Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations]
Birth cohort studies involve repeated surveys of large numbers of individuals from birth and throughout their lives. They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technol...
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Wellcome
2024-12-01
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| Online Access: | https://wellcomeopenresearch.org/articles/9-390/v2 |
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| author | Petr Danecek Amy Hough John Wright Karen Ho Nicholas J. Timpson Sarah J. Lindsay Davide Bonfanti Daniel S. Malawsky Rafaq Azad Deborah Plowman Sara Widaa Gemma Shireby Emla Fitzsimons David Bann Matthew E. Hurles Hilary C. Martin Susan M. Ring Dan Mason Michael A. Quail Wei Huang Vivek Iyer Mahmoud Koko Iaroslav Popov Laurie Fabian Gennadii Zakharov Ruth Y. Eberhardt Emma E. Wade Qin Qin Huang |
| author_facet | Petr Danecek Amy Hough John Wright Karen Ho Nicholas J. Timpson Sarah J. Lindsay Davide Bonfanti Daniel S. Malawsky Rafaq Azad Deborah Plowman Sara Widaa Gemma Shireby Emla Fitzsimons David Bann Matthew E. Hurles Hilary C. Martin Susan M. Ring Dan Mason Michael A. Quail Wei Huang Vivek Iyer Mahmoud Koko Iaroslav Popov Laurie Fabian Gennadii Zakharov Ruth Y. Eberhardt Emma E. Wade Qin Qin Huang |
| author_sort | Petr Danecek |
| collection | DOAJ |
| description | Birth cohort studies involve repeated surveys of large numbers of individuals from birth and throughout their lives. They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technologies. This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights ranging from population genetics to applications across the social sciences. Here we present quality-controlled whole exome sequencing data from three UK birth cohorts: the Avon Longitudinal Study of Parents and Children (8,436 children and 3,215 parents), the Millenium Cohort Study (7,667 children and 6,925 parents) and Born in Bradford (8,784 children and 2,875 parents). The overall objective of this coordinated effort is to make the resulting high-quality data widely accessible to the global research community in a timely manner. We describe how the datasets were generated and subjected to quality control at the sample, variant and genotype level. We then present some preliminary analyses to illustrate the quality of the datasets and probe potential sources of bias. We introduce measures of ultra-rare variant burden to the variables available for researchers working on these cohorts, and show that the exome-wide burden of deleterious protein-truncating variants, S het burden, is associated with educational attainment and cognitive test scores. The whole exome sequence data from these birth cohorts (CRAM & VCF files) are available through the European Genome-Phenome Archive, and here we provide guidance for their use. |
| format | Article |
| id | doaj-art-ff3a8201ba064f0bb8c65ad5b40f9a04 |
| institution | Kabale University |
| issn | 2398-502X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wellcome |
| record_format | Article |
| series | Wellcome Open Research |
| spelling | doaj-art-ff3a8201ba064f0bb8c65ad5b40f9a042025-01-21T01:00:00ZengWellcomeWellcome Open Research2398-502X2024-12-01925892Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations]Petr Danecek0Amy Hough1https://orcid.org/0000-0001-5212-1857John Wright2https://orcid.org/0000-0001-9572-7293Karen Ho3https://orcid.org/0000-0003-3478-9751Nicholas J. Timpson4https://orcid.org/0000-0002-7141-9189Sarah J. Lindsay5Davide Bonfanti6https://orcid.org/0000-0003-4092-7815Daniel S. Malawsky7Rafaq Azad8Deborah Plowman9https://orcid.org/0000-0002-6330-2669Sara Widaa10https://orcid.org/0009-0000-8017-8949Gemma Shireby11Emla Fitzsimons12David Bann13Matthew E. Hurles14Hilary C. Martin15Susan M. Ring16https://orcid.org/0000-0003-3103-9330Dan Mason17https://orcid.org/0000-0002-0026-9216Michael A. Quail18Wei Huang19Vivek Iyer20Mahmoud Koko21https://orcid.org/0000-0001-9512-0184Iaroslav Popov22https://orcid.org/0000-0001-7538-123XLaurie Fabian23https://orcid.org/0009-0007-3145-5357Gennadii Zakharov24Ruth Y. Eberhardt25Emma E. Wade26Qin Qin Huang27Human Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKBradford Institute for Health Research, Bradford Royal Infirmary, Bradford, England, BD9 6RJ, UKBradford Institute for Health Research, Bradford Royal Infirmary, Bradford, England, BD9 6RJ, UKPopulation Health Sciences, University of Bristol Medical School, Bristol, England, BS8 2BN, UKPopulation Health Sciences, University of Bristol Medical School, Bristol, England, BS8 2BN, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKBradford Institute for Health Research, Bradford Royal Infirmary, Bradford, England, BD9 6RJ, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKSequencing R&D, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKCentre for Longitudinal Studies, University College London Institute of Education, London, England, WC1H 0NU, UKCentre for Longitudinal Studies, University College London Institute of Education, London, England, WC1H 0NU, UKCentre for Longitudinal Studies, University College London Institute of Education, London, England, WC1H 0NU, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKPopulation Health Sciences, University of Bristol Medical School, Bristol, England, BS8 2BN, UKBradford Institute for Health Research, Bradford Royal Infirmary, Bradford, England, BD9 6RJ, UKSequencing R&D, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKPopulation Health Sciences, University of Bristol Medical School, Bristol, England, BS8 2BN, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKHuman Genetics, Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UKBirth cohort studies involve repeated surveys of large numbers of individuals from birth and throughout their lives. They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technologies. This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights ranging from population genetics to applications across the social sciences. Here we present quality-controlled whole exome sequencing data from three UK birth cohorts: the Avon Longitudinal Study of Parents and Children (8,436 children and 3,215 parents), the Millenium Cohort Study (7,667 children and 6,925 parents) and Born in Bradford (8,784 children and 2,875 parents). The overall objective of this coordinated effort is to make the resulting high-quality data widely accessible to the global research community in a timely manner. We describe how the datasets were generated and subjected to quality control at the sample, variant and genotype level. We then present some preliminary analyses to illustrate the quality of the datasets and probe potential sources of bias. We introduce measures of ultra-rare variant burden to the variables available for researchers working on these cohorts, and show that the exome-wide burden of deleterious protein-truncating variants, S het burden, is associated with educational attainment and cognitive test scores. The whole exome sequence data from these birth cohorts (CRAM & VCF files) are available through the European Genome-Phenome Archive, and here we provide guidance for their use.https://wellcomeopenresearch.org/articles/9-390/v2ALSPAC MCS BiB WES EGAeng |
| spellingShingle | Petr Danecek Amy Hough John Wright Karen Ho Nicholas J. Timpson Sarah J. Lindsay Davide Bonfanti Daniel S. Malawsky Rafaq Azad Deborah Plowman Sara Widaa Gemma Shireby Emla Fitzsimons David Bann Matthew E. Hurles Hilary C. Martin Susan M. Ring Dan Mason Michael A. Quail Wei Huang Vivek Iyer Mahmoud Koko Iaroslav Popov Laurie Fabian Gennadii Zakharov Ruth Y. Eberhardt Emma E. Wade Qin Qin Huang Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations] Wellcome Open Research ALSPAC MCS BiB WES EGA eng |
| title | Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_full | Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_fullStr | Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_full_unstemmed | Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_short | Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_sort | exome sequencing of uk birth cohorts version 2 peer review 2 approved 1 approved with reservations |
| topic | ALSPAC MCS BiB WES EGA eng |
| url | https://wellcomeopenresearch.org/articles/9-390/v2 |
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