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  • Authors: 
    Hunt, Harriet V; Rudzinski, Anna; Hongen Jiang; Ruiyun Wang; Thomas, Mark G; Jones, Martin K;
    Publisher: SAGE Journals
    Project: WT , EC | FOGLIP (249642), EC | BEAN (289966)

    Supplemental material, Table_S1_Chinese_Panicum_samples_and_genotypes_050218 for Genetic evidence for a western Chinese origin of broomcorn millet (Panicum miliaceum) by Harriet V Hunt, Anna Rudzinski, Hongen Jiang, Ruiyun Wang, Mark G Thomas and Martin K Jones in The Holocene

  • Authors: 
    University Of London, Institute Of Education; University College London, Institute Of Child Health;
    Publisher: UK Data Service
    Project: WT | Objective measurements of... (084686), UKRI | MRC Centre of Epidemiolog... (G0400546)

    <i>Background</i>:<br>The&nbsp;Millennium Cohort Study (MCS) is a large-scale, multi-purpose longitudinal dataset providing information about babies born at the beginning of the 21st century, their progress through life, and the families who are bringing them up, for the four countries of the United Kingdom. The original objectives of the first MCS survey, as laid down in the proposal to the Economic and Social Research Council (ESRC) in March 2000, were:<ul><li>to chart the initial conditions of social, economic and health advantages and disadvantages facing children born at the start of the 21st century, capturing information that the research community of the future will require</li><li>to provide a basis for comparing patterns of development with the preceding cohorts (the&nbsp;<i>National Child Development Study</i>, held at the UK Data Archive under GN 33004, and the&nbsp;<i>1970 Birth Cohort Study</i>, held under GN 33229)</li><li>to collect information on previously neglected topics, such as fathers' involvement in children's care and development</li><li>to focus on parents as the most immediate elements of the children's 'background', charting their experience as mothers and fathers of newborn babies in the year 2000, recording how they (and any other children in the family) adapted to the newcomer, and what their aspirations for her/his future may be</li><li>to emphasise intergenerational links including those back to the parents' own childhood</li><li>to investigate the wider social ecology of the family, including social networks, civic engagement and community facilities and services, splicing in geo-coded data when available</li></ul>Additional objectives subsequently included for MCS were:<ul><li>to provide control cases for the national evaluation of Sure Start (a government programme intended to alleviate child poverty and social exclusion)</li><li>to provide samples of adequate size to analyse and compare the smaller countries of the United Kingdom, and include disadvantaged areas of England</li></ul>The first sweep (MCS1) interviewed both mothers and (where resident) fathers (or father-figures) of infants included in the sample when the babies were nine months old, and the second sweep (MCS2) was carried out with the same respondents when the children were three years of age. The third sweep (MCS3) was conducted in 2006, when the children were aged five years old, the fourth sweep (MCS4) in 2008, when they were seven years old, the fifth sweep (MCS5) in 2012-2013, when they were eleven years old, the sixth sweep (MCS6) in 2015, when they were fourteen years old, and the seventh sweep (MCS7) in 2018, when they were seventeen years old.<br><br><i>End User Licence versions of MCS studies</i>:<br>The End User Licence (EUL) versions of MCS1, MCS2, MCS3, MCS4, MCS5, MCS6 and MCS7 are held under UK Data Archive SNs 4683, 5350, 5795, 6411, 7464, 8156 and 8682 respectively. The&nbsp;longitudinal family file is held under SN 8172.<br><br><i>Sub-sample studies</i>:<br>Some studies based on sub-samples of MCS have also been conducted, including a study of MCS respondent mothers who had received assisted fertility treatment, conducted in 2003 (see EUL SN 5559). Also, birth registration and maternity hospital episodes for the MCS respondents are held as a separate dataset (see EUL SN 5614).<br><br><div style=""><div style=""><span style="font-style: italic;">Release of Sweeps 1 to 4 to Long Format (Summer 2020)</span></div><div style="">To support longitudinal research and make it easier to compare data from different time points, all data from across all sweeps is now in a consistent format. The update affects the data from sweeps 1 to 4 (from 9 months to 7 years), which are updated from the old/wide to a new/long format to match the format of data of sweeps 5 and 6 (age 11 and 14 sweeps). The old/wide formatted datasets contained one row per family with multiple variables for different respondents. The new/long formatted datasets contain one row per respondent (per parent or per cohort member) for each MCS family. Additional updates have been made to all sweeps to harmonise variable labels and enhance anonymisation.&nbsp;<span style="font-style: italic;">&nbsp;</span></div></div><br><span style="font-style: italic;">MCS web pages</span>:<br>Further information about the MCS can be found on the&nbsp;<a href="https://cls.ucl.ac.uk/cls-studies/millennium-cohort-study/" target="_blank" style="background-color: rgb(255, 255, 255);">Centre for Longitudinal Studies</a>&nbsp;web pages.<br><br><i>How to access genetic and/or bio-medical sample data from a range of longitudinal surveys:</i><br>A useful overview of the governance routes for applying for genetic and bio-medical sample data, which are not available through the UK Data Service, can be found at&nbsp;<a href="http://www.metadac.ac.uk/data-access-through-metadac/" title="Governance of data and sample access" target="_blank" style="background-color: rgb(255, 255, 255);">Governance of data and sample access</a>&nbsp;on the METADAC (Managing Ethico-social, Technical and Administrative issues in Data Access) website.<br><br><b>Secure Access datasets</b>:<br>Secure Access versions of the MCS have more restrictive access conditions than versions available under the standard End User Licence or Special Licence (see 'Access data' tab above).<br><br>Secure Access versions of the MCS include:<br><ul><li>detailed sensitive variables not available under EUL. These have been grouped thematically and are held under SN 8753 (socio-economic, accommodation and occupational data), SN 8754 (self-reported health, behaviour and fertility), SN 8755 (demographics, language and religion) and SN 8756 (exact participation dates). These files replace previously available studies held under SNs 8456 and 8622-8627<br></li><li>detailed geographical identifier files which are grouped by sweep held under SN 7758 (MCS1), SN 7759 (MCS2), SN 7760 (MCS3), SN 7761 (MCS4), SN 7762 (MCS5 2001 Census Boundaries), SN 7763 (MCS5 2011 Census Boundaries), SN 8231 (MCS6 2001 Census Boundaries), SN 8232 (MCS6 2011 Census Boundaries), SN 8757 (MCS7), SN 8758 (MCS7 2001 Census Boundaries) and SN 8759 (MCS7 2011 Census Boundaries). These files replace previously available files grouped by geography SN 7049 (Ward level), SN 7050 (Lower Super Output Area level), and SN 7051 (Output Area level)</li><li>linked education administrative datasets for Key Stages 1, 2 and 4 held under SN 8481 (England).&nbsp; This replaces previously available datasets for Key Stage 1 (SN 6862) and Key Stage 2 (SN 7712)<br></li><li>linked education administrative datasets for Key Stage 1 held under SN 7414 (Scotland) and SN 7415 (Wales)</li><li>linked NHS Patient Episode Database for Wales (PEDW) for MCS1 – MCS5 held under SN 8302</li><li>Banded Distances to English Grammar Schools for MCS5 held under SN 8394</li><li>the exact date of interview held under SN 8456</li></ul>The linked education administrative datasets held under SNs 8481, 7414 and 7415 may be ordered alongside the MCS detailed geographical identifier files only if sufficient justification is provided in the application. The linked education administrative datasets are not available alongside the <span style="font-style: italic;">Hospital of Birth: Special Licence Access</span> dataset under SN 5724. Users are also only allowed access to either 2001 or 2011 of Geographical Identifiers Census Boundaries studies. So for MCS5 either SN 7762 (2001 Census Boundaries) or SN 7763 (2011 Census Boundaries), for the MCS6 users are only allowed either SN 8231 (2001 Census Boundaries) or SN 8232 (2011 Census Boundaries); and the same applies for MCS7 so either SN 8758 (2001 Census Boundaries) or SN 8759 (2011 Census Boundaries).<br><br>Researchers applying for access to the Secure Access MCS datasets should indicate on their ESRC Accredited Researcher application form the EUL dataset(s) that they also wish to access (selected from the MCS Series&nbsp;<a href="https://beta.ukdataservice.ac.uk/datacatalogue/series/series?id=2000031#!/access-data" target="_blank" style="background-color: rgb(255, 255, 255);">Access</a>&nbsp;web page).<br><br> <p><i>MCS4 Physical Activity Data, 2008</i><br> The MCS4 Physical Activity Data study surveyed levels and patterns of physical activity (PA) and sedentary behaviour (SB) among the MCS cohort. Children who took part in MCS4 (around age 7), were assessed using accelerometers issued to consenting child participants. These measurements were obtained primarily to understand the determinants and consequences of children's PA and SB in the context of the longitudinal biological, social, psychological, behavioural and environmental information collected earlier and to be collected subsequently at MCS home visits. Subsequently, an additional study investigating seasonal variation in levels and patterns of PA and SB was carried out in a sample of MCS children who had participated in the main accelerometer study during winter 2008/09. Repeat accelerometer measurements were obtained from these children during each of the three subsequent seasons during a single calendar year. For further information see the documentation and the main MCS4 survey, held at the UK Data Archive under SN 6411.</p><p><span style="font-weight: bold;">Latest edition information</span></p><p> </p><p>For the second edition (July 2021), raw accelerometer data taken from each child was added to the study, comprising 8,906 .dat files held in a separate zip file for download. These files contain raw accelerometer data from measurements. At least one file per participating child is included. The files are named according to the family ID followed by the file number.</p>

  • Open Access
    Authors: 
    Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Ardern Hulme-Beaman; Lebrasseur, Ophélie; Mikkel-Holger S. Sinding; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; +49 more
    Publisher: The Royal Society
    Project: NSF | Genetic Analysis of Indig... (1304810), EC | ArchSci2020 (676154), EC | UNDEAD (337574), UKRI | Animals, Lifeways and Lif... (AH/N504543/1), UKRI | Understanding Cultural Re... (AH/K006029/1), UKRI | Deciphering dog domestica... (NE/K003259/1), UKRI | Deciphering dog domestica... (NE/K005243/1), NSF | Genetic Analysis of Prehi... (1108175), EC | WhereWolf (655732), WT | Domestic animals as a mod... (210119)

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

  • Open Access
    Authors: 
    Pfrengle, Saskia; Neukamm, Judith; Guellil, Meriam; Keller, Marcel; Molak, Martyna; Avanzi, Charlotte; Kushniarevich, Alena; Montes, Núria; Neumann, Gunnar U.; Reiter, Ella; +29 more
    Publisher: figshare
    Project: WT , EC | LEPVORS (845479)

    Additional file 3: Table S5. SNP distance matrix.

  • Open Access
    Authors: 
    Pereira, Andreia; Mendonça, Maria Isabel; Borges, Sofia; Freitas, Sónia; Henriques, Eva; Rodrigues, Mariana; Freitas, Ana Isabel; Sousa, Ana Célia; Brehm, António; Reis, Roberto Palma Dos;
    Publisher: SciELO journals
    Project: WT

    Abstract Background: Genetic risk score can quantify individual’s predisposition to coronary artery disease; however, its usefulness as an independent risk predictor remains inconclusive. Objective: To evaluate the incremental predictive value of a genetic risk score to traditional risk factors associated with coronary disease. Methods: Thirty-three genetic variants previously associated with coronary disease were analyzed in a case-control population with 2,888 individuals. A multiplicative genetic risk score was calculated and then divided into quartiles, with the 1st quartile as the reference class. Coronary risk was determined by logistic regression analysis. Then, a second logistic regression was performed with traditional risk factors and the last quartile of the genetic risk score. Based on this model, two ROC curves were constructed with and without the genetic score and compared by the Delong test. Statistical significance was considered when p values were less than 0.05. Results: The last quartile of the multiplicative genetic risk score revealed a significant increase in coronary artery disease risk (OR = 2.588; 95% CI: 2.090-3.204; p < 0.0001). The ROC curve based on traditional risk factors estimated an AUC of 0.72, which increased to 0.74 when the genetic risk score was added, revealing a better fit of the model (p < 0.0001). Conclusions: In conclusion, a multilocus genetic risk score was associated with an increased risk for coronary disease in our population. The usual model of traditional risk factors can be improved by incorporating genetic data.

  • Open Access
    Authors: 
    Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Ardern Hulme-Beaman; Lebrasseur, Ophélie; Mikkel-Holger S. Sinding; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; +49 more
    Publisher: The Royal Society
    Project: EC | UNDEAD (337574), EC | WhereWolf (655732), WT | Domestic animals as a mod... (210119), UKRI | Understanding Cultural Re... (AH/K006029/1), UKRI | Animals, Lifeways and Lif... (AH/N504543/1), EC | ArchSci2020 (676154), NSF | Genetic Analysis of Indig... (1304810), UKRI | Deciphering dog domestica... (NE/K005243/1), NSF | Genetic Analysis of Prehi... (1108175), UKRI | Deciphering dog domestica... (NE/K003259/1)

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

  • Open Access
    Authors: 
    Riaan F. Rifkin; Surendra Vikram; Jean-Baptiste Ramond; Rey-Iglesia, Alba; Brand, Tina B.; Porraz, Guillaume; Val, Aurore; Hall, Grant; Woodborne, Stephan; Bailly, Matthieu Le; +7 more
    Publisher: figshare
    Project: WT

    Additional file 2: Table S1. Sequence reads for environmental- and subsistence-related taxa detected. Table S2. Information concerning 14C Accelerator Mass Spectrometry (AMS) dating. Table S3a. Processing protocol and results for isotope analyses. Table S3b. Results for isotope analyses (Merck standard). Table S3c. Results for isotope analyses (DL-Valine standard). Table S4. Abundance of bacterial taxonomic categories in the IM datasets. Table S5. Sequence read-length distribution for taxa identified in this study. Table S6. Significant KEGG pathways in the comparative IM datasets analysed. Table S7. Relative abundance of eighteen significant KEGG pathways in the IM cohorts. Table S8. Enrichment and depletion of KO metabolic gene categories in the comparative IM sample cohorts based on p-value (p=<0.05) designation. Table S9. Enrichment and depletion of KO metabolic gene categories in the comparative IM sample cohorts based on false discovery rate (FDR) corrected p-values (q=<0.05). Table S10. Enrichment and depletion of KO metabolic gene categories in the ancient and modern comparative IM sample cohort as calculated for the twenty-four authenticated ancient IM taxa. Table S11. Comparison of relative abundance of antibiotic resistance genes in the comparative IM cohorts. Table S12. Raw and filtered high-quality sequence read counts as related to the comparative IM datasets. Table S13. Information concerning the comparative NCBI genomes used during this study.

  • Open Access
    Authors: 
    Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Ardern Hulme-Beaman; Lebrasseur, Ophélie; Mikkel-Holger S. Sinding; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; +49 more
    Publisher: The Royal Society
    Project: UKRI | Animals, Lifeways and Lif... (AH/N504543/1), UKRI | Understanding Cultural Re... (AH/K006029/1), EC | ArchSci2020 (676154), EC | UNDEAD (337574), NSF | Genetic Analysis of Indig... (1304810), UKRI | Deciphering dog domestica... (NE/K005243/1), NSF | Genetic Analysis of Prehi... (1108175), UKRI | Deciphering dog domestica... (NE/K003259/1), EC | WhereWolf (655732), WT | Domestic animals as a mod... (210119)

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

  • Open Access
    Authors: 
    Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Ardern Hulme-Beaman; Lebrasseur, Ophélie; Mikkel-Holger S. Sinding; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; +49 more
    Publisher: The Royal Society
    Project: EC | UNDEAD (337574), UKRI | Deciphering dog domestica... (NE/K005243/1), NSF | Genetic Analysis of Prehi... (1108175), EC | ArchSci2020 (676154), NSF | Genetic Analysis of Indig... (1304810), UKRI | Understanding Cultural Re... (AH/K006029/1), UKRI | Animals, Lifeways and Lif... (AH/N504543/1), EC | WhereWolf (655732), WT | Domestic animals as a mod... (210119), UKRI | Deciphering dog domestica... (NE/K003259/1)

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

  • Open Access
    Authors: 
    Barson, Gemma; Griffiths, Ed;
    Publisher: Figshare
    Project: WT

    Additional file 1. A tarball of the current production release of the SeqTools source code at the time of writing.

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15 Research products, page 1 of 2
  • Authors: 
    Hunt, Harriet V; Rudzinski, Anna; Hongen Jiang; Ruiyun Wang; Thomas, Mark G; Jones, Martin K;
    Publisher: SAGE Journals
    Project: WT , EC | FOGLIP (249642), EC | BEAN (289966)

    Supplemental material, Table_S1_Chinese_Panicum_samples_and_genotypes_050218 for Genetic evidence for a western Chinese origin of broomcorn millet (Panicum miliaceum) by Harriet V Hunt, Anna Rudzinski, Hongen Jiang, Ruiyun Wang, Mark G Thomas and Martin K Jones in The Holocene

  • Authors: 
    University Of London, Institute Of Education; University College London, Institute Of Child Health;
    Publisher: UK Data Service
    Project: WT | Objective measurements of... (084686), UKRI | MRC Centre of Epidemiolog... (G0400546)

    <i>Background</i>:<br>The&nbsp;Millennium Cohort Study (MCS) is a large-scale, multi-purpose longitudinal dataset providing information about babies born at the beginning of the 21st century, their progress through life, and the families who are bringing them up, for the four countries of the United Kingdom. The original objectives of the first MCS survey, as laid down in the proposal to the Economic and Social Research Council (ESRC) in March 2000, were:<ul><li>to chart the initial conditions of social, economic and health advantages and disadvantages facing children born at the start of the 21st century, capturing information that the research community of the future will require</li><li>to provide a basis for comparing patterns of development with the preceding cohorts (the&nbsp;<i>National Child Development Study</i>, held at the UK Data Archive under GN 33004, and the&nbsp;<i>1970 Birth Cohort Study</i>, held under GN 33229)</li><li>to collect information on previously neglected topics, such as fathers' involvement in children's care and development</li><li>to focus on parents as the most immediate elements of the children's 'background', charting their experience as mothers and fathers of newborn babies in the year 2000, recording how they (and any other children in the family) adapted to the newcomer, and what their aspirations for her/his future may be</li><li>to emphasise intergenerational links including those back to the parents' own childhood</li><li>to investigate the wider social ecology of the family, including social networks, civic engagement and community facilities and services, splicing in geo-coded data when available</li></ul>Additional objectives subsequently included for MCS were:<ul><li>to provide control cases for the national evaluation of Sure Start (a government programme intended to alleviate child poverty and social exclusion)</li><li>to provide samples of adequate size to analyse and compare the smaller countries of the United Kingdom, and include disadvantaged areas of England</li></ul>The first sweep (MCS1) interviewed both mothers and (where resident) fathers (or father-figures) of infants included in the sample when the babies were nine months old, and the second sweep (MCS2) was carried out with the same respondents when the children were three years of age. The third sweep (MCS3) was conducted in 2006, when the children were aged five years old, the fourth sweep (MCS4) in 2008, when they were seven years old, the fifth sweep (MCS5) in 2012-2013, when they were eleven years old, the sixth sweep (MCS6) in 2015, when they were fourteen years old, and the seventh sweep (MCS7) in 2018, when they were seventeen years old.<br><br><i>End User Licence versions of MCS studies</i>:<br>The End User Licence (EUL) versions of MCS1, MCS2, MCS3, MCS4, MCS5, MCS6 and MCS7 are held under UK Data Archive SNs 4683, 5350, 5795, 6411, 7464, 8156 and 8682 respectively. The&nbsp;longitudinal family file is held under SN 8172.<br><br><i>Sub-sample studies</i>:<br>Some studies based on sub-samples of MCS have also been conducted, including a study of MCS respondent mothers who had received assisted fertility treatment, conducted in 2003 (see EUL SN 5559). Also, birth registration and maternity hospital episodes for the MCS respondents are held as a separate dataset (see EUL SN 5614).<br><br><div style=""><div style=""><span style="font-style: italic;">Release of Sweeps 1 to 4 to Long Format (Summer 2020)</span></div><div style="">To support longitudinal research and make it easier to compare data from different time points, all data from across all sweeps is now in a consistent format. The update affects the data from sweeps 1 to 4 (from 9 months to 7 years), which are updated from the old/wide to a new/long format to match the format of data of sweeps 5 and 6 (age 11 and 14 sweeps). The old/wide formatted datasets contained one row per family with multiple variables for different respondents. The new/long formatted datasets contain one row per respondent (per parent or per cohort member) for each MCS family. Additional updates have been made to all sweeps to harmonise variable labels and enhance anonymisation.&nbsp;<span style="font-style: italic;">&nbsp;</span></div></div><br><span style="font-style: italic;">MCS web pages</span>:<br>Further information about the MCS can be found on the&nbsp;<a href="https://cls.ucl.ac.uk/cls-studies/millennium-cohort-study/" target="_blank" style="background-color: rgb(255, 255, 255);">Centre for Longitudinal Studies</a>&nbsp;web pages.<br><br><i>How to access genetic and/or bio-medical sample data from a range of longitudinal surveys:</i><br>A useful overview of the governance routes for applying for genetic and bio-medical sample data, which are not available through the UK Data Service, can be found at&nbsp;<a href="http://www.metadac.ac.uk/data-access-through-metadac/" title="Governance of data and sample access" target="_blank" style="background-color: rgb(255, 255, 255);">Governance of data and sample access</a>&nbsp;on the METADAC (Managing Ethico-social, Technical and Administrative issues in Data Access) website.<br><br><b>Secure Access datasets</b>:<br>Secure Access versions of the MCS have more restrictive access conditions than versions available under the standard End User Licence or Special Licence (see 'Access data' tab above).<br><br>Secure Access versions of the MCS include:<br><ul><li>detailed sensitive variables not available under EUL. These have been grouped thematically and are held under SN 8753 (socio-economic, accommodation and occupational data), SN 8754 (self-reported health, behaviour and fertility), SN 8755 (demographics, language and religion) and SN 8756 (exact participation dates). These files replace previously available studies held under SNs 8456 and 8622-8627<br></li><li>detailed geographical identifier files which are grouped by sweep held under SN 7758 (MCS1), SN 7759 (MCS2), SN 7760 (MCS3), SN 7761 (MCS4), SN 7762 (MCS5 2001 Census Boundaries), SN 7763 (MCS5 2011 Census Boundaries), SN 8231 (MCS6 2001 Census Boundaries), SN 8232 (MCS6 2011 Census Boundaries), SN 8757 (MCS7), SN 8758 (MCS7 2001 Census Boundaries) and SN 8759 (MCS7 2011 Census Boundaries). These files replace previously available files grouped by geography SN 7049 (Ward level), SN 7050 (Lower Super Output Area level), and SN 7051 (Output Area level)</li><li>linked education administrative datasets for Key Stages 1, 2 and 4 held under SN 8481 (England).&nbsp; This replaces previously available datasets for Key Stage 1 (SN 6862) and Key Stage 2 (SN 7712)<br></li><li>linked education administrative datasets for Key Stage 1 held under SN 7414 (Scotland) and SN 7415 (Wales)</li><li>linked NHS Patient Episode Database for Wales (PEDW) for MCS1 – MCS5 held under SN 8302</li><li>Banded Distances to English Grammar Schools for MCS5 held under SN 8394</li><li>the exact date of interview held under SN 8456</li></ul>The linked education administrative datasets held under SNs 8481, 7414 and 7415 may be ordered alongside the MCS detailed geographical identifier files only if sufficient justification is provided in the application. The linked education administrative datasets are not available alongside the <span style="font-style: italic;">Hospital of Birth: Special Licence Access</span> dataset under SN 5724. Users are also only allowed access to either 2001 or 2011 of Geographical Identifiers Census Boundaries studies. So for MCS5 either SN 7762 (2001 Census Boundaries) or SN 7763 (2011 Census Boundaries), for the MCS6 users are only allowed either SN 8231 (2001 Census Boundaries) or SN 8232 (2011 Census Boundaries); and the same applies for MCS7 so either SN 8758 (2001 Census Boundaries) or SN 8759 (2011 Census Boundaries).<br><br>Researchers applying for access to the Secure Access MCS datasets should indicate on their ESRC Accredited Researcher application form the EUL dataset(s) that they also wish to access (selected from the MCS Series&nbsp;<a href="https://beta.ukdataservice.ac.uk/datacatalogue/series/series?id=2000031#!/access-data" target="_blank" style="background-color: rgb(255, 255, 255);">Access</a>&nbsp;web page).<br><br> <p><i>MCS4 Physical Activity Data, 2008</i><br> The MCS4 Physical Activity Data study surveyed levels and patterns of physical activity (PA) and sedentary behaviour (SB) among the MCS cohort. Children who took part in MCS4 (around age 7), were assessed using accelerometers issued to consenting child participants. These measurements were obtained primarily to understand the determinants and consequences of children's PA and SB in the context of the longitudinal biological, social, psychological, behavioural and environmental information collected earlier and to be collected subsequently at MCS home visits. Subsequently, an additional study investigating seasonal variation in levels and patterns of PA and SB was carried out in a sample of MCS children who had participated in the main accelerometer study during winter 2008/09. Repeat accelerometer measurements were obtained from these children during each of the three subsequent seasons during a single calendar year. For further information see the documentation and the main MCS4 survey, held at the UK Data Archive under SN 6411.</p><p><span style="font-weight: bold;">Latest edition information</span></p><p> </p><p>For the second edition (July 2021), raw accelerometer data taken from each child was added to the study, comprising 8,906 .dat files held in a separate zip file for download. These files contain raw accelerometer data from measurements. At least one file per participating child is included. The files are named according to the family ID followed by the file number.</p>

  • Open Access
    Authors: 
    Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Ardern Hulme-Beaman; Lebrasseur, Ophélie; Mikkel-Holger S. Sinding; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; +49 more
    Publisher: The Royal Society
    Project: NSF | Genetic Analysis of Indig... (1304810), EC | ArchSci2020 (676154), EC | UNDEAD (337574), UKRI | Animals, Lifeways and Lif... (AH/N504543/1), UKRI | Understanding Cultural Re... (AH/K006029/1), UKRI | Deciphering dog domestica... (NE/K003259/1), UKRI | Deciphering dog domestica... (NE/K005243/1), NSF | Genetic Analysis of Prehi... (1108175), EC | WhereWolf (655732), WT | Domestic animals as a mod... (210119)

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

  • Open Access
    Authors: 
    Pfrengle, Saskia; Neukamm, Judith; Guellil, Meriam; Keller, Marcel; Molak, Martyna; Avanzi, Charlotte; Kushniarevich, Alena; Montes, Núria; Neumann, Gunnar U.; Reiter, Ella; +29 more
    Publisher: figshare
    Project: WT , EC | LEPVORS (845479)

    Additional file 3: Table S5. SNP distance matrix.

  • Open Access
    Authors: 
    Pereira, Andreia; Mendonça, Maria Isabel; Borges, Sofia; Freitas, Sónia; Henriques, Eva; Rodrigues, Mariana; Freitas, Ana Isabel; Sousa, Ana Célia; Brehm, António; Reis, Roberto Palma Dos;
    Publisher: SciELO journals
    Project: WT

    Abstract Background: Genetic risk score can quantify individual’s predisposition to coronary artery disease; however, its usefulness as an independent risk predictor remains inconclusive. Objective: To evaluate the incremental predictive value of a genetic risk score to traditional risk factors associated with coronary disease. Methods: Thirty-three genetic variants previously associated with coronary disease were analyzed in a case-control population with 2,888 individuals. A multiplicative genetic risk score was calculated and then divided into quartiles, with the 1st quartile as the reference class. Coronary risk was determined by logistic regression analysis. Then, a second logistic regression was performed with traditional risk factors and the last quartile of the genetic risk score. Based on this model, two ROC curves were constructed with and without the genetic score and compared by the Delong test. Statistical significance was considered when p values were less than 0.05. Results: The last quartile of the multiplicative genetic risk score revealed a significant increase in coronary artery disease risk (OR = 2.588; 95% CI: 2.090-3.204; p < 0.0001). The ROC curve based on traditional risk factors estimated an AUC of 0.72, which increased to 0.74 when the genetic risk score was added, revealing a better fit of the model (p < 0.0001). Conclusions: In conclusion, a multilocus genetic risk score was associated with an increased risk for coronary disease in our population. The usual model of traditional risk factors can be improved by incorporating genetic data.

  • Open Access
    Authors: 
    Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Ardern Hulme-Beaman; Lebrasseur, Ophélie; Mikkel-Holger S. Sinding; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; +49 more
    Publisher: The Royal Society
    Project: EC | UNDEAD (337574), EC | WhereWolf (655732), WT | Domestic animals as a mod... (210119), UKRI | Understanding Cultural Re... (AH/K006029/1), UKRI | Animals, Lifeways and Lif... (AH/N504543/1), EC | ArchSci2020 (676154), NSF | Genetic Analysis of Indig... (1304810), UKRI | Deciphering dog domestica... (NE/K005243/1), NSF | Genetic Analysis of Prehi... (1108175), UKRI | Deciphering dog domestica... (NE/K003259/1)

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

  • Open Access
    Authors: 
    Riaan F. Rifkin; Surendra Vikram; Jean-Baptiste Ramond; Rey-Iglesia, Alba; Brand, Tina B.; Porraz, Guillaume; Val, Aurore; Hall, Grant; Woodborne, Stephan; Bailly, Matthieu Le; +7 more
    Publisher: figshare
    Project: WT

    Additional file 2: Table S1. Sequence reads for environmental- and subsistence-related taxa detected. Table S2. Information concerning 14C Accelerator Mass Spectrometry (AMS) dating. Table S3a. Processing protocol and results for isotope analyses. Table S3b. Results for isotope analyses (Merck standard). Table S3c. Results for isotope analyses (DL-Valine standard). Table S4. Abundance of bacterial taxonomic categories in the IM datasets. Table S5. Sequence read-length distribution for taxa identified in this study. Table S6. Significant KEGG pathways in the comparative IM datasets analysed. Table S7. Relative abundance of eighteen significant KEGG pathways in the IM cohorts. Table S8. Enrichment and depletion of KO metabolic gene categories in the comparative IM sample cohorts based on p-value (p=<0.05) designation. Table S9. Enrichment and depletion of KO metabolic gene categories in the comparative IM sample cohorts based on false discovery rate (FDR) corrected p-values (q=<0.05). Table S10. Enrichment and depletion of KO metabolic gene categories in the ancient and modern comparative IM sample cohort as calculated for the twenty-four authenticated ancient IM taxa. Table S11. Comparison of relative abundance of antibiotic resistance genes in the comparative IM cohorts. Table S12. Raw and filtered high-quality sequence read counts as related to the comparative IM datasets. Table S13. Information concerning the comparative NCBI genomes used during this study.

  • Open Access
    Authors: 
    Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Ardern Hulme-Beaman; Lebrasseur, Ophélie; Mikkel-Holger S. Sinding; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; +49 more
    Publisher: The Royal Society
    Project: UKRI | Animals, Lifeways and Lif... (AH/N504543/1), UKRI | Understanding Cultural Re... (AH/K006029/1), EC | ArchSci2020 (676154), EC | UNDEAD (337574), NSF | Genetic Analysis of Indig... (1304810), UKRI | Deciphering dog domestica... (NE/K005243/1), NSF | Genetic Analysis of Prehi... (1108175), UKRI | Deciphering dog domestica... (NE/K003259/1), EC | WhereWolf (655732), WT | Domestic animals as a mod... (210119)

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

  • Open Access
    Authors: 
    Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Ardern Hulme-Beaman; Lebrasseur, Ophélie; Mikkel-Holger S. Sinding; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; +49 more
    Publisher: The Royal Society
    Project: EC | UNDEAD (337574), UKRI | Deciphering dog domestica... (NE/K005243/1), NSF | Genetic Analysis of Prehi... (1108175), EC | ArchSci2020 (676154), NSF | Genetic Analysis of Indig... (1304810), UKRI | Understanding Cultural Re... (AH/K006029/1), UKRI | Animals, Lifeways and Lif... (AH/N504543/1), EC | WhereWolf (655732), WT | Domestic animals as a mod... (210119), UKRI | Deciphering dog domestica... (NE/K003259/1)

    Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

  • Open Access
    Authors: 
    Barson, Gemma; Griffiths, Ed;
    Publisher: Figshare
    Project: WT

    Additional file 1. A tarball of the current production release of the SeqTools source code at the time of writing.

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