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ASSOCIATION TESTING OF THE PROTEIN TYROSINE PHOSPHATASE 1B GENE (PTPN1) WITH TYPE 2 DIABETES IN 7,883 PEOPLE

Jose C. Florez 1,2,3,4, Christina M. Agapakis 1,3, Noël Burtt 3, Maria Sun 1,3, Peter Almgren 5, Lennart Råstam 6, Tiinamaija Tuomi 7, Daniel Gaudet 8, Thomas J. Hudson 9, Mark J. Daly 3, Kristin G. Ardlie 10, Joel N. Hirschhorn 3,11,12, Leif Groop 5 (*) and David Altshuler 1,2,3,4,11 (*)

1 Departments of Molecular Biology and 2 Medicine (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts; 3 Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Departments of 4 Medicine and 11 Genetics, Harvard Medical School, Boston, Massachusetts; Departments of 5 Endocrinology and 6 Clinical Science, University Hospital MAS, Lund University, Malmö, Sweden; 7 Department of Medicine, Helsinki University Central Hospital; Folkhalsan Genetic Institute, Folkhalsan Research Center; and Research Program for Molecular Medicine, University of Helsinki, Helsinki, Finland; 8 University of Montreal Community Genomic Center, Chicoutimi Hospital, Quebec, Canada; 9 McGill University and Genome Quebec Innovation Centre, Montreal, Canada; 10 Genomics Collaborative Division, SeraCare LifeSciences, Cambridge, Massachusetts; and 12 Divisions of Genetics and Endocrinology, Children’s Hospital, Boston, Massachusetts

(*) These authors jointly supervised the project

Diabetes. 2005 Jun;54(6):1884-91

Online supplementary information

Supplementary Table 1: Genotyping assays of SNPs in PTPN1
Genotyping assays for 42 SNPs in PTPN1, showing the sequences of the PCR primers and the extension probe, its direction (forward or reverse) and reasons for assay failure. Genotyping was performed by mass spectroscopy detection of allele-specific primer extension products (see text for details). SNPs in bold indicate those obtained from the HapMap website (www.hapmap.org). Failed HW, failed Hardy-Weinberg equilibrium in the CEPH reference panel; failed genotyping, genotyping rate <75% or >1 Mendel errors; MONO, monomorphic SNP in the CEPH reference panel. Thirty one of 42 SNPs passed assay design.

Supplementary Table 2: Genotype counts of individual SNPs in PTPN1
Allele counts for each of the 18 tag SNPs in our diabetic subsamples; for each SNP, the major allele is presented first. SNPs in bold comprise a block of tight LD as defined by Gabriel et al. (25) (see Fig. 1). (*) SNPs reportedly associated with T2D in Bento et al. (13). C/C, case/control.

Supplementary Table 3: Whole-body insulin sensitivity index according to PTPN1 haplotypes
The whole-body insulin sensitivity index (WB-ISI) was calculated in the 766 Scandinavian control subjects for whom we had OGTT data (22). Values were logarithmically transformed because of non-normality; they are expressed as mean ± S.D. Genotypic groups: A/A, homozygotes for haplotype A; A/X, carriers of haplotype A, excluding A/B heterozygotes; A/B, A/B heterozygotes; O/O, non-A, non-B haplotype carriers; B/X, carriers of haplotype B, excluding A/B heterozygotes; B/B, homozygotes for haplotype B; B/*, carriers of haplotype B, including A/B heterozygotes. ANOVA was used to compare >2 groups, and two-sided t tests were used to compare 2 groups.