{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T22:48:24Z","timestamp":1787870904468,"version":"build-2784847793"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.16341.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T00:00:00Z","timestamp":1631232000000}}],"reference-count":28,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T00:00:00Z","timestamp":1631232000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["669545"],"award-info":[{"award-number":["669545"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004963","name":"Seventh Framework Programme","doi-asserted-by":"publisher","award":["FP7\/2007-2013"],"award-info":[{"award-number":["FP7\/2007-2013"]}],"id":[{"id":"10.13039\/501100004963","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/N024397\/1"],"award-info":[{"award-number":["MR\/N024397\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UU_00011\/6"],"award-info":[{"award-number":["MC_UU_00011\/6"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000274","name":"British Heart Foundation","doi-asserted-by":"publisher","award":["CS\/16\/4\/32482"],"award-info":[{"award-number":["CS\/16\/4\/32482"]}],"id":[{"id":"10.13039\/501100000274","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000274","name":"British Heart Foundation","doi-asserted-by":"publisher","award":["FS\/17\/60\/33474"],"award-info":[{"award-number":["FS\/17\/60\/33474"]}],"id":[{"id":"10.13039\/501100000274","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015250","name":"NIHR Bristol Biomedical Research Centre","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015250","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014338","name":"National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care Yorkshire and Humber","doi-asserted-by":"publisher","award":["NIHR200166"],"award-info":[{"award-number":["NIHR200166"]}],"id":[{"id":"10.13039\/501100014338","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000269","name":"Economic and Social Research Council","doi-asserted-by":"publisher","award":["MR\/N024397\/1"],"award-info":[{"award-number":["MR\/N024397\/1"]}],"id":[{"id":"10.13039\/501100000269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000883","name":"University of Bristol","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000883","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01DK10324"],"award-info":[{"award-number":["R01DK10324"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","award":["NF-0616-10102"],"award-info":[{"award-number":["NF-0616-10102"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["101597, 083521"],"award-info":[{"award-number":["101597, 083521"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>Metabolomics is the quantification of small molecules, commonly known as metabolites. Collectively, these metabolites and their interactions within a biological system are known as the metabolome. The metabolome is a unique area of study, capturing influences from both genotype and environment. The availability of high-throughput technologies for quantifying large numbers of metabolites, as well as lipids and lipoprotein particles, has enabled detailed investigation of human metabolism in large-scale epidemiological studies. The Born in Bradford (BiB) cohort includes 12,453 women who experienced 13,776 pregnancies recruited between 2007-2011, their partners and their offspring. In this data note, we describe the metabolomic data available in BiB, profiled during pregnancy, in cord blood and during early life in the offspring. These include two platforms of metabolomic profiling: nuclear magnetic resonance and mass spectrometry. The maternal measures, taken at 26-28 weeks\u2019 gestation, can provide insight into the metabolome during pregnancy and how it relates to maternal and offspring health. The offspring cord blood measurements provide information on the fetal metabolome. These measures, alongside maternal pregnancy measures, can be used to explore how they may influence outcomes. The infant measures (taken around ages 12 and 24 months) provide a snapshot of the early life metabolome during a key phase of nutrition, environmental exposures, growth, and development. These metabolomic data can be examined alongside the BiB cohorts\u2019 extensive phenotype data from questionnaires, medical, educational and social record linkage, and other \u2018omics data.<\/ns3:p>","DOI":"10.12688\/wellcomeopenres.16341.2","type":"journal-article","created":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T10:50:14Z","timestamp":1631271014000},"page":"264","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":14,"title":["Metabolomics datasets in the Born in Bradford cohort"],"prefix":"10.12688","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4690-063X","authenticated-orcid":false,"given":"Kurt","family":"Taylor","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy","family":"McBride","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2488-4598","authenticated-orcid":false,"given":"Neil","family":"J Goulding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberley","family":"Burrows","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0026-9216","authenticated-orcid":false,"given":"Dan","family":"Mason","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0455-7469","authenticated-orcid":false,"given":"Lucy","family":"Pembrey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4549-7850","authenticated-orcid":false,"given":"Tiffany","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafaq","family":"Azad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9572-7293","authenticated-orcid":false,"given":"John","family":"Wright","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6793-2262","authenticated-orcid":false,"given":"Deborah","family":"A 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.18489.r45817, Ruifang Li-Gao, Leiden University Medical Center, Leiden, 04 Oct 2021, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/5-264\/v2#referee-response-45817","order":0,"name":"referee-response-45817","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.17967.r43230, Mengna Huang, Channing Division of Network Medicine, Department of Medicine, Brigham and Women\u2019s Hospital and Harvard Medical School, Boston, MA, 20 Apr 2021, version 1, 2 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/5-264\/v1#referee-response-43230","order":1,"name":"referee-response-43230","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Kurt Taylor<\/b>; \n<i>Posted: 06 Sep 2021<\/i>; 1. Page 4 \u2013 the total number of pregnancies in BiB was greater than the number of women enrolled in the study, and the recruitment period spanned over four years. In Figures 4A and 6, mostly it was the number of pregnancies that were presented \u2013 were these singleton birth? Were there women who contributed samples from more than one pregnancy? Same question for cord blood. In figure 4B, were children with NMR metabolomics all from independent families? Such information will have implications in statistical analysis and should be clarified.  \n<b>The reviewer makes a useful point, and we agree that having this information in the manuscript will be useful for readers and prospective users of the data. We have now added this information to Figures 4 and 6, which show that women with more than one pregnancy had one removed at random and those with multiple pregnancies were excluded.<\/b>  2.&nbsp;Page 4 \u2013 under \u201cPregnancy blood samples\u201d, step 4 indicated that 2 vials were used, while step 6 says 3 aliquots. This seems inconsistent.  \n<b>We thank the reviewer for pointing out this inconsistency, which we have now corrected by using only the term aliquot and clarifying the numbers:  <i>\u201c1) Storage racks were prepared.<\/i> <i>2) Participant details were checked, making sure that both the BiB study ID and hospital number on the specimen bottles matched those on the participant tracking forms.<\/i> <i>3) Tubes were centrifuged at 3500 rpm for 10 minutes at room temperature.<\/i> <i>4) A 1 ml automatic pipette was used to aliquot samples into 1.5 ml aliquots (<\/i><u>1-4 aliquots<\/u><i> dependent on sample volume).<\/i> <i>5) Vials were labelled with appropriate BiB study labels and the duplicate barcode label was placed in the corresponding space marked on BiB tracking form.<\/i> <i>6) Aliquots were then placed in racks in a -80&deg;C freezer.\u201d<\/i><\/b>  3.&nbsp;Page 7 \u2013 for validation of the MS platform, did the author conduct regression analysis with the MS glucose measure in association with BMI and HDP? This would of course be in a smaller sample size, but it would be interesting to see the results.  \n<b>We thank the reviewer for pointing this out. We agree that it would be useful to include this. Please see response 2, to reviewer 1 above. <\/b>  4.&nbsp;Page 10 \u2013 for the MS dataset, apart from the raw and scaled data sets from Metabolon, did the authors perform additional data processing (e.g. different imputation approach or log transformation)? There would usually be some metabolites with high missing percentages where imputing with the minimum (which I believe is what Metabolon usually does for imputation) would not be entirely appropriate for subsequent analysis. Is there any recommendation in terms of excluding them from subsequent analysis or applying a different analysis method?  \n<b>We agree with the reviewer. However, the data are provided by Metabolon following extensive quality control. We cannot give recommendations for analyses because it depends on the research question of the group using the data. For example, in some of our analyses we remove participants where there is little between person variation in a particular metabolite. We also convert xenobiotics where there is substantial missing data to binary variables (indicating exposure to e.g. a particular medication).<\/b>  5.&nbsp;Figure 7 \u2013 there should not be overlap between MS pregnancy dataset 1a and MS pregnancy dataset 2 according to descriptions on the bottom of Page 9?  \n<b>We thank the reviewer for identifying this mistake. We have amended the figure to show the overlap of \u20180\u2019.<\/b>  6.&nbsp;Page 14 \u2013 the authors mentioned that differences by ethnicity in distributions of NMR data were observed, I wonder if differences in diet plays a role here. It\u2019s not quite clear whether BiB collected dietary data from the main text?  \n<b>For clarity, we have added the following to the discussion section: <i>There is also scope to explore how diet could relate to the range of metabolomic measurements that BiB possesses. Further information on dietary variables can be found online in the BiB data dictionary https:\/\/borninbradford.github.io\/datadict\/.<\/i><\/b>  7.&nbsp;The article provided a good overview of the data available in pregnancy other than the metabolomics data. How much and what kind of data would be available during early life for the children? From the description of HELIX on Page 16, it seemed like BiB children were followed up to a median age of 6.6 years, were all children followed-up? Or just those in the ALL IN sub-study?  \n<b>For clarity, we have added a sentence in the \u201congoing and future research\u201d section: <i>To date, there is no published work using the offspring metabolomics data. Researchers can find information on planned follow up data elsewhere, to understand whether these data could be useful to their ongoing or future research (<\/i><i>https:\/\/doi.org\/10.1186\/s12889-019-7222-2<\/i><i>).<\/i><\/b>  8.&nbsp;Is there a plan to generate MS metabolomic data in the 12- and 24- months infant samples? Such data may complement the existing NMR data, and be important for studies like ALL IN.  \n<b>Currently there are no plans or funds to do this. Researchers who are interested in funding analyses on any available biosamples in BiB can submit an expression of interest to do so (https:\/\/borninbradford.nhs.uk\/research\/how-to-access-data\/). Because biosamples are finite these requests are assessed on several criteria, including the importance of the science, whether any existing assay results (including the metabolomic data described here) provide relevant data, whether other collaborators are already running similar assays and the volume required compared to current available sample volume.<\/b>  -----------------------------------  \n<b>ADDITIONAL SECTION TO THE REVISED DATANOTE  Since submitting the data not new versions of the two Metabolon MS data have been derived. We have added a new section called \u201csecond version of the Metabolon MS data\u201d in the \u201cissues for data users\u201d section. We describe why we obtained these new versions and some analyses of how they relate to the original versions. &nbsp;<\/b>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/5-264\/v2#referee-comment-4736","order":2,"name":"referee-comment-4736","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.18489.r79682, Sandi Azab, McMaster University, Hamilton, Ontario, 21 May 2024, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/5-264\/v2#referee-response-79682","order":3,"name":"referee-response-79682","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Core funding for BiB has been provided by the Wellcome Trust [101597], a joint grant from the UK Medical Research Council (MRC) and UK Economic and Social Science Research Council (ESRC) [MR\/N024397\/1], the British Heart Foundation [CS\/16\/4\/32482] and the National Institute for Health Research ARC Yorkshire and Humber [NIHR200166]. Funding for the metabolomics analyses has been provided by the US National Institutes of Health [R01 DK10324], the European Research Council (ERC) under the European Union\u2019s Seventh Framework Programme [FP7\/2007-2013] \/ ERC grant agreement no 669545 and the MRC via the MRC Integrative Epidemiology Unit Programme to D.A.L [MC_UU_00011\/6]. The work presented here is also supported by the University of Bristol British Heart Foundation Accelerator Award [AA\/18\/7\/34219]. K.T. is supported by a British Heart Foundation Doctoral Training Program [FS\/17\/60\/33474]. N.M. PhD studentship is funded by the National Institute for Health Research (NIHR) Biomedical Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol. K.T., N.M., N.J.G, K.B. and D.A.L. work in a unit that is supported by the University of Bristol and UK Medical Research Council [MC_UU_00011\/6]. D.A.L is a NIHR Senior Investigator [NF-0616-10102]. The ALL IN sub-study was supported by the Wellcome Trust [083521]. Funding was also provided by the National Institute for Health Research (NIHR) under its Collaboration for Applied Health Research and Care (CLAHRC) for Yorkshire and Humber","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}