Monthly Archives: February 2013
test-from-s1
Supplemental Material
Polymorphisms in Iron Homeostasis Genes and Urinary Cadmium Concentrations among Nonsmoking Women in Argentina and Bangladesh
Gerda Rentschler, Maria Kippler, Anna Axmon, Rubhana Raqib, Eva-Charlotte Ekström, Staffan Skerfving, Marie Vahter, Karin Broberg
Table of Contents: Page
Supplemental Material, Table S1 2
Genes and polymorphisms that were successfully genotyped.
Supplemental Material, Table S2
Polymorphisms that were genotyped but later excluded from the data evaluation. 4
Supplemental Material, Table S3 5
SNP-related modification of transcription factor binding sites
Supplemental Material, Table S4 7
Gene expression data for iron-related genes in the Andean women
Supplemental Material, Table S1. Genes and polymorphisms that were successfully genotyped (quality requirements: at least 90% of samples with clearly defined genotypesa) ).
Gene
Unigene Nrb Protein name Location |
rs nrc | Polymorphism typed | Allele frequencies
Argentinean Andes |
QCa
(%) |
Allele frequencies
Bangladesh |
QCa
(%) |
SLC11A2 | rs149411 | Intron C>T | 75/25 | 96 | 37/63 | 99 |
Hs.505545 | rs224572 | Intron G>A | 41/59 | 96 | 28/72 | 94 |
DMT1 | rs224574 | Intron C>T | 1/99 | 98 | 10/90 | 99 |
NRAMP2 | rs224575 | Intron G>A | 75/25 | 97 | 37/63 | 99 |
Chr 12q13 | rs364627 | Intron G>A | 1/99 | 96 | 10/90 | 93 |
rs407135 | Intron C>A | 8/92 | 97 | 34/66 | 100 | |
rs1005559 | Intron T>A | 7/93 | 97 | 24/76 | 96 | |
rs2269683 | Intron C>T | 34/66 | 96 | 9/91 | 99 | |
rs3809320 | Upstream T>A | 35/65 | 97 | 9/91 | 96 | |
rs6580779 | 5’ UTR G>T | 1/99 | 96 | 10/90 | 95 | |
rs12366756 | Intron G>A | 7/93 | 98 | 24/76 | 99 | |
rs12830073 | Intron T>C | 6/94 | 96 | 24/76 | 90 | |
SLC40A1 | rs1123110 | Intron C>T | 12/88 | 95 | 34/66 | 97 |
Hs.643005 | rs1439816 | Intron C>G | 12/88 | 97 | 22/78 | 100 |
FPN1 | rs4145237 | Intron C>G | 15/85 | 97 | 33/67 | 99 |
Chr 2q32 | rs4667287 | Intron C>A | 14/86 | 98 | 19/81 | 100 |
rs11884632 | Intron C>G | 0/100 | 98 | 13/87 | 98 | |
TF | rs12595 | Intron G>A | 58/43 | 98 | 41/59 | 99 |
Hs.518267 | rs1049296 | S589P T>C | 4/96 | 98 | 21/79 | 99 |
Transferrin | rs1130459 | 5’ UTR A>G | 6/94 | 98 | 25/75 | 97 |
Chr 3q22.1 | rs1799852 | L247L T>C | 12/88 | 97 | 21/79 | 99 |
rs2280673 | Intron C>A | 15/85 | 98 | 48/52 | 98 | |
rs2715627 | Intron C>T | 3/97 | 97 | 15/85 | 99 | |
rs3811647 | Intron A>G | 58/42 | 97 | 42/58 | 96 | |
rs4241357 | Intron G>T | 29/71 | 97 | 28/72 | 100 | |
rs4355280 | Intron G>A | 58/42 | 96 | 53/47 | 96 | |
rs4428180 | Intron G>A | 37/63 | 96 | 23/77 | 97 | |
rs4459901 | Intron C>T | 54/46 | 98 | 37/63 | 99 | |
rs4532136 | Intron A>G | 12/88 | 98 | 18/82 | 99 | |
rs6785596 | Intron A>T | 3/97 | 98 | 15/85 | 99 | |
rs6796795 | Intron G>A | 3/97 | 97 | 15/85 | 100 | |
rs8177184 | Intron G>A | 36/64 | 98 | 22/78 | 99 | |
rs8177186 | 5’ UTR T>G | 12/88 | 96 | 18/82 | 97 | |
rs8177190 | Intron T>C | 25/75 | 97 | 9/91 | 97 | |
rs8177191 | Intron A>G | 2/98 | 98 | 7/93 | 99 | |
rs8177213 | Intron C>A | 27/73 | 97 | 14/86 | 96 | |
rs8177235 | Intron A>G | 14/86 | 97 | 16/84 | 97 | |
rs41298977 | A76V T>C | 0/100 | 98 | 0/100 | 99 |
Supplemental Material, Table S1 (cont.)
Gene
Unigene Nrb Protein name Location |
rs nrc | Polymorphism typed | Allele frequencies
Argentinean Andes |
QCa
(%) |
Allele frequencies
Bangladesh |
QCa
(%) |
TFR2 | rs7385804 | Intron C>A | 18/82 | 96 (*) | 37/63 | 100 |
Hs.544932 | rs10247962 | Intron G>A | 2/98 | 98 | 24/76 | 99 |
TFR2 | rs34242818 | I238M G>C | 0/100 | 98 | 1/99 | 98 |
Chr 7q22 | ||||||
TFRC | rs2284889 | Intron T>C | 27/73 | 97 | 50/50 | 98 |
Hs.529618 | rs3736651 | Intron T>A | 43/57 | 96 | 21/79 | 99 |
TFRC | rs3761717 | Intron C>G | 73/27 | 97 | 49/51 | 94 |
Chr 3q29 | rs3804141 | Intron A>G | 26/74 | 97 (*) | 14/86 | 100 |
rs9859260 | Intron G>A | 73/27 | 97 | 50/50 | 95 | |
rs9859401 | Intron T>G | 27/73 | 97 | 49/51 | 95 | |
rs11185506 | Intron C>G | 27/73 | 97 | 49/51 | 98 | |
rs13072608 | Intron G>A | 73/27 | 97 | 49/51 | 96 | |
rs41301381 | L212V G>C | 0/100 | 98 | 0/100 | 100 |
a QC percent represents the percentage of samples with clearly defined genotypes (based on Sequenom mass spectrometry analysis). None of the SNPs showed Hardy-Weinberg disequilibrium in both populations. SNPs that demonstrated disequilibrium in one of the populations are marked with (*).
b Unigene accession number from NCBI (National Center for Biotechnology Information) Unigene Database (website: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene).
C rs numbers from NCBI SNP Database (website: http://www.ncbi.nlm.nih.gov/SNP).
d When applicable, amino acid position/gene region is denoted. The rare allele in Bangladesh is denoted first.
Supplemental Material, Table S2. Polymorphisms that were genotyped but later excluded from the data evaluation.
Gene | rs nra | Polymorphism typeb | QCc Argentinean Andes (%) | QCc Bangladesh (%) | Reason for exclusion |
SLC11A2 | rs224446 | 3′ UTR A>G | 82 | 88 | too low analytical quality |
rs17216051 | T298I C>T | 98 | 99 | no variants detected | |
rs17216086 | W500R T>C | 97 | 99 | no variants detected | |
rs17222449 | Q290R A>G | 97 | 99 | no variants detected | |
rs17222470 | H62Y C>T | 98 | 99 | no variants detected | |
SLC40A1 | rs11568350 | H248Q T>G | 97 | 99 | no variants detected |
rs45606432 | L443P T>C | 97 | 100 | no variants detected | |
TFRC | rs3817672 | S142G A>G | 78 | 89 | too low analytical quality |
a rs numbers from NCBI SNP Database (website: http://www.ncbi.nlm.nih.gov/SNP).
b When applicable, amino acid position/gene region is denoted.
c QC percent represents the percentage of samples with clearly defined genotypes (based on Sequenom mass spectrometry analysis).
Supplemental Material, Table S3. SNP-related modification of transcription factor binding sites according to the ElDorado databasea. SNPs analyzed were associated with concentrations of Cd biomarkers or ferritin (see Result section of the main text).
Gene
SNP |
Allele | Effect | Site affected
Family/Factor |
Description |
TFRC | ||||
rs3804141 | G -> A | new | HOXC/HOX_PBX | HOX/PBX binding sites |
G -> A | new | SNAP/PSE02 | Proximal sequence element (PSE) of RNA polymerase III-transcribed genes | |
TF | ||||
rs12595 | A -> G | lost | FKHD/HNF3.01 | Hepatocyte nuclear factor 3 (alpha, beta) (FOXA1, FOXA2) |
A -> G | new | HOMF/HMX2.02 | Hmx2/Nkx5-2 homeodomain transcription factor | |
A -> G | new | MYT1/MYT1.01 | MyT1 zinc finger transcription factor involved in primary neurogenesis | |
rs3811647 | G -> A | new | NR2F/TR2.01 | Nuclear hormone receptor TR2, DR5 binding sites |
rs4459901 | T -> C | new | CREB/CREB.02 | cAMP-responsive element binding protein |
T -> C | new | CREB/ATF1.01 | Activating transcription factor 1 | |
T -> C | new | CREB/CREB1.01 | cAMP-responsive element binding protein 1 | |
T -> C | new | E4FF/E4F.01 | GLI-Krueppel-related transcription factor, regulator of adenovirus E4 promoter | |
T -> C | new | HIFF/HIF1.01 | Hypoxia induced factor-1 (HIF-1) | |
T -> C | lost | LHXF/ISL1.01 | Pancreatic and intestinal lim-homeodomain factor | |
T -> C | lost | PDX1/PDX1.01 | Pdx1 (IDX1/IPF1) pancreatic and intestinal homeodomain TF | |
T -> C | lost | RXRF/RAR_RXR.03 | Retinoic acid receptor / retinoid X receptor heterodimer, DR5 sites |
Supplemental Material, Table S3 (cont.)
Gene
SNP |
Allele | Effect | Site affected
Family/Factor |
Description |
rs8177186 | G -> T | new | CART/PHOX2.01 | Phox2a (ARIX) and Phox2b |
G -> T | new | CART/CART1.01 | Cart-1 (cartilage homeoprotein 1) | |
G -> T | new | PARF/DBP.01 | Albumin D-box binding protein | |
G -> T | lost | TEAF/TEAD.01 | TEA domain-containing factors, transcriptional enhancer factors 1,3,4,5 | |
TFR2 | ||||
rs7385804 | C -> A | new | BCDF/PCE1.01 | Photoreceptor conserved element 1 |
C -> A | new | DLXF/DLX3.01 | Distal-less 3 homeodomain transcription factor | |
C -> A | new | HBOX/GSH2.01 | Homeodomain transcription factor Gsh-2 | |
C -> A | new | HOMF/MSX2.01 | Muscle segment homeobox 2, homologue of Drosophila (HOX 8) | |
C -> A | new | NKXH/NKX25.02 | Homeodomain factor Nkx-2.5/Csx, tinman homolog low affinity sites | |
C -> A | new | OCT1/OCT1.06 | Octamer-binding factor 1 | |
C -> A | lost | SORY/HBP1.01 | HMG box-containing protein 1 | |
C -> A | lost | TEAF/TEAD.01 | TEA domain-containing factors, transcriptional enhancer factors 1,3,4,5 |
a Version 08-2011 of the Genomatix software suite (http://www.genomatix.de/en/index.html)
Supplemental Material, Table S4. Gene expression data for iron-related genes measured in peripheral blood in the Andean women (N=72).
Gene | Probe | Probe |
Expressiona |
Spearman correlation coefficients (p-values) |
|||||
location |
Median |
(Range) |
TFb |
TFR2b |
TFRCb |
SLC11A2b |
SLC40A1b |
||
TF | ILMN_1768425 | exon 17 |
112 |
(86-147) |
|
|
|
|
|
TFR2 | ILMN_1724738 | exon 18 |
111 |
(91-138) |
0.18 (0.1) |
|
|
|
|
TFRC | ILMN_1674243 | exon 19 |
294 |
(168-773) |
0.05 (0.7) |
-0.12 (0.3) |
|
|
|
SLC11A2 | ILMN_1745034 | exon 19b |
132 |
(101-201) |
-0.19 (0.1) |
-0.21 (0.08) |
0.32 (0.006) |
|
|
SLC40A1 | ILMN_1761833 | exon 8 |
255 |
(117-570) |
0.15 (0.2) |
0.09 (0.4) |
0.56 (3.8E-07) |
0.17 (0.2) |
|
SLC40A1 | ILMN_2053103 | exon 8 |
400 |
(184-1021) |
0.22 (0.06) |
0.11 (0.3) |
0.55 (7.33E-07) |
0.25 (0.03) |
0.92 (1.5E-29) |
a Gene expression is presented in relative fluorescence units.
b P-values are written in parentheses.
Association of Osteoarthritis with Perfluorooctanoate and Perfluorooctane Sulfonate in NHANES 2003–2008
Sarah A. Uhl1, Tamarra James-Todd2, and Michelle L. Bell1
Read MoreManaging the Health Effects of Temperature in Response to Climate Change: Challenges Ahead
Cunrui Huang,1,2,3 Adrian G Barnett,1 Zhiwei Xu,1 Cordia Chu,2,3 Xiaoming Wang,4 Lyle R Turner,1 and Shilu Tong1
Read MoreONE Nano: NIEHS’s Strategic Initiative on the Health and Safety Effects of Engineered Nanomaterials
Thaddeus T. Schug1, Anne F. Johnson2, David M. Balshaw3, Stavros Garantziotis4, Nigel J. Walker5, Christopher Weis6, Srikanth S. Nadadur 1,and Linda S. Birnbaum6
Read MoreMaternal Exposure to Particulate Air Pollution and Term Birth Weight: A Multi-Country Evaluation of Effect and Heterogeneity
Payam Dadvand,1,2,3 Jennifer Parker,4 Michelle L. Bell,5 Matteo Bonzini,6 Michael Brauer,7 Lyndsey Darrow,8 Ulrike Gehring,9 Svetlana V. Glinianaia,10 Nelson Gouveia,11 Eun-hee Ha,12 Jong Han Leem,13 Edith H. van den Hooven,14,15 Bin Jalaludin,16,17,18 Bill M. Jesdale,19 Johanna Lepeule,20,21,22 Rachel Morello-Frosch,19,23 Geoffrey G. Morgan,24,25 Angela Cecilia Pesatori,26 Frank H. Pierik,15 Tanja Pless-Mulloli,10 David Q. Rich,27 Sheela Sathyanarayana,28 Juhee Seo,12 Rémy Slama,21,22 Matthew Strickland,8 Lillian Tamburic,29 Daniel Wartenberg,30 Mark J Nieuwenhuijsen,1,2,3 Tracey J. Woodruff31
Read MorePerformance in Omics Analyses of Blood Samples in Long-Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research
Dennie G.A.J. Hebels1, Panagiotis Georgiadis2, Hector C. Keun3,4, Toby J. Athersuch3,4, Paolo Vineis3, Roel Vermeulen5, Lützen Portengen5, Ingvar A. Bergdahl6, Göran Hallmans7, Domenico Palli8, Benedetta Bendinelli8, Vittorio Krogh9, Rosario Tumino10, Carlotta Sacerdote11,12, Salvatore Panico13, Jos C.S. Kleinjans1, Theo M.C.M. de Kok1, Martyn T. Smith14, and Soterios A. Kyrtopoulos2
Read MoreArsenic Exposure from Drinking Water and QT-Interval Prolongation: Results from the Health Effects of Arsenic Longitudinal Study
Yu Chen1, Fen Wu1, Faruque Parvez2, Alauddin Ahmed3, Mahbub Eunus3, Tyler R. McClintock4, Tazul Islam Patwary3, Tariqul Islam3, Anajan Kumar Ghosal3, Shahidul Islam3, Rabiul Hasan3, Diane Levy2, Golam Sarwar3, Vesna Slavkovich2, Alexander van Geen5, Joseph H. Graziano2, and Habibul Ahsan6
Read MoreEndocrine-Disrupting Chemicals (EDCs): In Vitro Mechanism of Estrogenic Activation and Differential Effects on ER Target Genes
Yin Li1, Colin J. Luh1, Katherine A. Burns1, Yukitomo Arao1, Zhongliang Jiang1, Christina T. Teng2, Raymond R. Tice2, and Kenneth S. Korach1
Read MoreEnvironmental and Occupational Interventions for Primary Prevention of Cancer: A Cross-Sectorial Policy Framework
Carolina Espina1, Miquel Porta2, Joachim Schüz3, Ildefonso Hernández Aguado4, Robert V. Percival5, Carlos Dora1, Terry Slevin6, Julietta Rodriguez Guzman7, Tim Meredith1, Philip J. Landrigan8, Maria Neira1
Read MoreRecent Advance Publications
- Association of Osteoarthritis with Perfluorooctanoate and Perfluorooctane Sulfonate in NHANES 2003–2008
- Managing the Health Effects of Temperature in Response to Climate Change: Challenges Ahead
- ONE Nano: NIEHS’s Strategic Initiative on the Health and Safety Effects of Engineered Nanomaterials
- Maternal Exposure to Particulate Air Pollution and Term Birth Weight: A Multi-Country Evaluation of Effect and Heterogeneity
- Performance in Omics Analyses of Blood Samples in Long-Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research
- Arsenic Exposure from Drinking Water and QT-Interval Prolongation: Results from the Health Effects of Arsenic Longitudinal Study
- Endocrine-Disrupting Chemicals (EDCs): In Vitro Mechanism of Estrogenic Activation and Differential Effects on ER Target Genes