givenname: Robert A. orcidid: 0000-0003-3634-3016 surname: Scott fullname: Scott, Robert A. email: robert.a.scott@gsk.com organization: GlaxoSmithKline – sequence: 51 givenname: Gonçalo R. surname: Abecasis fullname: Abecasis, Gonçalo R. organization: Regeneron Genetics Center – sequence: 52 givenname: Laura orcidid: 0000-0003-0006-5237 surname: Yerges-Armstrong fullname: Yerges-Armstrong, Laura email: laura.m.yerges-armstrong@gsk.com organization: GlaxoSmithKline – sequence: 53 givenname: Aris orcidid: 0000-0002-6830-3396 surname: Baras fullname: Baras, Aris email: aris.baras@regeneron.com organization: Regeneron Genetics Center |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33087929$$D View this record in MEDLINE/PubMed |
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| Title | Exome sequencing and characterization of 49,960 individuals in the UK Biobank |
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