DOI: 10.5255/ukda-sn-9437-1
title: Millennium Cohort Study: Polygenic Indices, 2015: Special Licence Access
title: Millennium Cohort Study - Multi-omics Data and Risk Scores
title: MCS

description: &lt;p&gt;&lt;i&gt;Background&lt;/i&gt;:&lt;br&gt;The 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:&lt;/p&gt;&lt;ul&gt;&lt;li&gt;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&lt;/li&gt;&lt;li&gt;to provide a basis for comparing patterns of development with the preceding cohorts (the &lt;i&gt;National Child Development Study&lt;/i&gt;, held at the UK Data Archive under GN 33004, and the &lt;i&gt;1970 Birth Cohort Study&lt;/i&gt;, held under GN 33229)&lt;/li&gt;&lt;li&gt;to collect information on previously neglected topics, such as fathers' involvement in children's care and development&lt;/li&gt;&lt;li&gt;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&lt;/li&gt;&lt;li&gt;to emphasise intergenerational links including those back to the parents' own childhood&lt;/li&gt;&lt;li&gt;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&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;Additional objectives subsequently included for MCS were:&lt;/p&gt;&lt;ul&gt;&lt;li&gt;to provide control cases for the national evaluation of Sure Start (a government programme intended to alleviate child poverty and social exclusion)&lt;/li&gt;&lt;li&gt;to provide samples of adequate size to analyse and compare the smaller countries of the United Kingdom, and include disadvantaged areas of England&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;Further information about the MCS can be found on the &lt;a href="https://cls.ucl.ac.uk/cls-studies/millennium-cohort-study/" target="_blank"&gt;Centre for Longitudinal Studies&lt;/a&gt; web pages.&lt;/p&gt;&lt;p&gt;The content of MCS studies, including questions, topics and variables can be explored via the &lt;a href="https://discovery.closer.ac.uk/item/uk.cls.mcs/0d8a7220-c61b-4542-967d-a40cb5aca430"&gt;CLOSER Discovery&lt;/a&gt; website. &lt;br&gt;&lt;/p&gt;&lt;p&gt;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, and the eighth sweep (MCS8) in 2023-2025, when they were 23 years old. .&lt;br&gt;&lt;br&gt;&lt;i&gt;Safeguarded versions of MCS studies&lt;/i&gt;:&lt;br&gt;The Safeguarded versions of MCS1, MCS2, MCS3, MCS4, MCS5, MCS6, MCS7 and MCS8 are held under UK Data Archive SNs 4683, 5350, 5795, 6411, 7464, 815, 8682 and 9509 respectively. The Longitudinal Files are held under SN 8172.&lt;br&gt;&lt;br&gt;&lt;span style="font-style: italic;"&gt;Polygenic Indices&lt;/span&gt;&lt;br&gt;Polygenic indices are available under Special Licence SN 9437. Derived summary scores have been created that combine the estimated effects of many different genes on a specific trait or characteristic, such as a person's risk of Alzheimer's disease, asthma, substance abuse, or mental health disorders, for example. These polygenic scores can be combined with existing survey data to offer a more nuanced understanding of how cohort members' outcomes may be shaped. &lt;br&gt;&lt;br&gt;&lt;span style="font-style: italic;"&gt;Sub-sample studies&lt;/span&gt;:&lt;br&gt;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).&lt;br&gt;&lt;br&gt;&lt;span style="font-style: italic;"&gt;Release of Sweeps 1 to 4 to Long Format (Summer 2020)&lt;br&gt;&lt;/span&gt;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. &lt;span style="font-style: italic;"&gt; &lt;br&gt;&lt;/span&gt;&lt;i&gt;&lt;br&gt;How to access genetic and/or bio-medical sample data from a range of longitudinal surveys:&lt;br&gt;&lt;/i&gt;For information on how to access biomedical data from MCS that are not held at the UKDS, see the &lt;a href="https://cls.ucl.ac.uk/data-access-training/genetic-data-and-biological-samples/" target="_blank"&gt;CLS Genetic data and biological samples&lt;/a&gt; webpage.&lt;br&gt;&lt;br&gt;&lt;span style="font-weight: bold;"&gt;Secure Access datasets&lt;/span&gt;:&lt;br&gt;Secure Access versions of the MCS have more restrictive access conditions than versions available under the standard Safeguarded Licence or Special Licence (see 'Access data' tab above).&lt;br&gt;&lt;br&gt;Secure Access versions of the MCS include:&lt;/p&gt;&lt;p&gt;&lt;/p&gt;&lt;p&gt;&lt;/p&gt;&lt;ul&gt;&lt;li&gt;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&lt;/li&gt;&lt;li&gt;detailed sensitive data from the MCS8 survey, and responses from triplets held under SN 9510&lt;/li&gt;&lt;li&gt;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)&lt;/li&gt;&lt;li&gt;linked education administrative datasets for Key Stages 1, 2, 4 and 5 held under SN 8481 (England).  This replaces previously available datasets for Key Stage 1 (SN 6862) and Key Stage 2 (SN 7712)&lt;br&gt;&lt;/li&gt;&lt;li&gt;linked education administrative datasets for Key Stage 1 held under SN 7414 (Scotland)&lt;/li&gt;&lt;li&gt;linked education administrative dataset for Key Stages 1, 2, 3 and 4 under SN 9085 (Wales)&lt;br&gt;&lt;/li&gt;&lt;li&gt;linked NHS Patient Episode Database for Wales (PEDW) for MCS1 – MCS5 held under SN 8302&lt;/li&gt;&lt;li&gt;linked Scottish Medical Records data held under SNs 8709, 8710, 8711, 8712, 8713 and 8714;&lt;/li&gt;&lt;li&gt;Banded Distances to English Grammar Schools for MCS5 held under SN 8394&lt;/li&gt;&lt;li&gt;linked Health Administrative Datasets (Hospital Episode Statistics) for England for years 2000-2019 held under SN 9030&lt;/li&gt;&lt;li&gt;linked Hospital of Birth data held under SN 5724.&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;The linked education administrative datasets held under SNs 8481,7414 and 9085 may be ordered alongside the MCS detailed geographical identifier files only if sufficient justification is provided in the application. &lt;br&gt;&lt;br&gt;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 &lt;a href="https://beta.ukdataservice.ac.uk/datacatalogue/series/series?id=2000031#!/access-data" target="_blank"&gt;Access&lt;/a&gt; web page).&lt;/p&gt;&lt;p&gt;&lt;/p&gt; 
&lt;p&gt;&lt;span style="font-style: italic;"&gt;SN 9437 - Millennium Cohort Study: Polygenic Indices, 2015: Special Licence Access&lt;/span&gt;&lt;br&gt;Polygenic indices (PGIs) aggregate Genome-wide Association Studies (GWAS) estimates across all measured single nucleotide polymorphisms (SNPs) to provide a single estimate of an individual’s genetic predisposition towards the trait under study. As such, SNPs can be considered as the building blocks of PGIs. It is important to note that the genetic predisposition represented by PGI is known inasmuch as it has been estimated accurately and reliably from a GWAS; not all SNPs are included in the GWAS or the GWAS estimates for a given SNP are inaccurate, then the genetic predisposition represented by the PGI will be lower than the true genetic predisposition.&lt;/p&gt;
&lt;p&gt;The PGIs have been developed using a consistent methodology that has been applied to harmonised genetic data across each cohort, enabling researchers to engage in consistent cross-cohort analysis for using derived genetic measures for the first time. All PGIs have been derived from large scale Genome-wide Association Studies (GWAS) with publicly available summary statistics. This approach is hoped to enable and encourage wider use of the genetic data collected in these studies. High level guidance on the use and interpretation of PGIs is provided.&lt;/p&gt;
&lt;p&gt;The PGIs were also developed in a consistent manner in a birth cohort born in 1946 (MRC National Survey of Health and Development, 1946c), which can be obtained by separate application to the Unit for Lifelong Health and Ageing at UCL.&lt;/p&gt;