1,052 results on '"Sampson, Joshua"'
Search Results
2. The Lateral Approach to Hip Arthroscopy
- Author
-
Sampson, Thomas G., primary and Sampson, Joshua D., additional
- Published
- 2024
- Full Text
- View/download PDF
3. Polygenic risk scores, radiation treatment exposures and subsequent cancer risk in childhood cancer survivors
- Author
-
Gibson, Todd M., Karyadi, Danielle M., Hartley, Stephen W., Arnold, Michael A., Berrington de Gonzalez, Amy, Conces, Miriam R., Howell, Rebecca M., Kapoor, Vidushi, Leisenring, Wendy M., Neglia, Joseph P., Sampson, Joshua N., Turcotte, Lucie M., Chanock, Stephen J., Armstrong, Gregory T., and Morton, Lindsay M.
- Published
- 2024
- Full Text
- View/download PDF
4. Increasing efficiency and reducing bias when assessing HPV vaccination efficacy by using non-targeted HPV strains
- Author
-
Etievant, Lola, Sampson, Joshua N., and Gail, Mitchell H.
- Subjects
Statistics - Applications - Abstract
Studies of vaccine efficacy often record both the incidence of vaccine-targeted virus strains (primary outcome) and the incidence of non-targeted strains (secondary outcome). However, standard estimates of vaccine efficacy on targeted strains ignore the data on non-targeted strains. Assuming non-targeted strains are unaffected by vaccination, we regard the secondary outcome as a negative control outcome and show how using such data can (i) increase the precision of the estimated vaccine efficacy against targeted strains in randomized trials, and (ii) reduce confounding bias of that same estimate in observational studies. For objective (i), we augment the primary outcome estimating equation with a function of the secondary outcome that is unbiased for zero. For objective (ii), we jointly estimate the treatment effects on the primary and secondary outcomes. If the bias induced by the unmeasured confounders is similar for both types of outcomes, as is plausible for factors that influence the general risk of infection, then we can use the estimated efficacy against the secondary outcomes to remove the bias from estimated efficacy against the primary outcome. We demonstrate the utility of these approaches in studies of HPV vaccines that only target a few highly carcinogenic strains. In this example, using non-targeted strains increased precision in randomized trials modestly but reduced bias in observational studies substantially., Comment: Etievant, L., Sampson, J.N. and Gail, M.H. (2022) Increasing efficiency and reducing bias when assessing HPV vaccination efficacy by using nontargeted HPV strains. Biometrics. 1-12
- Published
- 2022
- Full Text
- View/download PDF
5. Inflated expectations: Rare-variant association analysis using public controls
- Author
-
Kim, Jung, Karyadi, Danielle M, Hartley, Stephen W, Zhu, Bin, Wang, Mingyi, Wu, Dongjing, Song, Lei, Armstrong, Gregory T, Bhatia, Smita, Robison, Leslie L, Yasui, Yutaka, Carter, Brian, Sampson, Joshua N, Freedman, Neal D, Goldstein, Alisa M, Mirabello, Lisa, Chanock, Stephen J, Morton, Lindsay M, Savage, Sharon A, and Stewart, Douglas R
- Subjects
Epidemiology ,Biological Sciences ,Health Sciences ,Genetics ,Motivation ,High-Throughput Nucleotide Sequencing ,Polymorphism ,Single Nucleotide ,Software ,General Science & Technology - Abstract
The use of publicly available sequencing datasets as controls (hereafter, "public controls") in studies of rare variant disease associations has great promise but can increase the risk of false-positive discovery. The specific factors that could contribute to inflated distribution of test statistics have not been systematically examined. Here, we leveraged both public controls, gnomAD v2.1 and several datasets sequenced in our laboratory to systematically investigate factors that could contribute to the false-positive discovery, as measured by λΔ95, a measure to quantify the degree of inflation in statistical significance. Analyses of datasets in this investigation found that 1) the significantly inflated distribution of test statistics decreased substantially when the same variant caller and filtering pipelines were employed, 2) differences in library prep kits and sequencers did not affect the false-positive discovery rate and, 3) joint vs. separate variant-calling of cases and controls did not contribute to the inflation of test statistics. Currently available methods do not adequately adjust for the high false-positive discovery. These results, especially if replicated, emphasize the risks of using public controls for rare-variant association tests in which individual-level data and the computational pipeline are not readily accessible, which prevents the use of the same variant-calling and filtering pipelines on both cases and controls. A plausible solution exists with the emergence of cloud-based computing, which can make it possible to bring containerized analytical pipelines to the data (rather than the data to the pipeline) and could avert or minimize these issues. It is suggested that future reports account for this issue and provide this as a limitation in reporting new findings based on studies that cannot practically analyze all data on a single pipeline.
- Published
- 2023
6. Rest-activity rhythms and cognitive impairment and dementia in older women: Results from the Womens Health Initiative.
- Author
-
Xiao, Qian, Yaffe, Kristin, Sampson, Joshua, Chen, Jiu-Chiuan, Hayden, Kathleen, Henderson, Victor, LaCroix, Andrea, Rapp, Stephen, Shadyab, Aladdin, and Stone, Katie
- Subjects
circadian rhythm ,cognitive impairment ,dementia ,older women ,physical activity ,rest-activity rhythm ,sleep ,Aged ,Aging ,Cognitive Dysfunction ,Dementia ,Female ,Humans ,Rest ,Womens Health - Abstract
INTRODUCTION: Growing evidence suggests that impairment in rest-activity rhythms may be a risk factor for cognitive decline and impairment in the aging population. However, previous studies included only a limited set of rest-activity metrics and produced mixed findings. We studied a comprehensive set of parametric and nonparametric characteristics of rest-activity rhythms in relation to mild cognitive impairment (MCI) and probable dementia in a cohort of older women. METHODS: The prospective analysis included 763 women enrolled in two ancillary studies of the Womens Health Initiative (WHI): the WHI Memory Study-Epidemiology of Cognitive Health Outcomes and Objective Physical Activity and Cardiovascular Health studies. The association between accelerometry-based rest-activity parameters and centrally adjudicated MCI and probable dementia were determined using Cox regression models adjusted for sociodemographic characteristics, lifestyle factors, and comorbidities. RESULTS: Overall, the results support a prospective association between weakened rest-activity rhythms (e.g., reduced amplitude and overall rhythmicity) and adverse cognitive outcomes. Specifically, reduced overall rhythmicity (pseudo F statistic), lower amplitude and activity level (amplitude/relative amplitude, mesor, and activity level during active periods of the day [M10]), and later activity timing (acrophase and midpoint of M10) were associated with a higher risk for MCI and probable dementia. Women with lower amplitude and mesor also exhibited faster cognitive decline over follow-up. CONCLUSION: Weakened rest-activity rhythms may be predictive markers for cognitive decline, MCI, and dementia among older women.
- Published
- 2022
7. GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas
- Author
-
Machiela, Mitchell J., Huang, Wen-Yi, Wong, Wendy, Berndt, Sonja I., Sampson, Joshua, De Almeida, Jonas, Abubakar, Mustapha, Hislop, Jada, Chen, Kai-Ling, Dagnall, Casey, Diaz-Mayoral, Norma, Ferrell, Mary, Furr, Michael, Gonzalez, Alex, Hicks, Belynda, Hubbard, Aubrey K., Hutchinson, Amy, Jiang, Kevin, Jones, Kristine, Liu, Jia, Loftfield, Erikka, Loukissas, Jennifer, Mabie, Jerome, Merkle, Shannon, Miller, Eric, Minasian, Lori M., Nordgren, Ellen, Park, Brian, Pinsky, Paul, Riley, Thomas, Sandoval, Lorena, Saxena, Neeraj, Vogt, Aurelie, Wang, Jiahui, Williams, Craig, Wright, Patrick, Yeager, Meredith, Zhu, Bin, Zhu, Claire, Chanock, Stephen J., Garcia-Closas, Montserrat, and Freedman, Neal D.
- Published
- 2023
- Full Text
- View/download PDF
8. Lipidomics and pancreatic cancer risk in two prospective studies
- Author
-
Naudin, Sabine, Sampson, Joshua N., Moore, Steven C., Albanes, Demetrius, Freedman, Neal D., Weinstein, Stephanie J., and Stolzenberg-Solomon, Rachael
- Published
- 2023
- Full Text
- View/download PDF
9. HPV16 infection decreases vaccine-induced HPV16 antibody avidity: the CVT trial.
- Author
-
Tsang, Sabrina, Schiller, John, Porras, Carolina, Kemp, Troy, Herrero, Rolando, Schussler, John, Sierra, Monica, Cortes, Bernal, Hildesheim, Allan, Lowy, Douglas, Rodríguez, Ana, Romero, Byron, Çuburu, Nicolas, Shing, Jaimie, Pinto, Ligia, Sampson, Joshua, and Kreimer, Aimée
- Abstract
The HPV vaccine has shown sustained efficacy and consistent stabilization of antibody levels, even after a single dose. We defined the HPV16-VLP antibody avidity patterns over 11 years among women who received one- or three doses of the bivalent HPV vaccine in the Costa Rica HPV Vaccine Trial. Absolute HPV16 avidity was lower in women who received one compared to three doses, although the patterns were similar (increased in years 2 and 3 and remained stable over the remaining 8 years). HPV16 avidity among women who were HPV16-seropositive women at HPV vaccination, a marker of natural immune response to HPV16 infection, was significantly lower than those of HPV16-seronegative women, a difference that was more pronounced among one-dose recipients. No differences in HPV16 avidity were observed by HPV18 serostatus at vaccination, confirming the specificity of the findings. Importantly, point estimates for vaccine efficacy against incident, six-month persistent HPV16 infections was similar between women who were HPV16 seronegative and seropositive at the time of initial HPV vaccination for both one-dose and three-dose participants. It is therefore likely that this lower avidity level is still sufficient to enable antibody-mediated protection. It is encouraging for long-term HPV-vaccine protection that HPV16 antibody avidity was maintained for over a decade, even after a single dose.
- Published
- 2022
10. Nonparametric Parameters of 24-Hour Rest-Activity Rhythms and Long-Term Cognitive Decline and Incident Cognitive Impairment in Older Men.
- Author
-
Xiao, Qian, Sampson, Joshua N, LaCroix, Andrea Z, Shadyab, Aladdin H, Zeitzer, Jamie M, Ancoli-Israel, Sonia, Yaffe, Kristin, and Stone, Katie
- Subjects
Aging ,Behavioral and Social Science ,Mental Health ,Clinical Research ,Prevention ,Neurosciences ,Brain Disorders ,Mental health ,Actigraphy ,Aged ,Circadian Rhythm ,Cognitive Dysfunction ,Humans ,Male ,Prospective Studies ,Rest ,Circadian rhythms ,Cognitive impairment ,Dementia ,Older adults ,Rest and activity ,Osteoporotic Fractures in Men (MrOS) Study Group ,Clinical Sciences ,Gerontology - Abstract
Altered 24-hour rest-activity rhythms may be associated with cognitive impairment in older adults, but evidence from prospective studies is limited. Nonparametric methods were used to assess actigraphy-based activity patterns in 2 496 older men. Incident cognitive impairment was assessed 4 times over 12 years using the Modified Mini-Mental State Examination (3MS) and Trails B tests, self-reported medication use, and clinical diagnosis. The highest quartile (vs the lowest) of intradaily variability and the lowest quartiles (vs the highest) of interdaily stability and relative amplitude were associated with incident cognitive impairment (hazard ratio [95% confidence interval]: 1.82 [1.31-2.53], 1.36 [0.99-1.86], and 1.85 [1.33-2.56], respectively). A larger increase in intradaily variability over 7.5 years was associated with a greater subsequent decline in 3MS scores but not in Trails B performance. In conclusion, less stable and more variable rest-activity rhythms may represent early biomarkers of cognitive impairment in older men.
- Published
- 2022
11. Measuring diet by metabolomics: a 14-d controlled feeding study of weighed food intake
- Author
-
Playdon, Mary C., Tinker, Lesley F., Prentice, Ross L., Loftfield, Erikka, Hayden, Kathleen M., Van Horn, Linda, Sampson, Joshua N., Stolzenberg-Solomon, Rachael, Lampe, Johanna W., Neuhouser, Marian L., and Moore, Steven C.
- Published
- 2024
- Full Text
- View/download PDF
12. Risk Factors for Non–Human Papillomavirus (HPV) Type 16/18 Cervical Infections and Associated Lesions Among HPV DNA–Negative Women Vaccinated Against HPV-16/18 in the Costa Rica Vaccine Trial
- Author
-
Sierra, Mónica S, Tsang, Sabrina H, Hu, Shangying, Porras, Carolina, Herrero, Rolando, Kreimer, Aimée R, Schussler, John, Boland, Joseph, Wagner, Sarah, Cortes, Bernal, Rodríguez, Ana C, Quint, Wim, van Doorn, Leen-Jan, Schiffman, Mark, Sampson, Joshua N, Hildesheim, Allan, Cortés, Bernal, González, Paula, Jiménez, Silvia E, Rodríguez, Ana Cecilia, Lowy, Douglas R, Schiller, John T, Sherman, Mark, Wacholder, Sholom, Pinto, Ligia A, Kemp, Troy J, Sidawy, Mary K, Struijk, Linda, Palefsky, Joel M, Darragh, Teresa M, and Stoler, Mark H
- Subjects
Clinical Research ,Behavioral and Social Science ,Clinical Trials and Supportive Activities ,Sexually Transmitted Infections ,HPV and/or Cervical Cancer Vaccines ,Immunization ,Prevention ,HIV/AIDS ,Cervical Cancer ,Adolescent Sexual Activity ,Infectious Diseases ,Vaccine Related ,Pediatric ,Cancer ,Adolescent ,Adult ,Cervical Intraepithelial Neoplasia ,Costa Rica ,DNA ,Female ,Human papillomavirus 16 ,Human papillomavirus 18 ,Humans ,Papillomaviridae ,Papillomavirus Infections ,Papillomavirus Vaccines ,Pregnancy ,Risk Factors ,Treatment Outcome ,Uterine Cervical Neoplasms ,Young Adult ,Costa Rica Human Papillomavirus Vaccine Trial (CVT) Group ,Uterine Cervical Dysplasia ,CIN2+ ,HPV infection ,HPV vaccine ,incidence ,persistence ,progression ,Biological Sciences ,Medical and Health Sciences ,Microbiology - Abstract
BackgroundFactors that lead human papillomavirus (HPV) infections to persist and progress to cancer are not fully understood. We evaluated co-factors for acquisition, persistence, and progression of non-HPV-16/18 infections among HPV-vaccinated women.MethodsWe analyzed 2153 women aged 18-25 years randomized to the HPV-vaccine arm of the Costa Rica HPV Vaccine Trial. Women were HPV DNA negative for all types at baseline and followed for approximately 11 years. Generalized estimating equation methods were used to account for correlated observations. Time-dependent factors evaluated were age, sexual behavior, marital status, hormonally related factors, number of full-term pregnancies (FTPs), smoking behavior, and baseline body mass index.ResultsA total of 1777 incident oncogenic non-HPV-16/18 infections were detected in 12 292 visits (average, 0.14 infections/visit). Age and sexual behavior-related variables were associated with oncogenic non-HPV-16/18 acquisition. Twenty-six percent of incident infections persisted for ≥1 year. None of the factors evaluated were statistically associated with persistence of oncogenic non-HPV-16/18 infections. Risk of progression to Cervical Intraepithelial Neoplasia grade 2 or worst (CIN2+) increased with increasing age (P for trend = .001), injectable contraceptive use (relative risk, 2.61 [95% confidence interval, 1.19-5.73] ever vs never), and increasing FTPs (P for trend = .034).ConclusionsIn a cohort of HPV-16/18-vaccinated women, age and sexual behavior variables are associated with acquisition of oncogenic non-HPV-16/18 infections; no notable factors are associated with persistence of acquired infections; and age, parity, and hormonally related exposures are associated with progression to CIN2+.
- Published
- 2021
13. Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes
- Author
-
Berndt, Sonja I., Vijai, Joseph, Benavente, Yolanda, Camp, Nicola J., Nieters, Alexandra, Wang, Zhaoming, Smedby, Karin E., Kleinstern, Geffen, Hjalgrim, Henrik, Besson, Caroline, Skibola, Christine F., Morton, Lindsay M., Brooks-Wilson, Angela R., Teras, Lauren R., Breeze, Charles, Arias, Joshua, Adami, Hans-Olov, Albanes, Demetrius, Anderson, Kenneth C., Ansell, Stephen M., Bassig, Bryan, Becker, Nikolaus, Bhatti, Parveen, Birmann, Brenda M., Boffetta, Paolo, Bracci, Paige M., Brennan, Paul, Brown, Elizabeth E., Burdett, Laurie, Cannon-Albright, Lisa A., Chang, Ellen T., Chiu, Brian C. H., Chung, Charles C., Clavel, Jacqueline, Cocco, Pierluigi, Colditz, Graham, Conde, Lucia, Conti, David V., Cox, David G., Curtin, Karen, Casabonne, Delphine, De Vivo, Immaculata, Diepstra, Arjan, Diver, W. Ryan, Dogan, Ahmet, Edlund, Christopher K., Foretova, Lenka, Fraumeni, Jr, Joseph F., Gabbas, Attilio, Ghesquières, Hervé, Giles, Graham G., Glaser, Sally, Glenn, Martha, Glimelius, Bengt, Gu, Jian, Habermann, Thomas M., Haiman, Christopher A., Haioun, Corinne, Hofmann, Jonathan N., Holford, Theodore R., Holly, Elizabeth A., Hutchinson, Amy, Izhar, Aalin, Jackson, Rebecca D., Jarrett, Ruth F., Kaaks, Rudolph, Kane, Eleanor, Kolonel, Laurence N., Kong, Yinfei, Kraft, Peter, Kricker, Anne, Lake, Annette, Lan, Qing, Lawrence, Charles, Li, Dalin, Liebow, Mark, Link, Brian K., Magnani, Corrado, Maynadie, Marc, McKay, James, Melbye, Mads, Miligi, Lucia, Milne, Roger L., Molina, Thierry J., Monnereau, Alain, Montalvan, Rebecca, North, Kari E., Novak, Anne J., Onel, Kenan, Purdue, Mark P., Rand, Kristin A., Riboli, Elio, Riby, Jacques, Roman, Eve, Salles, Gilles, Sborov, Douglas W., Severson, Richard K., Shanafelt, Tait D., Smith, Martyn T., Smith, Alexandra, Song, Kevin W., Song, Lei, Southey, Melissa C., Spinelli, John J., Staines, Anthony, Stephens, Deborah, Sutherland, Heather J., Tkachuk, Kaitlyn, Thompson, Carrie A., Tilly, Hervé, Tinker, Lesley F., Travis, Ruth C., Turner, Jenny, Vachon, Celine M., Vajdic, Claire M., Van Den Berg, Anke, Van Den Berg, David J., Vermeulen, Roel C. H., Vineis, Paolo, Wang, Sophia S., Weiderpass, Elisabete, Weiner, George J., Weinstein, Stephanie, Doo, Nicole Wong, Ye, Yuanqing, Yeager, Meredith, Yu, Kai, Zeleniuch-Jacquotte, Anne, Zhang, Yawei, Zheng, Tongzhang, Ziv, Elad, Sampson, Joshua, Chatterjee, Nilanjan, Offit, Kenneth, Cozen, Wendy, Wu, Xifeng, Cerhan, James R., Chanock, Stephen J., Slager, Susan L., and Rothman, Nathaniel
- Published
- 2022
- Full Text
- View/download PDF
14. Pre-analytical Sample Handling Conditions and Their Effects on the Human Serum Metabolome in Epidemiological Studies
- Author
-
McClain, Kathleen M, Moore, Steven C, Sampson, Joshua N, Henderson, Theresa R, Gebauer, Sarah K, Newman, John W, Ross, Sharon, Pedersen, Theresa L, Baer, David J, and Zanetti, Krista A
- Subjects
Epidemiology ,Health Sciences ,Blood Specimen Collection ,Epidemiologic Studies ,Humans ,Metabolome ,Metabolomics ,Pilot Projects ,Temperature ,Time Factors ,bias ,metabolomics ,preclinical handling ,sample handling ,Mathematical Sciences ,Medical and Health Sciences - Abstract
Many epidemiologic studies use metabolomics for discovery-based research. The degree to which sample handling may influence findings, however, is poorly understood. In 2016, serum samples from 13 volunteers from the US Department of Agriculture's Beltsville Human Nutrition Research Center were subjected to different clotting (30 minutes/120 minutes) and refrigeration (0 minutes/24 hours) conditions, as well as different numbers (0/1/4) and temperatures (ice/refrigerator/room temperature) of thaws. The median absolute percent difference (APD) between metabolite levels and correlations between levels across conditions were estimated for 628 metabolites. The potential for handling artifacts to induce false-positive associations was estimated using variable hypothetical scenarios in which 1%-100% of case samples had different handling than control samples. All handling conditions influenced metabolite levels. Across metabolites, the median APD when extending clotting time was 9.08%. When increasing the number of thaws from 0 to 4, the median APD was 10.05% for ice and 5.54% for room temperature. Metabolite levels were correlated highly across conditions (all r's ≥ 0.84), indicating that relative ranks were preserved. However, if handling varied even modestly by case status, our hypotheticals showed that results can be biased and can result in false-positive findings. Sample handling affects levels of metabolites, and special care should be taken to minimize effects. Shorter room-temperature thaws should be preferred over longer ice thaws, and handling should be meticulously matched by case status.
- Published
- 2021
15. A metabolomic investigation of serum perfluorooctane sulfonate and perfluorooctanoate
- Author
-
Rhee, Jongeun, Loftfield, Erikka, Albanes, Demetrius, Layne, Tracy M., Stolzenberg-Solomon, Rachael, Liao, Linda M., Playdon, Mary C., Berndt, Sonja I., Sampson, Joshua N., Freedman, Neal D., Moore, Steven C., and Purdue, Mark P.
- Published
- 2023
- Full Text
- View/download PDF
16. Serum concentrations of per- and polyfluoroalkyl substances and risk of renal cell carcinoma in the Multiethnic Cohort Study
- Author
-
Rhee, Jongeun, Chang, Vicky C., Cheng, Iona, Calafat, Antonia M., Botelho, Julianne Cook, Shearer, Joseph J., Sampson, Joshua N., Setiawan, Veronica Wendy, Wilkens, Lynne R., Silverman, Debra T., Purdue, Mark P., and Hofmann, Jonathan N.
- Published
- 2023
- Full Text
- View/download PDF
17. Efficacy of the bivalent HPV vaccine against HPV 16/18-associated precancer: long-term follow-up results from the Costa Rica Vaccine Trial.
- Author
-
Porras, Carolina, Tsang, Sabrina H, Herrero, Rolando, Guillén, Diego, Darragh, Teresa M, Stoler, Mark H, Hildesheim, Allan, Wagner, Sarah, Boland, Joseph, Lowy, Douglas R, Schiller, John T, Schiffman, Mark, Schussler, John, Gail, Mitchell H, Quint, Wim, Ocampo, Rebeca, Morales, Jorge, Rodríguez, Ana C, Hu, Shangying, Sampson, Joshua N, Kreimer, Aimée R, and Costa Rica Vaccine Trial Group
- Subjects
Costa Rica Vaccine Trial Group ,Humans ,Papillomavirus Infections ,Vaccines ,Combined ,Treatment Outcome ,Immunization ,Double-Blind Method ,Time Factors ,Adolescent ,Adult ,Costa Rica ,Uterine Cervical Dysplasia ,Uterine Cervical Neoplasms ,Female ,Human papillomavirus 18 ,Human papillomavirus 16 ,Papillomavirus Vaccines ,Young Adult ,Neoplasm Grading ,Cervical Cancer ,Vaccine Related ,Cancer ,Biotechnology ,HPV and/or Cervical Cancer Vaccines ,Clinical Trials and Supportive Activities ,Prevention ,Clinical Research ,HIV/AIDS ,Sexually Transmitted Infections ,Infectious Diseases ,3.4 Vaccines ,Prevention of disease and conditions ,and promotion of well-being ,Infection ,Good Health and Well Being ,Oncology and Carcinogenesis ,Oncology & Carcinogenesis - Abstract
BackgroundOncogenic human papillomavirus (HPV) infections cause most cases of cervical cancer. Here, we report long-term follow-up results for the Costa Rica Vaccine Trial (publicly funded and initiated before licensure of the HPV vaccines), with the aim of assessing the efficacy of the bivalent HPV vaccine for preventing HPV 16/18-associated cervical intraepithelial neoplasia grade 2 or worse (CIN2+).MethodsWomen aged 18-25 years were enrolled in a randomised, double-blind, controlled trial in Costa Rica, between June 28, 2004, and Dec 21, 2005, designed to assess the efficacy of a bivalent vaccine for the prevention of infection with HPV 16/18 and associated precancerous lesions at the cervix. Participants were randomly assigned (1:1) to receive an HPV 16/18 AS04-adjuvanted vaccine or control hepatitis A vaccine. Vaccines were administered intramuscularly in three 0·5 mL doses at 0, 1, and 6 months and participants were followed up annually for 4 years. After the blinded phase, women in the HPV vaccine group were invited to enrol in the long-term follow-up study, which extended follow-up for 7 additional years. The control group received HPV vaccine and was replaced with a new unvaccinated control group. Women were followed up every 2 years until year 11. Investigators and patients were aware of treatment allocation for the follow-up phase. At each visit, clinicians collected cervical cells from sexually active women for cytology and HPV testing. Women with abnormal cytology were referred to colposcopy, biopsy, and treatment as needed. Women with negative results at the last screening visit (year 11) exited the long-term follow-up study. The analytical cohort for vaccine efficacy included women who were HPV 16/18 DNA-negative at vaccination. The primary outcome of this analysis was defined as histopathologically confirmed CIN2+ or cervical intraepithelial neoplasia grade 3 or worse associated with HPV 16/18 cervical infection detected at colposcopy referral. We calculated vaccine efficacy by year and cumulatively. This long-term follow-up study is registered with ClinicalTrials.gov, NCT00867464.Findings7466 women were enrolled in the Costa Rica Vaccine Trial; 3727 received the HPV vaccine and 3739 received the control vaccine. Between March 30, 2009, and July 5, 2012, 2635 women in the HPV vaccine group and 2836 women in the new unvaccinated control group were enrolled in the long-term follow-up study. 2635 women in the HPV vaccine group and 2677 women in the control group were included in the analysis cohort for years 0-4, and 2073 women from the HPV vaccine group and 2530 women from the new unvaccinated control group were included in the analysis cohort for years 7-11. Median follow-up time for the HPV group was 11·1 years (IQR 9·1-11·7), 4·6 years (4·3-5·3) for the original control group, and 6·2 years (5·5-6·9) for the new unvaccinated control group. At year 11, vaccine efficacy against incident HPV 16/18-associated CIN2+ was 100% (95% CI 89·2-100·0); 34 (1·5%) of 2233 unvaccinated women had a CIN2+ outcome compared with none of 1913 women in the HPV group. Cumulative vaccine efficacy against HPV 16/18-associated CIN2+ over the 11-year period was 97·4% (95% CI 88·0-99·6). Similar protection was observed against HPV 16/18-associated CIN3-specifically at year 11, vaccine efficacy was 100% (95% CI 78·8-100·0) and cumulative vaccine efficacy was 94·9% (73·7-99·4). During the long-term follow-up, no serious adverse events occurred that were deemed related to the HPV vaccine. The most common grade 3 or worse serious adverse events were pregnancy, puerperium, and perinatal conditions (in 255 [10%] of 2530 women in the unvaccinated control group and 201 [10%] of 2073 women in the HPV vaccine group). Four women in the unvaccinated control group and three in the HPV vaccine group died; no deaths were deemed to be related to the HPV vaccine.InterpretationThe bivalent HPV vaccine has high efficacy against HPV 16/18-associated precancer for more than a decade after initial vaccination, supporting the notion that invasive cervical cancer is preventable.FundingUS National Cancer Institute.
- Published
- 2020
18. A prospective nested case-control study of serum concentrations of per- and polyfluoroalkyl substances and aggressive prostate cancer risk
- Author
-
Rhee, Jongeun, Barry, Kathryn H., Huang, Wen-Yi, Sampson, Joshua N., Hofmann, Jonathan N., Silverman, Debra T., Calafat, Antonia M., Botelho, Julianne Cook, Kato, Kayoko, Purdue, Mark P., and Berndt, Sonja I.
- Published
- 2023
- Full Text
- View/download PDF
19. Correction: Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes
- Author
-
Berndt, Sonja I., Vijai, Joseph, Benavente, Yolanda, Camp, Nicola J., Nieters, Alexandra, Wang, Zhaoming, Smedby, Karin E., Kleinstern, Geffen, Hjalgrim, Henrik, Besson, Caroline, Skibola, Christine F., Morton, Lindsay M., Brooks-Wilson, Angela R., Teras, Lauren R., Breeze, Charles, Arias, Joshua, Adami, Hans-Olov, Albanes, Demetrius, Anderson, Kenneth C., Ansell, Stephen M., Bassig, Bryan, Becker, Nikolaus, Bhatti, Parveen, Birmann, Brenda M., Boffetta, Paolo, Bracci, Paige M., Brennan, Paul, Brown, Elizabeth E., Burdett, Laurie, Cannon-Albright, Lisa A., Chang, Ellen T., Chiu, Brian C. H., Chung, Charles C., Clavel, Jacqueline, Cocco, Pierluigi, Colditz, Graham, Conde, Lucia, Conti, David V., Cox, David G., Curtin, Karen, Casabonne, Delphine, De Vivo, Immaculata, Diepstra, Arjan, Diver, W. Ryan, Dogan, Ahmet, Edlund, Christopher K., Foretova, Lenka, Fraumeni, Jr, Joseph F., Gabbas, Attilio, Ghesquières, Hervé, Giles, Graham G., Glaser, Sally, Glenn, Martha, Glimelius, Bengt, Gu, Jian, Habermann, Thomas M., Haiman, Christopher A., Haioun, Corinne, Hofmann, Jonathan N., Holford, Theodore R., Holly, Elizabeth A., Hutchinson, Amy, Izhar, Aalin, Jackson, Rebecca D., Jarrett, Ruth F., Kaaks, Rudolph, Kane, Eleanor, Kolonel, Laurence N., Kong, Yinfei, Kraft, Peter, Kricker, Anne, Lake, Annette, Lan, Qing, Lawrence, Charles, Li, Dalin, Liebow, Mark, Link, Brian K., Magnani, Corrado, Maynadie, Marc, McKay, James, Melbye, Mads, Miligi, Lucia, Milne, Roger L., Molina, Thierry J., Monnereau, Alain, Montalvan, Rebecca, North, Kari E., Novak, Anne J., Onel, Kenan, Purdue, Mark P., Rand, Kristin A., Riboli, Elio, Riby, Jacques, Roman, Eve, Salles, Gilles, Sborov, Douglas W., Severson, Richard K., Shanafelt, Tait D., Smith, Martyn T., Smith, Alexandra, Song, Kevin W., Song, Lei, Southey, Melissa C., Spinelli, John J., Staines, Anthony, Stephens, Deborah, Sutherland, Heather J., Tkachuk, Kaitlyn, Thompson, Carrie A., Tilly, Hervé, Tinker, Lesley F., Travis, Ruth C., Turner, Jenny, Vachon, Celine M., Vajdic, Claire M., Van Den Berg, Anke, Van Den Berg, David J., Vermeulen, Roel C. H., Vineis, Paolo, Wang, Sophia S., Weiderpass, Elisabete, Weiner, George J., Weinstein, Stephanie, Doo, Nicole Wong, Ye, Yuanqing, Yeager, Meredith, Yu, Kai, Zeleniuch-Jacquotte, Anne, Zhang, Yawei, Zheng, Tongzhang, Ziv, Elad, Sampson, Joshua, Chatterjee, Nilanjan, Offit, Kenneth, Cozen, Wendy, Wu, Xifeng, Cerhan, James R., Chanock, Stephen J., Slager, Susan L., and Rothman, Nathaniel
- Published
- 2023
- Full Text
- View/download PDF
20. Evaluation of Durability of a Single Dose of the Bivalent HPV Vaccine: The CVT Trial.
- Author
-
Kreimer, Aimée, Sampson, Joshua, Porras, Carolina, Schiller, John, Kemp, Troy, Herrero, Rolando, Wagner, Sarah, Boland, Joseph, Schussler, John, Lowy, Douglas, Chanock, Stephen, Roberson, David, Sierra, Mónica, Tsang, Sabrina, Schiffman, Mark, Rodriguez, Ana, Cortes, Bernal, Gail, Mitchell, Hildesheim, Allan, Gonzalez, Paula, and Pinto, Ligia
- Subjects
Adolescent ,Adult ,Antibodies ,Viral ,Costa Rica ,Female ,Human papillomavirus 16 ,Human papillomavirus 18 ,Humans ,Papillomavirus Infections ,Papillomavirus Vaccines ,Vaccines ,Combined ,Young Adult - Abstract
BACKGROUND: The authors investigated the durability of vaccine efficacy (VE) against human papillomavirus (HPV)16 or 18 infections and antibody response among nonrandomly assigned women who received a single dose of the bivalent HPV vaccine compared with women who received multiple doses and unvaccinated women. METHODS: HPV infections were compared between HPV16 or 18-vaccinated women aged 18 to 25 years who received one (N = 112), two (N = 62), or three (N = 1365) doses, and age- and geography-matched unvaccinated women (N = 1783) in the long-term follow-up of the Costa Rica HPV Vaccine Trial. Cervical HPV infections were measured at two study visits, approximately 9 and 11 years after initial HPV vaccination, using National Cancer Institute next-generation sequencing TypeSeq1 assay. VE and 95% confidence intervals (CIs) were estimated. HPV16 or 18 antibody levels were measured in all one- and two-dose women, and a subset of three-dose women, using a virus-like particle-based enzyme-linked immunosorbent assay (n = 448). RESULTS: Median follow-up for the HPV-vaccinated group was 11.3 years (interquartile range = 10.9-11.7 years) and did not vary by dose group. VE against prevalent HPV16 or 18 infection was 80.2% (95% CI = 70.7% to 87.0%) among three-dose, 83.8% (95% CI = 19.5% to 99.2%) among two-dose, and 82.1% (95% CI = 40.2% to 97.0%) among single-dose women. HPV16 or 18 antibody levels did not qualitatively decline between years four and 11 regardless of the number of doses given, although one-dose titers continue to be statistically significantly lower compared with two- and three-dose titers. CONCLUSION: More than a decade after HPV vaccination, single-dose VE against HPV16 or 18 infection remained high and HPV16 or 18 antibodies remained stable. A single dose of bivalent HPV vaccine may induce sufficiently durable protection that obviates the need for more doses.
- Published
- 2020
21. Durability of Cross-Protection by Different Schedules of the Bivalent HPV Vaccine: The CVT Trial.
- Author
-
Tsang, Sabrina, Sampson, Joshua, Schussler, John, Porras, Carolina, Wagner, Sarah, Boland, Joseph, Cortes, Bernal, Lowy, Douglas, Schiller, John, Schiffman, Mark, Kemp, Troy, Rodriguez, Ana, Quint, Wim, Gail, Mitchell, Pinto, Ligia, Gonzalez, Paula, Hildesheim, Allan, Kreimer, Aimée, and Herrero, Rolando
- Subjects
Adolescent ,Adult ,Alphapapillomavirus ,Cohort Studies ,Costa Rica ,Cross Protection ,Female ,Human papillomavirus 31 ,Humans ,Immunization Schedule ,Papillomavirus Infections ,Papillomavirus Vaccines ,Prevalence ,Vaccines ,Combined ,Young Adult - Abstract
BACKGROUND: The Costa Rica HPV Vaccine Trial has documented cross-protection of the bivalent HPV vaccine against HPV31/33/45 up to 7 years after vaccination, even with one dose of the vaccine. However, the durability of such protection remains unknown. Here, we evaluate the efficacy of different schedules of the vaccine against HPV31/33/45 out to 11 years postvaccination, expanding to other nontargeted HPV types. METHODS: We compared the rates of HPV infection in vaccinated women with the rates in a comparable cohort of unvaccinated women. We estimated the average vaccine efficacy (VEavg) against incident infections and tested for a change in VE over time. RESULTS: Among 3-dose women, we observed statistically significant cross-protection against HPV31/33/45 (VEavg = 64.4%, 95% confidence interval [CI] = 57.7% to 70.0%). Additionally, we observed borderline, statistically significant cross-protection against HPV35 (VEavg = 23.2%, 95% CI = 0.3% to 40.8%) and HPV58 (VEavg = 21.2%, 95% CI = 4.2% to 35.3%). There was no decrease in VE over time (two-sided Ptrend > .05 for HPV31, -33, -35, -45, and -58). As a benchmark, VEavg against HPV16/18 was 82.0% (95% CI = 77.3% to 85.7%). Among 1-dose women, we observed comparable efficacy against HPV31/33/45 (VEavg = 54.4%, 95% CI = 21.0% to 73.7%). Acquisition of nonprotected HPV types was similar between vaccinated and unvaccinated women, indicating that the difference in HPV infection rates was not attributable to differential genital HPV exposure. CONCLUSIONS: Substantial cross-protection afforded by the bivalent vaccine against HPV31/33/45, and to a lesser extent, HPV35 and HPV58, was sustained and remained stable after 11 years postvaccination, reinforcing the notion that the bivalent vaccine is an effective option for protection against HPV-associated cancers.
- Published
- 2020
22. Efficacy of the AS04-Adjuvanted HPV16/18 Vaccine: Pooled Analysis of the Costa Rica Vaccine and PATRICIA Randomized Controlled Trials.
- Author
-
Tota, Joseph, Struyf, Frank, Sampson, Joshua, Gonzalez, Paula, Ryser, Martin, Herrero, Rolando, Schussler, John, Karkada, Naveen, Rodriguez, Ana, Folschweiller, Nicolas, Porras, Carolina, Schiffman, Mark, Schiller, John, Quint, Wim, Kreimer, Aimée, Wheeler, Cosette, and Hildesheim, Allan
- Subjects
Adjuvants ,Immunologic ,Adolescent ,Adult ,Costa Rica ,Female ,Human papillomavirus 16 ,Human papillomavirus 18 ,Humans ,Papillomavirus Infections ,Papillomavirus Vaccines ,Randomized Controlled Trials as Topic ,Retrospective Studies ,Treatment Outcome ,Uterine Cervical Neoplasms ,Young Adult ,Uterine Cervical Dysplasia - Abstract
BACKGROUND: The AS04-adjuvanted HPV16/18 (AS04-HPV16/18) vaccine provides excellent protection against targeted human papillomavirus (HPV) types and a variable degree of cross-protection against others, including types 6/11/31/33/45. High efficacy against any cervical intraepithelial neoplasia grade 3 or greater (CIN3+; >90%) suggests that lower levels of protection may exist for a wide range of oncogenic HPV types, which is difficult to quantify in individual trials. Pooling individual-level data from two randomized controlled trials, we aimed to evaluate AS04-HPV16/18 vaccine efficacy against incident HPV infections and cervical abnormalities . METHODS: Data were available from the Costa Rica Vaccine Trial (NCT00128661) and Papilloma Trial Against Cancer in Young Adults trial (NCT00122681), two large-scale, double-blind randomized controlled trials of the AS04-HPV16/18 vaccine. Primary analyses focused on disease-free women with no detectable cervicovaginal HPV at baseline. RESULTS: A total of 12 550 women were included in our primary analyses (HPV arm = 6271, control arm = 6279). Incidence of 6-month persistent oncogenic and nononcogenic infections, excluding known and accepted protected types 6/11/16/18/31/33/45 (focusing on 34/35/39/40/42/43/44/51/52/53/54/56/58/59/66/68/73/70/74), was statistically significantly lower in the HPV arm than in the control arm (efficacy = 9.9%, 95% confidence interval [CI] = 1.7% to 17.4%). Statistically significant efficacy (P
- Published
- 2020
23. Efficacy of the AS04-adjuvanted HPV-16/18 vaccine: Pooled analysis of the Costa Rica Vaccine and PATRICIA randomized controlled trials
- Author
-
Tota, Joseph E, Struyf, Frank, Sampson, Joshua N, Gonzalez, Paula, Ryser, Martin, Herrero, Rolando, Schussler, John, Karkada, Naveen, Rodriguez, Ana Cecilia, Folschweiller, Nicolas, Porras, Carolina, Schiffman, Mark, Schiller, John T, Quint, Wim, Kreimer, Aimée R, Wheeler, Cosette M, Hildesheim, Allan, Cortés, Bernal, González, Paula, Jiménez, Silvia E, Rodríguez, Ana Cecilia, Lowy, Douglas R, Wacholder, Sholom, Pinto, Ligia A, Kemp, Troy J, van Doorn, Leen-Jan, Struijk, Linda, Palefsky, Joel M, Darragh, Teresa M, Stoler, Mark H, Garland, SM, Skinner, SR, De Sutter, P, Poppe, WAJ, De Carvalho, NS, Teixeira, JC, Ferguson, L, Ferguson, M, Papp, K, Ramjattan, B, Orr, PH, Paavonen, J, Höpker, WD, Tobgui, S Jensen-El, Liverani, CA, Limson, GM, Marti, M Campins, Castro, M, Centeno, C, Chow, SN, Angsuwathana, S, Lewis, D, Ackerman, R, Caldwell, M, Chambers, C, Chatterjee, A, Harper, D, Sperling, R, Stapleton, J, Waldbaum, A, Lee, P, and Awedikian, Rafi
- Subjects
Sexually Transmitted Infections ,Immunization ,Cancer ,Biotechnology ,Infectious Diseases ,HPV and/or Cervical Cancer Vaccines ,Vaccine Related ,Clinical Research ,Clinical Trials and Supportive Activities ,Cervical Cancer ,Prevention ,HIV/AIDS ,Adjuvants ,Immunologic ,Adolescent ,Adult ,Costa Rica ,Female ,Human papillomavirus 16 ,Human papillomavirus 18 ,Humans ,Papillomavirus Infections ,Papillomavirus Vaccines ,Randomized Controlled Trials as Topic ,Retrospective Studies ,Treatment Outcome ,Uterine Cervical Neoplasms ,Young Adult ,Uterine Cervical Dysplasia ,Costa Rica Vaccine Trial and PATRICIA Study ,Oncology and Carcinogenesis ,Oncology & Carcinogenesis - Abstract
BackgroundThe AS04-adjuvanted HPV16/18 (AS04-HPV16/18) vaccine provides excellent protection against targeted human papillomavirus (HPV) types and a variable degree of cross-protection against others, including types 6/11/31/33/45. High efficacy against any cervical intraepithelial neoplasia grade 3 or greater (CIN3+; >90%) suggests that lower levels of protection may exist for a wide range of oncogenic HPV types, which is difficult to quantify in individual trials. Pooling individual-level data from two randomized controlled trials, we aimed to evaluate AS04-HPV16/18 vaccine efficacy against incident HPV infections and cervical abnormalities .MethodsData were available from the Costa Rica Vaccine Trial (NCT00128661) and Papilloma Trial Against Cancer in Young Adults trial (NCT00122681), two large-scale, double-blind randomized controlled trials of the AS04-HPV16/18 vaccine. Primary analyses focused on disease-free women with no detectable cervicovaginal HPV at baseline.ResultsA total of 12 550 women were included in our primary analyses (HPV arm = 6271, control arm = 6279). Incidence of 6-month persistent oncogenic and nononcogenic infections, excluding known and accepted protected types 6/11/16/18/31/33/45 (focusing on 34/35/39/40/42/43/44/51/52/53/54/56/58/59/66/68/73/70/74), was statistically significantly lower in the HPV arm than in the control arm (efficacy = 9.9%, 95% confidence interval [CI] = 1.7% to 17.4%). Statistically significant efficacy (P
- Published
- 2020
24. Metabolomic analysis of serum alpha-tocopherol among men in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study
- Author
-
Lawrence, Wayne R., Lim, Jung-Eun, Huang, Jiaqi, Sampson, Joshua N., Weinstein, Stephanie J., and Albanes, Demetrius
- Published
- 2022
- Full Text
- View/download PDF
25. Residential proximity to dioxin emissions and risk of breast cancer in the sister study cohort
- Author
-
Rhee, Jongeun, Medgyesi, Danielle N., Fisher, Jared A., White, Alexandra J., Sampson, Joshua N., Sandler, Dale P., Ward, Mary H., and Jones, Rena R.
- Published
- 2023
- Full Text
- View/download PDF
26. Evaluation of TypeSeq, a Novel High-Throughput, Low-Cost, Next-Generation Sequencing-Based Assay for Detection of 51 Human Papillomavirus Genotypes
- Author
-
Wagner, Sarah, Roberson, David, Boland, Joseph, Kreimer, Aimée R, Yeager, Meredith, Cullen, Michael, Mirabello, Lisa, Dunn, S Terence, Walker, Joan, Zuna, Rosemary, Porras, Carolina, Cortes, Bernal, Sampson, Joshua, Herrero, Rolando, Rodriguez, Ana Cecilia, Quint, Wim, Van Doorn, Leen-Jan, José, San, González, Paula, Jiménez, Silvia E, Rodríguez, Ana Cecilia, Hildesheim, Allan, Lowy, Douglas R, Schiffman, Mark, Schiller, John T, Sherman, Mark, Wacholder, Sholom, Pinto, Ligia A, Kemp, Troy J, Sidawy, Mary K, van Doorn, Leen-Jan, Struijk, Linda, Palefsky, Joel M, Darragh, Teresa M, Stoler, Mark H, and Wentzensen, Nicolas
- Subjects
Reproductive Medicine ,Biomedical and Clinical Sciences ,Biological Sciences ,Infectious Diseases ,Prevention ,Vaccine Related ,Cervical Cancer ,Biotechnology ,Genetics ,Cancer ,HIV/AIDS ,Sexually Transmitted Infections ,Immunization ,Adolescent ,Adult ,Aged ,Aged ,80 and over ,Costa Rica ,Costs and Cost Analysis ,Cross-Sectional Studies ,Female ,Genotype ,Genotyping Techniques ,High-Throughput Nucleotide Sequencing ,Humans ,Middle Aged ,Papillomaviridae ,Papillomavirus Infections ,Papillomavirus Vaccines ,Uterine Cervical Neoplasms ,Young Adult ,HPV ,TypeSeq ,vaccine efficacy ,genotyping ,screening ,CVT Group ,Medical and Health Sciences ,Microbiology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundHuman papillomaviruses (HPV) cause over 500 000 cervical cancers each year, most of which occur in low-resource settings. Human papillomavirus genotyping is important to study natural history and vaccine efficacy. We evaluated TypeSeq, a novel, next-generation, sequencing-based assay that detects 51 HPV genotypes, in 2 large international epidemiologic studies.MethodsTypeSeq was evaluated in 2804 cervical specimens from the Study to Understand Cervical Cancer Endpoints and Early Determinants (SUCCEED) and in 2357 specimens from the Costa Rica Vaccine Trial (CVT). Positive agreement and risks of precancer for individual genotypes were calculated for TypeSeq in comparison to Linear Array (SUCCEED). In CVT, positive agreement and vaccine efficacy were calculated for TypeSeq and SPF10-LiPA.ResultsWe observed high overall and positive agreement for most genotypes between TypeSeq and Linear Array in SUCCEED and SPF10-LiPA in CVT. There was no significant difference in risk of precancer between TypeSeq and Linear Array in SUCCEED or in estimates of vaccine efficacy between TypeSeq and SPF10-LiPA in CVT.ConclusionsThe agreement of TypeSeq with Linear Array and SPF10-LiPA, 2 well established standards for HPV genotyping, demonstrates its high accuracy. TypeSeq provides high-throughput, affordable HPV genotyping for world-wide studies of cervical precancer risk and of HPV vaccine efficacy.
- Published
- 2019
27. Mediation analysis using incomplete information from publicly available data sources
- Author
-
Derkach, Andriy, primary, Kantor, Elizabeth D., additional, Sampson, Joshua N., additional, and Pfeiffer, Ruth M., additional
- Published
- 2024
- Full Text
- View/download PDF
28. Methylation-based markers of aging and lifestyle-related factors and risk of breast cancer: a pooled analysis of four prospective studies
- Author
-
Dugué, Pierre-Antoine, Bodelon, Clara, Chung, Felicia F., Brewer, Hannah R., Ambatipudi, Srikant, Sampson, Joshua N., Cuenin, Cyrille, Chajès, Veronique, Romieu, Isabelle, Fiorito, Giovanni, Sacerdote, Carlotta, Krogh, Vittorio, Panico, Salvatore, Tumino, Rosario, Vineis, Paolo, Polidoro, Silvia, Baglietto, Laura, English, Dallas, Severi, Gianluca, Giles, Graham G., Milne, Roger L., Herceg, Zdenko, Garcia-Closas, Montserrat, Flanagan, James M., and Southey, Melissa C.
- Published
- 2022
- Full Text
- View/download PDF
29. A simple approximation to the bias of gene–environment interactions in case–control studies with silent disease
- Author
-
Lobach, Iryna, Sampson, Joshua, Lobach, Siarhei, Alekseyenko, Alexander, Piryatinska, Alexandra, He, Tao, and Zhang, Li
- Subjects
Epidemiology ,Biological Sciences ,Health Sciences ,Genetics ,Urologic Diseases ,Human Genome ,Cancer ,Aetiology ,2.1 Biological and endogenous factors ,Alleles ,Bias ,Case-Control Studies ,Computer Simulation ,Disease ,Gene-Environment Interaction ,Genome-Wide Association Study ,Humans ,Logistic Models ,Male ,Models ,Genetic ,Prostatic Neoplasms ,approximation ,bias ,prostate cancer ,silent disease ,Public Health and Health Services - Abstract
One of the most important research areas in case-control Genome-Wide Association Studies is to determine how the effect of a genotype varies across the environment or to measure the gene-environment interaction (G × E). We consider the scenario when some of the "healthy" controls actually have the disease and when the frequency of these latent cases varies by the environmental variable of interest. In this scenario, performing logistic regression with the clinically diagnosed disease status as an outcome variable and will result in biased estimates of G × E interaction. Here, we derive a general theoretical approximation to the bias in the estimates of the G × E interaction and show, through extensive simulation, that this approximation is accurate in finite samples. Moreover, we apply this approximation to evaluate the bias in the effect estimates of the genetic variants related to mitochondrial proteins a large-scale prostate cancer study.
- Published
- 2019
30. Gene–environment interactions in case–control studies with silent disease
- Author
-
Lobach, Iryna, Sampson, Joshua, Lobach, Siarhei, and Zhang, Li
- Subjects
Epidemiology ,Biological Sciences ,Health Sciences ,Genetics ,Human Genome ,Urologic Diseases ,Prostate Cancer ,Cancer ,Aetiology ,2.1 Biological and endogenous factors ,2.5 Research design and methodologies (aetiology) ,Bias ,Case-Control Studies ,Computer Simulation ,Disease ,Gene-Environment Interaction ,Genome-Wide Association Study ,Humans ,Male ,Models ,Genetic ,Polymorphism ,Single Nucleotide ,Prostatic Neoplasms ,case-control study ,gene-environment interactions ,prostate cancer ,pseudolikelihood ,silent disease ,Public Health and Health Services - Abstract
Genome-wide association studies (GWAS) often measure gene-environment interactions (G × E). We consider the problem of accurately estimating a G × E in a case-control GWAS when a subset of the controls have silent, or undiagnosed, disease and the frequency of the silent disease varies by the environmental variable. We show that using case-control status without accounting for misdiagnosis can lead to biased estimates of the G × E. We further propose a pseudolikelihood approach to remove the bias and accurately estimate how the relationship between the genetic variant and the true disease status varies by the environmental variable. We demonstrate our method in extensive simulations and apply our method to a GWAS of prostate cancer.
- Published
- 2018
31. Precancerous cervical lesions caused by non-vaccine-preventable HPV types after vaccination with the bivalent AS04-adjuvanted HPV vaccine: an analysis of the long-term follow-up study from the randomised Costa Rica HPV Vaccine Trial
- Author
-
Cortés, Bernal, González, Paula, Herrero, Rolando, Jiménez, Silvia E., Porras, Carolina, Rodríguez, Ana Cecilia, Hildesheim, Allan, Kreimer, Aimée R., Lowy, Douglas R., Schiffman, Mark, Schiller, John T., Sherman, Mark, Wacholder, Sholom, Pinto, Ligia A., Kemp, Troy J., Sidawy, Mary K., Quint, Wim, van Doorn, Leen-Jan, Struijk, Linda, Palefsky, Joel M., Darragh, Teresa M., Stoler, Mark H., Shing, Jaimie Z, Hu, Shangying, Sampson, Joshua N, Schussler, John, Schiller, John T, Lowy, Douglas R, Sierra, Mónica S, Carvajal, Loretto, and Kreimer, Aimée R
- Published
- 2022
- Full Text
- View/download PDF
32. Associations of serum trimethylamine N‐oxide and its precursors with colorectal cancer risk in the Prostate, Lung, Colorectal, Ovarian Cancer Screening Trial Cohort.
- Author
-
Byrd, Doratha A., Zouiouich, Semi, Karwa, Smriti, Li, Xinmin S., Wang, Zeneng, Sampson, Joshua N., Loftfield, Erikka, Huang, Wen‐Yi, Hazen, Stanley L., and Sinha, Rashmi
- Subjects
PROSTATE cancer ,COLORECTAL cancer ,LIQUID chromatography-mass spectrometry ,EARLY detection of cancer ,DISEASE risk factors - Abstract
Background: Dietary intake influences gut microbiome composition, which in turn may be associated with colorectal cancer (CRC). Associations of the gut microbiome with colorectal carcinogenesis may be mediated through bacterially regulated, metabolically active metabolites, including trimethylamine N‐oxide (TMAO) and its precursors, choline, L‐carnitine, and betaine. Methods: Prospective associations of circulating TMAO and its precursors with CRC risk were investigated. TMAO, choline, betaine, and L‐carnitine were measured in baseline serum samples from 761 incident CRC cases and 1:1 individually matched controls in the prospective Prostate, Lung, Colorectal, Ovarian Cancer Screening Trial Cohort using targeted fully quantitative liquid chromatography tandem mass spectrometry panels. Prospective associations of the metabolites with CRC risk, using multivariable conditional logistic regression, were measured. Associations of a priori–selected dietary exposures with the four metabolites were also investigated. Results: TMAO and its precursors were not associated with CRC risk overall, but TMAO and choline were positively associated with higher risk for distal CRC (continuous ORQ90 vs. Q10 [95% CI] = 1.90 [CI, 1.24–2.92; p =.003] and 1.26 [1.17–1.36; p <.0001], respectively). Conversely, choline was inversely associated with rectal cancer (ORQ90 vs. Q10 [95% CI] = 0.77 [0.76–0.79; p <.001]). Red meat, which was previously associated with CRC risk in the Prostate, Lung, Colorectal, Ovarian Cancer Screening Trial Cohort , was positively associated with TMAO (Spearman rho = 0.10; p =.0003). Conclusions: Serum TMAO and choline may be associated with higher risk of distal CRC, and red meat may be positively associated with serum TMAO. These findings provide insight into a potential microbially mediated mechanism underlying CRC etiology. In a prospective study among men and women in the United States, we measured circulating trimethylamine N‐oxide (TMAO), choline, betaine, and L‐carnitine and found that TMAO and choline were positively associated with distal colon cancers. Our findings support future studies into underlying mechanisms and potential TMAO‐targeted interventions to mitigate colorectal cancer risk. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
33. Maternal serum concentrations of per- and polyfluoroalkyl substances and childhood acute lymphoblastic leukemia.
- Author
-
Jones, Rena R, Madrigal, Jessica M, Troisi, Rebecca, Surcel, Heljä-Marja, Öhman, Hanna, Kivelä, Juha, Kiviranta, Hannu, Rantakokko, Panu, Koponen, Jani, Medgyesi, Danielle N, McGlynn, Katherine A, Sampson, Joshua, Albert, Paul S, and Ward, Mary H
- Subjects
FLUOROALKYL compounds ,LYMPHOBLASTIC leukemia ,ACUTE leukemia ,PLACENTAL growth factor ,PERSISTENT pollutants ,PERFLUOROOCTANE sulfonate - Abstract
Background Per- and polyfluoroalkyl substances (PFAS) are widespread and environmentally persistent chemicals with immunotoxic properties. Children are prenatally exposed through maternal transfer of PFAS to cord blood, but no studies have investigated the relationship with childhood leukemia. Methods We measured maternal serum levels of 19 PFAS in first-trimester samples collected in 1986-2010 and evaluated associations with acute lymphoblastic leukemia in full-term offspring (aged younger than 15 years) for 400 cases and 400 controls in the Finnish Maternity Cohort, matched on sample year, mother's age, gestational age, birth order, and child's sex. We analyzed continuous and categorical exposures, estimating odds ratios (ORs) and 95% confidence intervals (CIs) via conditional logistic regression adjusted for maternal smoking and correlated PFAS (ρ ≥ ±0.3). We also stratified by calendar period, mean diagnosis age, and the child's sex. Results N-methyl-perfluorooctane sulfonamidoacetic acid was associated with acute lymphoblastic leukemia in continuous models (per each doubling in levels: OR
perlog2 = 1.22, 95% CI = 1.07 to 1.39), with a positive exposure-response across categories (OR>90th percentile = 2.52, 95% CI = 1.33 to 4.78; Ptrend = .01). Although we found no relationship with perfluorooctane sulfonic acid overall, an association was observed in samples collected in 1986-1995, when levels were highest (median = 17.9 µg/L; ORperlog2 = 4.01, 95% CI = 1.62 to 9.93). A positive association with perfluorononanoic acid was suggested among first births (Pinteraction = .06). The N-methyl-perfluorooctane sulfonamidoacetic acid association was mainly limited to children diagnosed before age 5 years (Pinteraction = .02). We found no consistent patterns of association with other PFAS or differences by sex. Conclusions These novel data offer evidence of a relationship between some PFAS and risk of the most common childhood cancer worldwide, including associations with the highest levels of perfluorooctanesulfonic acid and with a precursor, N-methyl-perfluorooctane sulfonamidoacetic acid. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
34. Durability of Protection Afforded by Fewer Doses of the HPV16/18 Vaccine: The CVT Trial.
- Author
-
Safaeian, Mahboobeh, Sampson, Joshua, Pan, Yuanji, Porras, Carolina, Kemp, Troy, Herrero, Rolando, Quint, Wim, van Doorn, Leen, Schussler, John, Lowy, Douglas, Schiller, John, Schiffman, Mark, Rodriguez, Ana, Gail, Mitchell, Hildesheim, Allan, Gonzalez, Paula, Pinto, Ligia, and Kreimer, Aimée
- Subjects
Adolescent ,Adult ,Antibodies ,Viral ,Cervix Uteri ,DNA ,Viral ,Female ,Human papillomavirus 16 ,Human papillomavirus 18 ,Humans ,Papillomavirus Infections ,Papillomavirus Vaccines ,Uterine Cervical Diseases ,Young Adult - Abstract
BACKGROUND: Previously, we demonstrated similar human papillomavirus (HPV)16/18 vaccine efficacy estimates and stable HPV16/18 antibody levels four years postvaccination in a nonrandomized analysis of women who received a varying number of doses of the bivalent HPV16/18 vaccine. Here we extend data to seven years following initial vaccination. METHODS: We evaluated HPV16/18-vaccinated women who received one (n = 134), two (n 0/1 = 193, n 0/6 = 79), or three doses (n = 2043) to a median of 6.9 years postvaccination. Cervical HPV DNA was measured with the SPF10- DEIA-LiPA PCR system; HPV16/18-specific antibody levels were measured using enzyme-linked immunosorbent assays (n = 486). Infection and immunological measures were compared across vaccine dose groups. Prevalent HPV infection at year 7 was also compared with an unvaccinated control group (UCG). All statistical tests were two-sided. RESULTS: Among women in the three-dose, two-dose 0/6 , two-dose 0/1 , and one-dose groups, cumulative incident HPV16/18 infection rates (No. of events/No. of individuals) were 4.3% (88/2036, 95% confidence interval [CI] = 3.5% to 5.3%), 3.8% (3/78, 95% CI = 1.0% to 10.1%), 3.6% (7/192, 95% CI = 1.6% to 7.1%), and 1.5% (2/133, 95% CI = 0.3% to 4.9%; P = 1.00, .85, .17 comparing the two-dose 0/6 , two-dose 0/1 , and one-dose groups to the three-dose group, respectively). The prevalence of other carcinogenic and noncarcinogenic HPV types, excluding HPV16/18/31/33/45, were high and not statistically different among all dose groups, indicating that the low incidence of HPV16/18 in the one- and two-dose groups was not due to lack of exposure. At seven years, 100% of participants in all dose groups remained HPV16 and HPV18 seropositive. A non-statistically significant decrease in the geometric mean of the HPV16 antibody levels between years 4 and 7 was observed among women in the three-dose group: -10.8% (95% CI = -25.3% to 6.6%); two-dose (0/6 months) group: -17.3% (95% CI = -39.3% to 12.8%), two-dose (0/1 month) group: -6.9% (95% CI = -22.1% to 11.2%), and one-dose group: -5.5% (95% CI = -29.7% to 27.0%); results were similar for HPV18. CONCLUSIONS: At an average of seven years of follow-up, we observed similar low rates of HPV16/18 infections and slight, if any, decreases in HPV16/18 antibody levels by dose group.
- Published
- 2018
35. Case-control studies of gene-environment interactions. When a case might not be the case
- Author
-
Lobach, Iryna, Sampson, Joshua, Alekseyenko, Alexander, Lobach, Siarhei, and Zhang, Li
- Subjects
Epidemiology ,Biological Sciences ,Health Sciences ,Genetics ,Human Genome ,Generic health relevance ,Alzheimer Disease ,Bias ,Case-Control Studies ,Computer Simulation ,Gene-Environment Interaction ,Genome-Wide Association Study ,Genotype ,Humans ,Models ,Genetic ,Polymorphism ,Single Nucleotide ,General Science & Technology - Abstract
Case-control Genome-Wide Association Studies (GWAS) provide a rich resource for studying the genetic architecture of complex diseases. A key is to elucidate how the genetic effects vary by the environment, what is traditionally defined by Gene-Environment interactions (GxE). The overlooked complication is that multiple, distinct pathophysiologic mechanisms may lead to the same clinical diagnosis and often these mechanisms have distinct genetic bases. In this paper, we first show that using the clinically diagnosed status can lead to severely biased estimates of GxE interactions in situations when the frequency of the pathologic diagnosis of interest, as compared to other diagnoses, depends on the environment. We then propose a pseudo-likelihood solution to correct the bias. Finally, we demonstrate our method in extensive simulations and in a GWAS of Alzheimer's disease.
- Published
- 2018
36. An investigation of cross-sectional associations of a priori–selected dietary components with circulating bile acids
- Author
-
Byrd, Doratha A, Sinha, Rashmi, Weinstein, Stephanie J, Albanes, Demetrius, Freedman, Neal D, Sampson, Joshua, and Loftfield, Erikka
- Published
- 2021
- Full Text
- View/download PDF
37. Effects of Preanalytical Sample Collection and Handling on Comprehensive Metabolite Measurements in Human Urine Biospecimens
- Author
-
Braisted, John, primary, Henderson, Theresa, additional, Newman, John W., additional, Moore, Steven C., additional, Sampson, Joshua, additional, McClain, Kathleen, additional, Ross, Sharon, additional, Baer, David J., additional, Mathé, Ewy A., additional, and Zanetti, Krista A., additional
- Published
- 2024
- Full Text
- View/download PDF
38. Integrating Incomplete Data for Mediation Analysis
- Author
-
Derkach, Andriy, primary, Sampson, Joshua N., additional, and Pfeiffer, Ruth M., additional
- Published
- 2024
- Full Text
- View/download PDF
39. Maternal serum concentrations of per- and polyfluoroalkyl substances and childhood acute lymphoblastic leukemia
- Author
-
Jones, Rena R, primary, Madrigal, Jessica M, additional, Troisi, Rebecca, additional, Surcel, Heljä-Marja, additional, Öhman, Hanna, additional, Kivelä, Juha, additional, Kiviranta, Hannu, additional, Rantakokko, Panu, additional, Koponen, Jani, additional, Medgyesi, Danielle N, additional, McGlynn, Katherine A, additional, Sampson, Joshua, additional, Albert, Paul S, additional, and Ward, Mary H, additional
- Published
- 2023
- Full Text
- View/download PDF
40. A Visual, In‐Expensive, and Wireless Capillary Rheometer for Characterizing Wholly‐Cellular Bioinks
- Author
-
Du, Jianyi, primary, Lee, Stacey, additional, Sinha, Soham, additional, Solberg, Fredrik S., additional, Ho, Debbie L. L., additional, Sampson, Joshua P., additional, Wang, Qiuling, additional, Tam, Tony, additional, and Skylar‐Scott, Mark A., additional
- Published
- 2023
- Full Text
- View/download PDF
41. Association between ABO and Duffy blood types and circulating chemokines and cytokines
- Author
-
Van Alsten, Sarah C., Aversa, John G., Santo, Loredana, Camargo, M. Constanza, Kemp, Troy, Liu, Jia, Huang, Wen-Yi, Sampson, Joshua, and Rabkin, Charles S.
- Published
- 2021
- Full Text
- View/download PDF
42. Association of Estrogen Metabolism with Breast Cancer Risk in Different Cohorts of Postmenopausal Women
- Author
-
Sampson, Joshua N, Falk, Roni T, Schairer, Catherine, Moore, Steven C, Fuhrman, Barbara J, Dallal, Cher M, Bauer, Douglas C, Dorgan, Joanne F, Shu, Xiao-Ou, Zheng, Wei, Brinton, Louise A, Gail, Mitchell H, Ziegler, Regina G, Xu, Xia, Hoover, Robert N, and Gierach, Gretchen L
- Subjects
Cancer ,Breast Cancer ,Prevention ,Estrogen ,Clinical Research ,Aging ,Adult ,Aged ,Breast Neoplasms ,Chromatography ,Liquid ,Cohort Studies ,Estrogens ,Female ,Humans ,Hydroxylation ,Middle Aged ,Postmenopause ,Risk ,Tandem Mass Spectrometry ,Oncology and Carcinogenesis ,Oncology & Carcinogenesis - Abstract
Endogenous estradiol and estrone are linked causally to increased risks of breast cancer. In this study, we evaluated multiple competing hypotheses for how metabolism of these parent estrogens may influence risk. Prediagnostic concentrations of estradiol, estrone, and 13 metabolites were measured in 1,298 postmenopausal cases of breast cancer and 1,524 matched controls in four separate patient cohorts. The median time between sample collection and diagnosis was 4.4 to 12.7 years across the cohorts. Estrogen analytes were measured in serum or urine by liquid chromatography-tandem mass spectrometry. Total estrogen levels (summing all 15 estrogens/estrogen metabolites) were associated strongly and positively with breast cancer risk. Normalizing total estrogen levels, we also found that a relative increase in levels of 2-hydroxylation pathway metabolites, or in the ratio of 2-hydroxylation:16-hydroxylation pathway metabolites, were associated inversely with breast cancer risk. These associations varied by total estrogen levels, with the largest risk reductions occurring in women in the highest tertile. With appropriate validation, these findings suggest opportunities for breast cancer prevention by modifying individual estrogen metabolism profiles through either lifestyle alterations or chemopreventive strategies. Cancer Res; 77(4); 918-25. ©2017 AACR.
- Published
- 2017
43. Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies
- Author
-
Loftfield, Erikka, Vogtmann, Emily, Sampson, Joshua N, Moore, Steven C, Nelson, Heidi, Knight, Rob, Chia, Nicholas, and Sinha, Rashmi
- Subjects
Medical Biochemistry and Metabolomics ,Biomedical and Clinical Sciences ,Clinical Research ,Digestive Diseases ,Substance Misuse ,Adult ,Cryopreservation ,Epidemiologic Studies ,Feces ,Female ,Humans ,Male ,Metabolomics ,Middle Aged ,Reproducibility of Results ,Specimen Handling ,Young Adult ,Medical and Health Sciences ,Epidemiology ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundThe gut metabolome may be associated with the incidence and progression of numerous diseases. The composition of the gut metabolome can be captured by measuring metabolite levels in the feces. However, there are little data describing the effect of fecal sample collection methods on metabolomic measures.MethodsWe collected fecal samples from 18 volunteers using four methods: no solution, 95% ethanol, fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT). One set of samples was frozen after collection (day 0), and for 95% ethanol, FOBT, and FIT, a second set was frozen after 96 hours at room temperature. We evaluated (i) technical reproducibility within sample replicates, (ii) stability after 96 hours at room temperature for 95% ethanol, FOBT, and FIT, and (iii) concordance of metabolite measures with the putative "gold standard," day 0 samples without solution.ResultsIntraclass correlation coefficients (ICC) estimating technical reproducibility were high for replicate samples for each collection method. ICCs estimating stability at room temperature were high for 95% ethanol and FOBT (median ICC > 0.87) but not FIT (median ICC = 0.52). Similarly, Spearman correlation coefficients (rs) estimating metabolite concordance with the "gold standard" were higher for 95% ethanol (median rs = 0.82) and FOBT (median rs = 0.70) than for FIT (median rs = 0.40).ConclusionsMetabolomic measurements appear reproducible and stable in fecal samples collected with 95% ethanol or FOBT. Concordance with the "gold standard" is highest with 95% ethanol and acceptable with FOBT.ImpactFuture epidemiologic studies should collect feces using 95% ethanol or FOBT if interested in studying fecal metabolomics. Cancer Epidemiol Biomarkers Prev; 25(11); 1483-90. ©2016 AACR.
- Published
- 2016
44. Efficacy of the bivalent HPV vaccine against HPV 16/18-associated precancer: long-term follow-up results from the Costa Rica Vaccine Trial
- Author
-
Cortés, Bernal, González, Paula, Herrero, Rolando, Jiménez, Silvia E, Porras, Carolina, Rodríguez, Ana Cecilia, Hildesheim, Allan, Kreimer, Aimée R, Lowy, Douglas R, Schiffman, Mark, Schiller, John T, Sherman, Mark, Pinto, Ligia A, Kemp, Troy J, Sidawy, Mary K, Quint, Wim, Van Doorn, Leen-Jan, Struijk, Linda, Palefsky, Joel M, Darragh, Teresa M, Stoler, Mark H, Tsang, Sabrina H, Guillén, Diego, Wagner, Sarah, Boland, Joseph, Schussler, John, Gail, Mitchell H, Ocampo, Rebeca, Morales, Jorge, Rodríguez, Ana C, Hu, Shangying, and Sampson, Joshua N
- Published
- 2020
- Full Text
- View/download PDF
45. A Visual, In‐Expensive, and Wireless Capillary Rheometer for Characterizing Wholly‐Cellular Bioinks.
- Author
-
Du, Jianyi, Lee, Stacey, Sinha, Soham, Solberg, Fredrik S., Ho, Debbie L. L., Sampson, Joshua P., Wang, Qiuling, Tam, Tony, and Skylar‐Scott, Mark A.
- Published
- 2024
- Full Text
- View/download PDF
46. Prediagnostic serum concentrations of per‐ and polyfluoroalkyl substances and risk of papillary thyroid cancer in the Finnish Maternity Cohort.
- Author
-
Madrigal, Jessica M., Troisi, Rebecca, Surcel, Heljä‐Marja, Öhman, Hanna, Kivelä, Juha, Kiviranta, Hannu, Rantakokko, Panu, Koponen, Jani, Medgyesi, Danielle N., Kitahara, Cari M., McGlynn, Katherine A., Sampson, Joshua, Albert, Paul S., Ward, Mary H., and Jones, Rena R.
- Subjects
FLUOROALKYL compounds ,THYROID cancer ,SULFONIC acids ,PERFLUOROOCTANE sulfonate ,IODINE isotopes ,FOOD contamination ,THYROID gland - Abstract
Human exposure to per‐ and polyfluoroalkyl substances (PFAS) occurs globally through contaminated food, dust, and drinking water. Studies of PFAS and thyroid cancer have been limited. We conducted a nested case‐control study of prediagnostic serum levels of 19 PFAS and papillary thyroid cancer (400 cases, 400 controls) in the Finnish Maternity Cohort (pregnancies 1986‐2010; follow‐up through 2016), individually matched on sample year and age. We used conditional logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) for log2 transformed and categorical exposures, overall and stratified by calendar period, birth cohort, and median age at diagnosis. We adjusted for other PFAS with Spearman correlation rho = 0.3‐0.6. Seven PFAS, including perfluoroctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), N‐ethyl‐perfluorooctane sulfonamidoacetic acid (EtFOSAA), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), and perfluorohexane sulfonic acid (PFHxS) were detected in >50% of women. These PFAS were not associated with risk of thyroid cancer, except for PFHxS, which was inversely associated (OR log2 = 0.82, 95% CI: 0.70‐0.97). We observed suggestive but imprecise increased risks associated with PFOA, PFOS, and EtFOSAA for those diagnosed at ages <40 years, whereas associations were null or inverse among those diagnosed at 40+ years (P‐interaction:.02,.08,.13, respectively). There was little evidence of other interactions. These results show no clear association between PFAS and papillary thyroid cancer risk. Future work would benefit from evaluation of these relationships among those with higher exposure levels and during periods of early development when the thyroid gland may be more susceptible to environmental harms. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
47. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
- Author
-
Machiela, Mitchell J, Zhou, Weiyin, Karlins, Eric, Sampson, Joshua N, Freedman, Neal D, Yang, Qi, Hicks, Belynda, Dagnall, Casey, Hautman, Christopher, Jacobs, Kevin B, Abnet, Christian C, Aldrich, Melinda C, Amos, Christopher, Amundadottir, Laufey T, Arslan, Alan A, Beane-Freeman, Laura E, Berndt, Sonja I, Black, Amanda, Blot, William J, Bock, Cathryn H, Bracci, Paige M, Brinton, Louise A, Bueno-de-Mesquita, H Bas, Burdett, Laurie, Buring, Julie E, Butler, Mary A, Canzian, Federico, Carreon, Tania, Chaffee, Kari G, Chang, I-Shou, Chatterjee, Nilanjan, Chen, Chu, Chen, Constance, Chen, Kexin, Chung, Charles C, Cook, Linda S, Bou, Marta Crous, Cullen, Michael, Davis, Faith G, De Vivo, Immaculata, Ding, Ti, Doherty, Jennifer, Duell, Eric J, Epstein, Caroline G, Fan, Jin-Hu, Figueroa, Jonine D, Fraumeni, Joseph F, Friedenreich, Christine M, Fuchs, Charles S, Gallinger, Steven, Gao, Yu-Tang, Gapstur, Susan M, Garcia-Closas, Montserrat, Gaudet, Mia M, Gaziano, J Michael, Giles, Graham G, Gillanders, Elizabeth M, Giovannucci, Edward L, Goldin, Lynn, Goldstein, Alisa M, Haiman, Christopher A, Hallmans, Goran, Hankinson, Susan E, Harris, Curtis C, Henriksson, Roger, Holly, Elizabeth A, Hong, Yun-Chul, Hoover, Robert N, Hsiung, Chao A, Hu, Nan, Hu, Wei, Hunter, David J, Hutchinson, Amy, Jenab, Mazda, Johansen, Christoffer, Khaw, Kay-Tee, Kim, Hee Nam, Kim, Yeul Hong, Kim, Young Tae, Klein, Alison P, Klein, Robert, Koh, Woon-Puay, Kolonel, Laurence N, Kooperberg, Charles, Kraft, Peter, Krogh, Vittorio, Kurtz, Robert C, LaCroix, Andrea, Lan, Qing, Landi, Maria Teresa, Le Marchand, Loic, Li, Donghui, Liang, Xiaolin, Liao, Linda M, Lin, Dongxin, Liu, Jianjun, Lissowska, Jolanta, Lu, Lingeng, Magliocco, Anthony M, and Malats, Nuria
- Published
- 2016
48. Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies
- Author
-
Sinha, Rashmi, Chen, Jun, Amir, Amnon, Vogtmann, Emily, Shi, Jianxin, Inman, Kristin S, Flores, Roberto, Sampson, Joshua, Knight, Rob, and Chia, Nicholas
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Human Genome ,Genetics ,Clinical Research ,Adult ,Epidemiologic Studies ,Feces ,Female ,Humans ,Male ,Microbiota ,Middle Aged ,Young Adult ,Medical and Health Sciences ,Epidemiology ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundThe need to develop valid methods for sampling and analyzing fecal specimens for microbiome studies is increasingly important, especially for large population studies.MethodsSome of the most important attributes of any sampling method are reproducibility, stability, and accuracy. We compared seven fecal sampling methods [no additive, RNAlater, 70% ethanol, EDTA, dry swab, and pre/post development fecal occult blood test (FOBT)] using 16S rRNA microbiome profiling in two laboratories. We evaluated nine commonly used microbiome metrics: abundance of three phyla, two alpha-diversities, and four beta-diversities. We determined the technical reproducibility, stability at ambient temperature, and accuracy.ResultsAlthough microbiome profiles showed systematic biases according to sample method and time at ambient temperature, the highest source of variation was between individuals. All collection methods showed high reproducibility. FOBT and RNAlater resulted in the highest stability without freezing for 4 days. In comparison with no-additive samples, swab, FOBT, and 70% ethanol exhibited the greatest accuracy when immediately frozen.ConclusionsOverall, optimal stability and reproducibility were achieved using FOBT, making this a reasonable sample collection method for 16S analysis.ImpactHaving standardized method of collecting and storing stable fecal samples will allow future investigations into the role of gut microbiota in chronic disease etiology in large population studies.
- Published
- 2016
49. Prediagnostic serum concentrations of per‐ and polyfluoroalkyl substances and risk of papillary thyroid cancer in the Finnish Maternity Cohort
- Author
-
Madrigal, Jessica M., primary, Troisi, Rebecca, additional, Surcel, Heljä‐Marja, additional, Öhman, Hanna, additional, Kivelä, Juha, additional, Kiviranta, Hannu, additional, Rantakokko, Panu, additional, Koponen, Jani, additional, Medgyesi, Danielle N., additional, Kitahara, Cari M., additional, McGlynn, Katherine A., additional, Sampson, Joshua, additional, Albert, Paul S., additional, Ward, Mary H., additional, and Jones, Rena R., additional
- Published
- 2023
- Full Text
- View/download PDF
50. Leveraging local identity-by-descent increases the power of case/control GWAS with related individuals
- Author
-
Sampson, Joshua N., Wheeler, Bill, Li, Peng, and Shi, Jianxin
- Subjects
Statistics - Applications ,Quantitative Biology - Populations and Evolution - Abstract
Large case/control Genome-Wide Association Studies (GWAS) often include groups of related individuals with known relationships. When testing for associations at a given locus, current methods incorporate only the familial relationships between individuals. Here, we introduce the chromosome-based Quasi Likelihood Score (cQLS) statistic that incorporates local Identity-By-Descent (IBD) to increase the power to detect associations. In studies robust to population stratification, such as those with case/control sibling pairs, simulations show that the study power can be increased by over 50%. In our example, a GWAS examining late-onset Alzheimer's disease, the $p$-values among the most strongly associated SNPs in the APOE gene tend to decrease, with the smallest $p$-value decreasing from $1.23\times10^{-8}$ to $7.70\times 10^{-9}$. Furthermore, as a part of our simulations, we reevaluate our expectations about the use of families in GWAS. We show that, although adding only half as many unique chromosomes, genotyping affected siblings is more efficient than genotyping randomly ascertained cases. We also show that genotyping cases with a family history of disease will be less beneficial when searching for SNPs with smaller effect sizes., Comment: Published in at http://dx.doi.org/10.1214/14-AOAS715 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)
- Published
- 2014
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.