Faculty Appointments
Associate Professor of Medicine
Education
M.D., Medicine, University of Texas Southwestern Medical School, Dallas, TexasPh.D., Cellular & Molecular Biology, University of Texas Southwestern Medical School, Dallas, TexasA.B., Biochemistry & Molecular Biology, Harvard University, Cambridge, Massachusetts
Office Address
529 Light Hall
2215 Garland Ave
Nashville, TN 37232-0275
Nashville, TN 37232-0275
Research Description
Our research group investigates genetic predisposition to cancer and genetic determinants of cancer outcomes. We hope to elucidate causality and contribute to personalized medicine. We apply state-of-the-art genomics approaches and custom analytical tools in large-scale, data-driven projects.
We have had a longstanding interest in the genetics of familial prostate cancer. Infrequent families are disproportionately affected by this disease, reflecting an increased genetic burden. But there is considerable heterogeneity, with genetic causes differing between families, and even among men within a single family. The underlying alleles carry relatively strong risk for prostate cancer, singly and in aggregate, and are predictive of both risk and aggressiveness.
Although prostate cancer has the greatest heritability of all common cancers, its challenging complexity has required innovative approaches for study. We conducted the first pedigree-based linkage study as well as population-based GWAS of prostate cancer, leading to early recognition of the limitations of the approaches. This led to our conception of the familial case-control study design, comparing men in the tails of disease risk; independent cases, each with a strong family history, are compared to screened controls without a personal or family history of the disease. We have accrued 2,500 patients in this study and are sequencing their genomes and developing innovative statistical genetic approaches to reveal causal mutations.
Our second active project investigates the impact of mutations upon cancer survival within the Pan-Cancer Atlas, a study of 32 cancer types encompassing 10,652 cancer patients. In a landmark study, we discovered that a tumor's burden of pathogenic somatic mutations is remarkably predictive of both disease-specific and overall survival (P=5e-95). Patients with both low and high mutation burden fare notably better than those with an intermediate burden. Tumor mutation burden meaningfully distinguishes survival even among patients sharing a given cancer type, stage, and grade. Molecular mutation burden is a fundamental predictor of patient outcome, independently of anatomic stage and histologic grade. It is a key index of survival of analogous clinical utility to these traditional factors. We have now identified inherited genetic variation in Pan-Cancer Atlas patients to investigate its contribution to survival.
Past work by our group has included a collaborative breast cancer study with Drs. William Dupont and Melinda Sanders. This study investigated genetic, epidemiologic, and pathologic factors in the progression of premalignant breast lesions to invasive breast cancer. It investigated the Nashville Breast Cohort of 9,000 women with benign forms of breast disease who were followed for over two decades for the development of invasive breast cancer.
We have also previously developed genetic mapping resources for the zebrafish model organism. We identified two million SNPs, developed a high-resolution genetic map, characterized strain diversity, and first revealed the mechanism of genetic sex determination in this model organism.
We have had a longstanding interest in the genetics of familial prostate cancer. Infrequent families are disproportionately affected by this disease, reflecting an increased genetic burden. But there is considerable heterogeneity, with genetic causes differing between families, and even among men within a single family. The underlying alleles carry relatively strong risk for prostate cancer, singly and in aggregate, and are predictive of both risk and aggressiveness.
Although prostate cancer has the greatest heritability of all common cancers, its challenging complexity has required innovative approaches for study. We conducted the first pedigree-based linkage study as well as population-based GWAS of prostate cancer, leading to early recognition of the limitations of the approaches. This led to our conception of the familial case-control study design, comparing men in the tails of disease risk; independent cases, each with a strong family history, are compared to screened controls without a personal or family history of the disease. We have accrued 2,500 patients in this study and are sequencing their genomes and developing innovative statistical genetic approaches to reveal causal mutations.
Our second active project investigates the impact of mutations upon cancer survival within the Pan-Cancer Atlas, a study of 32 cancer types encompassing 10,652 cancer patients. In a landmark study, we discovered that a tumor's burden of pathogenic somatic mutations is remarkably predictive of both disease-specific and overall survival (P=5e-95). Patients with both low and high mutation burden fare notably better than those with an intermediate burden. Tumor mutation burden meaningfully distinguishes survival even among patients sharing a given cancer type, stage, and grade. Molecular mutation burden is a fundamental predictor of patient outcome, independently of anatomic stage and histologic grade. It is a key index of survival of analogous clinical utility to these traditional factors. We have now identified inherited genetic variation in Pan-Cancer Atlas patients to investigate its contribution to survival.
Past work by our group has included a collaborative breast cancer study with Drs. William Dupont and Melinda Sanders. This study investigated genetic, epidemiologic, and pathologic factors in the progression of premalignant breast lesions to invasive breast cancer. It investigated the Nashville Breast Cohort of 9,000 women with benign forms of breast disease who were followed for over two decades for the development of invasive breast cancer.
We have also previously developed genetic mapping resources for the zebrafish model organism. We identified two million SNPs, developed a high-resolution genetic map, characterized strain diversity, and first revealed the mechanism of genetic sex determination in this model organism.
Research Keywords
genetic, genetics, genomics, genome, inherited, heritable, heritability, family, familial, cancer, risk, survival, outcome, TMB, tumor mutation burden, prostate, prostate cancer, breast, breast cancer, pedigree, linkage, GWAS, statistics, statistical, informatics, bioinformatics, variant, variation, mutation, SNP, polymorphism, germline, somatic, personalized medicine, precision medicine, association study, computational, biobank, BioVU
Publications
Smith JR, Parl FF, Dupont WD. Mutation Burden Independently Predicts Survival in the Pan-Cancer Atlas. JCO Precis Oncol. 2023 Jun; 7: e2200571. PMID: 37276492, PMCID: PMC10309535, DOI: 10.1200/PO.22.00571, ISSN: 2473-4284.
Dupont WD, Breyer JP, Johnson SH, Plummer WD, Smith JR. Prostate cancer risk variants of the HOXB genetic locus. Sci Rep. 2021 May 5/31/2021; 11(1): 11385. PMID: 34059701, PMCID: PMC8167119, PII: 10.1038/s41598-021-89399-7, DOI: 10.1038/s41598-021-89399-7, ISSN: 2045-2322.
Dupont WD, Breyer JP, Plummer WD, Chang SS, Cookson MS, Smith JA, , Blue EE, Bamshad MJ, Smith JR. 8q24 genetic variation and comprehensive haplotypes altering familial risk of prostate cancer. Nat Commun. 2020 Mar 3/23/2020; 11(1): 1523. PMID: 32251286, PMCID: PMC7089954, PII: 10.1038/s41467-020-15122-1, DOI: 10.1038/s41467-020-15122-1, ISSN: 2041-1723.
Dupont WD, Breyer JP, Plummer WD, Chang SS, Cookson MS, Smith JA, , Blue EE, Bamshad MJ, Smith JR. 8q24 genetic variation and comprehensive haplotypes altering familial risk of prostate cancer. Nat Commun. 2020 Mar 3/23/2020; 11(1): 1523. PMID: 32251286, PMCID: PMC7089954, PII: 10.1038/s41467-020-15122-1, DOI: 10.1038/s41467-020-15122-1, ISSN: 2041-1723.
Breyer JP, Smith JR. Practical genotyping by single-nucleotide primer extension. Biol Methods Protoc. 2020; 5(1): bpaa002. PMID: 32382659, PMCID: PMC7200932, PII: bpaa002, DOI: 10.1093/biomethods/bpaa002, ISSN: 2396-8923.
Breyer JP, Smith JR. Practical genotyping by single-nucleotide primer extension. Biol Methods Protoc. 2020; 5(1): bpaa002. PMID: 32382659, PMCID: PMC7200932, PII: bpaa002, DOI: 10.1093/biomethods/bpaa002, ISSN: 2396-8923.
Degnim AC, Dupont WD, Radisky DC, Vierkant RA, Frank RD, Frost MH, Winham SJ, Sanders ME, Smith JR, Page DL, Hoskin TL, Vachon CM, Ghosh K, Hieken TJ, Denison LA, Carter JM, Hartmann LC, Visscher DW. Extent of atypical hyperplasia stratifies breast cancer risk in 2 independent cohorts of women. Cancer [print-electronic]. 2016 Oct; 122(19): 2971-8. PMID: 27352219, PMCID: PMC5030128, DOI: 10.1002/cncr.30153, ISSN: 1097-0142.
Degnim AC, Dupont WD, Radisky DC, Vierkant RA, Frank RD, Frost MH, Winham SJ, Sanders ME, Smith JR, Page DL, Hoskin TL, Vachon CM, Ghosh K, Hieken TJ, Denison LA, Carter JM, Hartmann LC, Visscher DW. Extent of atypical hyperplasia stratifies breast cancer risk in 2 independent cohorts of women. Cancer [print-electronic]. 2016 Oct; 122(19): 2971-8. PMID: 27352219, PMCID: PMC5030128, DOI: 10.1002/cncr.30153, ISSN: 1097-0142.
Solus JF, Chung CP, Oeser A, Li C, Rho YH, Bradley KM, Kawai VK, Smith JR, Stein CM. Genetics of serum concentration of IL-6 and TNFa in systemic lupus erythematosus and rheumatoid arthritis: a candidate gene analysis. Clin. Rheumatol [print-electronic]. 2015 Aug; 34(8): 1375-82. PMID: 25652333, PMCID: PMC4526456, DOI: 10.1007/s10067-015-2881-6, ISSN: 1434-9949.
Chung CP, Solus JF, Oeser A, Li C, Raggi P, Smith JR, Stein CM. A variant in the osteoprotegerin gene is associated with coronary atherosclerosis in patients with rheumatoid arthritis: results from a candidate gene study. Int J Mol Sci. 2015; 16(2): 3885-94. PMID: 25679449, PMCID: PMC4346932, PII: ijms16023885, DOI: 10.3390/ijms16023885, ISSN: 1422-0067.
Chung CP, Solus JF, Oeser A, Li C, Raggi P, Smith JR, Stein CM. Genetic variation and coronary atherosclerosis in patients with systemic lupus erythematosus. Lupus [print-electronic]. 2014 Aug; 23(9): 876-80. PMID: 24699314, PMCID: PMC4185017, PII: 0961203314530019, DOI: 10.1177/0961203314530019, ISSN: 1477-0962.
Breyer JP, Dorset DC, Clark TA, Bradley KM, Wahlfors TA, McReynolds KM, Maynard WH, Chang SS, Cookson MS, Smith JA, Schleutker J, Dupont WD, Smith JR. An expressed retrogene of the master embryonic stem cell gene POU5F1 is associated with prostate cancer susceptibility. Am. J. Hum. Genet [print-electronic]. 2014 Mar 3/6/2014; 94(3): 395-404. PMID: 24581739, PMCID: PMC3951923, PII: S0002-9297(14)00057-3, DOI: 10.1016/j.ajhg.2014.01.019, ISSN: 1537-6605.
Gray RS, Wilm TP, Smith J, Bagnat M, Dale RM, Topczewski J, Johnson SL, Solnica-Krezel L. Loss of col8a1a function during zebrafish embryogenesis results in congenital vertebral malformations. Dev. Biol [print-electronic]. 2014 Feb 2/1/2014; 386(1): 72-85. PMID: 24333517, PMCID: PMC3938106, PII: S0012-1606(13)00645-3, DOI: 10.1016/j.ydbio.2013.11.028, ISSN: 1095-564X.
Weng PH, Huang YL, Page JH, Chen JH, Xu J, Koutros S, Berndt S, Chanock S, Yeager M, Witte JS, Eeles RA, Easton DF, Neal DE, Donovan J, Hamdy FC, Muir KR, Giles G, Severi G, Smith JR, Balistreri CR, Shui IM, Chen YC. Polymorphisms of an innate immune gene, toll-like receptor 4, and aggressive prostate cancer risk: a systematic review and meta-analysis. PLoS ONE. 2014; 9(10): e110569. PMID: 25360682, PMCID: PMC4215920, PII: PONE-D-14-21052, DOI: 10.1371/journal.pone.0110569, ISSN: 1932-6203.
Kodaman N, Aldrich MC, Smith JR, Signorello LB, Bradley K, Breyer J, Cohen SS, Long J, Cai Q, Giles J, Bush WS, Blot WJ, Matthews CE, Williams SM. A small number of candidate gene SNPs reveal continental ancestry in African Americans. Ann. Hum. Genet. 2013 Jan; 77(1): 56-66. PMID: 23278390, PMCID: PMC3677760, DOI: 10.1111/j.1469-1809.2012.00738.x, ISSN: 1469-1809.
Higginbotham KS, Breyer JP, McReynolds KM, Bradley KM, Schuyler PA, Plummer WD, Freudenthal ME, Trentham-Dietz A, Newcomb PA, Parl FF, Sanders ME, Page DL, Egan KM, Dupont WD, Smith JR. A multistage genetic association study identifies breast cancer risk loci at 10q25 and 16q24. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2012 Sep; 21(9): 1565-73. PMID: 22806168, PMCID: PMC3707501, PII: 1055-9965.EPI-12-0386, DOI: 10.1158/1055-9965.EPI-12-0386, ISSN: 1538-7755.
Breyer JP, Avritt TG, McReynolds KM, Dupont WD, Smith JR. Confirmation of the HOXB13 G84E germline mutation in familial prostate cancer. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2012 Aug; 21(8): 1348-53. PMID: 22714738, PMCID: PMC3415588, PII: 1055-9965.EPI-12-0495, DOI: 10.1158/1055-9965.EPI-12-0495, ISSN: 1538-7755.
Edwards TL, Velez Edwards DR, Villegas R, Cohen SS, Buchowski MS, Fowke JH, Schlundt D, Long J, Cai Q, Zheng W, Shu XO, Hargreaves MK, Smith J, Williams SM, Signorello LB, Blot WJ, Matthews CE. HTR1B, ADIPOR1, PPARGC1A, and CYP19A1 and obesity in a cohort of Caucasians and African Americans: an evaluation of gene-environment interactions and candidate genes. Am. J. Epidemiol [print-electronic]. 2012 Jan 1/1/2012; 175(1): 11-21. PMID: 22106445, PMCID: PMC3244609, PII: kwr272, DOI: 10.1093/aje/kwr272, ISSN: 1476-6256.
Melville DB, Montero-Balaguer M, Levic DS, Bradley K, Smith JR, Hatzopoulos AK, Knapik EW. The feelgood mutation in zebrafish dysregulates COPII-dependent secretion of select extracellular matrix proteins in skeletal morphogenesis. Dis Model Mech [print-electronic]. 2011 Nov; 4(6): 763-76. PMID: 21729877, PMCID: PMC3209646, PII: dmm.007625, DOI: 10.1242/dmm.007625, ISSN: 1754-8411.
Cohen SS, Gammon MD, North KE, Millikan RC, Lange EM, Williams SM, Zheng W, Cai Q, Long J, Smith JR, Signorello LB, Blot WJ, Matthews CE. ADIPOQ, ADIPOR1, and ADIPOR2 polymorphisms in relation to serum adiponectin levels and BMI in black and white women. Obesity (Silver Spring) [print-electronic]. 2011 Oct; 19(10): 2053-62. PMID: 21273992, PMCID: PMC3474141, PII: oby2010346, DOI: 10.1038/oby.2010.346, ISSN: 1930-739X.
Crooke PS, Justenhoven C, Brauch H, , Dawling S, Roodi N, Higginbotham KS, Plummer WD, Schuyler PA, Sanders ME, Page DL, Smith JR, Dupont WD, Parl FF. Estrogen metabolism and exposure in a genotypic-phenotypic model for breast cancer risk prediction. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2011 Jul; 20(7): 1502-15. PMID: 21610218, PMCID: PMC3472969, PII: 1055-9965.EPI-11-0060, DOI: 10.1158/1055-9965.EPI-11-0060, ISSN: 1538-7755.
Higginbotham KS, Breyer JP, Bradley KM, Schuyler PA, Plummer WD, Freudenthal ME, Trentham-Dietz A, Newcomb PA, Sanders ME, Page DL, Parl FF, Egan KM, Dupont WD, Smith JR. A multistage association study identifies a breast cancer genetic locus at NCOA7. Cancer Res [print-electronic]. 2011 Jun 6/1/2011; 71(11): 3881-8. PMID: 21610108, PMCID: PMC3137260, PII: 0008-5472.CAN-10-2653, DOI: 10.1158/0008-5472.CAN-10-2653, ISSN: 1538-7445.
Bradley KM, Breyer JP, Melville DB, Broman KW, Knapik EW, Smith JR. An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci. G3 (Bethesda). 2011 Jun 6/1/2011; 1(1): 3-9. PMID: 21949597, PMCID: PMC3178105, DOI: 10.1534/g3.111.000190, ISSN: 2160-1836.
Signorello LB, Shi J, Cai Q, Zheng W, Williams SM, Long J, Cohen SS, Li G, Hollis BW, Smith JR, Blot WJ. Common variation in vitamin D pathway genes predicts circulating 25-hydroxyvitamin D Levels among African Americans. PLoS ONE [print-electronic]. 2011; 6(12): e28623. PMID: 22205958, PMCID: PMC3244405, PII: PONE-D-11-12638, DOI: 10.1371/journal.pone.0028623, ISSN: 1932-6203.
Signorello LB, Williams SM, Zheng W, Smith JR, Long J, Cai Q, Hargreaves MK, Hollis BW, Blot WJ. Blood vitamin d levels in relation to genetic estimation of African ancestry. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2010 Sep; 19(9): 2325-31. PMID: 20647395, PMCID: PMC2938736, PII: 1055-9965.EPI-10-0482, DOI: 10.1158/1055-9965.EPI-10-0482, ISSN: 1538-7755.
Dupont WD, Breyer JP, Bradley KM, Schuyler PA, Plummer WD, Sanders ME, Page DL, Smith JR. Protein phosphatase 2A subunit gene haplotypes and proliferative breast disease modify breast cancer risk. Cancer. 2010 Jan 1/1/2010; 116(1): 8-19. PMID: 19890961, PMCID: PMC2807897, DOI: 10.1002/cncr.24702, ISSN: 0008-543X.
Gudmundsson J, Sulem P, Gudbjartsson DF, Blondal T, Gylfason A, Agnarsson BA, Benediktsdottir KR, Magnusdottir DN, Orlygsdottir G, Jakobsdottir M, Stacey SN, Sigurdsson A, Wahlfors T, Tammela T, Breyer JP, McReynolds KM, Bradley KM, Saez B, Godino J, Navarrete S, Fuertes F, Murillo L, Polo E, Aben KK, van Oort IM, Suarez BK, Helfand BT, Kan D, Zanon C, Frigge ML, Kristjansson K, Gulcher JR, Einarsson GV, Jonsson E, Catalona WJ, Mayordomo JI, Kiemeney LA, Smith JR, Schleutker J, Barkardottir RB, Kong A, Thorsteinsdottir U, Rafnar T, Stefansson K. Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nat. Genet [print-electronic]. 2009 Oct; 41(10): 1122-6. PMID: 19767754, PMCID: PMC3562712, PII: ng.448, DOI: 10.1038/ng.448, ISSN: 1546-1718.
Breyer JP, McReynolds KM, Yaspan BL, Bradley KM, Dupont WD, Smith JR. Genetic variants and prostate cancer risk: candidate replication and exploration of viral restriction genes. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2009 Jul; 18(7): 2137-44. PMID: 19567509, PMCID: PMC2813685, PII: 1055-9965.EPI-08-1223, DOI: 10.1158/1055-9965.EPI-08-1223, ISSN: 1538-7755.
Breyer JP, Sanders ME, Airey DC, Cai Q, Yaspan BL, Schuyler PA, Dai Q, Boulos F, Olivares MG, Bradley KM, Gao YT, Page DL, Dupont WD, Zheng W, Smith JR. Heritable variation of ERBB2 and breast cancer risk. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2009 Apr; 18(4): 1252-8. PMID: 19336545, PMCID: PMC2730036, PII: 1055-9965.EPI-08-1202, DOI: 10.1158/1055-9965.EPI-08-1202, ISSN: 1055-9965.
Love HD, Booton SE, Boone BE, Breyer JP, Koyama T, Revelo MP, Shappell SB, Smith JR, Hayward SW. Androgen regulated genes in human prostate xenografts in mice: relation to BPH and prostate cancer. PLoS ONE. 2009; 4(12): e8384. PMID: 20027305, PMCID: PMC2793011, DOI: 10.1371/journal.pone.0008384, ISSN: 1932-6203.
Ciarleglio CM, Ryckman KK, Servick SV, Hida A, Robbins S, Wells N, Hicks J, Larson SA, Wiedermann JP, Carver K, Hamilton N, Kidd KK, Kidd JR, Smith JR, Friedlaender J, McMahon DG, Williams SM, Summar ML, Johnson CH. Genetic differences in human circadian clock genes among worldwide populations. J. Biol. Rhythms. 2008 Aug; 23(4): 330-40. PMID: 18663240, PMCID: PMC2579796, PII: 23/4/330, DOI: 10.1177/0748730408320284, ISSN: 0748-7304.
Ye C, Gao YT, Wen W, Breyer JP, Shu XO, Smith JR, Zheng W, Cai Q. Association of mitochondrial DNA displacement loop (CA)n dinucleotide repeat polymorphism with breast cancer risk and survival among Chinese women. Cancer Epidemiol. Biomarkers Prev. 2008 Aug; 17(8): 2117-22. PMID: 18708405, PMCID: PMC2643086, PII: 17/8/2117, DOI: 10.1158/1055-9965.EPI-07-2798, ISSN: 1055-9965.
Yaspan BL, McReynolds KM, Elmore JB, Breyer JP, Bradley KM, Smith JR. A haplotype at chromosome Xq27.2 confers susceptibility to prostate cancer. Hum. Genet [print-electronic]. 2008 May; 123(4): 379-86. PMID: 18350320, PMCID: PMC2811403, DOI: 10.1007/s00439-008-0486-8, ISSN: 1432-1203.
Gudmundsson J, Sulem P, Rafnar T, Bergthorsson JT, Manolescu A, Gudbjartsson D, Agnarsson BA, Sigurdsson A, Benediktsdottir KR, Blondal T, Jakobsdottir M, Stacey SN, Kostic J, Kristinsson KT, Birgisdottir B, Ghosh S, Magnusdottir DN, Thorlacius S, Thorleifsson G, Zheng SL, Sun J, Chang BL, Elmore JB, Breyer JP, McReynolds KM, Bradley KM, Yaspan BL, Wiklund F, Stattin P, Lindström S, Adami HO, McDonnell SK, Schaid DJ, Cunningham JM, Wang L, Cerhan JR, St Sauver JL, Isaacs SD, Wiley KE, Partin AW, Walsh PC, Polo S, Ruiz-Echarri M, Navarrete S, Fuertes F, Saez B, Godino J, Weijerman PC, Swinkels DW, Aben KK, Witjes JA, Suarez BK, Helfand BT, Frigge ML, Kristjansson K, Ober C, Jonsson E, Einarsson GV, Xu J, Gronberg H, Smith JR, Thibodeau SN, Isaacs WB, Catalona WJ, Mayordomo JI, Kiemeney LA, Barkardottir RB, Gulcher JR, Thorsteinsdottir U, Kong A, Stefansson K. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat. Genet [print-electronic]. 2008 Mar; 40(3): 281-3. PMID: 18264098, PMCID: PMC3598012, PII: ng.89, DOI: 10.1038/ng.89, ISSN: 1546-1718.
Cai Q, Kataoka N, Li C, Wen W, Smith JR, Gao YT, Shu XO, Zheng W. Haplotype analyses of CYP19A1 gene variants and breast cancer risk: results from the Shanghai Breast Cancer Study. Cancer Epidemiol. Biomarkers Prev. 2008 Jan; 17(1): 27-32. PMID: 18199708, PMCID: PMC2633134, PII: 17/1/27, DOI: 10.1158/1055-9965.EPI-07-0688, ISSN: 1055-9965.
Yaspan BL, Breyer JP, Cai Q, Dai Q, Elmore JB, Amundson I, Bradley KM, Shu XO, Gao YT, Dupont WD, Zheng W, Smith JR. Haplotype analysis of CYP11A1 identifies promoter variants associated with breast cancer risk. Cancer Res. 2007 Jun 6/15/2007; 67(12): 5673-82. PMID: 17575134, PMCID: PMC2805128, PII: 67/12/5673, DOI: 10.1158/0008-5472.CAN-07-0467, ISSN: 0008-5472.
Bradley KM, Elmore JB, Breyer JP, Yaspan BL, Jessen JR, Knapik EW, Smith JR. A major zebrafish polymorphism resource for genetic mapping. Genome Biol. 2007; 8(4): R55. PMID: 17428331, PMCID: PMC1896001, PII: gb-2007-8-4-r55, DOI: 10.1186/gb-2007-8-4-r55, ISSN: 1474-760X.
Baffoe-Bonnie AB, Smith JR, Stephan DA, Schleutker J, Carpten JD, Kainu T, Gillanders EM, Matikainen M, Teslovich TM, Tammela T, Sood R, Balshem AM, Scarborough SD, Xu J, Isaacs WB, Trent JM, Kallioniemi OP, Bailey-Wilson JE. A major locus for hereditary prostate cancer in Finland: localization by linkage disequilibrium of a haplotype in the HPCX region. Hum. Genet [print-electronic]. 2005 Aug; 117(4): 307-16. PMID: 15906096, DOI: 10.1007/s00439-005-1306-z, ISSN: 0340-6717.
Owens SE, Broman KW, Wiltshire T, Elmore JB, Bradley KM, Smith JR, Southard-Smith EM. Genome-wide linkage identifies novel modifier loci of aganglionosis in the Sox10Dom model of Hirschsprung disease. Hum. Mol. Genet [print-electronic]. 2005 Jun 6/1/2005; 14(11): 1549-58. PMID: 15843399, PII: ddi163, DOI: 10.1093/hmg/ddi163, ISSN: 0964-6906.
Boyapati SM, Shu XO, Ruan ZX, Cai Q, Smith JR, Wen W, Gao YT, Zheng W. Polymorphisms in ER-alpha gene interact with estrogen receptor status in breast cancer survival. Clin. Cancer Res. 2005 Feb 2/1/2005; 11(3): 1093-8. PMID: 15709176, PII: 11/3/1093, ISSN: 1078-0432.
Wen W, Gao YT, Shu XO, Yu H, Cai Q, Smith JR, Zheng W. Insulin-like growth factor-I gene polymorphism and breast cancer risk in Chinese women. Int. J. Cancer. 2005 Jan 1/10/2005; 113(2): 307-11. PMID: 15386404, DOI: 10.1002/ijc.20571, ISSN: 0020-7136.
Cantrell VA, Owens SE, Chandler RL, Airey DC, Bradley KM, Smith JR, Southard-Smith EM. Interactions between Sox10 and EdnrB modulate penetrance and severity of aganglionosis in the Sox10Dom mouse model of Hirschsprung disease. Hum. Mol. Genet [print-electronic]. 2004 Oct 10/1/2004; 13(19): 2289-301. PMID: 15294878, PII: ddh243, DOI: 10.1093/hmg/ddh243, ISSN: 0964-6906.
Adegoke OJ, Shu XO, Gao YT, Cai Q, Breyer J, Smith J, Zheng W. Genetic polymorphisms in uridine diphospho-glucuronosyltransferase 1A1 (UGT1A1) and risk of breast cancer. Breast Cancer Res. Treat. 2004 Jun; 85(3): 239-45. PMID: 15111762, PII: 5267594, DOI: 10.1023/B:BREA.0000025419.26423.b8, ISSN: 0167-6806.
Zheng W, Gao YT, Shu XO, Wen W, Cai Q, Dai Q, Smith JR. Population-based case-control study of CYP11A gene polymorphism and breast cancer risk. Cancer Epidemiol. Biomarkers Prev. 2004 May; 13(5): 709-14. PMID: 15159300, PII: 13/5/709, ISSN: 1055-9965.
Cai Q, Gao YT, Wen W, Shu XO, Jin F, Smith JR, Zheng W. Association of breast cancer risk with a GT dinucleotide repeat polymorphism upstream of the estrogen receptor-alpha gene. Cancer Res. 2003 Sep 9/15/2003; 63(18): 5727-30. PMID: 14522892, ISSN: 0008-5472.
Ho GY, Knapp M, Freije D, Nelson WG, Smith JR, Carpten JD, Bailey-Wilson JE, Beaty TH, Petersen G, Xu J, Kamensky V, Walsh PC, Isaacs WB. Transmission/disequilibrium tests of androgen receptor and glutathione S-transferase pi variants in prostate cancer families. Int. J. Cancer. 2002 Apr 4/20/2002; 98(6): 938-42. PMID: 11948476, PII: 10.1002/ijc.10290, ISSN: 0020-7136.
Carpten J, Nupponen N, Isaacs S, Sood R, Robbins C, Xu J, Faruque M, Moses T, Ewing C, Gillanders E, Hu P, Bujnovszky P, Makalowska I, Baffoe-Bonnie A, Faith D, Smith J, Stephan D, Wiley K, Brownstein M, Gildea D, Kelly B, Jenkins R, Hostetter G, Matikainen M, Schleutker J, Klinger K, Connors T, Xiang Y, Wang Z, De Marzo A, Papadopoulos N, Kallioniemi OP, Burk R, Meyers D, Grönberg H, Meltzer P, Silverman R, Bailey-Wilson J, Walsh P, Isaacs W, Trent J. Germline mutations in the ribonuclease L gene in families showing linkage with HPC1. Nat. Genet [print-electronic]. 2002 Feb; 30(2): 181-4. PMID: 11799394, PII: ng823, DOI: 10.1038/ng823, ISSN: 1061-4036.
Stephan DA, Howell GR, Teslovich TM, Coffey AJ, Smith L, Bailey-Wilson JE, Malechek L, Gildea D, Smith JR, Gillanders EM, Schleutker J, Hu P, Steingruber HE, Dhami P, Robbins CM, Makalowska I, Carpten JD, Sood R, Mumm S, Reinbold R, Bonner TI, Baffoe-Bonnie A, Bubendorf L, Heiskanen M, Kallioneimi OP, Baxevanis AD, Joseph SS, Zucchi I, Burk RD, Isaacs W, Ross MT, Trent JM. Physical and transcript map of the hereditary prostate cancer region at xq27. Genomics. 2002 Jan; 79(1): 41-50. PMID: 11827456, PII: S0888754301966819, DOI: 10.1006/geno.2001.6681, ISSN: 0888-7543.
Smith, J., Collins, F., and Gelehrter, T. Molecular Genetics of Common Disease. In: The Genetic Basis of Common Diseases, Second Edition, edited by King, Rotter, and Motulsky. (Oxford Univesity Press). 2002.
Xu J, Zheng SL, Chang B, Smith JR, Carpten JD, Stine OC, Isaacs SD, Wiley KE, Henning L, Ewing C, Bujnovszky P, Bleeker ER, Walsh PC, Trent JM, Meyers DA, Isaacs WB. Linkage of prostate cancer susceptibility loci to chromosome 1. Hum. Genet. 2001 Apr; 108(4): 335-45. PMID: 11379880, ISSN: 0340-6717.
Schleutker J, Matikainen M, Smith J, Koivisto P, Baffoe-Bonnie A, Kainu T, Gillanders E, Sankila R, Pukkala E, Carpten J, Stephan D, Tammela T, Brownstein M, Bailey-Wilson J, Trent J, Kallioniemi OP. A genetic epidemiological study of hereditary prostate cancer (HPC) in Finland: frequent HPCX linkage in families with late-onset disease. Clin. Cancer Res. 2000 Dec; 6(12): 4810-5. PMID: 11156239, ISSN: 1078-0432.
Bergthorsson JT, Johannesdottir G, Arason A, Benediktsdottir KR, Agnarsson BA, Bailey-Wilson JE, Gillanders E, Smith J, Trent J, Barkardottir RB. Analysis of HPC1, HPCX, and PCaP in Icelandic hereditary prostate cancer. Hum. Genet. 2000 Oct; 107(4): 372-5. PMID: 11129338, ISSN: 0340-6717.
Xu J. Combined analysis of hereditary prostate cancer linkage to 1q24-25: results from 772 hereditary prostate cancer families from the International Consortium for Prostate Cancer Genetics. Am. J. Hum. Genet. 2000 Mar; 66(3): 945-57. PMID: 10712209, PMCID: PMC1288175, PII: S0002-9297(07)64021-X, ISSN: 0002-9297.
Carpten JD, Makalowska I, Robbins CM, Scott N, Sood R, Connors TD, Bonner TI, Smith JR, Faruque MU, Stephan DA, Pinkett H, Morgenbesser SD, Su K, Graham C, Gregory SG, Williams H, McDonald L, Baxevanis AD, Klingler KW, Landes GM, Trent JM. A 6-Mb high-resolution physical and transcription map encompassing the hereditary prostate cancer 1 (HPC1) region. Genomics. 2000 Feb 2/15/2000; 64(1): 1-14. PMID: 10708513, PII: S0888-7543(99)96051-2, DOI: 10.1006/geno.1999.6051, ISSN: 0888-7543.
Berry R, Schaid DJ, Smith JR, French AJ, Schroeder JJ, McDonnell SK, Peterson BJ, Wang ZY, Carpten JD, Roberts SG, Tester DJ, Blute ML, Trent JM, Thibodeau SN. Linkage analyses at the chromosome 1 loci 1q24-25 (HPC1), 1q42.2-43 (PCAP), and 1p36 (CAPB) in families with hereditary prostate cancer. Am. J. Hum. Genet. 2000 Feb; 66(2): 539-46. PMID: 10677314, PMCID: PMC1288107, PII: S0002-9297(07)63428-4, DOI: 10.1086/302771, ISSN: 0002-9297.
Grönberg H, Smith J, Emanuelsson M, Jonsson BA, Bergh A, Carpten J, Isaacs W, Xu J, Meyers D, Trent J, Damber JE. In Swedish families with hereditary prostate cancer, linkage to the HPC1 locus on chromosome 1q24-25 is restricted to families with early-onset prostate cancer. Am. J. Hum. Genet. 1999 Jul; 65(1): 134-40. PMID: 10364525, PMCID: PMC1378083, PII: S0002-9297(07)63736-7, DOI: 10.1086/302447, ISSN: 0002-9297.
Carpten, J., Smith, J., Stephan, D., Isaacs, W., Trent, J. Searching for Prostate Cancer Genes. Science and Medicine. 1998; 5: 26-35.
Grönberg H, Xu J, Smith JR, Carpten JD, Isaacs SD, Freije D, Bova GS, Danber JE, Bergh A, Walsh PC, Collins FS, Trent JM, Meyers DA, Isaacs WB. Early age at diagnosis in families providing evidence of linkage to the hereditary prostate cancer locus (HPC1) on chromosome 1. Cancer Res. 1997 Nov 11/1/1997; 57(21): 4707-9. PMID: 9354426, ISSN: 0008-5472.
Grönberg H, Isaacs SD, Smith JR, Carpten JD, Bova GS, Freije D, Xu J, Meyers DA, Collins FS, Trent JM, Walsh PC, Isaacs WB. Characteristics of prostate cancer in families potentially linked to the hereditary prostate cancer 1 (HPC1) locus. JAMA. 1997 Oct 10/15/1997; 278(15): 1251-5. PMID: 9333266, ISSN: 0098-7484.
Ghosh S, Karanjawala ZE, Hauser ER, Ally D, Knapp JI, Rayman JB, Musick A, Tannenbaum J, Te C, Shapiro S, Eldridge W, Musick T, Martin C, Smith JR, Carpten JD, Brownstein MJ, Powell JI, Whiten R, Chines P, Nylund SJ, Magnuson VL, Boehnke M, Collins FS. Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group. Genome Res. 1997 Feb; 7(2): 165-78. PMID: 9049634, ISSN: 1088-9051.
Brownstein, M., Carpten, J., and Smith, J. Modulation of Nontemplated Nucleotide Addition by Taq DNA Polymerase: Primer Modifications that Facilitate Genotyping. Biotechniques. 1996; 20: 1004-10.
Smith, J., Freije, D., Carpten, J., Gronberg, H., Xu, J., Isaacs, S., Brownstein, M., Bova, G., Guo, H., Bujnovszky, P., Nusskern, D., Damber, J., Bergh, A., Emanuelsson, M., Kallioniemi, O., Walker-Daniels, J., Bailey-Wilson, J., Beaty, T., Meyers, D., Walsh, P., Collins, F., Trent, J., and Isaacs, W. Major Susceptibility Locus for Prostate Cancer on Chromosome 1 Suggested by a Genome-Wide Search. Science. 1996; 274((Nov 22)): 1371-4.
Smith JR, Carpten JD, Brownstein MJ, Ghosh S, Magnuson VL, Gilbert DA, Trent JM, Collins FS. Approach to genotyping errors caused by nontemplated nucleotide addition by Taq DNA polymerase. Genome Res. 1995 Oct; 5(3): 312-7. PMID: 8593617, ISSN: 1088-9051.
Smith JR, Osborne TF, Goldstein JL, Brown MS. Identification of nucleotides responsible for enhancer activity of sterol regulatory element in low density lipoprotein receptor gene. J. Biol. Chem. 1990 Feb 2/5/1990; 265(4): 2306-10. PMID: 2298751, ISSN: 0021-9258.
Smith JR, Osborne TF, Brown MS, Goldstein JL, Gil G. Multiple sterol regulatory elements in promoter for hamster 3-hydroxy-3-methylglutaryl-coenzyme A synthase. J. Biol. Chem. 1988 Dec 12/5/1988; 263(34): 18480-7. PMID: 2903862, ISSN: 0021-9258.
Gil G, Smith JR, Goldstein JL, Slaughter CA, Orth K, Brown MS, Osborne TF. Multiple genes encode nuclear factor 1-like proteins that bind to the promoter for 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Proc. Natl. Acad. Sci. U.S.A. 1988 Dec; 85(23): 8963-7. PMID: 3194401, PMCID: PMC282633, ISSN: 0027-8424.
Gil G, Smith JR, Goldstein JL, Brown MS. Optional exon in the 5'-untranslated region of 3-hydroxy-3-methylglutaryl coenzyme A synthase gene: conserved sequence and splicing pattern in humans and hamsters. Proc. Natl. Acad. Sci. U.S.A. 1987 Apr; 84(7): 1863-6. PMID: 3470763, PMCID: PMC304541, ISSN: 0027-8424.
Dupont WD, Breyer JP, Johnson SH, Plummer WD, Smith JR. Prostate cancer risk variants of the HOXB genetic locus. Sci Rep. 2021 May 5/31/2021; 11(1): 11385. PMID: 34059701, PMCID: PMC8167119, PII: 10.1038/s41598-021-89399-7, DOI: 10.1038/s41598-021-89399-7, ISSN: 2045-2322.
Dupont WD, Breyer JP, Plummer WD, Chang SS, Cookson MS, Smith JA, , Blue EE, Bamshad MJ, Smith JR. 8q24 genetic variation and comprehensive haplotypes altering familial risk of prostate cancer. Nat Commun. 2020 Mar 3/23/2020; 11(1): 1523. PMID: 32251286, PMCID: PMC7089954, PII: 10.1038/s41467-020-15122-1, DOI: 10.1038/s41467-020-15122-1, ISSN: 2041-1723.
Dupont WD, Breyer JP, Plummer WD, Chang SS, Cookson MS, Smith JA, , Blue EE, Bamshad MJ, Smith JR. 8q24 genetic variation and comprehensive haplotypes altering familial risk of prostate cancer. Nat Commun. 2020 Mar 3/23/2020; 11(1): 1523. PMID: 32251286, PMCID: PMC7089954, PII: 10.1038/s41467-020-15122-1, DOI: 10.1038/s41467-020-15122-1, ISSN: 2041-1723.
Breyer JP, Smith JR. Practical genotyping by single-nucleotide primer extension. Biol Methods Protoc. 2020; 5(1): bpaa002. PMID: 32382659, PMCID: PMC7200932, PII: bpaa002, DOI: 10.1093/biomethods/bpaa002, ISSN: 2396-8923.
Breyer JP, Smith JR. Practical genotyping by single-nucleotide primer extension. Biol Methods Protoc. 2020; 5(1): bpaa002. PMID: 32382659, PMCID: PMC7200932, PII: bpaa002, DOI: 10.1093/biomethods/bpaa002, ISSN: 2396-8923.
Degnim AC, Dupont WD, Radisky DC, Vierkant RA, Frank RD, Frost MH, Winham SJ, Sanders ME, Smith JR, Page DL, Hoskin TL, Vachon CM, Ghosh K, Hieken TJ, Denison LA, Carter JM, Hartmann LC, Visscher DW. Extent of atypical hyperplasia stratifies breast cancer risk in 2 independent cohorts of women. Cancer [print-electronic]. 2016 Oct; 122(19): 2971-8. PMID: 27352219, PMCID: PMC5030128, DOI: 10.1002/cncr.30153, ISSN: 1097-0142.
Degnim AC, Dupont WD, Radisky DC, Vierkant RA, Frank RD, Frost MH, Winham SJ, Sanders ME, Smith JR, Page DL, Hoskin TL, Vachon CM, Ghosh K, Hieken TJ, Denison LA, Carter JM, Hartmann LC, Visscher DW. Extent of atypical hyperplasia stratifies breast cancer risk in 2 independent cohorts of women. Cancer [print-electronic]. 2016 Oct; 122(19): 2971-8. PMID: 27352219, PMCID: PMC5030128, DOI: 10.1002/cncr.30153, ISSN: 1097-0142.
Solus JF, Chung CP, Oeser A, Li C, Rho YH, Bradley KM, Kawai VK, Smith JR, Stein CM. Genetics of serum concentration of IL-6 and TNFa in systemic lupus erythematosus and rheumatoid arthritis: a candidate gene analysis. Clin. Rheumatol [print-electronic]. 2015 Aug; 34(8): 1375-82. PMID: 25652333, PMCID: PMC4526456, DOI: 10.1007/s10067-015-2881-6, ISSN: 1434-9949.
Chung CP, Solus JF, Oeser A, Li C, Raggi P, Smith JR, Stein CM. A variant in the osteoprotegerin gene is associated with coronary atherosclerosis in patients with rheumatoid arthritis: results from a candidate gene study. Int J Mol Sci. 2015; 16(2): 3885-94. PMID: 25679449, PMCID: PMC4346932, PII: ijms16023885, DOI: 10.3390/ijms16023885, ISSN: 1422-0067.
Chung CP, Solus JF, Oeser A, Li C, Raggi P, Smith JR, Stein CM. Genetic variation and coronary atherosclerosis in patients with systemic lupus erythematosus. Lupus [print-electronic]. 2014 Aug; 23(9): 876-80. PMID: 24699314, PMCID: PMC4185017, PII: 0961203314530019, DOI: 10.1177/0961203314530019, ISSN: 1477-0962.
Breyer JP, Dorset DC, Clark TA, Bradley KM, Wahlfors TA, McReynolds KM, Maynard WH, Chang SS, Cookson MS, Smith JA, Schleutker J, Dupont WD, Smith JR. An expressed retrogene of the master embryonic stem cell gene POU5F1 is associated with prostate cancer susceptibility. Am. J. Hum. Genet [print-electronic]. 2014 Mar 3/6/2014; 94(3): 395-404. PMID: 24581739, PMCID: PMC3951923, PII: S0002-9297(14)00057-3, DOI: 10.1016/j.ajhg.2014.01.019, ISSN: 1537-6605.
Gray RS, Wilm TP, Smith J, Bagnat M, Dale RM, Topczewski J, Johnson SL, Solnica-Krezel L. Loss of col8a1a function during zebrafish embryogenesis results in congenital vertebral malformations. Dev. Biol [print-electronic]. 2014 Feb 2/1/2014; 386(1): 72-85. PMID: 24333517, PMCID: PMC3938106, PII: S0012-1606(13)00645-3, DOI: 10.1016/j.ydbio.2013.11.028, ISSN: 1095-564X.
Weng PH, Huang YL, Page JH, Chen JH, Xu J, Koutros S, Berndt S, Chanock S, Yeager M, Witte JS, Eeles RA, Easton DF, Neal DE, Donovan J, Hamdy FC, Muir KR, Giles G, Severi G, Smith JR, Balistreri CR, Shui IM, Chen YC. Polymorphisms of an innate immune gene, toll-like receptor 4, and aggressive prostate cancer risk: a systematic review and meta-analysis. PLoS ONE. 2014; 9(10): e110569. PMID: 25360682, PMCID: PMC4215920, PII: PONE-D-14-21052, DOI: 10.1371/journal.pone.0110569, ISSN: 1932-6203.
Kodaman N, Aldrich MC, Smith JR, Signorello LB, Bradley K, Breyer J, Cohen SS, Long J, Cai Q, Giles J, Bush WS, Blot WJ, Matthews CE, Williams SM. A small number of candidate gene SNPs reveal continental ancestry in African Americans. Ann. Hum. Genet. 2013 Jan; 77(1): 56-66. PMID: 23278390, PMCID: PMC3677760, DOI: 10.1111/j.1469-1809.2012.00738.x, ISSN: 1469-1809.
Higginbotham KS, Breyer JP, McReynolds KM, Bradley KM, Schuyler PA, Plummer WD, Freudenthal ME, Trentham-Dietz A, Newcomb PA, Parl FF, Sanders ME, Page DL, Egan KM, Dupont WD, Smith JR. A multistage genetic association study identifies breast cancer risk loci at 10q25 and 16q24. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2012 Sep; 21(9): 1565-73. PMID: 22806168, PMCID: PMC3707501, PII: 1055-9965.EPI-12-0386, DOI: 10.1158/1055-9965.EPI-12-0386, ISSN: 1538-7755.
Breyer JP, Avritt TG, McReynolds KM, Dupont WD, Smith JR. Confirmation of the HOXB13 G84E germline mutation in familial prostate cancer. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2012 Aug; 21(8): 1348-53. PMID: 22714738, PMCID: PMC3415588, PII: 1055-9965.EPI-12-0495, DOI: 10.1158/1055-9965.EPI-12-0495, ISSN: 1538-7755.
Edwards TL, Velez Edwards DR, Villegas R, Cohen SS, Buchowski MS, Fowke JH, Schlundt D, Long J, Cai Q, Zheng W, Shu XO, Hargreaves MK, Smith J, Williams SM, Signorello LB, Blot WJ, Matthews CE. HTR1B, ADIPOR1, PPARGC1A, and CYP19A1 and obesity in a cohort of Caucasians and African Americans: an evaluation of gene-environment interactions and candidate genes. Am. J. Epidemiol [print-electronic]. 2012 Jan 1/1/2012; 175(1): 11-21. PMID: 22106445, PMCID: PMC3244609, PII: kwr272, DOI: 10.1093/aje/kwr272, ISSN: 1476-6256.
Melville DB, Montero-Balaguer M, Levic DS, Bradley K, Smith JR, Hatzopoulos AK, Knapik EW. The feelgood mutation in zebrafish dysregulates COPII-dependent secretion of select extracellular matrix proteins in skeletal morphogenesis. Dis Model Mech [print-electronic]. 2011 Nov; 4(6): 763-76. PMID: 21729877, PMCID: PMC3209646, PII: dmm.007625, DOI: 10.1242/dmm.007625, ISSN: 1754-8411.
Cohen SS, Gammon MD, North KE, Millikan RC, Lange EM, Williams SM, Zheng W, Cai Q, Long J, Smith JR, Signorello LB, Blot WJ, Matthews CE. ADIPOQ, ADIPOR1, and ADIPOR2 polymorphisms in relation to serum adiponectin levels and BMI in black and white women. Obesity (Silver Spring) [print-electronic]. 2011 Oct; 19(10): 2053-62. PMID: 21273992, PMCID: PMC3474141, PII: oby2010346, DOI: 10.1038/oby.2010.346, ISSN: 1930-739X.
Crooke PS, Justenhoven C, Brauch H, , Dawling S, Roodi N, Higginbotham KS, Plummer WD, Schuyler PA, Sanders ME, Page DL, Smith JR, Dupont WD, Parl FF. Estrogen metabolism and exposure in a genotypic-phenotypic model for breast cancer risk prediction. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2011 Jul; 20(7): 1502-15. PMID: 21610218, PMCID: PMC3472969, PII: 1055-9965.EPI-11-0060, DOI: 10.1158/1055-9965.EPI-11-0060, ISSN: 1538-7755.
Higginbotham KS, Breyer JP, Bradley KM, Schuyler PA, Plummer WD, Freudenthal ME, Trentham-Dietz A, Newcomb PA, Sanders ME, Page DL, Parl FF, Egan KM, Dupont WD, Smith JR. A multistage association study identifies a breast cancer genetic locus at NCOA7. Cancer Res [print-electronic]. 2011 Jun 6/1/2011; 71(11): 3881-8. PMID: 21610108, PMCID: PMC3137260, PII: 0008-5472.CAN-10-2653, DOI: 10.1158/0008-5472.CAN-10-2653, ISSN: 1538-7445.
Bradley KM, Breyer JP, Melville DB, Broman KW, Knapik EW, Smith JR. An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci. G3 (Bethesda). 2011 Jun 6/1/2011; 1(1): 3-9. PMID: 21949597, PMCID: PMC3178105, DOI: 10.1534/g3.111.000190, ISSN: 2160-1836.
Signorello LB, Shi J, Cai Q, Zheng W, Williams SM, Long J, Cohen SS, Li G, Hollis BW, Smith JR, Blot WJ. Common variation in vitamin D pathway genes predicts circulating 25-hydroxyvitamin D Levels among African Americans. PLoS ONE [print-electronic]. 2011; 6(12): e28623. PMID: 22205958, PMCID: PMC3244405, PII: PONE-D-11-12638, DOI: 10.1371/journal.pone.0028623, ISSN: 1932-6203.
Signorello LB, Williams SM, Zheng W, Smith JR, Long J, Cai Q, Hargreaves MK, Hollis BW, Blot WJ. Blood vitamin d levels in relation to genetic estimation of African ancestry. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2010 Sep; 19(9): 2325-31. PMID: 20647395, PMCID: PMC2938736, PII: 1055-9965.EPI-10-0482, DOI: 10.1158/1055-9965.EPI-10-0482, ISSN: 1538-7755.
Dupont WD, Breyer JP, Bradley KM, Schuyler PA, Plummer WD, Sanders ME, Page DL, Smith JR. Protein phosphatase 2A subunit gene haplotypes and proliferative breast disease modify breast cancer risk. Cancer. 2010 Jan 1/1/2010; 116(1): 8-19. PMID: 19890961, PMCID: PMC2807897, DOI: 10.1002/cncr.24702, ISSN: 0008-543X.
Gudmundsson J, Sulem P, Gudbjartsson DF, Blondal T, Gylfason A, Agnarsson BA, Benediktsdottir KR, Magnusdottir DN, Orlygsdottir G, Jakobsdottir M, Stacey SN, Sigurdsson A, Wahlfors T, Tammela T, Breyer JP, McReynolds KM, Bradley KM, Saez B, Godino J, Navarrete S, Fuertes F, Murillo L, Polo E, Aben KK, van Oort IM, Suarez BK, Helfand BT, Kan D, Zanon C, Frigge ML, Kristjansson K, Gulcher JR, Einarsson GV, Jonsson E, Catalona WJ, Mayordomo JI, Kiemeney LA, Smith JR, Schleutker J, Barkardottir RB, Kong A, Thorsteinsdottir U, Rafnar T, Stefansson K. Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nat. Genet [print-electronic]. 2009 Oct; 41(10): 1122-6. PMID: 19767754, PMCID: PMC3562712, PII: ng.448, DOI: 10.1038/ng.448, ISSN: 1546-1718.
Breyer JP, McReynolds KM, Yaspan BL, Bradley KM, Dupont WD, Smith JR. Genetic variants and prostate cancer risk: candidate replication and exploration of viral restriction genes. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2009 Jul; 18(7): 2137-44. PMID: 19567509, PMCID: PMC2813685, PII: 1055-9965.EPI-08-1223, DOI: 10.1158/1055-9965.EPI-08-1223, ISSN: 1538-7755.
Breyer JP, Sanders ME, Airey DC, Cai Q, Yaspan BL, Schuyler PA, Dai Q, Boulos F, Olivares MG, Bradley KM, Gao YT, Page DL, Dupont WD, Zheng W, Smith JR. Heritable variation of ERBB2 and breast cancer risk. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2009 Apr; 18(4): 1252-8. PMID: 19336545, PMCID: PMC2730036, PII: 1055-9965.EPI-08-1202, DOI: 10.1158/1055-9965.EPI-08-1202, ISSN: 1055-9965.
Love HD, Booton SE, Boone BE, Breyer JP, Koyama T, Revelo MP, Shappell SB, Smith JR, Hayward SW. Androgen regulated genes in human prostate xenografts in mice: relation to BPH and prostate cancer. PLoS ONE. 2009; 4(12): e8384. PMID: 20027305, PMCID: PMC2793011, DOI: 10.1371/journal.pone.0008384, ISSN: 1932-6203.
Ciarleglio CM, Ryckman KK, Servick SV, Hida A, Robbins S, Wells N, Hicks J, Larson SA, Wiedermann JP, Carver K, Hamilton N, Kidd KK, Kidd JR, Smith JR, Friedlaender J, McMahon DG, Williams SM, Summar ML, Johnson CH. Genetic differences in human circadian clock genes among worldwide populations. J. Biol. Rhythms. 2008 Aug; 23(4): 330-40. PMID: 18663240, PMCID: PMC2579796, PII: 23/4/330, DOI: 10.1177/0748730408320284, ISSN: 0748-7304.
Ye C, Gao YT, Wen W, Breyer JP, Shu XO, Smith JR, Zheng W, Cai Q. Association of mitochondrial DNA displacement loop (CA)n dinucleotide repeat polymorphism with breast cancer risk and survival among Chinese women. Cancer Epidemiol. Biomarkers Prev. 2008 Aug; 17(8): 2117-22. PMID: 18708405, PMCID: PMC2643086, PII: 17/8/2117, DOI: 10.1158/1055-9965.EPI-07-2798, ISSN: 1055-9965.
Yaspan BL, McReynolds KM, Elmore JB, Breyer JP, Bradley KM, Smith JR. A haplotype at chromosome Xq27.2 confers susceptibility to prostate cancer. Hum. Genet [print-electronic]. 2008 May; 123(4): 379-86. PMID: 18350320, PMCID: PMC2811403, DOI: 10.1007/s00439-008-0486-8, ISSN: 1432-1203.
Gudmundsson J, Sulem P, Rafnar T, Bergthorsson JT, Manolescu A, Gudbjartsson D, Agnarsson BA, Sigurdsson A, Benediktsdottir KR, Blondal T, Jakobsdottir M, Stacey SN, Kostic J, Kristinsson KT, Birgisdottir B, Ghosh S, Magnusdottir DN, Thorlacius S, Thorleifsson G, Zheng SL, Sun J, Chang BL, Elmore JB, Breyer JP, McReynolds KM, Bradley KM, Yaspan BL, Wiklund F, Stattin P, Lindström S, Adami HO, McDonnell SK, Schaid DJ, Cunningham JM, Wang L, Cerhan JR, St Sauver JL, Isaacs SD, Wiley KE, Partin AW, Walsh PC, Polo S, Ruiz-Echarri M, Navarrete S, Fuertes F, Saez B, Godino J, Weijerman PC, Swinkels DW, Aben KK, Witjes JA, Suarez BK, Helfand BT, Frigge ML, Kristjansson K, Ober C, Jonsson E, Einarsson GV, Xu J, Gronberg H, Smith JR, Thibodeau SN, Isaacs WB, Catalona WJ, Mayordomo JI, Kiemeney LA, Barkardottir RB, Gulcher JR, Thorsteinsdottir U, Kong A, Stefansson K. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat. Genet [print-electronic]. 2008 Mar; 40(3): 281-3. PMID: 18264098, PMCID: PMC3598012, PII: ng.89, DOI: 10.1038/ng.89, ISSN: 1546-1718.
Cai Q, Kataoka N, Li C, Wen W, Smith JR, Gao YT, Shu XO, Zheng W. Haplotype analyses of CYP19A1 gene variants and breast cancer risk: results from the Shanghai Breast Cancer Study. Cancer Epidemiol. Biomarkers Prev. 2008 Jan; 17(1): 27-32. PMID: 18199708, PMCID: PMC2633134, PII: 17/1/27, DOI: 10.1158/1055-9965.EPI-07-0688, ISSN: 1055-9965.
Yaspan BL, Breyer JP, Cai Q, Dai Q, Elmore JB, Amundson I, Bradley KM, Shu XO, Gao YT, Dupont WD, Zheng W, Smith JR. Haplotype analysis of CYP11A1 identifies promoter variants associated with breast cancer risk. Cancer Res. 2007 Jun 6/15/2007; 67(12): 5673-82. PMID: 17575134, PMCID: PMC2805128, PII: 67/12/5673, DOI: 10.1158/0008-5472.CAN-07-0467, ISSN: 0008-5472.
Bradley KM, Elmore JB, Breyer JP, Yaspan BL, Jessen JR, Knapik EW, Smith JR. A major zebrafish polymorphism resource for genetic mapping. Genome Biol. 2007; 8(4): R55. PMID: 17428331, PMCID: PMC1896001, PII: gb-2007-8-4-r55, DOI: 10.1186/gb-2007-8-4-r55, ISSN: 1474-760X.
Baffoe-Bonnie AB, Smith JR, Stephan DA, Schleutker J, Carpten JD, Kainu T, Gillanders EM, Matikainen M, Teslovich TM, Tammela T, Sood R, Balshem AM, Scarborough SD, Xu J, Isaacs WB, Trent JM, Kallioniemi OP, Bailey-Wilson JE. A major locus for hereditary prostate cancer in Finland: localization by linkage disequilibrium of a haplotype in the HPCX region. Hum. Genet [print-electronic]. 2005 Aug; 117(4): 307-16. PMID: 15906096, DOI: 10.1007/s00439-005-1306-z, ISSN: 0340-6717.
Owens SE, Broman KW, Wiltshire T, Elmore JB, Bradley KM, Smith JR, Southard-Smith EM. Genome-wide linkage identifies novel modifier loci of aganglionosis in the Sox10Dom model of Hirschsprung disease. Hum. Mol. Genet [print-electronic]. 2005 Jun 6/1/2005; 14(11): 1549-58. PMID: 15843399, PII: ddi163, DOI: 10.1093/hmg/ddi163, ISSN: 0964-6906.
Boyapati SM, Shu XO, Ruan ZX, Cai Q, Smith JR, Wen W, Gao YT, Zheng W. Polymorphisms in ER-alpha gene interact with estrogen receptor status in breast cancer survival. Clin. Cancer Res. 2005 Feb 2/1/2005; 11(3): 1093-8. PMID: 15709176, PII: 11/3/1093, ISSN: 1078-0432.
Wen W, Gao YT, Shu XO, Yu H, Cai Q, Smith JR, Zheng W. Insulin-like growth factor-I gene polymorphism and breast cancer risk in Chinese women. Int. J. Cancer. 2005 Jan 1/10/2005; 113(2): 307-11. PMID: 15386404, DOI: 10.1002/ijc.20571, ISSN: 0020-7136.
Cantrell VA, Owens SE, Chandler RL, Airey DC, Bradley KM, Smith JR, Southard-Smith EM. Interactions between Sox10 and EdnrB modulate penetrance and severity of aganglionosis in the Sox10Dom mouse model of Hirschsprung disease. Hum. Mol. Genet [print-electronic]. 2004 Oct 10/1/2004; 13(19): 2289-301. PMID: 15294878, PII: ddh243, DOI: 10.1093/hmg/ddh243, ISSN: 0964-6906.
Adegoke OJ, Shu XO, Gao YT, Cai Q, Breyer J, Smith J, Zheng W. Genetic polymorphisms in uridine diphospho-glucuronosyltransferase 1A1 (UGT1A1) and risk of breast cancer. Breast Cancer Res. Treat. 2004 Jun; 85(3): 239-45. PMID: 15111762, PII: 5267594, DOI: 10.1023/B:BREA.0000025419.26423.b8, ISSN: 0167-6806.
Zheng W, Gao YT, Shu XO, Wen W, Cai Q, Dai Q, Smith JR. Population-based case-control study of CYP11A gene polymorphism and breast cancer risk. Cancer Epidemiol. Biomarkers Prev. 2004 May; 13(5): 709-14. PMID: 15159300, PII: 13/5/709, ISSN: 1055-9965.
Cai Q, Gao YT, Wen W, Shu XO, Jin F, Smith JR, Zheng W. Association of breast cancer risk with a GT dinucleotide repeat polymorphism upstream of the estrogen receptor-alpha gene. Cancer Res. 2003 Sep 9/15/2003; 63(18): 5727-30. PMID: 14522892, ISSN: 0008-5472.
Ho GY, Knapp M, Freije D, Nelson WG, Smith JR, Carpten JD, Bailey-Wilson JE, Beaty TH, Petersen G, Xu J, Kamensky V, Walsh PC, Isaacs WB. Transmission/disequilibrium tests of androgen receptor and glutathione S-transferase pi variants in prostate cancer families. Int. J. Cancer. 2002 Apr 4/20/2002; 98(6): 938-42. PMID: 11948476, PII: 10.1002/ijc.10290, ISSN: 0020-7136.
Carpten J, Nupponen N, Isaacs S, Sood R, Robbins C, Xu J, Faruque M, Moses T, Ewing C, Gillanders E, Hu P, Bujnovszky P, Makalowska I, Baffoe-Bonnie A, Faith D, Smith J, Stephan D, Wiley K, Brownstein M, Gildea D, Kelly B, Jenkins R, Hostetter G, Matikainen M, Schleutker J, Klinger K, Connors T, Xiang Y, Wang Z, De Marzo A, Papadopoulos N, Kallioniemi OP, Burk R, Meyers D, Grönberg H, Meltzer P, Silverman R, Bailey-Wilson J, Walsh P, Isaacs W, Trent J. Germline mutations in the ribonuclease L gene in families showing linkage with HPC1. Nat. Genet [print-electronic]. 2002 Feb; 30(2): 181-4. PMID: 11799394, PII: ng823, DOI: 10.1038/ng823, ISSN: 1061-4036.
Stephan DA, Howell GR, Teslovich TM, Coffey AJ, Smith L, Bailey-Wilson JE, Malechek L, Gildea D, Smith JR, Gillanders EM, Schleutker J, Hu P, Steingruber HE, Dhami P, Robbins CM, Makalowska I, Carpten JD, Sood R, Mumm S, Reinbold R, Bonner TI, Baffoe-Bonnie A, Bubendorf L, Heiskanen M, Kallioneimi OP, Baxevanis AD, Joseph SS, Zucchi I, Burk RD, Isaacs W, Ross MT, Trent JM. Physical and transcript map of the hereditary prostate cancer region at xq27. Genomics. 2002 Jan; 79(1): 41-50. PMID: 11827456, PII: S0888754301966819, DOI: 10.1006/geno.2001.6681, ISSN: 0888-7543.
Smith, J., Collins, F., and Gelehrter, T. Molecular Genetics of Common Disease. In: The Genetic Basis of Common Diseases, Second Edition, edited by King, Rotter, and Motulsky. (Oxford Univesity Press). 2002.
Xu J, Zheng SL, Chang B, Smith JR, Carpten JD, Stine OC, Isaacs SD, Wiley KE, Henning L, Ewing C, Bujnovszky P, Bleeker ER, Walsh PC, Trent JM, Meyers DA, Isaacs WB. Linkage of prostate cancer susceptibility loci to chromosome 1. Hum. Genet. 2001 Apr; 108(4): 335-45. PMID: 11379880, ISSN: 0340-6717.
Schleutker J, Matikainen M, Smith J, Koivisto P, Baffoe-Bonnie A, Kainu T, Gillanders E, Sankila R, Pukkala E, Carpten J, Stephan D, Tammela T, Brownstein M, Bailey-Wilson J, Trent J, Kallioniemi OP. A genetic epidemiological study of hereditary prostate cancer (HPC) in Finland: frequent HPCX linkage in families with late-onset disease. Clin. Cancer Res. 2000 Dec; 6(12): 4810-5. PMID: 11156239, ISSN: 1078-0432.
Bergthorsson JT, Johannesdottir G, Arason A, Benediktsdottir KR, Agnarsson BA, Bailey-Wilson JE, Gillanders E, Smith J, Trent J, Barkardottir RB. Analysis of HPC1, HPCX, and PCaP in Icelandic hereditary prostate cancer. Hum. Genet. 2000 Oct; 107(4): 372-5. PMID: 11129338, ISSN: 0340-6717.
Xu J. Combined analysis of hereditary prostate cancer linkage to 1q24-25: results from 772 hereditary prostate cancer families from the International Consortium for Prostate Cancer Genetics. Am. J. Hum. Genet. 2000 Mar; 66(3): 945-57. PMID: 10712209, PMCID: PMC1288175, PII: S0002-9297(07)64021-X, ISSN: 0002-9297.
Carpten JD, Makalowska I, Robbins CM, Scott N, Sood R, Connors TD, Bonner TI, Smith JR, Faruque MU, Stephan DA, Pinkett H, Morgenbesser SD, Su K, Graham C, Gregory SG, Williams H, McDonald L, Baxevanis AD, Klingler KW, Landes GM, Trent JM. A 6-Mb high-resolution physical and transcription map encompassing the hereditary prostate cancer 1 (HPC1) region. Genomics. 2000 Feb 2/15/2000; 64(1): 1-14. PMID: 10708513, PII: S0888-7543(99)96051-2, DOI: 10.1006/geno.1999.6051, ISSN: 0888-7543.
Berry R, Schaid DJ, Smith JR, French AJ, Schroeder JJ, McDonnell SK, Peterson BJ, Wang ZY, Carpten JD, Roberts SG, Tester DJ, Blute ML, Trent JM, Thibodeau SN. Linkage analyses at the chromosome 1 loci 1q24-25 (HPC1), 1q42.2-43 (PCAP), and 1p36 (CAPB) in families with hereditary prostate cancer. Am. J. Hum. Genet. 2000 Feb; 66(2): 539-46. PMID: 10677314, PMCID: PMC1288107, PII: S0002-9297(07)63428-4, DOI: 10.1086/302771, ISSN: 0002-9297.
Grönberg H, Smith J, Emanuelsson M, Jonsson BA, Bergh A, Carpten J, Isaacs W, Xu J, Meyers D, Trent J, Damber JE. In Swedish families with hereditary prostate cancer, linkage to the HPC1 locus on chromosome 1q24-25 is restricted to families with early-onset prostate cancer. Am. J. Hum. Genet. 1999 Jul; 65(1): 134-40. PMID: 10364525, PMCID: PMC1378083, PII: S0002-9297(07)63736-7, DOI: 10.1086/302447, ISSN: 0002-9297.
Carpten, J., Smith, J., Stephan, D., Isaacs, W., Trent, J. Searching for Prostate Cancer Genes. Science and Medicine. 1998; 5: 26-35.
Grönberg H, Xu J, Smith JR, Carpten JD, Isaacs SD, Freije D, Bova GS, Danber JE, Bergh A, Walsh PC, Collins FS, Trent JM, Meyers DA, Isaacs WB. Early age at diagnosis in families providing evidence of linkage to the hereditary prostate cancer locus (HPC1) on chromosome 1. Cancer Res. 1997 Nov 11/1/1997; 57(21): 4707-9. PMID: 9354426, ISSN: 0008-5472.
Grönberg H, Isaacs SD, Smith JR, Carpten JD, Bova GS, Freije D, Xu J, Meyers DA, Collins FS, Trent JM, Walsh PC, Isaacs WB. Characteristics of prostate cancer in families potentially linked to the hereditary prostate cancer 1 (HPC1) locus. JAMA. 1997 Oct 10/15/1997; 278(15): 1251-5. PMID: 9333266, ISSN: 0098-7484.
Ghosh S, Karanjawala ZE, Hauser ER, Ally D, Knapp JI, Rayman JB, Musick A, Tannenbaum J, Te C, Shapiro S, Eldridge W, Musick T, Martin C, Smith JR, Carpten JD, Brownstein MJ, Powell JI, Whiten R, Chines P, Nylund SJ, Magnuson VL, Boehnke M, Collins FS. Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group. Genome Res. 1997 Feb; 7(2): 165-78. PMID: 9049634, ISSN: 1088-9051.
Brownstein, M., Carpten, J., and Smith, J. Modulation of Nontemplated Nucleotide Addition by Taq DNA Polymerase: Primer Modifications that Facilitate Genotyping. Biotechniques. 1996; 20: 1004-10.
Smith, J., Freije, D., Carpten, J., Gronberg, H., Xu, J., Isaacs, S., Brownstein, M., Bova, G., Guo, H., Bujnovszky, P., Nusskern, D., Damber, J., Bergh, A., Emanuelsson, M., Kallioniemi, O., Walker-Daniels, J., Bailey-Wilson, J., Beaty, T., Meyers, D., Walsh, P., Collins, F., Trent, J., and Isaacs, W. Major Susceptibility Locus for Prostate Cancer on Chromosome 1 Suggested by a Genome-Wide Search. Science. 1996; 274((Nov 22)): 1371-4.
Smith JR, Carpten JD, Brownstein MJ, Ghosh S, Magnuson VL, Gilbert DA, Trent JM, Collins FS. Approach to genotyping errors caused by nontemplated nucleotide addition by Taq DNA polymerase. Genome Res. 1995 Oct; 5(3): 312-7. PMID: 8593617, ISSN: 1088-9051.
Smith JR, Osborne TF, Goldstein JL, Brown MS. Identification of nucleotides responsible for enhancer activity of sterol regulatory element in low density lipoprotein receptor gene. J. Biol. Chem. 1990 Feb 2/5/1990; 265(4): 2306-10. PMID: 2298751, ISSN: 0021-9258.
Smith JR, Osborne TF, Brown MS, Goldstein JL, Gil G. Multiple sterol regulatory elements in promoter for hamster 3-hydroxy-3-methylglutaryl-coenzyme A synthase. J. Biol. Chem. 1988 Dec 12/5/1988; 263(34): 18480-7. PMID: 2903862, ISSN: 0021-9258.
Gil G, Smith JR, Goldstein JL, Slaughter CA, Orth K, Brown MS, Osborne TF. Multiple genes encode nuclear factor 1-like proteins that bind to the promoter for 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Proc. Natl. Acad. Sci. U.S.A. 1988 Dec; 85(23): 8963-7. PMID: 3194401, PMCID: PMC282633, ISSN: 0027-8424.
Gil G, Smith JR, Goldstein JL, Brown MS. Optional exon in the 5'-untranslated region of 3-hydroxy-3-methylglutaryl coenzyme A synthase gene: conserved sequence and splicing pattern in humans and hamsters. Proc. Natl. Acad. Sci. U.S.A. 1987 Apr; 84(7): 1863-6. PMID: 3470763, PMCID: PMC304541, ISSN: 0027-8424.