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417 results on '"Hudson, TJ"'

1. Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development.

Author: Smith, EN, Ghia, EM, DeBoever, CM, Rassenti, LZ, Jepsen, K, Yoon, K-A, Matsui, H, Rozenzhak, S, Alakus, H, Shepard, PJ, Dai, Y, Khosroheidari, M, Bina, M, Gunderson, KL, Messer, K, Muthuswamy, L, Hudson, TJ, Harismendy, O, Barrett, CL, Jamieson, CHM, Carson, DA, Kipps, TJ, and Frazer, KA
Subjects: Humans, Disease Progression, DNA Methylation, Epigenesis, Genetic, CpG Islands, Mutation, Leukemia, Lymphocytic, Chronic, B-Cell, Clonal Evolution, Polycomb-Group Proteins, Lymphoma, Human Genome, Rare Diseases, Cancer, Genetics, Hematology, 2.1 Biological and endogenous factors, Cardiorespiratory Medicine and Haematology, Oncology and Carcinogenesis
Abstract: We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.
Published: 2015

2. Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures

Author: Georgeson, P, Harrison, TA, Pope, BJ, Zaidi, SH, Qu, C, Steinfelder, RS, Lin, Y, Joo, JE, Mahmood, K, Clendenning, M, Walker, R, Amitay, EL, Berndt, S, Brenner, H, Campbell, PT, Cao, Y, Chan, AT, Chang-Claude, J, Doheny, KF, Drew, DA, Figueiredo, JC, French, AJ, Gallinger, S, Giannakis, M, Giles, GG, Gsur, A, Gunter, MJ, Hoffmeister, M, Hsu, L, Huang, W-Y, Limburg, P, Manson, JE, Moreno, V, Nassir, R, Nowak, JA, Obon-Santacana, M, Ogino, S, Phipps, A, Potter, JD, Schoen, RE, Sun, W, Toland, AE, Trinh, QM, Ugai, T, Macrae, FA, Rosty, C, Hudson, TJ, Jenkins, MA, Thibodeau, SN, Winship, IM, Peters, U, Buchanan, DD, Georgeson, P, Harrison, TA, Pope, BJ, Zaidi, SH, Qu, C, Steinfelder, RS, Lin, Y, Joo, JE, Mahmood, K, Clendenning, M, Walker, R, Amitay, EL, Berndt, S, Brenner, H, Campbell, PT, Cao, Y, Chan, AT, Chang-Claude, J, Doheny, KF, Drew, DA, Figueiredo, JC, French, AJ, Gallinger, S, Giannakis, M, Giles, GG, Gsur, A, Gunter, MJ, Hoffmeister, M, Hsu, L, Huang, W-Y, Limburg, P, Manson, JE, Moreno, V, Nassir, R, Nowak, JA, Obon-Santacana, M, Ogino, S, Phipps, A, Potter, JD, Schoen, RE, Sun, W, Toland, AE, Trinh, QM, Ugai, T, Macrae, FA, Rosty, C, Hudson, TJ, Jenkins, MA, Thibodeau, SN, Winship, IM, Peters, U, and Buchanan, DD
Abstract: Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk of colorectal cancer. We test 5649 colorectal cancers to evaluate the discriminatory potential of a tumor mutational signature specific to MUTYH for identifying biallelic carriers and classifying variants of uncertain clinical significance (VUS). Using a tumor and matched germline targeted multi-gene panel approach, our classifier identifies all biallelic MUTYH carriers and all known non-carriers in an independent test set of 3019 colorectal cancers (accuracy = 100% (95% confidence interval 99.87-100%)). All monoallelic MUTYH carriers are classified with the non-MUTYH carriers. The classifier provides evidence for a pathogenic classification for two VUS and a benign classification for five VUS. Somatic hotspot mutations KRAS p.G12C and PIK3CA p.Q546K are associated with colorectal cancers from biallelic MUTYH carriers compared with non-carriers (p = 2 × 10-23 and p = 6 × 10-11, respectively). Here, we demonstrate the potential application of mutational signatures to tumor sequencing workflows to improve the identification of biallelic MUTYH carriers.
Published: 2022

3. Association between germline variants and somatic mutations in colorectal cancer.

Author: Barfield, R, Qu, C, Steinfelder, RS, Zeng, C, Harrison, TA, Brezina, S, Buchanan, DD, Campbell, PT, Casey, G, Gallinger, S, Giannakis, M, Gruber, SB, Gsur, A, Hsu, L, Huyghe, JR, Moreno, V, Newcomb, PA, Ogino, S, Phipps, AI, Slattery, ML, Thibodeau, SN, Trinh, QM, Toland, AE, Hudson, TJ, Sun, W, Zaidi, SH, Peters, U, Barfield, R, Qu, C, Steinfelder, RS, Zeng, C, Harrison, TA, Brezina, S, Buchanan, DD, Campbell, PT, Casey, G, Gallinger, S, Giannakis, M, Gruber, SB, Gsur, A, Hsu, L, Huyghe, JR, Moreno, V, Newcomb, PA, Ogino, S, Phipps, AI, Slattery, ML, Thibodeau, SN, Trinh, QM, Toland, AE, Hudson, TJ, Sun, W, Zaidi, SH, and Peters, U
Abstract: Colorectal cancer (CRC) is a heterogeneous disease with evidence of distinct tumor types that develop through different somatically altered pathways. To better understand the impact of the host genome on somatically mutated genes and pathways, we assessed associations of germline variations with somatic events via two complementary approaches. We first analyzed the association between individual germline genetic variants and the presence of non-silent somatic mutations in genes in 1375 CRC cases with genome-wide SNPs data and a tumor sequencing panel targeting 205 genes. In the second analysis, we tested if germline variants located within previously identified regions of somatic allelic imbalance were associated with overall CRC risk using summary statistics from a recent large scale GWAS (n≃125 k CRC cases and controls). The first analysis revealed that a variant (rs78963230) located within a CNA region associated with TLR3 was also associated with a non-silent mutation within gene FBXW7. In the secondary analysis, the variant rs2302274 located in CDX1/PDGFRB frequently gained/lost in colorectal tumors was associated with overall CRC risk (OR = 0.96, p = 7.50e-7). In summary, we demonstrate that an integrative analysis of somatic and germline variation can lead to new insights about CRC.
Published: 2022

4. Genetic architectures of proximal and distal colorectal cancer are partly distinct

Author: Huyghe, JR, Harrison, TA, Bien, SA, Hampel, H, Figueiredo, JC, Schmit, SL, Conti, D, Chen, S, Qu, C, Lin, Y, Barfield, R, Baron, JA, Cross, AJ, Diergaarde, B, Duggan, D, Harlid, S, Imaz, L, Kang, HM, Levine, DM, Perduca, V, Perez-Cornago, A, Sakoda, LC, Schumacher, FR, Slattery, ML, Toland, AE, van Duijnhoven, FJB, Van Guelpen, B, Agudo, A, Albanes, D, Alonso, MH, Anderson, K, Arnau-Collell, C, Arndt, V, Banbury, BL, Bassik, MC, Berndt, S, Bezieau, S, Bishop, DT, Boehm, J, Boeing, H, Boutron-Ruault, M-C, Brenner, H, Brezina, S, Buch, S, Buchanan, DD, Burnett-Hartman, A, Caan, BJ, Campbell, PT, Carr, PR, Castells, A, Castellvi-Bel, S, Chan, AT, Chang-Claude, J, Chanock, SJ, Curtis, KR, de la Chapelle, A, Easton, DF, English, DR, Feskens, EJM, Gala, M, Gallinger, SJ, Gauderman, WJ, Giles, GG, Goodman, PJ, Grady, WM, Grove, JS, Gsur, A, Gunter, MJ, Haile, RW, Hampe, J, Hoffmeister, M, Hopper, JL, Hsu, W-L, Huang, W-Y, Hudson, TJ, Jenab, M, Jenkins, MA, Joshi, AD, Keku, TO, Kooperberg, C, Kuhn, T, Kury, S, Le Marchand, L, Lejbkowicz, F, Li, C, Li, L, Lieb, W, Lindblom, A, Lindor, NM, Mannisto, S, Markowitz, SD, Milne, RL, Moreno, L, Murphy, N, Nassir, R, Offit, K, Ogino, S, Panico, S, Parfrey, PS, Pearlman, R, Pharoah, PDP, Phipps, A, Platz, EA, Potter, JD, Prentice, RL, Qi, L, Raskin, L, Rennert, G, Rennert, HS, Riboli, E, Schafmayer, C, Schoen, RE, Seminara, D, Song, M, Su, Y-R, Tangen, CM, Thibodeau, SN, Thomas, DC, Trichopoulou, A, Ulrich, CM, Visvanathan, K, Vodicka, P, Vodickova, L, Vymetalkova, V, Weigl, K, Weinstein, SJ, White, E, Wolk, A, Woods, MO, Wu, AH, Abecasis, GR, Nickerson, DA, Scacheri, PC, Kundaje, A, Casey, G, Gruber, SB, Hsu, L, Moreno, V, Hayes, RB, Newcomb, PA, Peters, U, Huyghe, JR, Harrison, TA, Bien, SA, Hampel, H, Figueiredo, JC, Schmit, SL, Conti, D, Chen, S, Qu, C, Lin, Y, Barfield, R, Baron, JA, Cross, AJ, Diergaarde, B, Duggan, D, Harlid, S, Imaz, L, Kang, HM, Levine, DM, Perduca, V, Perez-Cornago, A, Sakoda, LC, Schumacher, FR, Slattery, ML, Toland, AE, van Duijnhoven, FJB, Van Guelpen, B, Agudo, A, Albanes, D, Alonso, MH, Anderson, K, Arnau-Collell, C, Arndt, V, Banbury, BL, Bassik, MC, Berndt, S, Bezieau, S, Bishop, DT, Boehm, J, Boeing, H, Boutron-Ruault, M-C, Brenner, H, Brezina, S, Buch, S, Buchanan, DD, Burnett-Hartman, A, Caan, BJ, Campbell, PT, Carr, PR, Castells, A, Castellvi-Bel, S, Chan, AT, Chang-Claude, J, Chanock, SJ, Curtis, KR, de la Chapelle, A, Easton, DF, English, DR, Feskens, EJM, Gala, M, Gallinger, SJ, Gauderman, WJ, Giles, GG, Goodman, PJ, Grady, WM, Grove, JS, Gsur, A, Gunter, MJ, Haile, RW, Hampe, J, Hoffmeister, M, Hopper, JL, Hsu, W-L, Huang, W-Y, Hudson, TJ, Jenab, M, Jenkins, MA, Joshi, AD, Keku, TO, Kooperberg, C, Kuhn, T, Kury, S, Le Marchand, L, Lejbkowicz, F, Li, C, Li, L, Lieb, W, Lindblom, A, Lindor, NM, Mannisto, S, Markowitz, SD, Milne, RL, Moreno, L, Murphy, N, Nassir, R, Offit, K, Ogino, S, Panico, S, Parfrey, PS, Pearlman, R, Pharoah, PDP, Phipps, A, Platz, EA, Potter, JD, Prentice, RL, Qi, L, Raskin, L, Rennert, G, Rennert, HS, Riboli, E, Schafmayer, C, Schoen, RE, Seminara, D, Song, M, Su, Y-R, Tangen, CM, Thibodeau, SN, Thomas, DC, Trichopoulou, A, Ulrich, CM, Visvanathan, K, Vodicka, P, Vodickova, L, Vymetalkova, V, Weigl, K, Weinstein, SJ, White, E, Wolk, A, Woods, MO, Wu, AH, Abecasis, GR, Nickerson, DA, Scacheri, PC, Kundaje, A, Casey, G, Gruber, SB, Hsu, L, Moreno, V, Hayes, RB, Newcomb, PA, and Peters, U
Abstract: OBJECTIVE: An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined. DESIGN: To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling. RESULTS: We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer. CONCLUSION: Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.
Published: 2021

5. Cumulative Burden of Colorectal Cancer Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer

Author: Archambault, AN, Su, Y-R, Jeon, J, Thomas, M, Lin, Y, Conti, DV, Win, AK, Sakoda, LC, Lansdorp-Vogelaar, I, Peterse, EFP, Zauber, AG, Duggan, D, Holowatyj, AN, Huyghe, JR, Brenner, H, Cotterchio, M, Bezieau, S, Schmit, SL, Edlund, CK, Southey, MC, MacInnis, RJ, Campbell, PT, Chang-Claude, J, Slattery, ML, Chan, AT, Joshi, AD, Song, M, Cao, Y, Woods, MO, White, E, Weinstein, SJ, Ulrich, CM, Hoffmeister, M, Bien, SA, Harrison, TA, Hampe, J, Li, CI, Schafmayer, C, Offit, K, Pharoah, PD, Moreno, V, Lindblom, A, Wolk, A, Wu, AH, Li, L, Gunter, MJ, Gsur, A, Keku, TO, Pearlman, R, Bishop, DT, Castellvi-Bel, S, Moreira, L, Vodicka, P, Kampman, E, Giles, GG, Albanes, D, Baron, JA, Berndt, SI, Brezina, S, Buch, S, Buchanan, DD, Trichopoulou, A, Severi, G, Chirlaque, M-D, Sanchez, M-J, Palli, D, Kuhn, T, Murphy, N, Cross, AJ, Burnett-Hartman, AN, Chanock, SJ, de la Chapelle, A, Easton, DF, Elliott, F, English, DR, Feskens, EJM, FitzGerald, LM, Goodman, PJ, Hopper, JL, Hudson, TJ, Hunter, DJ, Jacobs, EJ, Joshu, CE, Kury, S, Markowitz, SD, Milne, RL, Platz, EA, Rennert, G, Rennert, HS, Schumacher, FR, Sandler, RS, Seminara, D, Tangen, CM, Thibodeau, SN, Toland, AE, van Duijnhoven, FJB, Visvanathan, K, Vodickova, L, Potter, JD, Mannisto, S, Weigl, K, Figueiredo, J, Martin, V, Larsson, SC, Parfrey, PS, Huang, W-Y, Lenz, H-J, Castelao, JE, Gago-Dominguez, M, Munoz-Garzon, V, Mancao, C, Haiman, CA, Wilkens, LR, Siegel, E, Barry, E, Younghusband, B, Van Guelpen, B, Harlid, S, Zeleniuch-Jacquotte, A, Liang, PS, Du, M, Casey, G, Lindor, NM, Le Marchand, L, Gallinger, SJ, Jenkins, MA, Newcomb, PA, Gruber, SB, Schoen, RE, Hampel, H, Corley, DA, Hsu, L, Peters, U, Hayes, RB, Archambault, AN, Su, Y-R, Jeon, J, Thomas, M, Lin, Y, Conti, DV, Win, AK, Sakoda, LC, Lansdorp-Vogelaar, I, Peterse, EFP, Zauber, AG, Duggan, D, Holowatyj, AN, Huyghe, JR, Brenner, H, Cotterchio, M, Bezieau, S, Schmit, SL, Edlund, CK, Southey, MC, MacInnis, RJ, Campbell, PT, Chang-Claude, J, Slattery, ML, Chan, AT, Joshi, AD, Song, M, Cao, Y, Woods, MO, White, E, Weinstein, SJ, Ulrich, CM, Hoffmeister, M, Bien, SA, Harrison, TA, Hampe, J, Li, CI, Schafmayer, C, Offit, K, Pharoah, PD, Moreno, V, Lindblom, A, Wolk, A, Wu, AH, Li, L, Gunter, MJ, Gsur, A, Keku, TO, Pearlman, R, Bishop, DT, Castellvi-Bel, S, Moreira, L, Vodicka, P, Kampman, E, Giles, GG, Albanes, D, Baron, JA, Berndt, SI, Brezina, S, Buch, S, Buchanan, DD, Trichopoulou, A, Severi, G, Chirlaque, M-D, Sanchez, M-J, Palli, D, Kuhn, T, Murphy, N, Cross, AJ, Burnett-Hartman, AN, Chanock, SJ, de la Chapelle, A, Easton, DF, Elliott, F, English, DR, Feskens, EJM, FitzGerald, LM, Goodman, PJ, Hopper, JL, Hudson, TJ, Hunter, DJ, Jacobs, EJ, Joshu, CE, Kury, S, Markowitz, SD, Milne, RL, Platz, EA, Rennert, G, Rennert, HS, Schumacher, FR, Sandler, RS, Seminara, D, Tangen, CM, Thibodeau, SN, Toland, AE, van Duijnhoven, FJB, Visvanathan, K, Vodickova, L, Potter, JD, Mannisto, S, Weigl, K, Figueiredo, J, Martin, V, Larsson, SC, Parfrey, PS, Huang, W-Y, Lenz, H-J, Castelao, JE, Gago-Dominguez, M, Munoz-Garzon, V, Mancao, C, Haiman, CA, Wilkens, LR, Siegel, E, Barry, E, Younghusband, B, Van Guelpen, B, Harlid, S, Zeleniuch-Jacquotte, A, Liang, PS, Du, M, Casey, G, Lindor, NM, Le Marchand, L, Gallinger, SJ, Jenkins, MA, Newcomb, PA, Gruber, SB, Schoen, RE, Hampel, H, Corley, DA, Hsu, L, Peters, U, and Hayes, RB
Abstract: BACKGROUND & AIMS: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. METHODS: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. RESULTS: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28-4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80-3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10-5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61-5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70-3.00). Sensitivity analyses were consistent with these findings. CONCLUSIONS: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be mo
Published: 2020

6. Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival

Author: Zaidi, SH, Harrison, TA, Phipps, A, Steinfelder, R, Trinh, QM, Qu, C, Banbury, BL, Georgeson, P, Grasso, CS, Giannakis, M, Adams, JB, Alwers, E, Amitay, EL, Barfield, RT, Berndt, S, Borozan, I, Brenner, H, Brezina, S, Buchanan, DD, Cao, Y, Chan, AT, Chang-Claude, J, Connolly, CM, Drew, DA, Farris, AB, Figueiredo, JC, French, AJ, Fuchs, CS, Garraway, LA, Gruber, S, Guinter, MA, Hamilton, SR, Harlid, S, Heisler, LE, Hidaka, A, Hopper, JL, Huang, W-Y, Huyghe, JR, Jenkins, MA, Krzyzanowski, PM, Lemire, M, Lin, Y, Luo, X, Mardis, ER, McPherson, JD, Miller, JK, Moreno, V, Mu, XJ, Nishihara, R, Papadopoulos, N, Pasternack, D, Quist, MJ, Rafikova, A, Reid, EEG, Shinbrot, E, Shirts, BH, Stein, LD, Teney, CD, Timms, L, Um, CY, Van Guelpen, B, Van Tassel, M, Wang, X, Wheeler, DA, Yung, CK, Hsu, L, Ogino, S, Gsur, A, Newcomb, PA, Gallinger, S, Hoffmeister, M, Campbell, PT, Thibodeau, SN, Sun, W, Hudson, TJ, Peters, U, Zaidi, SH, Harrison, TA, Phipps, A, Steinfelder, R, Trinh, QM, Qu, C, Banbury, BL, Georgeson, P, Grasso, CS, Giannakis, M, Adams, JB, Alwers, E, Amitay, EL, Barfield, RT, Berndt, S, Borozan, I, Brenner, H, Brezina, S, Buchanan, DD, Cao, Y, Chan, AT, Chang-Claude, J, Connolly, CM, Drew, DA, Farris, AB, Figueiredo, JC, French, AJ, Fuchs, CS, Garraway, LA, Gruber, S, Guinter, MA, Hamilton, SR, Harlid, S, Heisler, LE, Hidaka, A, Hopper, JL, Huang, W-Y, Huyghe, JR, Jenkins, MA, Krzyzanowski, PM, Lemire, M, Lin, Y, Luo, X, Mardis, ER, McPherson, JD, Miller, JK, Moreno, V, Mu, XJ, Nishihara, R, Papadopoulos, N, Pasternack, D, Quist, MJ, Rafikova, A, Reid, EEG, Shinbrot, E, Shirts, BH, Stein, LD, Teney, CD, Timms, L, Um, CY, Van Guelpen, B, Van Tassel, M, Wang, X, Wheeler, DA, Yung, CK, Hsu, L, Ogino, S, Gsur, A, Newcomb, PA, Gallinger, S, Hoffmeister, M, Campbell, PT, Thibodeau, SN, Sun, W, Hudson, TJ, and Peters, U
Abstract: Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR = 0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR = 1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features.
Published: 2020

7. Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer (vol 138, pg 307, 2019)

Author: Bien, SA, Su, Y-R, Conti, DV, Harrison, TA, Qu, C, Guo, X, Lu, Y, Albanes, D, Auer, PL, Banbury, BL, Berndt, SI, Bezieau, S, Brenner, H, Buchanan, DD, Caan, BJ, Campbell, PT, Carlson, CS, Chan, AT, Chang-Claude, J, Chen, S, Connolly, CM, Easton, DF, Feskens, EJM, Gallinger, S, Giles, GG, Gunter, MJ, Hampe, J, Huyghe, JR, Hoffmeister, M, Hudson, TJ, Jacobs, EJ, Jenkins, MA, Kampman, E, Kang, HM, Kuehn, T, Kury, S, Lejbkowicz, F, Le Marchand, L, Milne, RL, Li, L, Li, CI, Lindblom, A, Lindor, NM, Martin, V, McNeil, CE, Melas, M, Moreno, V, Newcomb, PA, Offit, K, Pharaoh, PDP, Potter, JD, Riboli, E, Rennert, G, Sala, N, Schafmayer, C, Scacheri, PC, Schmit, SL, Severi, G, Slattery, ML, Smith, JD, Trichopoulou, A, Tumino, R, Ulrich, CM, van Duijnhoven, FJB, Van Guelpen, B, Weinstein, SJ, White, E, Wolk, A, Woods, MO, Wu, AH, Abecasis, GR, Casey, G, Nickerson, DA, Gruber, SB, Hsu, L, Zheng, W, Peters, U, Bien, SA, Su, Y-R, Conti, DV, Harrison, TA, Qu, C, Guo, X, Lu, Y, Albanes, D, Auer, PL, Banbury, BL, Berndt, SI, Bezieau, S, Brenner, H, Buchanan, DD, Caan, BJ, Campbell, PT, Carlson, CS, Chan, AT, Chang-Claude, J, Chen, S, Connolly, CM, Easton, DF, Feskens, EJM, Gallinger, S, Giles, GG, Gunter, MJ, Hampe, J, Huyghe, JR, Hoffmeister, M, Hudson, TJ, Jacobs, EJ, Jenkins, MA, Kampman, E, Kang, HM, Kuehn, T, Kury, S, Lejbkowicz, F, Le Marchand, L, Milne, RL, Li, L, Li, CI, Lindblom, A, Lindor, NM, Martin, V, McNeil, CE, Melas, M, Moreno, V, Newcomb, PA, Offit, K, Pharaoh, PDP, Potter, JD, Riboli, E, Rennert, G, Sala, N, Schafmayer, C, Scacheri, PC, Schmit, SL, Severi, G, Slattery, ML, Smith, JD, Trichopoulou, A, Tumino, R, Ulrich, CM, van Duijnhoven, FJB, Van Guelpen, B, Weinstein, SJ, White, E, Wolk, A, Woods, MO, Wu, AH, Abecasis, GR, Casey, G, Nickerson, DA, Gruber, SB, Hsu, L, Zheng, W, and Peters, U
Abstract: Every author has erroneously been assigned to the affiliation "62". The affiliation 62 belongs to the author Graham Casey.
Published: 2019

8. Novel Common Genetic Susceptibility Loci for Colorectal Cancer

Author: Schmit, SL, Edlund, CK, Schumacher, FR, Gong, J, Harrison, TA, Huyghe, JR, Qu, C, Melas, M, Van den Berg, DJ, Wang, H, Tring, S, Plummer, SJ, Albanes, D, Alonso, MH, Amos, CI, Anton, K, Aragaki, AK, Arndt, V, Barry, EL, Berndt, SI, Bezieau, S, Bien, S, Bloomer, A, Boehm, J, Boutron-Ruault, M-C, Brenner, H, Brezina, S, Buchanan, DD, Butterbach, K, Caan, BJ, Campbell, PT, Carlson, CS, Castelao, JE, Chan, AT, Chang-Claude, J, Chanock, SJ, Cheng, I, Cheng, Y-W, Chin, LS, Church, JM, Church, T, Coetzee, GA, Cotterchio, M, Correa, MC, Curtis, KR, Duggan, D, Easton, DF, English, D, Feskens, EJM, Fischer, R, FitzGerald, LM, Fortini, BK, Fritsche, LG, Fuchs, CS, Gago-Dominguez, M, Gala, M, Gallinger, SJ, Gauderman, WJ, Giles, GG, Giovannucci, EL, Gogarten, SM, Gonzalez-Villalpando, C, Gonzalez-Villalpando, EM, Grady, WM, Greenson, JK, Gsur, A, Gunter, M, Haiman, CA, Hampe, J, Harlid, S, Harju, JF, Hayes, RB, Hofer, P, Hoffmeister, M, Hopper, JL, Huang, S-C, Huerta, JM, Hudson, TJ, Hunter, DJ, Idos, GE, Iwasaki, M, Jackson, RD, Jacobs, EJ, Jee, SH, Jenkins, MA, Jia, W-H, Jiao, S, Joshi, AD, Kolonel, LN, Kono, S, Kooperberg, C, Krogh, V, Kuehn, T, Kury, S, LaCroix, A, Laurie, CA, Lejbkowicz, F, Lemire, M, Lenz, H-J, Levine, D, Li, CI, Li, L, Lieb, W, Lin, Y, Lindor, NM, Liu, Y-R, Loupakis, F, Lu, Y, Luh, F, Ma, J, Mancao, C, Manion, FJ, Markowitz, SD, Martin, V, Matsuda, K, Matsuo, K, McDonnell, KJ, McNeil, CE, Milne, R, Molina, AJ, Mukherjee, B, Murphy, N, Newcomb, PA, Offit, K, Omichessan, H, Palli, D, Cotore, JPP, Perez-Mayoral, J, Pharoah, PD, Potter, JD, Raskin, L, Rennert, G, Rennert, HS, Riggs, BM, Schafmayer, C, Schoen, RE, Sellers, TA, Seminara, D, Severi, G, Shi, W, Shibata, D, Shu, X-O, Siegel, EM, Slattery, ML, Southey, M, Stadler, ZK, Stern, MC, Stintzing, S, Taverna, D, Thibodeau, SN, Thomas, DC, Trichopoulou, A, Tsugane, S, Ulrich, CM, van Duijnhoven, FJB, van Guelpan, B, Vijai, J, Virtamo, J, Weinstein, SJ, White, E, Win, AK, Wolk, A, Woods, M, Wu, AH, Wu, K, Xiang, Y-B, Yen, Y, Zanke, BW, Zeng, Y-X, Zhang, B, Zubair, N, Kweon, S-S, Figueiredo, JC, Zheng, W, Le Marchand, L, Lindblom, A, Moreno, V, Peters, U, Casey, G, Hsu, L, Conti, DV, Gruber, SB, Schmit, SL, Edlund, CK, Schumacher, FR, Gong, J, Harrison, TA, Huyghe, JR, Qu, C, Melas, M, Van den Berg, DJ, Wang, H, Tring, S, Plummer, SJ, Albanes, D, Alonso, MH, Amos, CI, Anton, K, Aragaki, AK, Arndt, V, Barry, EL, Berndt, SI, Bezieau, S, Bien, S, Bloomer, A, Boehm, J, Boutron-Ruault, M-C, Brenner, H, Brezina, S, Buchanan, DD, Butterbach, K, Caan, BJ, Campbell, PT, Carlson, CS, Castelao, JE, Chan, AT, Chang-Claude, J, Chanock, SJ, Cheng, I, Cheng, Y-W, Chin, LS, Church, JM, Church, T, Coetzee, GA, Cotterchio, M, Correa, MC, Curtis, KR, Duggan, D, Easton, DF, English, D, Feskens, EJM, Fischer, R, FitzGerald, LM, Fortini, BK, Fritsche, LG, Fuchs, CS, Gago-Dominguez, M, Gala, M, Gallinger, SJ, Gauderman, WJ, Giles, GG, Giovannucci, EL, Gogarten, SM, Gonzalez-Villalpando, C, Gonzalez-Villalpando, EM, Grady, WM, Greenson, JK, Gsur, A, Gunter, M, Haiman, CA, Hampe, J, Harlid, S, Harju, JF, Hayes, RB, Hofer, P, Hoffmeister, M, Hopper, JL, Huang, S-C, Huerta, JM, Hudson, TJ, Hunter, DJ, Idos, GE, Iwasaki, M, Jackson, RD, Jacobs, EJ, Jee, SH, Jenkins, MA, Jia, W-H, Jiao, S, Joshi, AD, Kolonel, LN, Kono, S, Kooperberg, C, Krogh, V, Kuehn, T, Kury, S, LaCroix, A, Laurie, CA, Lejbkowicz, F, Lemire, M, Lenz, H-J, Levine, D, Li, CI, Li, L, Lieb, W, Lin, Y, Lindor, NM, Liu, Y-R, Loupakis, F, Lu, Y, Luh, F, Ma, J, Mancao, C, Manion, FJ, Markowitz, SD, Martin, V, Matsuda, K, Matsuo, K, McDonnell, KJ, McNeil, CE, Milne, R, Molina, AJ, Mukherjee, B, Murphy, N, Newcomb, PA, Offit, K, Omichessan, H, Palli, D, Cotore, JPP, Perez-Mayoral, J, Pharoah, PD, Potter, JD, Raskin, L, Rennert, G, Rennert, HS, Riggs, BM, Schafmayer, C, Schoen, RE, Sellers, TA, Seminara, D, Severi, G, Shi, W, Shibata, D, Shu, X-O, Siegel, EM, Slattery, ML, Southey, M, Stadler, ZK, Stern, MC, Stintzing, S, Taverna, D, Thibodeau, SN, Thomas, DC, Trichopoulou, A, Tsugane, S, Ulrich, CM, van Duijnhoven, FJB, van Guelpan, B, Vijai, J, Virtamo, J, Weinstein, SJ, White, E, Win, AK, Wolk, A, Woods, M, Wu, AH, Wu, K, Xiang, Y-B, Yen, Y, Zanke, BW, Zeng, Y-X, Zhang, B, Zubair, N, Kweon, S-S, Figueiredo, JC, Zheng, W, Le Marchand, L, Lindblom, A, Moreno, V, Peters, U, Casey, G, Hsu, L, Conti, DV, and Gruber, SB
Abstract: BACKGROUND: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk. METHODS: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided. RESULTS: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0. CONCLUSIONS: T
Published: 2019

9. Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer

Author: Bien, SA, Su, Y-R, Conti, DV, Harrison, TA, Qu, C, Guo, X, Lu, Y, Albanes, D, Auer, PL, Banbury, BL, Berndt, SI, Bezieau, S, Brenner, H, Buchanan, DD, Caan, BJ, Campbell, PT, Carlson, CS, Chan, AT, Chang-Claude, J, Chen, S, Connolly, CM, Easton, DF, Feskens, EJM, Gallinger, S, Giles, GG, Gunter, MJ, Hampe, J, Huyghe, JR, Hoffmeister, M, Hudson, TJ, Jacobs, EJ, Jenkins, MA, Kampman, E, Kang, HM, Kuehn, T, Kury, S, Lejbkowicz, F, Le Marchand, L, Milne, RL, Li, L, Li, CI, Lindblom, A, Lindor, NM, Martin, V, McNeil, CE, Melas, M, Moreno, V, Newcomb, PA, Offit, K, Pharaoh, PDP, Potter, JD, Riboli, E, Rennert, G, Sala, N, Schafmayer, C, Scacheri, PC, Schmit, SL, Severi, G, Slattery, ML, Smith, JD, Trichopoulou, A, Tumino, R, Ulrich, CM, van Duijnhoven, FJB, Van Guelpen, B, Weinstein, SJ, White, E, Wolk, A, Woods, MO, Wu, AH, Abecasis, GR, Casey, G, Nickerson, DA, Gruber, SB, Hsu, L, Zheng, W, Peters, U, Bien, SA, Su, Y-R, Conti, DV, Harrison, TA, Qu, C, Guo, X, Lu, Y, Albanes, D, Auer, PL, Banbury, BL, Berndt, SI, Bezieau, S, Brenner, H, Buchanan, DD, Caan, BJ, Campbell, PT, Carlson, CS, Chan, AT, Chang-Claude, J, Chen, S, Connolly, CM, Easton, DF, Feskens, EJM, Gallinger, S, Giles, GG, Gunter, MJ, Hampe, J, Huyghe, JR, Hoffmeister, M, Hudson, TJ, Jacobs, EJ, Jenkins, MA, Kampman, E, Kang, HM, Kuehn, T, Kury, S, Lejbkowicz, F, Le Marchand, L, Milne, RL, Li, L, Li, CI, Lindblom, A, Lindor, NM, Martin, V, McNeil, CE, Melas, M, Moreno, V, Newcomb, PA, Offit, K, Pharaoh, PDP, Potter, JD, Riboli, E, Rennert, G, Sala, N, Schafmayer, C, Scacheri, PC, Schmit, SL, Severi, G, Slattery, ML, Smith, JD, Trichopoulou, A, Tumino, R, Ulrich, CM, van Duijnhoven, FJB, Van Guelpen, B, Weinstein, SJ, White, E, Wolk, A, Woods, MO, Wu, AH, Abecasis, GR, Casey, G, Nickerson, DA, Gruber, SB, Hsu, L, Zheng, W, and Peters, U
Abstract: Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10- 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10- 4, replication P = 6.7 × 10- 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight in
Published: 2019

10. Discovery of common and rare genetic risk variants for colorectal cancer

Author: Huyghe, JR, Bien, SA, Harrison, TA, Kang, HM, Chen, S, Schmit, SL, Conti, DV, Qu, C, Jeon, J, Edlund, CK, Greenside, P, Wainberg, M, Schumacher, FR, Smith, JD, Levine, DM, Nelson, SC, Sinnott-Armstrong, NA, Albanes, D, Alonso, MH, Anderson, K, Arnau-Collell, C, Arndt, V, Bamia, C, Banbury, BL, Baron, JA, Berndt, SI, Bezieau, S, Bishop, DT, Boehm, J, Boeing, H, Brenner, H, Brezina, S, Buch, S, Buchanan, DD, Burnett-Hartman, A, Butterbach, K, Caan, BJ, Campbell, PT, Carlson, CS, Castellvi-Bel, S, Chan, AT, Chang-Claude, J, Chanock, SJ, Chirlaque, M-D, Cho, SH, Connolly, CM, Cross, AJ, Cuk, K, Curtis, KR, de la Chapelle, A, Doheny, KF, Duggan, D, Easton, DF, Elias, SG, Elliott, F, English, DR, Feskens, EJM, Figueiredo, JC, Fischer, R, FitzGerald, LM, Forman, D, Gala, M, Gallinger, S, Gauderman, WJ, Giles, GG, Gillanders, E, Gong, J, Goodman, PJ, Grady, WM, Grove, JS, Gsur, A, Gunter, MJ, Haile, RW, Hampe, J, Hampel, H, Harlid, S, Hayes, RB, Hofer, P, Hoffmeister, M, Hopper, JL, Hsu, W-L, Huang, W-Y, Hudson, TJ, Hunter, DJ, Ibanez-Sanz, G, Idos, GE, Ingersoll, R, Jackson, RD, Jacobs, EJ, Jenkins, MA, Joshi, AD, Joshu, CE, Keku, TO, Key, TJ, Kim, HR, Kobayashi, E, Kolonel, LN, Kooperberg, C, Kuehn, T, Kury, S, Kweon, S-S, Larsson, SC, Laurie, CA, Le Marchand, L, Leal, SM, Lee, SC, Lejbkowicz, F, Lemire, M, Li, CI, Li, L, Lieb, W, Lin, Y, Lindblom, A, Lindor, NM, Ling, H, Louie, TL, Mannisto, S, Markowitz, SD, Martin, V, Masala, G, McNeil, CE, Melas, M, Milne, RL, Moreno, L, Murphy, N, Myte, R, Naccarati, A, Newcomb, PA, Offit, K, Ogino, S, Onland-Moret, NC, Pardini, B, Parfrey, PS, Pearlman, R, Perduca, V, Pharoah, PDP, Pinchev, M, Platz, EA, Prentice, RL, Pugh, E, Raskin, L, Rennert, G, Rennert, HS, Riboli, E, Rodriguez-Barranco, M, Romm, J, Sakoda, LC, Schafmayer, C, Schoen, RE, Seminara, D, Shah, M, Shelford, T, Shin, M-H, Shulman, K, Sieri, S, Slattery, ML, Southey, MC, Stadler, ZK, Stegmaier, C, Su, Y-R, Tangen, CM, Thibodeau, SN, Thomas, DC, Thomas, SS, Toland, AE, Trichopoulou, A, Ulrich, CM, Van den Berg, DJ, van Duijnhoven, FJB, Van Guelpen, B, van Kranen, H, Vijai, J, Visvanathan, K, Vodicka, P, Vodickova, L, Vymetalkova, V, Weigl, K, Weinstein, SJ, White, E, Win, AK, Wolf, CR, Wolk, A, Woods, MO, Wu, AH, Zaidi, SH, Zanke, BW, Zhang, Q, Zheng, W, Scacheri, PC, Potter, JD, Bassik, MC, Kundaje, A, Casey, G, Moreno, V, Abecasis, GR, Nickerson, DA, Gruber, SB, Hsu, L, Peters, U, Huyghe, JR, Bien, SA, Harrison, TA, Kang, HM, Chen, S, Schmit, SL, Conti, DV, Qu, C, Jeon, J, Edlund, CK, Greenside, P, Wainberg, M, Schumacher, FR, Smith, JD, Levine, DM, Nelson, SC, Sinnott-Armstrong, NA, Albanes, D, Alonso, MH, Anderson, K, Arnau-Collell, C, Arndt, V, Bamia, C, Banbury, BL, Baron, JA, Berndt, SI, Bezieau, S, Bishop, DT, Boehm, J, Boeing, H, Brenner, H, Brezina, S, Buch, S, Buchanan, DD, Burnett-Hartman, A, Butterbach, K, Caan, BJ, Campbell, PT, Carlson, CS, Castellvi-Bel, S, Chan, AT, Chang-Claude, J, Chanock, SJ, Chirlaque, M-D, Cho, SH, Connolly, CM, Cross, AJ, Cuk, K, Curtis, KR, de la Chapelle, A, Doheny, KF, Duggan, D, Easton, DF, Elias, SG, Elliott, F, English, DR, Feskens, EJM, Figueiredo, JC, Fischer, R, FitzGerald, LM, Forman, D, Gala, M, Gallinger, S, Gauderman, WJ, Giles, GG, Gillanders, E, Gong, J, Goodman, PJ, Grady, WM, Grove, JS, Gsur, A, Gunter, MJ, Haile, RW, Hampe, J, Hampel, H, Harlid, S, Hayes, RB, Hofer, P, Hoffmeister, M, Hopper, JL, Hsu, W-L, Huang, W-Y, Hudson, TJ, Hunter, DJ, Ibanez-Sanz, G, Idos, GE, Ingersoll, R, Jackson, RD, Jacobs, EJ, Jenkins, MA, Joshi, AD, Joshu, CE, Keku, TO, Key, TJ, Kim, HR, Kobayashi, E, Kolonel, LN, Kooperberg, C, Kuehn, T, Kury, S, Kweon, S-S, Larsson, SC, Laurie, CA, Le Marchand, L, Leal, SM, Lee, SC, Lejbkowicz, F, Lemire, M, Li, CI, Li, L, Lieb, W, Lin, Y, Lindblom, A, Lindor, NM, Ling, H, Louie, TL, Mannisto, S, Markowitz, SD, Martin, V, Masala, G, McNeil, CE, Melas, M, Milne, RL, Moreno, L, Murphy, N, Myte, R, Naccarati, A, Newcomb, PA, Offit, K, Ogino, S, Onland-Moret, NC, Pardini, B, Parfrey, PS, Pearlman, R, Perduca, V, Pharoah, PDP, Pinchev, M, Platz, EA, Prentice, RL, Pugh, E, Raskin, L, Rennert, G, Rennert, HS, Riboli, E, Rodriguez-Barranco, M, Romm, J, Sakoda, LC, Schafmayer, C, Schoen, RE, Seminara, D, Shah, M, Shelford, T, Shin, M-H, Shulman, K, Sieri, S, Slattery, ML, Southey, MC, Stadler, ZK, Stegmaier, C, Su, Y-R, Tangen, CM, Thibodeau, SN, Thomas, DC, Thomas, SS, Toland, AE, Trichopoulou, A, Ulrich, CM, Van den Berg, DJ, van Duijnhoven, FJB, Van Guelpen, B, van Kranen, H, Vijai, J, Visvanathan, K, Vodicka, P, Vodickova, L, Vymetalkova, V, Weigl, K, Weinstein, SJ, White, E, Win, AK, Wolf, CR, Wolk, A, Woods, MO, Wu, AH, Zaidi, SH, Zanke, BW, Zhang, Q, Zheng, W, Scacheri, PC, Potter, JD, Bassik, MC, Kundaje, A, Casey, G, Moreno, V, Abecasis, GR, Nickerson, DA, Gruber, SB, Hsu, L, and Peters, U
Abstract: To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
Published: 2019

11. ABCA1 regulatory variants influence coronary artery disease independent of effects on plasma lipid levels

Author: Zwarts, KY, Clee, SM, Zwinderman, AH, Engert, JC, Singaraja, R, Loubser, O, James, E, Roomp, K, Hudson, TJ, Jukema, JW, Kastelein, JJP, and Hayden, MR
Published: 2002

12. Large-scale candidate gene association studies of type 2 diabetes

Author: Hirschhom, JN, Altshuler, D, Lindgren, CM, Klannemark, M, Daly, M, Vohl, MC, Nemesh, J, Lane, C, Bolk, S, Hudson, TJ, Groop, L, and Lander, ES
Published: 2016

13. A second generation human haplotype map of over 3.1 million SNPs

Author: Frazer, KA, Ballinger, DG, Cox, DR, Hinds, DA, Stuve, LL, Gibbs, RA, Belmont, JW, Boudreau, A, Hardenbol, P, Leal, SM, Pasternak, S, Wheeler, DA, Willis, TD, Yu, F, Yang, H, Zeng, C, Gao, Y, Hu, H, Hu, W, Li, C, Lin, W, Liu, S, Pan, H, Tang, X, Wang, J, Wang, W, Yu, J, Zhang, B, Zhang, Q, Zhao, H, Zhou, J, Gabriel, SB, Barry, R, Blumenstiel, B, Camargo, A, Defelice, M, Faggart, M, Goyette, M, Gupta, S, Moore, J, Nguyen, H, Onofrio, RC, Parkin, M, Roy, J, Stahl, E, Winchester, E, Ziaugra, L, Altshuler, D, Shen, Y, Yao, Z, Huang, W, Chu, X, He, Y, Jin, L, Liu, Y, Sun, W, Wang, H, Wang, Y, Xiong, X, Xu, L, Waye, MM, Tsui, SK, Xue, H, Wong, JT, Galver, LM, Fan, JB, Gunderson, K, Murray, SS, Oliphant, AR, Chee, MS, Montpetit, A, Chagnon, F, Ferretti, V, Leboeuf, M, Olivier, JF, Phillips, MS, Roumy, S, Sallée, C, Verner, A, Hudson, TJ, Kwok, PY, Cai, D, Koboldt, DC, Miller, RD, Pawlikowska, L, Taillon-Miller, P, Xiao, M, Tsui, LC, Mak, W, Song, YQ, Tam, PK, Nakamura, Y, Kawaguchi, T, Kitamoto, T, Morizono, T, Nagashima, A, Ohnishi, Y, Sekine, A, Tanaka, T, Tsunoda, T, Deloukas, P, Bird, CP, Delgado, M, Dermitzakis, ET, Gwilliam, R, Hunt, S, Morrison, J, Powell, D, Stranger, BE, Whittaker, P, Bentley, DR, Daly, MJ, de Bakker, PI, Barrett, J, Chretien, YR, Maller, J, McCarroll, S, Patterson, N, Pe'er, I, Price, A, Purcell, S, Richter, DJ, Sabeti, P, Saxena, R, Schaffner, SF, Sham, PC, Varilly, P, Stein, LD, Krishnan, L, Smith, AV, Tello-Ruiz, MK, Thorisson, GA, Chakravarti, A, Chen, PE, Cutler, DJ, Kashuk, CS, Lin, S, Abecasis, GR, Guan, W, Li, Y, Munro, HM, Qin, ZS, Thomas, DJ, McVean, G, Auton, A, Bottolo, L, Cardin, N, Eyheramendy, S, Freeman, C, Marchini, J, Myers, S, Spencer, C, Stephens, M, Donnelly, P, Cardon, LR, Clarke, G, Evans, DM, Morris, AP, Weir, BS, Mullikin, JC, Sherry, ST, Feolo, M, Skol, A, Zhang, H, Matsuda, I, Fukushima, Y, Macer, DR, Suda, E, Rotimi, CN, Adebamowo, CA, Ajayi, I, Aniagwu, T, Marshall, PA, Nkwodimmah, C, Royal, CD, Leppert, MF, Dixon, M, Peiffer, A, Qiu, R, Kent, A, Kato, K, Niikawa, N, Adewole, IF, Knoppers, BM, Foster, MW, Clayton, EW, Watkin, J, Muzny, D, Nazareth, L, Sodergren, E, Weinstock, GM, Yakub, I, Birren, BW, Wilson, RK, Fulton, LL, Rogers, J, Burton, J, Carter, NP, Clee, CM, Griffiths, M, Jones, MC, McLay, K, Plumb, RW, Ross, MT, Sims, SK, Willey, DL, Chen, Z, Han, H, Kang, L, Godbout, M, Wallenburg, JC, L'Archevêque, P, Bellemare, G, Saeki, K, An, D, Fu, H, Li, Q, Wang, Z, Wang, R, Holden, AL, Brooks, LD, McEwen, JE, Guyer, MS, Wang, VO, Peterson, JL, Shi, M, Spiegel, J, Sung, LM, Zacharia, LF, Collins, FS, Kennedy, K, Jamieson, R, and Stewart, J
Subjects: Male, Recombination, Genetic, Genetics, Linkage disequilibrium, education.field_of_study, Multidisciplinary, Homozygote, Racial Groups, Haplotype, Population, Single-nucleotide polymorphism, Tag SNP, Biology, Polymorphism, Single Nucleotide, Linkage Disequilibrium, Article, Haplotypes, Humans, Female, Selection, Genetic, International HapMap Project, education, Imputation (genetics), Genetic association
Abstract: We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r 2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r 2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations. ©2007 Nature Publishing Group., link_to_OA_fulltext
Published: 2016

14. CYP24A1 variant modifies the association between use of oestrogen plus progestogen therapy and colorectal cancer risk

Author: Garcia-Albeniz, X, Rudolph, A, Hutter, C, White, E, Lin, Y, Rosse, SA, Figueiredo, JC, Harrison, TA, Jiao, S, Brenner, H, Casey, G, Hudson, TJ, Thornquist, M, Le Marchand, L, Potter, J, Slattery, ML, Zanke, B, Baron, JA, Caan, BJ, Chanock, SJ, Berndt, SI, Stelling, D, Fuchs, CS, Hoffmeister, M, Butterbach, K, Du, M, Gauderman, WJ, Gunter, MJ, Lemire, M, Ogino, S, Lin, J, Hayes, RB, Haile, RW, Schoen, RE, SWarnick, G, Jenkins, MA, Thibodeau, SN, Schumacher, FR, Lindor, NM, Kolonel, LN, Hopper, JL, Gong, J, Seminara, D, Pflugeisen, BM, Ulrich, CM, Qu, C, Duggan, D, Cotterchio, M, Campbell, PT, Carlson, CS, Newcomb, PA, Giovannucci, E, Hsu, L, Chan, AT, Peters, U, Chang-Claude, J, Garcia-Albeniz, X, Rudolph, A, Hutter, C, White, E, Lin, Y, Rosse, SA, Figueiredo, JC, Harrison, TA, Jiao, S, Brenner, H, Casey, G, Hudson, TJ, Thornquist, M, Le Marchand, L, Potter, J, Slattery, ML, Zanke, B, Baron, JA, Caan, BJ, Chanock, SJ, Berndt, SI, Stelling, D, Fuchs, CS, Hoffmeister, M, Butterbach, K, Du, M, Gauderman, WJ, Gunter, MJ, Lemire, M, Ogino, S, Lin, J, Hayes, RB, Haile, RW, Schoen, RE, SWarnick, G, Jenkins, MA, Thibodeau, SN, Schumacher, FR, Lindor, NM, Kolonel, LN, Hopper, JL, Gong, J, Seminara, D, Pflugeisen, BM, Ulrich, CM, Qu, C, Duggan, D, Cotterchio, M, Campbell, PT, Carlson, CS, Newcomb, PA, Giovannucci, E, Hsu, L, Chan, AT, Peters, U, and Chang-Claude, J
Abstract: BACKGROUND: Menopausal hormone therapy (MHT) use has been consistently associated with a decreased risk of colorectal cancer (CRC) in women. Our aim was to use a genome-wide gene-environment interaction analysis to identify genetic modifiers of CRC risk associated with use of MHT. METHODS: We included 10 835 postmenopausal women (5419 cases and 5416 controls) from 10 studies. We evaluated use of any MHT, oestrogen-only (E-only) and combined oestrogen-progestogen (E+P) hormone preparations. To test for multiplicative interactions, we applied the empirical Bayes (EB) test as well as the Wald test in conventional case-control logistic regression as primary tests. The Cocktail test was used as secondary test. RESULTS: The EB test identified a significant interaction between rs964293 at 20q13.2/CYP24A1 and E+P (interaction OR (95% CIs)=0.61 (0.52-0.72), P=4.8 × 10(-9)). The secondary analysis also identified this interaction (Cocktail test OR=0.64 (0.52-0.78), P=1.2 × 10(-5) (alpha threshold=3.1 × 10(-4)). The ORs for association between E+P and CRC risk by rs964293 genotype were as follows: C/C, 0.96 (0.61-1.50); A/C, 0.61 (0.39-0.95) and A/A, 0.40 (0.22-0.73), respectively. CONCLUSIONS: Our results indicate that rs964293 modifies the association between E+P and CRC risk. The variant is located near CYP24A1, which encodes an enzyme involved in vitamin D metabolism. This novel finding offers additional insight into downstream pathways of CRC etiopathogenesis.
Published: 2016

15. Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer

Author: Williams, SM, Gong, J, Hutter, CM, Newcomb, PA, Ulrich, CM, Bien, SA, Campbell, PT, Baron, JA, Berndt, SI, Bezieau, S, Brenner, H, Casey, G, Chan, AT, Chang-Claude, J, Du, M, Duggan, D, Figueiredo, JC, Gallinger, S, Giovannucci, EL, Haile, RW, Harrison, TA, Hayes, RB, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jeon, J, Jenkins, MA, Kocarnik, J, Kury, S, Le Marchand, L, Lin, Y, Lindor, NM, Nishihara, R, Ogino, S, Potter, JD, Rudolph, A, Schoen, RE, Schrotz-King, P, Seminara, D, Slattery, ML, Thibodeau, SN, Thornquist, M, Toth, R, Wallace, R, White, E, Jiao, S, Lemire, M, Hsu, L, Peters, U, Williams, SM, Gong, J, Hutter, CM, Newcomb, PA, Ulrich, CM, Bien, SA, Campbell, PT, Baron, JA, Berndt, SI, Bezieau, S, Brenner, H, Casey, G, Chan, AT, Chang-Claude, J, Du, M, Duggan, D, Figueiredo, JC, Gallinger, S, Giovannucci, EL, Haile, RW, Harrison, TA, Hayes, RB, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jeon, J, Jenkins, MA, Kocarnik, J, Kury, S, Le Marchand, L, Lin, Y, Lindor, NM, Nishihara, R, Ogino, S, Potter, JD, Rudolph, A, Schoen, RE, Schrotz-King, P, Seminara, D, Slattery, ML, Thibodeau, SN, Thornquist, M, Toth, R, Wallace, R, White, E, Jiao, S, Lemire, M, Hsu, L, and Peters, U
Abstract: Genome-wide association studies (GWAS) have identified many genetic susceptibility loci for colorectal cancer (CRC). However, variants in these loci explain only a small proportion of familial aggregation, and there are likely additional variants that are associated with CRC susceptibility. Genome-wide studies of gene-environment interactions may identify variants that are not detected in GWAS of marginal gene effects. To study this, we conducted a genome-wide analysis for interaction between genetic variants and alcohol consumption and cigarette smoking using data from the Colon Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Interactions were tested using logistic regression. We identified interaction between CRC risk and alcohol consumption and variants in the 9q22.32/HIATL1 (Pinteraction = 1.76×10-8; permuted p-value 3.51x10-8) region. Compared to non-/occasional drinking light to moderate alcohol consumption was associated with a lower risk of colorectal cancer among individuals with rs9409565 CT genotype (OR, 0.82 [95% CI, 0.74-0.91]; P = 2.1×10-4) and TT genotypes (OR,0.62 [95% CI, 0.51-0.75]; P = 1.3×10-6) but not associated among those with the CC genotype (p = 0.059). No genome-wide statistically significant interactions were observed for smoking. If replicated our suggestive finding of a genome-wide significant interaction between genetic variants and alcohol consumption might contribute to understanding colorectal cancer etiology and identifying subpopulations with differential susceptibility to the effect of alcohol on CRC risk.
Published: 2016

16. Common variants in the obesity-associated genes FTO and MC4R are not associated with risk of colorectal cancer

Author: Yang, B, Thrift, AP, Figueiredo, JC, Jenkins, MA, Schumacher, FR, Conti, DV, Lin, Y, Win, AK, Limburg, PJ, Berndt, SI, Brenner, H, Chan, AT, Chang-Claude, J, Hoffmeister, M, Hudson, TJ, Le Marchand, L, Newcomb, PA, Slattery, ML, White, E, Peters, U, Casey, G, Campbell, PT, Yang, B, Thrift, AP, Figueiredo, JC, Jenkins, MA, Schumacher, FR, Conti, DV, Lin, Y, Win, AK, Limburg, PJ, Berndt, SI, Brenner, H, Chan, AT, Chang-Claude, J, Hoffmeister, M, Hudson, TJ, Le Marchand, L, Newcomb, PA, Slattery, ML, White, E, Peters, U, Casey, G, and Campbell, PT
Abstract: BACKGROUND: Obesity is a convincing risk factor for colorectal cancer. Genetic variants in or near FTO and MC4R are consistently associated with body mass index and other body size measures, but whether they are also associated with colorectal cancer risk is unclear. METHODS: In the discovery stage, we tested associations of 677 FTO and 323 MC4R single nucleotide polymorphisms (SNPs) 100kb upstream and 300kb downstream from each respective locus with risk of colorectal cancer in data from the Colon Cancer Family Registry (CCFR: 1960 cases; 1777 controls). Next, all SNPs that were nominally statistically significant (p<0.05) in the discovery stage were included in replication analyses in data from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO: 9716 cases; 9844 controls). RESULTS: In the discovery stage, 43 FTO variants and 18 MC4R variants were associated with colorectal cancer risk (p<0.05). No SNPs remained statistically significant in the replication analysis after accounting for multiple comparisons. CONCLUSION: We found no evidence that individual variants in or near the obesity-related genes FTO and MC4R are associated with risk of colorectal cancer.
Published: 2016

17. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants

Author: Wang, J, Du, M, Jiao, S, Bien, SA, Gala, M, Abecasis, G, Bezieau, S, Brenner, H, Butterbach, K, Caan, BJ, Carlson, CS, Casey, G, Chang-Claude, J, Conti, DV, Curtis, KR, Duggan, D, Gallinger, S, Haile, RW, Harrison, TA, Hayes, RB, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jenkins, MA, Kury, S, Le Marchand, L, Leal, SM, Newcomb, PA, Nickerson, DA, Potter, JD, Schoen, RE, Schumacher, FR, Seminara, D, Slattery, ML, Hsu, L, Chan, AT, White, E, Berndt, SI, Peters, U, Wang, J, Du, M, Jiao, S, Bien, SA, Gala, M, Abecasis, G, Bezieau, S, Brenner, H, Butterbach, K, Caan, BJ, Carlson, CS, Casey, G, Chang-Claude, J, Conti, DV, Curtis, KR, Duggan, D, Gallinger, S, Haile, RW, Harrison, TA, Hayes, RB, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jenkins, MA, Kury, S, Le Marchand, L, Leal, SM, Newcomb, PA, Nickerson, DA, Potter, JD, Schoen, RE, Schumacher, FR, Seminara, D, Slattery, ML, Hsu, L, Chan, AT, White, E, Berndt, SI, and Peters, U
Abstract: Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).
Published: 2016

18. Is rigorousretrospective harmonization possible? Application of the DataSHaPER approachacross 53 large studies

Author: Fortier I, Doiron D, Little J, Ferretti V, L'Heureux F, Stolk RP, Knoppers BM, Hudson TJ, Burton PR, International Harmonization Initiative, PANICO, SALVATORE, Fortier, I, Doiron, D, Little, J, Ferretti, V, L'Heureux, F, Stolk, Rp, Knoppers, Bm, Hudson, Tj, Burton, Pr, International Harmonization, Initiative, and Panico, Salvatore
Published: 2011

19. BCL2 Splice Isoform Switching Promotes Leukemia Stem Cell Survival and Sensitivity to a Novel Pan BCL2 Inhibitor

Author: GOFF D, SMITH KM, SHIH AY, COURT RECART A, SADARANGANI A, GERON I, CHUANG R, BALAIAN L, WEI J, KITADA S, ZHAI D, GOTLIB J, MINDEN MD, SCHAIRER A, LEU H, MA W, JIANG Q, RUSERT J, DAO KHT, SHAZAND K, VOLAR M, DE BORJA R, MCPHERSON JD, HUDSON TJ, BARRETT CL, FRAZER KA, WENTWORTH P, MORRIS SR, GOLDSTEIN LSB, PELLECHIA M, REED JC, JAMIESON C., MARTINELLI, GIOVANNI, GOFF D, SMITH KM, SHIH AY, COURT-RECART A, SADARANGANI A, GERON I, CHUANG R, BALAIAN L, WEI J, KITADA S, ZHAI D, GOTLIB J, MINDEN MD, MARTINELLI G, SCHAIRER A, LEU H, MA W, JIANG Q, RUSERT J, DAO KHT, SHAZAND K, VOLAR M, DE BORJA R, MCPHERSON JD, HUDSON TJ, BARRETT CL, FRAZER KA, WENTWORTH P, MORRIS SR, GOLDSTEIN LSB, PELLECHIA M, REED JC, and JAMIESON C
Subjects: SPLICE VARIANT
Published: 2011

20. Meta-analysis identifies seven susceptibility loci involved in the atopic March

Author: Marenholz, I, Esparza-Gordillo, J, Rüschendorf, F, Bauerfeind, A, Strachan, DP, Spycher, BD, Baurecht, H, Margaritte-Jeannin, P, Sääf, A, Kerkhof, M, Ege, M, Baltic, S, Matheson, MC, Li, J, Michel, S, Ang, WQ, McArdle, W, Arnold, A, Homuth, G, Demenais, F, Bouzigon, E, Söderhäll, C, Pershagen, G, De Jongste, JC, Postma, DS, Braun-Fahrländer, C, Horak, E, Ogorodova, LM, Puzyrev, VP, Bragina, EY, Hudson, TJ, Morin, C, Duffy, DL, Marks, GB, Robertson, CF, Montgomery, GW, Musk, B, Thompson, PJ, Martin, NG, James, A, Sleiman, P, Toskala, E, Rodriguez, E, Fölster-Holst, R, Franke, A, Lieb, W, Gieger, C, Heinzmann, A, Rietschel, E, Keil, T, Cichon, S, Nöthen, MM, Pennell, CE, Sly, PD, Schmidt, CO, Matanovic, A, Schneider, V, Heinig, M, Hübner, N, Holt, PG, Lau, S, Kabesch, M, Weidinger, S, Hakonarson, H, Ferreira, MAR, Laprise, C, Freidin, MB, Genuneit, J, Koppelman, GH, Melén, E, Dizier, MH, Henderson, AJ, Lee, YA, Marenholz, I, Esparza-Gordillo, J, Rüschendorf, F, Bauerfeind, A, Strachan, DP, Spycher, BD, Baurecht, H, Margaritte-Jeannin, P, Sääf, A, Kerkhof, M, Ege, M, Baltic, S, Matheson, MC, Li, J, Michel, S, Ang, WQ, McArdle, W, Arnold, A, Homuth, G, Demenais, F, Bouzigon, E, Söderhäll, C, Pershagen, G, De Jongste, JC, Postma, DS, Braun-Fahrländer, C, Horak, E, Ogorodova, LM, Puzyrev, VP, Bragina, EY, Hudson, TJ, Morin, C, Duffy, DL, Marks, GB, Robertson, CF, Montgomery, GW, Musk, B, Thompson, PJ, Martin, NG, James, A, Sleiman, P, Toskala, E, Rodriguez, E, Fölster-Holst, R, Franke, A, Lieb, W, Gieger, C, Heinzmann, A, Rietschel, E, Keil, T, Cichon, S, Nöthen, MM, Pennell, CE, Sly, PD, Schmidt, CO, Matanovic, A, Schneider, V, Heinig, M, Hübner, N, Holt, PG, Lau, S, Kabesch, M, Weidinger, S, Hakonarson, H, Ferreira, MAR, Laprise, C, Freidin, MB, Genuneit, J, Koppelman, GH, Melén, E, Dizier, MH, Henderson, AJ, and Lee, YA
Abstract: Eczema often precedes the development of asthma in a disease course called the a € atopic marcha €. To unravel the genes underlying this characteristic pattern of allergic disease, we conduct a multi-stage genome-wide association study on infantile eczema followed by childhood asthma in 12 populations including 2,428 cases and 17,034 controls. Here we report two novel loci specific for the combined eczema plus asthma phenotype, which are associated with allergic disease for the first time; rs9357733 located in EFHC1 on chromosome 6p12.3 (OR 1.27; P=2.1 × 10 a'8) and rs993226 between TMTC2 and SLC6A15 on chromosome 12q21.3 (OR 1.58; P=5.3 × 10 a'9). Additional susceptibility loci identified at genome-wide significance are FLG (1q21.3), IL4/KIF3A (5q31.1), AP5B1/OVOL1 (11q13.1), C11orf30/LRRC32 (11q13.5) and IKZF3 (17q21). We show that predominantly eczema loci increase the risk for the atopic march. Our findings suggest that eczema may play an important role in the development of asthma after eczema.
Published: 2015

21. Genome-wide association study of colorectal cancer identifies six new susceptibility loci

Author: Schumacher, FR, Schmit, SL, Jiao, S, Edlund, CK, Wang, H, Zhang, B, Hsu, L, Huang, S-C, Fischer, CP, Harju, JF, Idos, GE, Lejbkowicz, F, Manion, FJ, McDonnell, K, McNeil, CE, Melas, M, Rennert, HS, Shi, W, Thomas, DC, Van Den Berg, DJ, Hutter, CM, Aragaki, AK, Butterbach, K, Caan, BJ, Carlson, CS, Chanock, SJ, Curtis, KR, Fuchs, CS, Gala, M, Giocannucci, EL, Gogarten, SM, Hayes, RB, Henderson, B, Hunter, DJ, Jackson, RD, Kolonel, LN, Kooperberg, C, Kury, S, LaCroix, A, Laurie, CC, Laurie, CA, Lemire, M, Levine, D, Ma, J, Makar, KW, Qu, C, Taverna, D, Ulrich, CM, Wu, K, Kono, S, West, DW, Berndt, SI, Bezieau, S, Brenner, H, Campbell, PT, Chan, AT, Chang-Claude, J, Coetzee, GA, Conti, DV, Duggan, D, Figueiredo, JC, Fortini, BK, Gallinger, SJ, Gauderman, WJ, Giles, G, Green, R, Haile, R, Harrison, TA, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jacobs, E, Iwasaki, M, Jee, SH, Jenkins, M, Jia, W-H, Joshi, A, Li, L, Lindor, NM, Matsuo, K, Moreno, V, Mukherjee, B, Newcomb, PA, Potter, JD, Raskin, L, Rennert, G, Rosse, S, Severi, G, Schoen, RE, Seminara, D, Shu, X-O, Slattery, ML, Tsugane, S, White, E, Xiang, Y-B, Zanke, BW, Zheng, W, Le Marchand, L, Casey, G, Gruber, SB, Peters, U, Schumacher, FR, Schmit, SL, Jiao, S, Edlund, CK, Wang, H, Zhang, B, Hsu, L, Huang, S-C, Fischer, CP, Harju, JF, Idos, GE, Lejbkowicz, F, Manion, FJ, McDonnell, K, McNeil, CE, Melas, M, Rennert, HS, Shi, W, Thomas, DC, Van Den Berg, DJ, Hutter, CM, Aragaki, AK, Butterbach, K, Caan, BJ, Carlson, CS, Chanock, SJ, Curtis, KR, Fuchs, CS, Gala, M, Giocannucci, EL, Gogarten, SM, Hayes, RB, Henderson, B, Hunter, DJ, Jackson, RD, Kolonel, LN, Kooperberg, C, Kury, S, LaCroix, A, Laurie, CC, Laurie, CA, Lemire, M, Levine, D, Ma, J, Makar, KW, Qu, C, Taverna, D, Ulrich, CM, Wu, K, Kono, S, West, DW, Berndt, SI, Bezieau, S, Brenner, H, Campbell, PT, Chan, AT, Chang-Claude, J, Coetzee, GA, Conti, DV, Duggan, D, Figueiredo, JC, Fortini, BK, Gallinger, SJ, Gauderman, WJ, Giles, G, Green, R, Haile, R, Harrison, TA, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jacobs, E, Iwasaki, M, Jee, SH, Jenkins, M, Jia, W-H, Joshi, A, Li, L, Lindor, NM, Matsuo, K, Moreno, V, Mukherjee, B, Newcomb, PA, Potter, JD, Raskin, L, Rennert, G, Rosse, S, Severi, G, Schoen, RE, Seminara, D, Shu, X-O, Slattery, ML, Tsugane, S, White, E, Xiang, Y-B, Zanke, BW, Zheng, W, Le Marchand, L, Casey, G, Gruber, SB, and Peters, U
Abstract: Genetic susceptibility to colorectal cancer is caused by rare pathogenic mutations and common genetic variants that contribute to familial risk. Here we report the results of a two-stage association study with 18,299 cases of colorectal cancer and 19,656 controls, with follow-up of the most statistically significant genetic loci in 4,725 cases and 9,969 controls from two Asian consortia. We describe six new susceptibility loci reaching a genome-wide threshold of P<5.0E-08. These findings provide additional insight into the underlying biological mechanisms of colorectal cancer and demonstrate the scientific value of large consortia-based genetic epidemiology studies.
Published: 2015

22. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

Author: Alioto, TS, Buchhalter, I, Derdak, S, Hutter, B, Eldridge, MD, Hovig, E, Heisler, LE, Beck, TA, Simpson, JT, Tonon, L, Sertier, A-S, Patch, A-M, Jaeger, N, Ginsbach, P, Drews, R, Paramasivam, N, Kabbe, R, Chotewutmontri, S, Diessl, N, Previti, C, Schmidt, S, Brors, B, Feuerbach, L, Heinold, M, Groebner, S, Korshunov, A, Tarpey, PS, Butler, AP, Hinton, J, Jones, D, Menzies, A, Raine, K, Shepherd, R, Stebbings, L, Teague, JW, Ribeca, P, Giner, FC, Beltran, S, Raineri, E, Dabad, M, Heath, SC, Gut, M, Denroche, RE, Harding, NJ, Yamaguchi, TN, Fujimoto, A, Nakagawa, H, Quesada, C, Valdes-Mas, R, Nakken, S, Vodak, D, Bower, L, Lynch, AG, Anderson, CL, Waddell, N, Pearson, JV, Grimmond, SM, Peto, M, Spellman, P, He, M, Kandoth, C, Lee, S, Zhang, J, Letourneau, L, Ma, S, Seth, S, Torrents, D, Xi, L, Wheeler, DA, Lopez-Otin, C, Campo, E, Campbell, PJ, Boutros, PC, Puente, XS, Gerhard, DS, Pfister, SM, McPherson, JD, Hudson, TJ, Schlesner, M, Lichter, P, Eils, R, Jones, DTW, Gut, IG, Alioto, TS, Buchhalter, I, Derdak, S, Hutter, B, Eldridge, MD, Hovig, E, Heisler, LE, Beck, TA, Simpson, JT, Tonon, L, Sertier, A-S, Patch, A-M, Jaeger, N, Ginsbach, P, Drews, R, Paramasivam, N, Kabbe, R, Chotewutmontri, S, Diessl, N, Previti, C, Schmidt, S, Brors, B, Feuerbach, L, Heinold, M, Groebner, S, Korshunov, A, Tarpey, PS, Butler, AP, Hinton, J, Jones, D, Menzies, A, Raine, K, Shepherd, R, Stebbings, L, Teague, JW, Ribeca, P, Giner, FC, Beltran, S, Raineri, E, Dabad, M, Heath, SC, Gut, M, Denroche, RE, Harding, NJ, Yamaguchi, TN, Fujimoto, A, Nakagawa, H, Quesada, C, Valdes-Mas, R, Nakken, S, Vodak, D, Bower, L, Lynch, AG, Anderson, CL, Waddell, N, Pearson, JV, Grimmond, SM, Peto, M, Spellman, P, He, M, Kandoth, C, Lee, S, Zhang, J, Letourneau, L, Ma, S, Seth, S, Torrents, D, Xi, L, Wheeler, DA, Lopez-Otin, C, Campo, E, Campbell, PJ, Boutros, PC, Puente, XS, Gerhard, DS, Pfister, SM, McPherson, JD, Hudson, TJ, Schlesner, M, Lichter, P, Eils, R, Jones, DTW, and Gut, IG
Abstract: As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.
Published: 2015

23. Genetic determinants of telomere length and risk of common cancers: a Mendelian randomization study

Author: Zhang, C, Doherty, JA, Burgess, S, Hung, RJ, Lindstroem, S, Kraft, P, Gong, J, Amos, CI, Sellers, TA, Monteiro, ANA, Chenevix-Trench, G, Bickeboeller, H, Risch, A, Brennan, P, Mckay, JD, Houlston, RS, Landi, MT, Timofeeva, MN, Wang, Y, Heinrich, J, Kote-Jarai, Z, Eeles, RA, Muir, K, Wiklund, F, Gronberg, H, Berndt, SI, Chanock, SJ, Schumacher, F, Haiman, CA, Henderson, BE, Al Olama, AA, Andrulis, IL, Hopper, JL, Chang-Claude, J, John, EM, Malone, KE, Gammon, MD, Ursin, G, Whittemore, AS, Hunter, DJ, Gruber, SB, Knight, JA, Hou, L, Le Marchand, L, Newcomb, PA, Hudson, TJ, Chan, AT, Li, L, Woods, MO, Ahsan, H, Pierce, BL, Zhang, C, Doherty, JA, Burgess, S, Hung, RJ, Lindstroem, S, Kraft, P, Gong, J, Amos, CI, Sellers, TA, Monteiro, ANA, Chenevix-Trench, G, Bickeboeller, H, Risch, A, Brennan, P, Mckay, JD, Houlston, RS, Landi, MT, Timofeeva, MN, Wang, Y, Heinrich, J, Kote-Jarai, Z, Eeles, RA, Muir, K, Wiklund, F, Gronberg, H, Berndt, SI, Chanock, SJ, Schumacher, F, Haiman, CA, Henderson, BE, Al Olama, AA, Andrulis, IL, Hopper, JL, Chang-Claude, J, John, EM, Malone, KE, Gammon, MD, Ursin, G, Whittemore, AS, Hunter, DJ, Gruber, SB, Knight, JA, Hou, L, Le Marchand, L, Newcomb, PA, Hudson, TJ, Chan, AT, Li, L, Woods, MO, Ahsan, H, and Pierce, BL
Abstract: Epidemiological studies have reported inconsistent associations between telomere length (TL) and risk for various cancers. These inconsistencies are likely attributable, in part, to biases that arise due to post-diagnostic and post-treatment TL measurement. To avoid such biases, we used a Mendelian randomization approach and estimated associations between nine TL-associated SNPs and risk for five common cancer types (breast, lung, colorectal, ovarian and prostate cancer, including subtypes) using data on 51 725 cases and 62 035 controls. We then used an inverse-variance weighted average of the SNP-specific associations to estimate the association between a genetic score representing long TL and cancer risk. The long TL genetic score was significantly associated with increased risk of lung adenocarcinoma (P = 6.3 × 10(-15)), even after exclusion of a SNP residing in a known lung cancer susceptibility region (TERT-CLPTM1L) P = 6.6 × 10(-6)). Under Mendelian randomization assumptions, the association estimate [odds ratio (OR) = 2.78] is interpreted as the OR for lung adenocarcinoma corresponding to a 1000 bp increase in TL. The weighted TL SNP score was not associated with other cancer types or subtypes. Our finding that genetic determinants of long TL increase lung adenocarcinoma risk avoids issues with reverse causality and residual confounding that arise in observational studies of TL and disease risk. Under Mendelian randomization assumptions, our finding suggests that longer TL increases lung adenocarcinoma risk. However, caution regarding this causal interpretation is warranted in light of the potential issue of pleiotropy, and a more general interpretation is that SNPs influencing telomere biology are also implicated in lung adenocarcinoma risk.
Published: 2015

24. Genome-wide association study of colorectal cancer identifies six new susceptibility loci (vol 6, 7138, 2015)

Author: Schumacher, FR, Schmit, SL, Jiao, S, Edlund, CK, Wang, H, Zhang, B, Hsu, L, Huang, S-C, Fischer, CP, Harju, JF, Idos, GE, Lejbkowicz, F, Manion, FJ, McDonnell, K, McNeil, CE, Melas, M, Rennert, HS, Shi, W, Thomas, DC, Van den Berg, DJ, Hutter, CM, Aragaki, AK, Butterbach, K, Caan, BJ, Carlson, CS, Chanock, SJ, Curtis, KR, Fuchs, CS, Gala, M, Giovannucci, EL, Gogarten, SM, Hayes, RB, Henderson, B, Hunter, DJ, Jackson, RD, Kolonel, LN, Kooperberg, C, Kuery, S, LaCroix, A, Laurie, CC, Laurie, CA, Lemire, M, Levine, D, Ma, J, Makar, KW, Qu, C, Taverna, D, Ulrich, CM, Wu, K, Kono, S, West, DW, Berndt, SI, Bezieau, S, Brenner, H, Campbell, PT, Chan, AT, Chang-Claude, J, Coetzee, GA, Conti, DV, Duggan, D, Figueiredo, JC, Fortini, BK, Gallinger, SJ, Gauderman, WJ, Giles, G, Green, R, Haile, R, Harrison, TA, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jacobs, E, Iwasaki, M, Jee, SH, Jenkins, M, Jia, W-H, Joshi, A, Li, L, Lindor, NM, Matsuo, K, Moreno, V, Mukherjee, B, Newcomb, PA, Potter, JD, Raskin, L, Rennert, G, Rosse, S, Severi, G, Schoen, RE, Seminara, D, Shu, X-O, Slattery, ML, Tsugane, S, White, E, Xiang, Y-B, Zanke, BW, Zheng, W, Le Marchand, L, Casey, G, Gruber, SB, Peters, U, Schumacher, FR, Schmit, SL, Jiao, S, Edlund, CK, Wang, H, Zhang, B, Hsu, L, Huang, S-C, Fischer, CP, Harju, JF, Idos, GE, Lejbkowicz, F, Manion, FJ, McDonnell, K, McNeil, CE, Melas, M, Rennert, HS, Shi, W, Thomas, DC, Van den Berg, DJ, Hutter, CM, Aragaki, AK, Butterbach, K, Caan, BJ, Carlson, CS, Chanock, SJ, Curtis, KR, Fuchs, CS, Gala, M, Giovannucci, EL, Gogarten, SM, Hayes, RB, Henderson, B, Hunter, DJ, Jackson, RD, Kolonel, LN, Kooperberg, C, Kuery, S, LaCroix, A, Laurie, CC, Laurie, CA, Lemire, M, Levine, D, Ma, J, Makar, KW, Qu, C, Taverna, D, Ulrich, CM, Wu, K, Kono, S, West, DW, Berndt, SI, Bezieau, S, Brenner, H, Campbell, PT, Chan, AT, Chang-Claude, J, Coetzee, GA, Conti, DV, Duggan, D, Figueiredo, JC, Fortini, BK, Gallinger, SJ, Gauderman, WJ, Giles, G, Green, R, Haile, R, Harrison, TA, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jacobs, E, Iwasaki, M, Jee, SH, Jenkins, M, Jia, W-H, Joshi, A, Li, L, Lindor, NM, Matsuo, K, Moreno, V, Mukherjee, B, Newcomb, PA, Potter, JD, Raskin, L, Rennert, G, Rosse, S, Severi, G, Schoen, RE, Seminara, D, Shu, X-O, Slattery, ML, Tsugane, S, White, E, Xiang, Y-B, Zanke, BW, Zheng, W, Le Marchand, L, Casey, G, Gruber, SB, and Peters, U
Published: 2015

25. Association of Aspirin and NSAID Use With Risk of Colorectal Cancer According to Genetic Variants

Author: Nan, H, Hutter, CM, Lin, Y, Jacobs, EJ, Ulrich, CM, White, E, Baron, JA, Berndt, SI, Brenner, H, Butterbach, K, Caan, BJ, Campbell, PT, Carlson, CS, Casey, G, Chang-Claude, J, Chanock, SJ, Cotterchio, M, Duggan, D, Figueiredo, JC, Fuchs, CS, Giovannucci, EL, Gong, J, Haile, RW, Harrison, TA, Hayes, RB, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jenkins, MA, Jiao, S, Lindor, NM, Lemire, M, Le Marchand, L, Newcomb, PA, Ogino, S, Pflugeisen, BM, Potter, JD, Qu, C, Rosse, SA, Rudolph, A, Schoen, RE, Schumacher, FR, Seminara, D, Slattery, ML, Thibodeau, SN, Thomas, F, Thornquist, M, Warnick, GS, Zanke, BW, Gauderman, WJ, Peters, U, Hsu, L, Chan, AT, Nan, H, Hutter, CM, Lin, Y, Jacobs, EJ, Ulrich, CM, White, E, Baron, JA, Berndt, SI, Brenner, H, Butterbach, K, Caan, BJ, Campbell, PT, Carlson, CS, Casey, G, Chang-Claude, J, Chanock, SJ, Cotterchio, M, Duggan, D, Figueiredo, JC, Fuchs, CS, Giovannucci, EL, Gong, J, Haile, RW, Harrison, TA, Hayes, RB, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jenkins, MA, Jiao, S, Lindor, NM, Lemire, M, Le Marchand, L, Newcomb, PA, Ogino, S, Pflugeisen, BM, Potter, JD, Qu, C, Rosse, SA, Rudolph, A, Schoen, RE, Schumacher, FR, Seminara, D, Slattery, ML, Thibodeau, SN, Thomas, F, Thornquist, M, Warnick, GS, Zanke, BW, Gauderman, WJ, Peters, U, Hsu, L, and Chan, AT
Abstract: IMPORTANCE: Use of aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with lower risk of colorectal cancer. OBJECTIVE: To identify common genetic markers that may confer differential benefit from aspirin or NSAID chemoprevention, we tested gene × environment interactions between regular use of aspirin and/or NSAIDs and single-nucleotide polymorphisms (SNPs) in relation to risk of colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS: Case-control study using data from 5 case-control and 5 cohort studies initiated between 1976 and 2003 across the United States, Canada, Australia, and Germany and including colorectal cancer cases (n=8634) and matched controls (n=8553) ascertained between 1976 and 2011. Participants were all of European descent. EXPOSURES: Genome-wide SNP data and information on regular use of aspirin and/or NSAIDs and other risk factors. MAIN OUTCOMES AND MEASURES: Colorectal cancer. RESULTS: Regular use of aspirin and/or NSAIDs was associated with lower risk of colorectal cancer (prevalence, 28% vs 38%; odds ratio [OR], 0.69 [95% CI, 0.64-0.74]; P = 6.2 × 10(-28)) compared with nonregular use. In the conventional logistic regression analysis, the SNP rs2965667 at chromosome 12p12.3 near the MGST1 gene showed a genome-wide significant interaction with aspirin and/or NSAID use (P = 4.6 × 10(-9) for interaction). Aspirin and/or NSAID use was associated with a lower risk of colorectal cancer among individuals with rs2965667-TT genotype (prevalence, 28% vs 38%; OR, 0.66 [95% CI, 0.61-0.70]; P = 7.7 × 10(-33)) but with a higher risk among those with rare (4%) TA or AA genotypes (prevalence, 35% vs 29%; OR, 1.89 [95% CI, 1.27-2.81]; P = .002). In case-only interaction analysis, the SNP rs16973225 at chromosome 15q25.2 near the IL16 gene showed a genome-wide significant interaction with use of aspirin and/or NSAIDs (P = 8.2 × 10(-9) for interaction). Regular use was associated with a lower risk of colorectal cancer among individuals
Published: 2015

26. A genome-wide association study for colorectal cancer identifies a risk locus in 14q23.1

Author: Lemire, M, Qu, C, Loo, LWM, Zaidi, SHE, Wang, H, Berndt, SI, Bezieau, S, Brenner, H, Campbell, PT, Chan, AT, Chang-Claude, J, Du, M, Edlund, CK, Gallinger, S, Haile, RW, Harrison, TA, Hoffmeister, M, Hopper, JL, Hou, L, Hsu, L, Jacobs, EJ, Jenkins, MA, Jeon, J, Kuery, S, Li, L, Lindor, NM, Newcomb, PA, Potter, JD, Rennert, G, Rudolph, A, Schoen, RE, Schumacher, FR, Seminara, D, Severi, G, Slattery, ML, White, E, Woods, MO, Cotterchio, M, Le Marchand, L, Casey, G, Gruber, SB, Peters, U, Hudson, TJ, Lemire, M, Qu, C, Loo, LWM, Zaidi, SHE, Wang, H, Berndt, SI, Bezieau, S, Brenner, H, Campbell, PT, Chan, AT, Chang-Claude, J, Du, M, Edlund, CK, Gallinger, S, Haile, RW, Harrison, TA, Hoffmeister, M, Hopper, JL, Hou, L, Hsu, L, Jacobs, EJ, Jenkins, MA, Jeon, J, Kuery, S, Li, L, Lindor, NM, Newcomb, PA, Potter, JD, Rennert, G, Rudolph, A, Schoen, RE, Schumacher, FR, Seminara, D, Severi, G, Slattery, ML, White, E, Woods, MO, Cotterchio, M, Le Marchand, L, Casey, G, Gruber, SB, Peters, U, and Hudson, TJ
Abstract: Over 50 loci associated with colorectal cancer (CRC) have been uncovered by genome-wide association studies (GWAS). Identifying additional loci has the potential to help elucidate aspects of the underlying biological processes leading to better understanding of the pathogenesis of the disease. We re-evaluated a GWAS by excluding controls that have family history of CRC or personal history of colorectal polyps, as we hypothesized that their inclusion reduces power to detect associations. This is supported empirically and through simulations. Two-phase GWAS analysis was performed in a total of 16,517 cases and 14,487 controls. We identified rs17094983, a SNP associated with risk of CRC [p = 2.5 × 10(-10); odds ratio estimated by re-including all controls (OR) = 0.87, 95% confidence interval (CI) 0.83-0.91; minor allele frequency (MAF) = 13%]. Results were replicated in samples of African descent (1894 cases and 4703 controls; p = 0.01; OR = 0.86, 95% CI 0.77-0.97; MAF = 16 %). Gene expression data in 195 colon adenocarcinomas and 59 normal colon tissues from two different studies revealed that this locus has genotypes that are associated with RTN1 (Reticulon 1) expression (p = 0.001), a protein-coding gene involved in survival and proliferation of cancer cells which is highly expressed in normal colon tissues but has significantly reduced expression in tumor cells (p = 1.3 × 10(-8)).
Published: 2015

27. Pleiotropic effects of genetic risk variants for other cancers on colorectal cancer risk: PAGE, GECCO and CCFR consortia

Author: Cheng, I, Kocarnik, JM, Dumitrescu, L, Lindor, NM, Chang-Claude, J, Avery, CL, Caberto, CP, Love, S-A, Slattery, ML, Chan, AT, Baron, JA, Hindorff, LA, Park, SL, Schumacher, FR, Hoffmeister, M, Kraft, P, Butler, AM, Duggan, DJ, Hou, L, Carlson, CS, Monroe, KR, Lin, Y, Carty, CL, Mann, S, Ma, J, Giovannucci, EL, Fuchs, CS, Newcomb, PA, Jenkins, MA, Hopper, JL, Haile, RW, Conti, DV, Campbell, PT, Potter, JD, Caan, BJ, Schoen, RE, Hayes, RB, Chanock, SJ, Berndt, SI, Kuery, S, Bezieau, S, Ambite, JL, Kumaraguruparan, G, Richardson, DM, Goodloe, RJ, Dilks, HH, Baker, P, Zanke, BW, Lemire, M, Gallinger, S, Hsu, L, Jiao, S, Harrison, TA, Seminara, D, Haiman, CA, Kooperberg, C, Wilkens, LR, Hutter, CM, White, E, Crawford, DC, Heiss, G, Hudson, TJ, Brenner, H, Bush, WS, Casey, G, Le Marchand, L, Peters, U, Cheng, I, Kocarnik, JM, Dumitrescu, L, Lindor, NM, Chang-Claude, J, Avery, CL, Caberto, CP, Love, S-A, Slattery, ML, Chan, AT, Baron, JA, Hindorff, LA, Park, SL, Schumacher, FR, Hoffmeister, M, Kraft, P, Butler, AM, Duggan, DJ, Hou, L, Carlson, CS, Monroe, KR, Lin, Y, Carty, CL, Mann, S, Ma, J, Giovannucci, EL, Fuchs, CS, Newcomb, PA, Jenkins, MA, Hopper, JL, Haile, RW, Conti, DV, Campbell, PT, Potter, JD, Caan, BJ, Schoen, RE, Hayes, RB, Chanock, SJ, Berndt, SI, Kuery, S, Bezieau, S, Ambite, JL, Kumaraguruparan, G, Richardson, DM, Goodloe, RJ, Dilks, HH, Baker, P, Zanke, BW, Lemire, M, Gallinger, S, Hsu, L, Jiao, S, Harrison, TA, Seminara, D, Haiman, CA, Kooperberg, C, Wilkens, LR, Hutter, CM, White, E, Crawford, DC, Heiss, G, Hudson, TJ, Brenner, H, Bush, WS, Casey, G, Le Marchand, L, and Peters, U
Abstract: OBJECTIVE: Genome-wide association studies have identified a large number of single nucleotide polymorphisms (SNPs) associated with a wide array of cancer sites. Several of these variants demonstrate associations with multiple cancers, suggesting pleiotropic effects and shared biological mechanisms across some cancers. We hypothesised that SNPs previously associated with other cancers may additionally be associated with colorectal cancer. In a large-scale study, we examined 171 SNPs previously associated with 18 different cancers for their associations with colorectal cancer. DESIGN: We examined 13 338 colorectal cancer cases and 40 967 controls from three consortia: Population Architecture using Genomics and Epidemiology (PAGE), Genetic Epidemiology of Colorectal Cancer (GECCO), and the Colon Cancer Family Registry (CCFR). Study-specific logistic regression results, adjusted for age, sex, principal components of genetic ancestry, and/or study specific factors (as relevant) were combined using fixed-effect meta-analyses to evaluate the association between each SNP and colorectal cancer risk. A Bonferroni-corrected p value of 2.92×10(-4) was used to determine statistical significance of the associations. RESULTS: Two correlated SNPs--rs10090154 and rs4242382--in Region 1 of chromosome 8q24, a prostate cancer susceptibility region, demonstrated statistically significant associations with colorectal cancer risk. The most significant association was observed with rs4242382 (meta-analysis OR=1.12; 95% CI 1.07 to 1.18; p=1.74×10(-5)), which also demonstrated similar associations across racial/ethnic populations and anatomical sub-sites. CONCLUSIONS: This is the first study to clearly demonstrate Region 1 of chromosome 8q24 as a susceptibility locus for colorectal cancer; thus, adding colorectal cancer to the list of cancer sites linked to this particular multicancer risk region at 8q24.
Published: 2014

28. Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer

Author: Houlston, RS, Webb, E, Broderick, P, Pittman, AM, Di Bernardo, MC, Lubbe, S, Chandler, I, Vijayakrishnan, J, Sullivan, K, Penegar, S, Carvajal-Carmona, L, Howarth, K, Jaeger, E, Spain, SL, Walther, A, Barclay, E, Martin, L, Gorman, M, Domingo, E, Teixeira, AS, Kerr, D, Cazier, J-B, Niittymaki, I, Tuupanen, S, Karhu, A, Aaltonen, LA, Tomlinson, IPM, Farrington, SM, Tenesa, A, Prendergast, JGD, Barnetson, RA, Cetnarskyj, R, Porteous, ME, Pharoah, PDP, Koessler, T, Hampe, J, Buch, S, Schafmayer, C, Tepel, J, Schreiber, S, Voelzke, H, Chang-Claude, J, Hoffmeister, M, Brenner, H, Zanke, BW, Montpetit, A, Hudson, TJ, Gallinger, S, Campbell, H, Dunlop, MG, Study, COGENT, Consor, CCAS, Consortium, C, and Assoc, ICCG
Subjects: Male, Colorectal cancer, Single-nucleotide polymorphism, Genome-wide association study, Biology, Genome, Article, 03 medical and health sciences, 0302 clinical medicine, Germline mutation, medicine, Genetics, Humans, Genetic Predisposition to Disease, 030304 developmental biology, Aged, 0303 health sciences, Genome, Human, Case-control study, Middle Aged, medicine.disease, 3. Good health, 030220 oncology & carcinogenesis, Meta-analysis, Case-Control Studies, Human genome, Female, Colorectal Neoplasms, Genome-Wide Association Study
Abstract: Genome-wide association (GWA) studies have identified multiple loci at which common variants modestly influence the risk of developing colorectal cancer (CRC). To enhance power to identify additional loci with similar effect sizes, we conducted a meta-analysis of two GWA studies, comprising 13,315 individuals genotyped for 38,710 common tagging SNPs. We undertook replication testing in up to eight independent case-control series comprising 27,418 subjects. We identified four previously unreported CRC risk loci at 14q22.2 (rs4444235, BMP4; P = 8.1 x 10(-10)), 16q22.1 (rs9929218, CDH1; P = 1.2 x 10(-8)), 19q13.1 (rs10411210, RHPN2; P = 4.6 x 10(-9)) and 20p12.3 (rs961253; P = 2.0 x 10(-10)). These findings underscore the value of large sample series for discovery and follow-up of genetic variants contributing to the etiology of CRC.
Published: 2008

29. An extremes of outcome strategy provides evidence for multiple sclerosis severity being determined by alleles at the HLA-DRB1 locus

Author: Deluca, Gc, Ramagopalan, Sv, Herrera, Bm, Dyment, Da, Lincoln, Mr, Montpetit, A, Pugliatti, Maura, Risch, N, Sadovnick, D, Esiri, M, Sotgiu, S, Hudson, Tj, and Ebers, G. C.
Subjects: NO
Published: 2008

30. Genome-wide detection and characterization of positive selection in human populations

Author: Sabeti, PC, Varilly, P, Fry, B, Lohmueller, J, Hostetter, E, Cotsapas, C, Xie, X, Byrne, EH, McCarroll, SA, Gaudet, R, Schaffner, SF, Lander, ES, Frazer, KA, Ballinger, DG, Cox, DR, Hinds, DA, Stuve, LL, Gibbs, RA, Belmont, JW, Boudreau, A, Hardenbol, P, Leal, SM, Pasternak, S, Wheeler, DA, Willis, TD, Yu, F, Yang, H, Zeng, C, Gao, Y, Hu, H, Hu, W, Li, C, Lin, W, Liu, S, Pan, H, Tang, X, Wang, J, Wang, W, Yu, J, Zhang, B, Zhang, Q, Zhao, H, Zhou, J, Gabriel, SB, Barry, R, Blumenstiel, B, Camargo, A, Defelice, M, Faggart, M, Goyette, M, Gupta, S, Moore, J, Nguyen, H, Onofrio, RC, Parkin, M, Roy, J, Stahl, E, Winchester, E, Ziaugra, L, Altshuler, D, Shen, Y, Yao, Z, Huang, W, Chu, X, He, Y, Jin, L, Liu, Y, Sun, W, Wang, H, Wang, Y, Xiong, X, Xu, L, Waye, MM, Tsui, SK, Xue, H, Wong, JT, Galver, LM, Fan, JB, Gunderson, K, Murray, SS, Oliphant, AR, Chee, MS, Montpetit, A, Chagnon, F, Ferretti, V, Leboeuf, M, Olivier, JF, Phillips, MS, Roumy, S, Sallée, C, Verner, A, Hudson, TJ, Kwok, PY, Cai, D, Koboldt, DC, Miller, RD, Pawlikowska, L, Taillon-Miller, P, Xiao, M, Tsui, LC, Mak, W, Song, YQ, Tam, PK, Nakamura, Y, Kawaguchi, T, Kitamoto, T, Morizono, T, Nagashima, A, Ohnishi, Y, Sekine, A, Tanaka, T, Tsunoda, T, Deloukas, P, Bird, CP, Delgado, M, Dermitzakis, ET, Gwilliam, R, Hunt, S, Morrison, J, Powell, D, Stranger, BE, Whittaker, P, Bentley, DR, Daly, MJ, de Bakker, PI, Barrett, J, Chretien, YR, Maller, J, McCarroll, S, Patterson, N, Pe'er, I, Price, A, Purcell, S, Richter, DJ, Sabeti, P, Saxena, R, Sham, PC, Stein, LD, Krishnan, L, Smith, AV, Tello-Ruiz, MK, Thorisson, GA, Chakravarti, A, Chen, PE, Cutler, DJ, Kashuk, CS, Lin, S, Abecasis, GR, Guan, W, Li, Y, Munro, HM, Qin, ZS, Thomas, DJ, McVean, G, Auton, A, Bottolo, L, Cardin, N, Eyheramendy, S, Freeman, C, Marchini, J, Myers, S, Spencer, C, Stephens, M, Donnelly, P, Cardon, LR, Clarke, G, Evans, DM, Morris, AP, Weir, BS, Johnson, TA, Mullikin, JC, Sherry, ST, Feolo, M, Skol, A, Zhang, H, Matsuda, I, Fukushima, Y, Macer, DR, Suda, E, Rotimi, CN, Adebamowo, CA, Ajayi, I, Aniagwu, T, Marshall, PA, Nkwodimmah, C, Royal, CD, Leppert, MF, Dixon, M, Peiffer, A, Qiu, R, Kent, A, Kato, K, Niikawa, N, Adewole, IF, Knoppers, BM, Foster, MW, Clayton, EW, Watkin, J, Muzny, D, Nazareth, L, Sodergren, E, Weinstock, GM, Yakub, I, Birren, BW, Wilson, RK, Fulton, LL, Rogers, J, Burton, J, Carter, NP, Clee, CM, Griffiths, M, Jones, MC, McLay, K, Plumb, RW, Ross, MT, Sims, SK, Willey, DL, Chen, Z, Han, H, Kang, L, Godbout, M, Wallenburg, JC, L'Archevêque, P, Bellemare, G, Saeki, K, An, D, Fu, H, Li, Q, Wang, Z, Wang, R, Holden, AL, Brooks, LD, McEwen, JE, Guyer, MS, Wang, VO, Peterson, JL, Shi, M, Spiegel, J, Sung, LM, Zacharia, LF, Collins, FS, Kennedy, K, Jamieson, R, and Stewart, J
Subjects: Models, Molecular, Population, Single-nucleotide polymorphism, Human genetic variation, Biology, Polymorphism, Single Nucleotide, Article, Antiporters, Gene Frequency, Humans, International HapMap Project, Selection, Genetic, education, Selection (genetic algorithm), Genetics, education.field_of_study, Multidisciplinary, Natural selection, Geography, Edar Receptor, Genome, Human, Haplotype, Regional Index: Eurasia, Protein Structure, Tertiary, Europe, Genetics, Population, Haplotypes, Human genome
Abstract: With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia. ©2007 Nature Publishing Group., link_to_OA_fulltext
Published: 2007

31. Genetic Predictors of Circulating 25-Hydroxyvitamin D and Risk of Colorectal Cancer

Author: Hiraki, LT, Qu, C, Hutter, CM, Baron, JA, Berndt, SI, Bezieau, S, Brenner, H, Caan, BJ, Casey, G, Chang-Claude, J, Chanock, SJ, Conti, DV, Duggan, D, Fuchs, CS, Gallinger, S, Giovannucci, EL, Harrison, TA, Hayes, RB, Hazra, A, Henderson, B, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jenkins, MA, Kuery, SE, Le Marchand, L, Lemire, M, Ma, J, Manson, JE, Nan, H, Newcomb, PA, Ng, K, Potter, JD, Schoen, RE, Schumacher, FR, Seminara, D, Slattery, ML, Wactawski-Wende, J, White, E, Wu, K, Zanke, BW, Kraft, P, Peters, U, Chan, AT, Hiraki, LT, Qu, C, Hutter, CM, Baron, JA, Berndt, SI, Bezieau, S, Brenner, H, Caan, BJ, Casey, G, Chang-Claude, J, Chanock, SJ, Conti, DV, Duggan, D, Fuchs, CS, Gallinger, S, Giovannucci, EL, Harrison, TA, Hayes, RB, Hazra, A, Henderson, B, Hoffmeister, M, Hopper, JL, Hudson, TJ, Jenkins, MA, Kuery, SE, Le Marchand, L, Lemire, M, Ma, J, Manson, JE, Nan, H, Newcomb, PA, Ng, K, Potter, JD, Schoen, RE, Schumacher, FR, Seminara, D, Slattery, ML, Wactawski-Wende, J, White, E, Wu, K, Zanke, BW, Kraft, P, Peters, U, and Chan, AT
Abstract: BACKGROUND: Experimental evidence has demonstrated an antineoplastic role for vitamin D in the colon, and higher circulating 25-hydroxyvitamin D [25(OH)D] levels are consistently associated with a lower risk of colorectal cancer. Genome-wide association studies have identified loci associated with levels of circulating 25(OH)D. The identified single-nucleotide polymorphisms (SNPs) from four gene regions collectively explain approximately 5% of the variance in circulating 25(OH)D. METHODS: We investigated whether five polymorphisms in GC, CYP2R1, CYP24A1, and DHCR7/NADSYN1, genes previously shown to be associated with circulating 25(OH)D levels, were associated with colorectal cancer risk in 10,061 cases and 12,768 controls drawn from 13 studies included in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and Colon Cancer Family Registry (CCFR). We conducted a meta-analysis of crude and multivariate-adjusted logistic regression models to calculate odds ratios and associated confidence intervals for SNPs individually, SNPs simultaneously, and for a vitamin D additive genetic risk score (GRS). RESULTS: We did not observe a statistically significant association between the 25(OH)D-associated SNPs and colorectal cancer marginally, conditionally, or as a GRS, or for colon or rectal cancer separately. CONCLUSIONS: Our findings do not support an association between SNPs associated with circulating 25(OH)D and risk of colorectal cancer. Additional work is warranted to investigate the complex relationship between 25(OH)D and colorectal cancer risk. IMPACT: There was no association observed between genetic markers of circulating 25(OH)D and colorectal cancer. These genetic markers account for a small proportion of the variance in 25(OH)D.
Published: 2013

32. Meta-analysis of new genome-wide association studies of colorectal cancer risk

Author: Peters, U, Hutter, CM, Hsu, L, Schumacher, FR, Conti, DV, Carlson, CS, Edlund, CK, Haile, RW, Gallinger, S, Zanke, BW, Lemire, M, Rangrej, J, Vijayaraghavan, R, Chan, AT, Hazra, A, Hunter, DJ, Ma, J, Fuchs, CS, Giovannucci, EL, Kraft, P, Liu, Y, Chen, L, Jiao, S, Makar, KW, Taverna, D, Gruber, SB, Rennert, G, Moreno, V, Ulrich, CM, Woods, MO, Green, RC, Parfrey, PS, Prentice, RL, Kooperberg, C, Jackson, RD, LaCroix, AZ, Caan, BJ, Hayes, RB, Berndt, SI, Chanock, SJ, Schoen, RE, Chang-Claude, J, Hoffmeister, M, Brenner, H, Frank, B, Bezieau, S, Kuery, S, Slattery, ML, Hopper, JL, Jenkins, MA, Le Marchand, L, Lindor, NM, Newcomb, PA, Seminara, D, Hudson, TJ, Duggan, DJ, Potter, JD, Casey, G, Peters, U, Hutter, CM, Hsu, L, Schumacher, FR, Conti, DV, Carlson, CS, Edlund, CK, Haile, RW, Gallinger, S, Zanke, BW, Lemire, M, Rangrej, J, Vijayaraghavan, R, Chan, AT, Hazra, A, Hunter, DJ, Ma, J, Fuchs, CS, Giovannucci, EL, Kraft, P, Liu, Y, Chen, L, Jiao, S, Makar, KW, Taverna, D, Gruber, SB, Rennert, G, Moreno, V, Ulrich, CM, Woods, MO, Green, RC, Parfrey, PS, Prentice, RL, Kooperberg, C, Jackson, RD, LaCroix, AZ, Caan, BJ, Hayes, RB, Berndt, SI, Chanock, SJ, Schoen, RE, Chang-Claude, J, Hoffmeister, M, Brenner, H, Frank, B, Bezieau, S, Kuery, S, Slattery, ML, Hopper, JL, Jenkins, MA, Le Marchand, L, Lindor, NM, Newcomb, PA, Seminara, D, Hudson, TJ, Duggan, DJ, Potter, JD, and Casey, G
Abstract: Colorectal cancer is the second leading cause of cancer death in developed countries. Genome-wide association studies (GWAS) have successfully identified novel susceptibility loci for colorectal cancer. To follow up on these findings, and try to identify novel colorectal cancer susceptibility loci, we present results for GWAS of colorectal cancer (2,906 cases, 3,416 controls) that have not previously published main associations. Specifically, we calculated odds ratios and 95% confidence intervals using log-additive models for each study. In order to improve our power to detect novel colorectal cancer susceptibility loci, we performed a meta-analysis combining the results across studies. We selected the most statistically significant single nucleotide polymorphisms (SNPs) for replication using ten independent studies (8,161 cases and 9,101 controls). We again used a meta-analysis to summarize results for the replication studies alone, and for a combined analysis of GWAS and replication studies. We measured ten SNPs previously identified in colorectal cancer susceptibility loci and found eight to be associated with colorectal cancer (p value range 0.02 to 1.8 × 10(-8)). When we excluded studies that have previously published on these SNPs, five SNPs remained significant at p < 0.05 in the combined analysis. No novel susceptibility loci were significant in the replication study after adjustment for multiple testing, and none reached genome-wide significance from a combined analysis of GWAS and replication. We observed marginally significant evidence for a second independent SNP in the BMP2 region at chromosomal location 20p12 (rs4813802; replication p value 0.03; combined p value 7.3 × 10(-5)). In a region on 5p33.15, which includes the coding regions of the TERT-CLPTM1L genes and has been identified in GWAS to be associated with susceptibility to at least seven other cancers, we observed a marginally significant association with rs2853668 (replication p value 0.03; co
Published: 2012

33. Genome-Wide Search for Gene-Gene Interactions in Colorectal Cancer

Author: Yu, Z, Jiao, S, Hsu, L, Berndt, S, Bezieau, S, Brenner, H, Buchanan, D, Caan, BJ, Campbell, PT, Carlson, CS, Casey, G, Chan, AT, Chang-Claude, J, Chanock, S, Conti, DV, Curtis, KR, Duggan, D, Gallinger, S, Gruber, SB, Harrison, TA, Hayes, RB, Henderson, BE, Hoffmeister, M, Hopper, JL, Hudson, TJ, Hutter, CM, Jackson, RD, Jenkins, MA, Kantor, ED, Kolonel, LN, Kuery, S, Le Marchand, L, Lemire, M, Newcomb, PA, Potter, JD, Qu, C, Rosse, SA, Schoen, RE, Schumacher, FR, Seminara, D, Slattery, ML, Ulrich, CM, Zanke, BW, Peters, U, Yu, Z, Jiao, S, Hsu, L, Berndt, S, Bezieau, S, Brenner, H, Buchanan, D, Caan, BJ, Campbell, PT, Carlson, CS, Casey, G, Chan, AT, Chang-Claude, J, Chanock, S, Conti, DV, Curtis, KR, Duggan, D, Gallinger, S, Gruber, SB, Harrison, TA, Hayes, RB, Henderson, BE, Hoffmeister, M, Hopper, JL, Hudson, TJ, Hutter, CM, Jackson, RD, Jenkins, MA, Kantor, ED, Kolonel, LN, Kuery, S, Le Marchand, L, Lemire, M, Newcomb, PA, Potter, JD, Qu, C, Rosse, SA, Schoen, RE, Schumacher, FR, Seminara, D, Slattery, ML, Ulrich, CM, Zanke, BW, and Peters, U
Abstract: Genome-wide association studies (GWAS) have successfully identified a number of single-nucleotide polymorphisms (SNPs) associated with colorectal cancer (CRC) risk. However, these susceptibility loci known today explain only a small fraction of the genetic risk. Gene-gene interaction (GxG) is considered to be one source of the missing heritability. To address this, we performed a genome-wide search for pair-wise GxG associated with CRC risk using 8,380 cases and 10,558 controls in the discovery phase and 2,527 cases and 2,658 controls in the replication phase. We developed a simple, but powerful method for testing interaction, which we term the Average Risk Due to Interaction (ARDI). With this method, we conducted a genome-wide search to identify SNPs showing evidence for GxG with previously identified CRC susceptibility loci from 14 independent regions. We also conducted a genome-wide search for GxG using the marginal association screening and examining interaction among SNPs that pass the screening threshold (p<10(-4)). For the known locus rs10795668 (10p14), we found an interacting SNP rs367615 (5q21) with replication p = 0.01 and combined p = 4.19×10(-8). Among the top marginal SNPs after LD pruning (n = 163), we identified an interaction between rs1571218 (20p12.3) and rs10879357 (12q21.1) (nominal combined p = 2.51×10(-6); Bonferroni adjusted p = 0.03). Our study represents the first comprehensive search for GxG in CRC, and our results may provide new insight into the genetic etiology of CRC.
Published: 2012

34. Genome-wide meta-analysis of common variant differences between men and women

Author: Boraska, V, Jeroncic, A, Colonna, V, Southam, L, Nyholt, DR, Rayner, NW, Perry, JRB, Toniolo, D, Albrecht, E, Ang, W, Bandinelli, S, Barbalic, M, Barroso, I, Beckmann, JS, Biffar, R, Boomsma, D, Campbell, H, Corre, T, Erdmann, J, Esko, T, Fischer, K (Kirsten), Franceschini, N, Frayling, TM, Girotto, G, Gonzalez, JR, Harris, TB, Heath, AC, Heid, IM, Hoffmann, W, Hofman, Bert, Horikoshi, M, Zhao, JH, Jackson, AU, Hottenga, JJ (Jouke Jan), Jula, A, Kahonen, M, Khaw, KT, Kiemeney, LA, Klopp, N, Kutalik, Z, Lagou, V, Launer, LJ (Lenore), Lehtimaki, T, Lemire, M, Lokki, ML, Loley, C, Luan, JA, Mangino, M, Leach, IM, Medland, SE, Mihailov, E, Montgomery, GW, Navis, G, Newnham, J, Nieminen, MS, Palotie, A, Panoutsopoulou, K, Peters, A, Pirastu, N, Polasek, O, Rehnstrom, K, Ripatti, S, Ritchie, GRS, Rivadeneira, Fernando, Robino, A, Samani, NJ, Shin, SY, Sinisalo, J, Smit, JH, Soranzo, N, Stolk, Lisette, Swinkels, DW, Tanaka, T, Teumer, A, Tonjes, A, Traglia, M, Tuomilehto, J, Valsesia, A, van Gilst, WH, van Meurs, Joyce, Smith, AV, Viikari, J, Vink, JM, Waeber, G, Warrington, NM, Widen, E, Willemsen, G, Wright, AF, Zanke, BW, Zgaga, L, Boehnke, M, d'Adamo, AP, de Geus, ED, Demerath, EW, Heijer, Mariska, Eriksson, JG, Ferrucci, L, Gieger, C, Gudnason, V, Hayward, C, Hengstenberg, C, Hudson, TJ, Jarvelin, MR, Kogevinas, M, Loos, RJF, Martin, NG, Metspalu, A, Pennell, CE, Penninx, BW, Perola, M, Raitakari, O, Salomaa, V, Schreiber, S, Schunkert, H, Spector, TD, Stumvoll, M, Uitterlinden, André, Ulivi, S, van der Harst, P, Vollenweider, P, Volzke, H, Wareham, NJ, Wichmann, HE, Wilson, JF, Rudan, I, Xue, YL, Zeggini, E, Boraska, V, Jeroncic, A, Colonna, V, Southam, L, Nyholt, DR, Rayner, NW, Perry, JRB, Toniolo, D, Albrecht, E, Ang, W, Bandinelli, S, Barbalic, M, Barroso, I, Beckmann, JS, Biffar, R, Boomsma, D, Campbell, H, Corre, T, Erdmann, J, Esko, T, Fischer, K (Kirsten), Franceschini, N, Frayling, TM, Girotto, G, Gonzalez, JR, Harris, TB, Heath, AC, Heid, IM, Hoffmann, W, Hofman, Bert, Horikoshi, M, Zhao, JH, Jackson, AU, Hottenga, JJ (Jouke Jan), Jula, A, Kahonen, M, Khaw, KT, Kiemeney, LA, Klopp, N, Kutalik, Z, Lagou, V, Launer, LJ (Lenore), Lehtimaki, T, Lemire, M, Lokki, ML, Loley, C, Luan, JA, Mangino, M, Leach, IM, Medland, SE, Mihailov, E, Montgomery, GW, Navis, G, Newnham, J, Nieminen, MS, Palotie, A, Panoutsopoulou, K, Peters, A, Pirastu, N, Polasek, O, Rehnstrom, K, Ripatti, S, Ritchie, GRS, Rivadeneira, Fernando, Robino, A, Samani, NJ, Shin, SY, Sinisalo, J, Smit, JH, Soranzo, N, Stolk, Lisette, Swinkels, DW, Tanaka, T, Teumer, A, Tonjes, A, Traglia, M, Tuomilehto, J, Valsesia, A, van Gilst, WH, van Meurs, Joyce, Smith, AV, Viikari, J, Vink, JM, Waeber, G, Warrington, NM, Widen, E, Willemsen, G, Wright, AF, Zanke, BW, Zgaga, L, Boehnke, M, d'Adamo, AP, de Geus, ED, Demerath, EW, Heijer, Mariska, Eriksson, JG, Ferrucci, L, Gieger, C, Gudnason, V, Hayward, C, Hengstenberg, C, Hudson, TJ, Jarvelin, MR, Kogevinas, M, Loos, RJF, Martin, NG, Metspalu, A, Pennell, CE, Penninx, BW, Perola, M, Raitakari, O, Salomaa, V, Schreiber, S, Schunkert, H, Spector, TD, Stumvoll, M, Uitterlinden, André, Ulivi, S, van der Harst, P, Vollenweider, P, Volzke, H, Wareham, NJ, Wichmann, HE, Wilson, JF, Rudan, I, Xue, YL, and Zeggini, E
Abstract: The male-to-female sex ratio at birth is constant across world populations with an average of 1.06 (106 male to 100 female live births) for populations of European descent. The sex ratio is considered to be affected by numerous biological and environmental factors and to have a heritable component. The aim of this study was to investigate the presence of common allele modest effects at autosomal and chromosome X variants that could explain the observed sex ratio at birth. We conducted a large-scale genome-wide association scan (GWAS) meta-analysis across 51 studies, comprising overall 114 863 individuals (61 094 women and 53 769 men) of European ancestry and 2 623 828 common (minor allele frequency 0.05) single-nucleotide polymorphisms (SNPs). Allele frequencies were compared between men and women for directly-typed and imputed variants within each study. Forward-time simulations for unlinked, neutral, autosomal, common loci were performed under the demographic model for European populations with a fixed sex ratio and a random mating scheme to assess the probability of detecting significant allele frequency differences. We do not detect any genome-wide significant (P 5 10(8)) common SNP differences between men and women in this well-powered meta-analysis. The simulated data provided results entirely consistent with these findings. This large-scale investigation across approximate to 115 000 individuals shows no detectable contribution from common genetic variants to the observed skew in the sex ratio. The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased traits.
Published: 2012

35. Quality, quantity and harmony: The DataSHaPER approach to integrating data across bioclinical studies

Author: Fortier, I, Burton, PR, Robson, PJ, Ferretti, V, Little, J, L'Heureux, F, Deschênes, M, Knoppers, BM, Doiron, D, Keers, JC, Linksted, P, Harris, JR, Lachance, G, Boileau, C, Pedersen, NL, Hamilton, CM, Hveem, K, Borugian, MJ, Gallagher, RP, McLaughlin, J, Parker, L, Potter, JD, Gallacher, J, Kaaks, R, Liu, B, Sprosen, T, Vilain, A, Atkinson, SA, Rengifo, A, Morton, R, Metspalu, A, Erich Wichmann, H, Tremblay, M, Chisholm, RL, Garcia-Montero, A, Hillege, H, Litton, JE, Palmer, LJ, Perola, M, Wolffenbuttel, BHR, Peltonen, L, Hudson, TJ, Fortier, I, Burton, PR, Robson, PJ, Ferretti, V, Little, J, L'Heureux, F, Deschênes, M, Knoppers, BM, Doiron, D, Keers, JC, Linksted, P, Harris, JR, Lachance, G, Boileau, C, Pedersen, NL, Hamilton, CM, Hveem, K, Borugian, MJ, Gallagher, RP, McLaughlin, J, Parker, L, Potter, JD, Gallacher, J, Kaaks, R, Liu, B, Sprosen, T, Vilain, A, Atkinson, SA, Rengifo, A, Morton, R, Metspalu, A, Erich Wichmann, H, Tremblay, M, Chisholm, RL, Garcia-Montero, A, Hillege, H, Litton, JE, Palmer, LJ, Perola, M, Wolffenbuttel, BHR, Peltonen, L, and Hudson, TJ
Abstract: Background: Vast sample sizes are often essential in the quest to disentangle the complex interplay of the genetic, lifestyle, environmental and social factors that determine the aetiology and progression of chronic diseases. The pooling of information between studies is therefore of central importance to contemporary bioscience. However, there are many technical, ethico-legal and scientific challenges to be overcome if an effective, valid, pooled analysis is to be achieved. Perhaps most critically, any data that are to be analysed in this way must be adequately 'harmonized'. This implies that the collection and recording of information and data must be done in a manner that is sufficiently similar in the different studies to allow valid synthesis to take place. Methods: This conceptual article describes the origins, purpose and scientific foundations of the DataSHaPER (DataSchema and Harmonization Platform for Epidemiological Research; http://www.datashaper.org), which has been created by a multidisciplinary consortium of experts that was pulled together and coordinated by three international organizations: P3G (Public Population Project in Genomics), PHOEBE (Promoting Harmonization of Epidemiological Biobanks in Europe) and CPT (Canadian Partnership for Tomorrow Project). Results: The DataSHaPER provides a flexible, structured approach to the harmonization and pooling of information between studies. Its two primary components, the 'DataSchema' and 'Harmonization Platforms', together support the preparation of effective data-collection protocols and provide a central reference to facilitate harmonization. The DataSHaPER supports both 'prospective' and 'retrospective' harmonization. Conclusion: It is hoped that this article will encourage readers to investigate the project further: the more the research groups and studies are actively involved, the more effective the DataSHaPER programme will ultimately be. Published by Oxford University Press on behalf of the Inter
Published: 2010

36. International network of cancer genome projects

Author: Hudson, TJ, Anderson, W, Aretz, A, Barker, AD, Bell, C, Bernabe, RR, Bhan, MK, Calvo, F, Eerola, I, Gerhard, DS, Guttmacher, A, Guyer, M, Hemsley, FM, Jennings, JL, Kerr, D, Klatt, P, Kolar, P, Kusuda, J, Lane, DP, Laplace, F, Lu, Y, Nettekoven, G, Ozenberger, B, Peterson, J, Rao, TS, Remacle, J, Schafer, AJ, Shibata, T, Stratton, MR, Vockley, JG, Watanabe, K, Yang, H, Yuen, MMF, Knoppers, M, Bobrow, M, Cambon-Thomsen, A, Dressler, LG, Dyke, SOM, Joly, Y, Kato, K, Kennedy, KL, Nicolas, P, Parker, MJ, Rial-Sebbag, E, Romeo-Casabona, CM, Shaw, KM, Wallace, S, Wiesner, GL, Zeps, N, Lichter, P, Biankin, AV, Chabannon, C, Chin, L, Clement, B, de Alava, E, Degos, F, Ferguson, ML, Geary, P, Hayes, DN, Johns, AL, Nakagawa, H, Penny, R, Piris, MA, Sarin, R, Scarpa, A, van de Vijver, M, Futreal, PA, Aburatani, H, Bayes, M, Bowtell, DDL, Campbell, PJ, Estivill, X, Grimmond, SM, Gut, I, Hirst, M, Lopez-Otin, C, Majumder, P, Marra, M, Ning, Z, Puente, XS, Ruan, Y, Stunnenberg, HG, Swerdlow, H, Velculescu, VE, Wilson, RK, Xue, HH, Yang, L, Spellman, PT, Bader, GD, Boutros, PC, Flicek, P, Getz, G, Guigo, R, Guo, G, Haussler, D, Heath, S, Hubbard, TJ, Jiang, T, Jones, SM, Li, Q, Lopez-Bigas, N, Luo, R, Pearson, JV, Quesada, V, Raphael, BJ, Sander, C, Speed, TP, Stuart, JM, Teague, JW, Totoki, Y, Tsunoda, T, Valencia, A, Wheeler, DA, Wu, H, Zhao, S, Zhou, G, Stein, LD, Lathrop, M, Ouellette, BFF, Thomas, G, Yoshida, T, Axton, M, Gunter, C, McPherson, JD, Miller, LJ, Kasprzyk, A, Zhang, J, Haider, SA, Wang, J, Yung, CK, Cross, A, Liang, Y, Gnaneshan, S, Guberman, J, Hsu, J, Chalmers, DRC, Hasel, KW, Kaan, TSH, Knoppers, BM, Lowrance, WW, Masui, T, Rodriguez, LL, Vergely, C, Cloonan, N, Defazio, A, Eshleman, JR, Etemadmoghadam, D, Gardiner, BA, Kench, JG, Sutherland, RL, Tempero, MA, Waddell, NJ, Wilson, PJ, Gallinger, S, Tsao, M-S, Shaw, PA, Petersen, GM, Mukhopadhyay, D, DePinho, RA, Thayer, S, Muthuswamy, L, Shazand, K, Beck, T, Sam, M, Timms, L, Ballin, V, Ji, J, Zhang, X, Chen, F, Hu, X, Yang, Q, Tian, G, Zhang, L, Xing, X, Li, X, Zhu, Z, Yu, Y, Yu, J, Tost, J, Brennan, P, Holcatova, I, Zaridze, D, Brazma, A, Egevad, L, Prokhortchouk, E, Banks, RE, Uhlen, M, Viksna, J, Ponten, F, Skryabin, K, Birney, E, Borg, A, Borresen-Dale, A-L, Caldas, C, Foekens, JA, Martin, S, Reis-Filho, JS, Richardson, AL, Sotiriou, C, van't Veer, L, Birnbaum, D, Blanche, H, Boucher, P, Boyault, S, Masson-Jacquemier, JD, Pauporte, I, Pivot, X, Vincent-Salomon, A, Tabone, E, Theillet, C, Treilleux, I, Bioulac-Sage, P, Decaens, T, Franco, D, Gut, M, Samuel, D, Zucman-Rossi, J, Eils, R, Brors, B, Korbel, JO, Korshunov, A, Landgraf, P, Lehrach, H, Pfister, S, Radlwimmer, B, Reifenberger, G, Taylor, MD, von Kalle, C, Majumder, PP, Pederzoli, P, Lawlor, RT, Delledonne, M, Bardelli, A, Gress, T, Klimstra, D, Zamboni, G, Nakamura, Y, Miyano, S, Fujimoto, A, Campo, E, de Sanjose, S, Montserrat, E, Gonzalez-Diaz, M, Jares, P, Himmelbaue, H, Bea, S, Aparicio, S, Easton, DF, Collins, FS, Compton, CC, Lander, ES, Burke, W, Green, AR, Hamilton, SR, Kallioniemi, OP, Ley, TJ, Liu, ET, Wainwright, BJ, Hudson, TJ, Anderson, W, Aretz, A, Barker, AD, Bell, C, Bernabe, RR, Bhan, MK, Calvo, F, Eerola, I, Gerhard, DS, Guttmacher, A, Guyer, M, Hemsley, FM, Jennings, JL, Kerr, D, Klatt, P, Kolar, P, Kusuda, J, Lane, DP, Laplace, F, Lu, Y, Nettekoven, G, Ozenberger, B, Peterson, J, Rao, TS, Remacle, J, Schafer, AJ, Shibata, T, Stratton, MR, Vockley, JG, Watanabe, K, Yang, H, Yuen, MMF, Knoppers, M, Bobrow, M, Cambon-Thomsen, A, Dressler, LG, Dyke, SOM, Joly, Y, Kato, K, Kennedy, KL, Nicolas, P, Parker, MJ, Rial-Sebbag, E, Romeo-Casabona, CM, Shaw, KM, Wallace, S, Wiesner, GL, Zeps, N, Lichter, P, Biankin, AV, Chabannon, C, Chin, L, Clement, B, de Alava, E, Degos, F, Ferguson, ML, Geary, P, Hayes, DN, Johns, AL, Nakagawa, H, Penny, R, Piris, MA, Sarin, R, Scarpa, A, van de Vijver, M, Futreal, PA, Aburatani, H, Bayes, M, Bowtell, DDL, Campbell, PJ, Estivill, X, Grimmond, SM, Gut, I, Hirst, M, Lopez-Otin, C, Majumder, P, Marra, M, Ning, Z, Puente, XS, Ruan, Y, Stunnenberg, HG, Swerdlow, H, Velculescu, VE, Wilson, RK, Xue, HH, Yang, L, Spellman, PT, Bader, GD, Boutros, PC, Flicek, P, Getz, G, Guigo, R, Guo, G, Haussler, D, Heath, S, Hubbard, TJ, Jiang, T, Jones, SM, Li, Q, Lopez-Bigas, N, Luo, R, Pearson, JV, Quesada, V, Raphael, BJ, Sander, C, Speed, TP, Stuart, JM, Teague, JW, Totoki, Y, Tsunoda, T, Valencia, A, Wheeler, DA, Wu, H, Zhao, S, Zhou, G, Stein, LD, Lathrop, M, Ouellette, BFF, Thomas, G, Yoshida, T, Axton, M, Gunter, C, McPherson, JD, Miller, LJ, Kasprzyk, A, Zhang, J, Haider, SA, Wang, J, Yung, CK, Cross, A, Liang, Y, Gnaneshan, S, Guberman, J, Hsu, J, Chalmers, DRC, Hasel, KW, Kaan, TSH, Knoppers, BM, Lowrance, WW, Masui, T, Rodriguez, LL, Vergely, C, Cloonan, N, Defazio, A, Eshleman, JR, Etemadmoghadam, D, Gardiner, BA, Kench, JG, Sutherland, RL, Tempero, MA, Waddell, NJ, Wilson, PJ, Gallinger, S, Tsao, M-S, Shaw, PA, Petersen, GM, Mukhopadhyay, D, DePinho, RA, Thayer, S, Muthuswamy, L, Shazand, K, Beck, T, Sam, M, Timms, L, Ballin, V, Ji, J, Zhang, X, Chen, F, Hu, X, Yang, Q, Tian, G, Zhang, L, Xing, X, Li, X, Zhu, Z, Yu, Y, Yu, J, Tost, J, Brennan, P, Holcatova, I, Zaridze, D, Brazma, A, Egevad, L, Prokhortchouk, E, Banks, RE, Uhlen, M, Viksna, J, Ponten, F, Skryabin, K, Birney, E, Borg, A, Borresen-Dale, A-L, Caldas, C, Foekens, JA, Martin, S, Reis-Filho, JS, Richardson, AL, Sotiriou, C, van't Veer, L, Birnbaum, D, Blanche, H, Boucher, P, Boyault, S, Masson-Jacquemier, JD, Pauporte, I, Pivot, X, Vincent-Salomon, A, Tabone, E, Theillet, C, Treilleux, I, Bioulac-Sage, P, Decaens, T, Franco, D, Gut, M, Samuel, D, Zucman-Rossi, J, Eils, R, Brors, B, Korbel, JO, Korshunov, A, Landgraf, P, Lehrach, H, Pfister, S, Radlwimmer, B, Reifenberger, G, Taylor, MD, von Kalle, C, Majumder, PP, Pederzoli, P, Lawlor, RT, Delledonne, M, Bardelli, A, Gress, T, Klimstra, D, Zamboni, G, Nakamura, Y, Miyano, S, Fujimoto, A, Campo, E, de Sanjose, S, Montserrat, E, Gonzalez-Diaz, M, Jares, P, Himmelbaue, H, Bea, S, Aparicio, S, Easton, DF, Collins, FS, Compton, CC, Lander, ES, Burke, W, Green, AR, Hamilton, SR, Kallioniemi, OP, Ley, TJ, Liu, ET, and Wainwright, BJ
Abstract: The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
Published: 2010

37. The International HapMap Project

Author: Gibbs, RA, Belmont, JW, Hardenbol, P., Willis, TD, Yu, FL, Yang, HM, Ch'ang, LY, Huang, W., Liu, B., Shen, Y., Tam, PKH, Foster, MW, Jasperse, M., Knoppers, BM, Kwok, PY, Licinio, J., Long, JC, Marshall, PA, Ossorio, PN, Wang, VO, Rotimi, CN, Tsui, LC, Royal, CDM, Spallone, P., Terry, SF, Lander, ES, Lai, EH, Nickerson, DA, Abecasis, GR, Altshuler, D., Bentley, DR, Boehnke, M., Waye, MMY, Cardon, LR, Daly, MJ, Deloukas, P., Douglas, JA, Gabriel, SB, Hudson, RR, Hudson, TJ, Kruglyak, L., Nakamura, Y., Wong, JTF, Nussbaum, RL, Schaffner, SF, Sherry, ST, Stein, LD, Tanaka, T., Zeng, CQ, Zhang, QR, Chee, MS, Galver, LM, Kruglyak, S., Murray, SS, Oliphant, AR, Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, MS, Verner, A., Duan, SH, Lind, DL, Miller, RD, Rice, JP, Saccone, NL, Taillon-Miller, P., Xiao, M., Sekine, A., Sorimachi, K., Tanaka, Y., Tsunoda, T., Yoshino, E., Hunt, S., Powell, D., Qiu, RZ, Ken, A., Dunston, GM, Kato, K., Niikawa, N., Clayton, EW, Watkin, J., Sodergren, E., Weinstock, GM, Wilson, RK, Fulton, LL, Rogers, J., Birren, BW, Han, H., Wang, HG, Godbout, M., Wallenburg, JC, L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, AL, Collins, FS, Brooks, LD, McEwen, JE, Guyer, MS, Jordan, E., Peterson, JL, Spiegel, J., Sung, LM, Zacharia, LF, Kennedy, K., Dunn, MG, Seabrook, R., Shillito, M., Skene, B., Stewart, JG, Valle, DL, Jorde, LB, Chakravarti, A., Cho, MK, Duster, T., Gibbs, RA, Belmont, JW, Hardenbol, P., Willis, TD, Yu, FL, Yang, HM, Ch'ang, LY, Huang, W., Liu, B., Shen, Y., Tam, PKH, Foster, MW, Jasperse, M., Knoppers, BM, Kwok, PY, Licinio, J., Long, JC, Marshall, PA, Ossorio, PN, Wang, VO, Rotimi, CN, Tsui, LC, Royal, CDM, Spallone, P., Terry, SF, Lander, ES, Lai, EH, Nickerson, DA, Abecasis, GR, Altshuler, D., Bentley, DR, Boehnke, M., Waye, MMY, Cardon, LR, Daly, MJ, Deloukas, P., Douglas, JA, Gabriel, SB, Hudson, RR, Hudson, TJ, Kruglyak, L., Nakamura, Y., Wong, JTF, Nussbaum, RL, Schaffner, SF, Sherry, ST, Stein, LD, Tanaka, T., Zeng, CQ, Zhang, QR, Chee, MS, Galver, LM, Kruglyak, S., Murray, SS, Oliphant, AR, Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, MS, Verner, A., Duan, SH, Lind, DL, Miller, RD, Rice, JP, Saccone, NL, Taillon-Miller, P., Xiao, M., Sekine, A., Sorimachi, K., Tanaka, Y., Tsunoda, T., Yoshino, E., Hunt, S., Powell, D., Qiu, RZ, Ken, A., Dunston, GM, Kato, K., Niikawa, N., Clayton, EW, Watkin, J., Sodergren, E., Weinstock, GM, Wilson, RK, Fulton, LL, Rogers, J., Birren, BW, Han, H., Wang, HG, Godbout, M., Wallenburg, JC, L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, AL, Collins, FS, Brooks, LD, McEwen, JE, Guyer, MS, Jordan, E., Peterson, JL, Spiegel, J., Sung, LM, Zacharia, LF, Kennedy, K., Dunn, MG, Seabrook, R., Shillito, M., Skene, B., Stewart, JG, Valle, DL, Jorde, LB, Chakravarti, A., Cho, MK, and Duster, T.
Published: 2003

38. PHP93 ASSESSMENT OF METABOLIC MONITORING OF PATIENTS PRESCRIBED SECOND GENERATION ANTIPSYCHOTICS (SGAS) USING ELECTRONIC MEDICAL RECORD (EMR) DATA

Author: Dhamane, AD, primary, Martin, B, additional, Brixner, D, additional, Hudson, TJ, additional, and Said, Q, additional
Published: 2010
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39. La puce à ADN en médecine et en science.

Author: Lee, P, primary and Hudson, TJ, additional
Published: 2000
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40. Cancer genomics: technology, discovery, and translation.

Author: Tran B, Dancey JE, Kamel-Reid S, McPherson JD, Bedard PL, Brown AM, Zhang T, Shaw P, Onetto N, Stein L, Hudson TJ, Neel BG, and Siu LL
Published: 2012

41. An empirical basis for standardizing adherence measures derived from administrative claims data among diabetic patients.

Author: Karve S, Cleves MA, Helms M, Hudson TJ, West DS, and Martin BC
Published: 2008
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42. Association of common variation in the HNF1alpha gene region with risk of type 2 diabetes.

Author: Winckler W, Burtt NP, Holmkvist J, Cervin C, de Bakker PIW, Sun M, Almgren P, Tuomi T, Gaudet D, Hudson TJ, Ardlie KG, Daly MJ, Hirschhorn JN, Altshuler D, Groop L, Winckler, Wendy, Burtt, Noël P, Holmkvist, Johan, Cervin, Camilla, and de Bakker, Paul I W
Abstract: It is currently unclear how often genes that are mutated to cause rare, early-onset monogenic forms of disease also harbor common variants that contribute to the more typical polygenic form of each disease. The gene for MODY3 diabetes, HNF1alpha, lies in a region that has shown linkage to late-onset type 2 diabetes (12q24, NIDDM2), and previous association studies have suggested a weak trend toward association for common missense variants in HNF1alpha with glucose-related traits. Based on genotyping of 79 common SNPs in the 118 kb spanning HNF1alpha, we selected 21 haplotype tag single nucleotide polymorphisms (SNPs) and genotyped them in >4,000 diabetic patients and control subjects from Sweden, Finland, and Canada. Several SNPs from the coding region and 5' of the gene demonstrated nominal association with type 2 diabetes, with the most significant marker (rs1920792) having an odds ratio of 1.17 and a P value of 0.002. We then genotyped three SNPs with the strongest evidence for association to type 2 diabetes (rs1920792, I27L, and A98V) in an additional 4,400 type 2 diabetic and control subjects from North America and Poland and compared our results with those of the original sample and of Weedon et al. None of the results were consistently observed across all samples, with the possible exception of a modest association of the rare (3-5%) A98V variant. These results indicate that common variants in HNF1alpha either play no role in type 2 diabetes, a very small role, or a role that cannot be consistently observed without consideration of as yet unmeasured genetic or environmental modifiers. [ABSTRACT FROM AUTHOR]
Published: 2005
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43. Association of vitamin D receptor genetic variants with susceptibility to asthma and atopy.

Author: Poon AH, Laprise C, Lemire M, Montpetit A, Sinnett D, Schurr E, and Hudson TJ
Abstract: Genome scans for asthma have identified suggestive or significant linkages on 17 different chromosomes, including chromosome 12, region q13-23, housing the vitamin D receptor (VDR) gene. Through interaction with VDR, 1,25-dihydroxyvitamin D3 mediates numerous biological activities, such as regulation of helper T-cell development and subsequent cytokine secretion profiles. Variants of the VDR have been found to be associated with immune-mediated diseases that are characterized by an imbalance in helper T-cell development, such as Crohn's disease and tuberculosis. The VDR, hence, is a good candidate to be investigated for association with asthma, which is characterized by enhanced helper T-cell type 2 activity. Here, we examined VDR genetic variants in an asthma family-based cohort from Quebec. We report six variants to be strongly associated with asthma and four with atopy (0.0005 < or = p < or = 0.05). Analysis of the linkage disequilibrium pattern and haplotypes also revealed significant association with both phenotypes (0.0004 < or = p < or = 0.01). The findings have been replicated by another research team in a second but not in a third cohort. These results identify VDR variants as genetic risk factors for asthma/atopy and implicate a non-human leukocyte antigen immunoregulatory molecule in the pathogenesis of asthma and atopy. [ABSTRACT FROM AUTHOR]
Published: 2004
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44. The effect of guideline implementation strategies on akathisia outcomes in schizophrenia.

Author: Williams DK, Thrush CR, Armitage TL, Owen RR, Hudson TJ, and Thapa P
Abstract: Background: The purpose of this study was to examine the effect of a conceptually driven, multicomponent strategy for implementing guidelines to improve akathisia in schizophrenia.Methods: Patients included in the study were recruited from 6 Veterans Affairs Medical Centers (VAMCs) that were split into geographically matched pairs with 3 VAMCs receiving basic education and 3 receiving enhanced intervention to promote guideline-concordant treatment and patient adherence.Results: Of 293 patients with baseline and 6-month follow-up Barnes Akathisia Rating Scale (BARS) scores, results of both nonparametric and parametric repeated measures ANOVA showed several significant site-pair intervention effects, though the patterns were not consistent across the site-pairs. Logistic regression results controlling for baseline akathisia diagnosis and for patient covariates showed varying effects of the intervention among site-pairs as well. Exploratory results for differences in akathisia in those on novel versus conventional antipsychotics are also presented.Conclusions: Akathisia tended to improve over time, but the enhanced guideline-implementation strategy did not consistently result in lower prevalence and severity of akathisia at all sites, apparently due to considerable differences in patient or site characteristics. [ABSTRACT FROM AUTHOR]
Published: 2003

45. Personalized medicine: a transformative approach is needed.

Author: Hudson TJ and Hudson, Thomas J
Published: 2009
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46. Finding genetic modifiers of cystic fibrosis.

Author: Haston CK and Hudson TJ
Published: 2005

47. A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality.

Author: Loo VG, Poirier L, Miller MA, Oughton M, Libman MD, Michaud S, Bourgault A, Nguyen T, Frenette C, Kelly M, Vibien A, Brassard P, Fenn S, Dewar K, Hudson TJ, Horn R, René P, Monczak Y, Dascal A, and Loo, Vivian G
Abstract: Background: In March 2003, several hospitals in Quebec, Canada, noted a marked increase in the incidence of Clostridium difficile-associated diarrhea.Methods: In 2004 we conducted a prospective study at 12 Quebec hospitals to determine the incidence of nosocomial C. difficile-associated diarrhea and its complications and a case-control study to identify risk factors for the disease. Isolates of C. difficile were typed by pulsed-field gel electrophoresis and analyzed for binary toxin genes and partial deletions in the toxin A and B repressor gene tcdC. Antimicrobial susceptibility was evaluated in a subgroup of isolates.Results: A total of 1703 patients with 1719 episodes of nosocomial C. difficile-associated diarrhea were identified. The incidence was 22.5 per 1000 admissions. The 30-day attributable mortality rate was 6.9 percent. Case patients were more likely than matched controls to have received fluoroquinolones (odds ratio, 3.9; 95 percent confidence interval, 2.3 to 6.6) or cephalosporins (odds ratio, 3.8; 95 percent confidence interval, 2.2 to 6.6). A predominant strain, resistant to fluoroquinolones, was found in 129 of 157 isolates (82.2 percent), and the binary toxin genes and partial deletions in the tcdC gene were present in 132 isolates (84.1 percent).Conclusions: A strain of C. difficile that was resistant to fluoroquinolones and had binary toxin and a partial deletion of the tcdC gene was responsible for this outbreak of C. difficile-associated diarrhea. Exposure to fluoroquinolones or cephalosporins was a risk factor. [ABSTRACT FROM AUTHOR]
Published: 2005

48. Are gaps in rates of retention on buprenorphine for treatment of opioid use disorder closing among veterans across different races and ethnicities? A retrospective cohort study.

Author: Hayes CJ, Raciborski RA, Martin BC, Gordon AJ, Hudson TJ, Brown CC, Pro G, and Cucciare MA
Subjects: Humans, Retrospective Studies, Male, Female, United States epidemiology, Middle Aged, Adult, Ethnicity statistics & numerical data, United States Department of Veterans Affairs statistics & numerical data, Racial Groups statistics & numerical data, Buprenorphine therapeutic use, Veterans statistics & numerical data, Opioid-Related Disorders drug therapy, Opioid-Related Disorders epidemiology, Opioid-Related Disorders ethnology, Opiate Substitution Treatment statistics & numerical data
Abstract: Introduction: The U.S. Veterans Health Administration has undertaken several initiatives to improve veterans' access to and retention on buprenorphine because it prevents overdose and reduces drug-related morbidity. We aimed to determine whether improvements in retention duration over time was equitable across veterans of different races and ethnicities., Methods: This retrospective cohort study was conducted among veterans who initiated buprenorphine from federal fiscal years (FY) 2006 to 2020 after diagnosis of opioid use disorder. Using an accelerated failure time model, we estimated the association between time to buprenorphine discontinuation and FY of initiation, race and ethnicity, and other control covariates. We followed veterans from buprenorphine initiation until they discontinued or had a censoring event. We then estimated the predicted median days retained on buprenorphine, the average marginal effect of initiating in a later FY, the same measure by race and ethnicity, the incremental effect of the various racial and ethnic identities in contrast to non-Hispanic White, and the total change in the size of the gap over the 15 years of the study between veterans with a minoritized racial or ethnic identity compared to non-Hispanic White veterans., Results: Most of the 31,797 veterans in the sample were non-Hispanic White (74.5 %), from urban areas (83.5 %), male (92.0 %), and had significant comorbidities, most frequently anxiety disorders (51.0 %) and depression (63.0 %). Overall, 49.8 % of veterans were retained at least 180 days. The average marginal effect of FY was 7.0 days [95%CI:5.3, 8.8] but was significantly smaller among veterans identifying as Black or African American [3.2 days; 95%CI:2.4, 4.1] or Asian [3.6 days; 95%CI:1.6, 5.7] compared to veterans who identify as non-Hispanic White [7.9 days; 95%CI:5.9, 9.9]. Additional measures of change were significant for veterans identifying as Hispanic White or with two or more races., Conclusion: Although buprenorphine retention in OUD treatment improved for all veterans over the 15-year study period, veterans from most minoritized racial and ethnic groups fell further behind as gains in duration on therapy accrued primarily to non-Hispanic White veterans. Targeted interventions addressing specific challenges experienced by veterans with minoritized identities are needed to close gaps in retention on buprenorphine., Competing Interests: Declaration of competing interest None., (Published by Elsevier Inc.)
Published: 2024
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49. Average Daily Dose Trajectories for Episodes of Buprenorphine Treatment for Opioid Use Disorder.

Author: Hayes CJ, Martin BC, Hoggatt KJ, Cucciare MA, Hudson TJ, and Gordon AJ
Subjects: Humans, Female, Male, Adult, Middle Aged, United States epidemiology, Analgesics, Opioid administration & dosage, Analgesics, Opioid therapeutic use, Analgesics, Opioid adverse effects, United States Department of Veterans Affairs, Narcotic Antagonists administration & dosage, Narcotic Antagonists therapeutic use, Buprenorphine administration & dosage, Buprenorphine therapeutic use, Opioid-Related Disorders drug therapy, Opioid-Related Disorders epidemiology, Opiate Substitution Treatment methods
Abstract: Background: High-dose (≥24 mg) buprenorphine daily doses (BDD) may be important in treating patients with opioid use disorder (OUD) to improve retention and prevent overdose, particularly in the context of increased illicit fentanyl use. This study sought to: (1) identify trajectories for average BDD among patients initiating buprenorphine treatment for OUD and (2) assess patient characteristics associated with these identified trajectories., Methods: Buprenorphine treatment episodes among patients in the US Veterans Healthcare Administration (VHA) from federal fiscal years 2006 to 2020 were identified. Group-based trajectory modeling (GBTM) was used to identify BDD trajectories based on weekly averages of BDD over the 180 days after buprenorphine episode initiation., Results: A total of 79 303 buprenorphine treatment episodes among 44 583 patients were included in the analytic sample. GBTM identified 9 latent trajectories for BDD: (1) moderate dose, early discontinuation (10.1%), (2) moderate dose, delayed discontinuation (4.5%), (3) moderate dose, moderate-paced discontinuation (5.2%), (4) low-moderate dose, delayed discontinuation (7.0%), and (5) low-moderate dose, early discontinuation (21.1%), (6) low dose retention (9.6%), (7) low-moderate dose retention (16.7%), (8) moderate dose retention (18.6%), and (9) high dose retention (7.4%). Patient BDD can broadly be characterized as low [2-4 mg/day], low-moderate (6-8 mg/day), moderate (12-18 mg/day), and high dose (≥ 24 mg/day). Patients with episodes in the high BDD trajectory have the lowest social risk (eg, lowest rate of past-year history of homelessness) and the lowest diagnosed rate of physical and mental health-related comorbidities compared to those following other trajectories., Conclusions: BDD ranges widely and patient characteristics are significantly different between those episodes following differing BDD trajectories. Future research on the association between BDD and subsequent patient outcomes (eg, overdose) needs to carefully consider these differences in baseline characteristics., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Published: 2024
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50. On the function of TRAP substrate-binding proteins: Conformational variation of the sialic acid binding protein SiaP.

Author: King-Hudson TJ, Davies JS, Quan S, Currie MJ, Tillett ZD, Copping J, Panjikar S, Friemann R, Allison JR, North RA, and Dobson RCJ
Abstract: Tripartite ATP-independent periplasmic (TRAP) transporters are analogous to ABC transporters in that they use a substrate-binding protein to scavenge metabolites (e.g., N-acetylneuraminate) and deliver them to the membrane components for import. TRAP substrate-binding proteins are thought to bind the substrate using a two-state (open and closed) induced-fit mechanism. We solved the structure of the TRAP N-acetylneuraminate substrate-binding protein from Aggregatibacter actinomycetemcomitans (AaSiaP) in both the open ligand-free and closed liganded conformations. Surprisingly, we also observed an intermediate conformation, where AaSiaP is mostly closed and is bound to a non-cognate ligand, acetate, which hints at how N-acetylneuraminate binding stabilizes a fully closed state. AaSiaP preferentially binds N-acetylneuraminate (K D = 0.4 μM) compared to N-glycolylneuraminate (K D = 4.4 μM), which is explained by the closed-N-acetylneuraminate bound structure. Small-angle X-ray scattering data alongside molecular dynamics simulations suggest the AaSiaP adopts a more open state in solution than in a crystal. However, the open unliganded conformation can also sample closed conformations. Molecular dynamics simulations also demonstrate the importance of water molecules for stabilizing the closed conformation. Although our data is consistent with an induced fit model of binding, we suggest that the open unliganded conformation may sample multiple states capable of binding substrate. The mechanism by which the ligand is released for import remains to be determined., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
Published: 2024
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