Open Access Research article

Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19

John H Lillvis1, Yoshiki Kyo19, Gerard Tromp2, Guy M Lenk110, Ming Li3, Qing Lu34, Robert P Igo4, Natzi Sakalihasan5, Robert E Ferrell6, Charles M Schworer2, Zoran Gatalica7, Susan Land18 and Helena Kuivaniemi2*

Author Affiliations

1 Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA

2 Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, 100 North Academy Avenue, Pennsylvania 17822-2610, USA

3 Department of Epidemiology, Michigan State University, East Lansing, Michigan, USA

4 Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA

5 Department of Cardiovascular Surgery, University Hospital of Liège, Liège, Belgium

6 Department of Human Genetics, University of Pittsburgh, School of Public Health, Pittsburgh, Pennsylvania, USA

7 Department of Pathology, Creighton University School of Medicine, Omaha, Nebraska, USA

8 Applied Genomics Technology Center, Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA

9 Department of Cardiovascular Surgery, Higashihiroshima Medical Center, Hiroshima, Japan

10 Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA

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BMC Medical Genetics 2011, 12:14  doi:10.1186/1471-2350-12-14

Published: 19 January 2011

Additional files

Additional File 1:

Table S1. List of all 55 SNPs chosen for the study. Each SNP genotyped for this study ordered by chromosomal coordinate. SNP RefSeq number, gene symbol, minor allele, chromosome 19 coordinate, p-value for HWE test, MAF in the entire population and for Canadian and Belgian populations separately (cases and controls separately), p-values for the allelic test for combined analysis as well as for Canadian and Belgian population separately, and LRT p-values are provided in tabular format. RefSeq numbers contain hyperlinks to the NCBI site.

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Additional File 2:

Table S2. Genomic DNA samples used for sequencing of CEBPG and CD22. For each sample used in sequencing, case/control status, nationality of origin, sex and sequencing status of CD22 and CEBPG provided in tabular format.

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Additional File 3:

Table S3. cDNA samples used for sequencing of PEPD. Case/control status, nationality of origin, sex and family history of each individual whose sample was used in the sequencing of PEPD provided in tabular format.

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Additional File 4:

Table S4. PCR primer pairs for CEPBG, PEPD and CD22. For each PCR reaction, a description of each reaction, primer pair sequences and orientation, product sizes, annealing temperatures, and the cycling times and magnesium chloride concentrations used provided in tabular format.

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Additional File 5:

Table S5. Sequencing primers used for CEBPG, PEPD and CD22. For each sequencing reaction, a description of the reaction, the primer sequences and orientation, and predicted melting points for primer provided in tabular format.

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Additional File 6:

Table S6. Human tissue samples used in immunohistochemical analysis of CD22 and PEPD. Donor age, sex, case/control status and control cause of death if known.

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Additional File 7:

Figure S1. Linkage disequilibrium (LD) plots of genotyped SNPs in CEBPG and PEPD for cases (A) and controls (B) separately. LD at the CEBPG/PEPD locus plotted separately for cases and controls using r2 as the statistic. Approximate locations of genes and SNPs were plotted along the x-axis above plots. Nominally associated SNPs are indicated with an asterisk.

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Additional File 8:

Figure S2. LD plots of genotyped SNPs in CD22 for cases (A) and controls (B) separately. LD at the CD22 locus plotted separately for cases and controls using r2 as the statistic. Approximate location of CD22 and SNPs were plotted along the x-axis above plots. Nominally associated SNPs are indicated with an asterisk.

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Additional File 9:

Table S7. PEPD sequence changes by sample number. Table showing genotype at each sequence variant detected by sequencing in each individual sequenced. Sample numbers refer to Additional file 3, Table S3, and sequence change number refers to Table 4.

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Additional File 10:

Table S8. Flanking sequences of the PEPD sequence variants. Gene feature, 15 bp flanking sequences and SNP identifier, if available, for each sequence variant.

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Additional File 11:

Table S9. CD22 sequence changes by sample number. Table showing genotype at each sequence variant detected by sequencing in each individual sequenced. Sample numbers refer to Additional file 2, Table S2, and sequence change number refers to Table 5.

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Additional File 12:

Table S10. Flanking sequences of the CD22 sequence variants. Gene feature, 15 bp flanking sequences and SNP identifier, if available, for each sequence variant.

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