JDRF/Wellcome Trust

Diabetes and Inflammation Laboratory

DNA references and sample sources:

Sample collections used at the JDRF/WT DIL

This page serves 3 purposes:

  • some journals set an upper limit of e.g. 25 references for a short article. If we have performed extensive genotyping only to find a null result, references to DNA collections could take 8 or more of those precious citations slots, so we have decided to assemble them here. [DNA references]
  • we are increasingly performing non-DNA lab work: which collections have which sample-type is shown. [Sample counts]
  • from April 1st 2013, all submitted papers with RCUK funding should state where to access sample collections used - this gives links to access committees where known. [Basis on which samples held, and sample sources]

DNA references

 
DNA set 1: cell-lined, multiplex families
Collection
(our code, if different)
Country Reference/URL PubMed ID
Human Biological Data Interchange (HBDI) US Lernmark, A. (1991). Human cell lines from families available for diabetes research (Letter). Diabetologia 34, 61 2055345
UK Diabetes Warren 1 repository (WARREN, aka BDA or Diabetes UK) UK Bain, S.C., Todd, J.A. & Barnett, A. H. (1990). The British Diabetic Association: Warren Repository. Autoimmunity 7, 83-85 2151758
 
DNA set 2: non-cell-lined, simplex families
Northern Ireland family colection (BELFAST) UK Patterson, C.C., Carson, D.J., Hadden, D.R., Waugh, N.R. & Cole, S.K. (1994). A case-control investigation of perinatal risk factors for childhood IDDM in Northern Ireland and Scotland. Diabetes Care 17, 376-381 8062603
Bristol UK Wadsworth, E.J., Shield, J.P., Hunt, L.P. & Baum, J.D. (1997). A case-control study of environmental factors associated with diabetes in the under 5s. Diabetic Medicine 14(5), 390-396 9171256
DiMe and IDDMGen (FIN) Finland Tuomilehto, J., Lounamaa, R., Tuomilehto-Wolf, E., Reunanen, A., Virtala, E., Kaprio, E.A. & Akerblom, H.K. (1992). Epidemiology of childhood diabetes mellitus in Finland: background of a nationwide study of type 1 (insulin-dependent) diabetes mellitus: the Childhood Diabetes in Finland (DiMe) Study Group. Diabetologia 35, 70-76 1541383
Norwegian Norway Undlien, D.E., Akselsen, H.E., Joner, G., Dahl-Jorgensen, K., Aagenaes, O., Sovik, O., Thorsby, E. & Ronningen, K.S. (1995). No difference in the parental origin of susceptibility HLA class II haplotypes among Norwegian patients with insulin-dependent diabetes mellitus. Am. J. Hum. Genet. 57, 1511-1514 8533785
Romanian 1995 and 1999 (ROM) Romania Ionescu-Tirgoviste, C., Guja, C., Herr, M., Cucca, E., Welsh, K., Bunce, M., Marshall, S. & Todd, J.A. (2001). Low frequency of HLA DRB1*03-DQB1*02 and DQB1*0302 haplotypes in Romania is consistent with the country's low incidence of type I diabetes. Diabetologia 44 (Suppl. 3), B60-B66 11724419
Type 1 Diabetes Genetics Consortium family collection (T1DGC) worldwide Rich, S.S., Concannon, P.P., Erlich, H.H., Julier, C., Morahan, G., Nerup, J., Pociot, F. & Todd, J.A. (2006). The Type 1 Diabetes Genetics Consortium. Ann N Y Acad Sci 1079, 1-8 17130525
Yorkshire UK Feltbower, R.G., McKinney, P.A., Parslow, R.C., Stephenson, C.R., & Bodansky, H.J. (2003). Type 1 diabetes in Yorkshire, UK: time trends in 0--14 and 15--29-year-olds, age at onset and age-period-cohort modelling. Diabetic Medicine 20, 437-441. 12786676
 
Case-control collections
UK GRID diabetic cases (UK GRID) UK http://www.childhood-diabetes.org.uk/grid.shtml  
National Child Development Study, aka 1958 British birth cohort - controls for diabetic cases (1958BC, aka 58C, B58C) UK Power, C., & Elliott, J. (2006) Cohort profile: 1958 British birth cohort (National Child Development Study). Int J Epidemiol, 35(1), 34-41 16155052
UK Blood Services controls (UKBS-CC aka UKBS, NBS) UK link to Wellcome Trust launch story, explaining UKBS involvement in human genetics  
Graves' cases from autoimmune thyroid disease UK National Collection (GRAVES) UK Ueda, H., Howson, J.M.M., Esposito, L., Heward, J., Snook, H., Chamberlain, G., Rainbow, D.B., Hunter, K.M.D., Smith, A.N., Di Genova, G., Herr, M.H., Dahlman, I., Payne, F., Smyth, D., Lowe, C., Twells, R.C.J., Howlett, S., Healy, B., Nutlan, S., Rance, H.E., Everett, V., Smink, L.J., Lam, A.C.H., Cordell, H.J., Walker, N.M., Bordin, C., Hulme, J., Motzo, C., Cucca, F., Hess, J.F., Metzker, M.L., Rogers, J., Gregory, S., Allahabadia, A., Nithiyananthan, R., Tuomilehto-Wolf, E., Tuomilehto, J., Bingley, P., Gillespie, K.M., Undlien, D.E., Ronningen, K.S., Guja, C., Ionescu-Tirgoviste, C., Savage, D.A., Maxwell, A.P., Carson, D.J., Patterson, C.C., Franklyn, J.A., Clayton, D.G., Peterson, L.B., Wicker, L.S., Todd, J.A. & Gough, S.C.L. (2003) Association of the T cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature, 423, 506-511 12724780
 
Additional genotyping resources
Cambridge BioResource (CBR) UK Subjects are genotyped for selection into further research, and/or for research itself
http://www.cambridgebioresource.org.uk/
 
Genes and Phenotypes of Type 1 Diabetes (IP, was CB) UK Our small-scale direct recruitment for immunophenotyping experiments
http://www.t1-diabetes.org.uk/
 
Diabetes UK, Warren 3 trios (DUK) UK Patel, A., Scott, W.R., Lympany, P.A., Rippin, J.D., Gill, G.V., the Warren 3/UK GoKind Study Group, Barnett, A.H., & Bain, S.C. (2005). The TGF-beta1 gene codon 10 polymorphism contributes to the genetic predisposition to nephropathy in Type 1 diabetes. Diabetic Medicine 22:1, 69-73 15606694
Genetics of Kidneys in Diabetes, cases (GoKIND) UK Used as additional cases. Part of wider GoKIND group. Reference as for DUK above  
Oxford Regional Prospective Study, cases and families (ORPS) UK Schultz, C.J., Konopelska-Bahu, T., Dalton, R.N., Carroll, T.A., Stratton, I., Gale, E.A. et al. for the Oxford Regional Prospective Study Group (1999). Microalbuminuria prevalence varies with age, sex and puberty in children with insulin-dependent mellitus followed in a longitudinal study from diagnosis. Diabetes Care 22, 495-502 10097935
 
Misc reference samples
Centre d'Etude du Polymorphisme Humain - especially HapMap samples (CEPH) US Samples used for sequencing
http://ccr.coriell.org/Sections/Collections/NHGRI/hapmap.aspx?PgId=266&coll=GM
 
International Histocompatibility Working Group [IHWG] International Cell and Gene Bank (REFERENCE) worldwide HLA reference samples
http://www.ihwg.org/cellbank/dna/refpan.html
 
Human Random Control Reference Panel (ECACC) UK Samples formerly used as controls
http://www.ecacc.org.uk/detail2.asp?itemid=92962
 

Sample counts

 
Sample counts by collection code
Collection code blood PBL cell line DNA amplified DNA plasma sera
HBDI -- -- -- 2,200 -- -- --
WARREN -- -- 2,050 2,200 -- -- --
 
BELFAST -- -- -- 950 -- -- --
BRISTOL -- -- -- 650 -- -- --
FIN -- -- -- 7,900 -- 50 --
NORWEGIAN -- -- -- 1,550 -- -- --
ROM -- -- -- 1,500 -- -- --
T1DGC -- -- -- 4,000 -- -- --
YORKSHIRE -- -- -- 300 -- -- --
 
UK GRID tbc tbc 9,800 9,800 1,450 8,750 --
1958BC -- -- -- 8,200 700 -- --
UKBS-CC -- -- -- 3,200 -- -- --
GRAVES -- -- -- 4,200 -- -- --
 
CBR 11450 -- -- tbc -- tbc tbc
IP 1450 -- -- tbc -- tbc tbc
DUK -- -- -- 400 -- -- --
GOKIND -- -- 1,250 1,200 -- -- --
ORPS -- -- -- 500 -- -- --
 
CEPH -- -- 50 800 -- -- --
REFERENCE -- -- -- 50 -- -- --
ECACC -- -- 500 500 -- -- --

Notes:

  • figures for CBR and IP need updating - and splitting between saliva- and blood-derived DNA - as at January 2013
  • counts are of distinct subjects, rather than samples
  • counts are rounded to nearest 50
  • DNA counts will, in some cases, include exhausted samples where data is retained

Basis on which samples held, and sample sources

Collection code basis on which samples held available from
HBDI resourceHBDI
WARREN resourceECACC
 
BELFAST collaboration--
BRISTOL collaboration--
FIN collaboration--
NORWEGIAN collaboration--
ROM collaboration--
T1DGC resource NIDDK Central Repository
YORKSHIRE collaboration--
 
UK GRID resource JDRF/WT DIL, NIDDK Central Repository
1958BC resource 1958BC at Leicester
UKBS-CC collaboration as resource - Department of Haemetology, Cambridge, UK - via PIs webpage, currently
GRAVES collaboration --
 
CBR resource Cambridge BioResource
IP resourceJDRF/WT DIL
DUK collaboration--
GOKIND collaboration--
ORPS collaboration--
 
CEPH resourceCoriell
REFERENCE resourceIHWG
ECACC resourceECACC

Notes:

  • The Diabetes UK Warren 3 (DUK) and GoKIND samples we use collaboratively are now part of a wider resource