المؤلفون: Lindsay M. Morton, Olivia W. Lee, Danielle M. Karyadi, Tetiana I. Bogdanova, Chip Stewart, Stephen W. Hartley, Charles E. Breeze, Sara J. Schonfeld, Elizabeth K. Cahoon, Vladimir Drozdovitch, Sergii Masiuk, Mykola Chepurny, Liudmyla Yu Zurnadzhy, Jieqiong Dai, Marko Krznaric, Meredith Yeager, Amy Hutchinson, Belynda D. Hicks, Casey L. Dagnall, Mia K. Steinberg, Kristine Jones, Komal Jain, Ben Jordan, Mitchell J. Machiela, Eric T. Dawson, Vibha Vij, Julie M. Gastier-Foster, Jay Bowen, Kiyohiko Mabuchi, Maureen Hatch, Amy Berrington de Gonzalez, Gad Getz, Mykola D. Tronko, Gerry A. Thomas, Stephen J. Chanock

المصدر: Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)

مصطلحات موضوعية: Science

الوصف: Abstract Childhood radioactive iodine exposure from the Chornobyl accident increased papillary thyroid carcinoma (PTC) risk. While cervical lymph node metastases (cLNM) are well-recognized in pediatric PTC, the PTC metastatic process and potential radiation association are poorly understood. Here, we analyze cLNM occurrence among 428 PTC with genomic landscape analyses and known drivers (131I-exposed = 349, unexposed = 79; mean age = 27.9 years). We show that cLNM are more frequent in PTC with fusion (55%) versus mutation (30%) drivers, although the proportion varies by specific driver gene (RET-fusion = 71%, BRAF-mutation = 38%, RAS-mutation = 5%). cLNM frequency is not associated with other characteristics, including radiation dose. cLNM molecular profiling (N = 47) demonstrates 100% driver concordance with matched primary PTCs and highly concordant mutational spectra. Transcriptome analysis reveals 17 differentially expressed genes, particularly in the HOXC cluster and BRINP3; the strongest differentially expressed microRNA also is near HOXC10. Our findings underscore the critical role of driver alterations and provide promising candidates for elucidating the biological underpinnings of PTC cLNM.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2041-1723Test

الوصول الحر: https://doaj.org/article/43b4a3f2d4b34656b884b3b550e5f0f9Test

المؤلفون: Zeni Wu, Ruth M. Pfeiffer, Doratha A. Byrd, Yunhu Wan, Daniel Ansong, Joe-Nat Clegg-Lamptey, Beatrice Wiafe-Addai, Lawrence Edusei, Ernest Adjei, Nicholas Titiloye, Florence Dedey, Francis Aitpillah, Joseph Oppong, Verna Vanderpuye, Ernest Osei-Bonsu, Casey L. Dagnall, Kristine Jones, Amy Hutchinson, Belynda D. Hicks, Thomas U. Ahearn, Rob Knight, Richard Biritwum, Joel Yarney, Seth Wiafe, Baffour Awuah, Kofi Nyarko, Montserrat Garcia-Closas, Rashmi Sinha, Jonine D. Figueroa, Louise A. Brinton, Britton Trabert, Emily Vogtmann

المصدر: Microbiology Spectrum, Vol 11, Iss 4 (2023)

مصطلحات موضوعية: estrogens, fecal microbiome, oral microbiome, postmenopausal African women, Microbiology, QR1-502

الوصف: ABSTRACT The human fecal and oral microbiome may play a role in the etiology of breast cancer through modulation of endogenous estrogen metabolism. This study aimed to investigate associations of circulating estrogens and estrogen metabolites with the fecal and oral microbiome in postmenopausal African women. A total of 117 women with fecal (N = 110) and oral (N = 114) microbiome data measured by 16S rRNA gene sequencing, and estrogens and estrogen metabolites data measured by liquid chromatography tandem mass spectrometry were included. The outcomes were measures of the microbiome and the independent variables were the estrogens and estrogen metabolites. Estrogens and estrogen metabolites were associated with the fecal microbial Shannon index (global P

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2165-0497Test

الوصول الحر: https://doaj.org/article/7910c0285efa4e909fd0c1af4c22781fTest

المؤلفون: Yukiko Yano, Emily Vogtmann, Alaina H. Shreves, Stephanie J. Weinstein, Amanda Black, Norma Diaz-Mayoral, Yunhu Wan, Weiyin Zhou, Xing Hua, Casey L. Dagnall, Amy Hutchinson, Kristine Jones, Belynda D. Hicks, Kathleen Wyatt, Michelle Brotzman, Nicole Gerlanc, Wen-Yi Huang, Paul S. Albert, Nicolas Wentzensen, Christian C. Abnet

المصدر: PLoS ONE, Vol 18, Iss 4 (2023)

مصطلحات موضوعية: Medicine, Science

الوصف: Oral bacteria play important roles in human health and disease. Oral samples collected using ethanol-containing mouthwash are widely used for oral microbiome studies. However, ethanol is flammable and not ideal for transportation/storage in large quantities, and some individuals may avoid ethanol due to the burning sensation or due to various personal, medical, religious, and/or cultural factors. Here, we compared ethanol-free and ethanol-containing mouthwashes using multiple microbiome metrics and assessed the stability of the mouthwash samples stored up to 10 days before processing. Forty volunteers provided oral wash samples collected using ethanol-free and ethanol-containing mouthwashes. From each sample, one aliquot was immediately frozen, one was stored at 4°C for 5 days and frozen, while the third aliquot was stored for 5 days at 4°C and 5 days at ambient temperature to mimic shipping delays and then frozen. DNA was extracted, the 16S rRNA gene V4 region was amplified and sequenced, and bioinformatic processing was performed using QIIME 2. Microbiome metrics measured in the two mouthwash types were very similar, with intraclass correlation coefficients (ICCs) for alpha and beta diversity metrics greater than 0.85. Relative abundances of some taxa were significantly different, but ICCs of the top four most abundant phyla and genera were high (> 0.75) for the comparability of the mouthwashes. Stability during delayed processing was also high for both mouthwashes based on alpha and beta diversity measures and relative abundances of the top four phyla and genera (ICCs ≥ 0.90). These results demonstrate ethanol-free mouthwash performs similarly to ethanol-containing mouthwash for microbial analyses, and both mouthwashes are stable for at least 10 days without freezing prior to laboratory processing. Ethanol-free mouthwash is suitable for collecting and shipping oral wash samples, and these results have important implications for planning future epidemiologic studies of the oral microbiome.

وصف الملف: electronic resource

العلاقة: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138257/?tool=EBITest; https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/108f3562f2bc483ab19811c49cb8a635Test

المؤلفون: Mary L. McMaster, Sonja I. Berndt, Jianqing Zhang, Susan L. Slager, Shengchao Alfred Li, Claire M. Vajdic, Karin E. Smedby, Huihuang Yan, Brenda M. Birmann, Elizabeth E. Brown, Alex Smith, Geffen Kleinstern, Mervin M. Fansler, Christine Mayr, Bin Zhu, Charles C. Chung, Ju-Hyun Park, Laurie Burdette, Belynda D. Hicks, Amy Hutchinson, Lauren R. Teras, Hans-Olov Adami, Paige M. Bracci, James McKay, Alain Monnereau, Brian K. Link, Roel C. H. Vermeulen, Stephen M. Ansell, Ann Maria, W. Ryan Diver, Mads Melbye, Akinyemi I. Ojesina, Peter Kraft, Paolo Boffetta, Jacqueline Clavel, Edward Giovannucci, Caroline M. Besson, Federico Canzian, Ruth C. Travis, Paolo Vineis, Elisabete Weiderpass, Rebecca Montalvan, Zhaoming Wang, Meredith Yeager, Nikolaus Becker, Yolanda Benavente, Paul Brennan, Lenka Foretova, Marc Maynadie, Alexandra Nieters, Silvia de Sanjose, Anthony Staines, Lucia Conde, Jacques Riby, Bengt Glimelius, Henrik Hjalgrim, Nisha Pradhan, Andrew L. Feldman, Anne J. Novak, Charles Lawrence, Bryan A. Bassig, Qing Lan, Tongzhang Zheng, Kari E. North, Lesley F. Tinker, Wendy Cozen, Richard K. Severson, Jonathan N. Hofmann, Yawei Zhang, Rebecca D. Jackson, Lindsay M. Morton, Mark P. Purdue, Nilanjan Chatterjee, Kenneth Offit, James R. Cerhan, Stephen J. Chanock, Nathaniel Rothman, Joseph Vijai, Lynn R. Goldin, Christine F. Skibola, Neil E. Caporaso

المصدر: Nature Communications, Vol 9, Iss 1, Pp 1-12 (2018)

مصطلحات موضوعية: Science

الوصف: Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a non-Hodgkin-type B cell lymphoma. Here, the authors identify two risk loci for WM/LPL in a two-stage GWAS involving a family-oversampling approach and provide evidence for a functional role of the non-coding SNP rs116446171.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2041-1723Test

الوصول الحر: https://doaj.org/article/4f8f4ed337f247598d7a3f86722ba590Test

المؤلفون: Yukiko Yano, Xing Hua, Yunhu Wan, Shalabh Suman, Bin Zhu, Casey L. Dagnall, Amy Hutchinson, Kristine Jones, Belynda D. Hicks, Jianxin Shi, Christian C. Abnet, Emily Vogtmann

المصدر: mSystems, Vol 5, Iss 4 (2020)

مصطلحات موضوعية: oral microbiome, collection method, epidemiology, Microbiology, QR1-502

الوصف: ABSTRACT Epidemiologic studies use various biosample collection methods to study associations between human oral microbiota and health outcomes. However, the agreement between the different methods is unclear. We compared a commercially available OMNIgene ORAL kit to three alternative collection methods: Saccomanno’s fixative, Scope mouthwash, and nonethanol mouthwash. Oral samples were collected from 40 individuals over 4 visits. Two samples were collected from each subject per visit: one with OMNIgene and one with an alternative method. DNA was extracted using the DSP DNA Virus Pathogen kit, and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using MiSeq. Oral collection methods were compared based on alpha and beta diversity metrics and phylum- and genus-level relative abundances. All alpha diversity metrics were significantly lower for Saccomanno’s fixative than for OMNIgene (P < 0.001), whereas the two mouthwashes were more similar to OMNIgene. Principal-coordinate analysis (PCoA) using the Bray-Curtis and weighted UniFrac beta diversity matrices showed large differences in the microbial compositions of samples collected with Saccomanno’s compared to those with OMNIgene and the mouthwashes. Clustering by collection method was not observed in unweighted UniFrac PCoA plots, suggesting differences in relative abundances but not specific taxa detected by the collection methods. Relative abundances of most taxa were significantly different between OMNIgene and the other methods at each taxonomic level, with Saccomanno’s showing the least agreement with OMNIgene. There were clear differences in oral microbial communities between the four oral collection methods, particularly for Saccomanno’s fixative. IMPORTANCE We compared four different oral collection methods for studying the human oral microbiome: an OMNIgene ORAL kit, Scope mouthwash, nonethanol mouthwash, and Saccomanno’s fixative. Our study shows that the type of the collection method can have a large impact on the results of an oral microbiome analysis. We recommend that one consistent oral collection method should be used for all oral microbiome comparisons. While Scope and nonethanol mouthwashes are less expensive and provide results similar to those with OMNIgene, Saccomanno’s fixative may be unfavorable due to the microbial differences detected in this study. Our results will help guide the design of future oral microbiome studies.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2379-5077Test

الوصول الحر: https://doaj.org/article/3fbaac9f709e4519b5d082b6b3531be9Test

المؤلفون: Casey L. Dagnall, Lindsay M. Morton, Belynda D. Hicks, Shengchao Li, Weiyin Zhou, Eric Karlins, Kedest Teshome, Salma Chowdhury, Kerrie S. Lashley, Joshua N. Sampson, Leslie L. Robison, Gregory T. Armstrong, Smita Bhatia, Gretchen A. Radloff, Stella M. Davies, Margaret A. Tucker, Meredith Yeager, Stephen J. Chanock

المصدر: BMC Genomics, Vol 19, Iss 1, Pp 1-10 (2018)

مصطلحات موضوعية: Whole genome amplification, Genome-wide association study, High-density microarray, CCSS clinical trial, Biotechnology, TP248.13-248.65, Genetics, QH426-470

الوصف: Abstract Background The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray. Results Overall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input. Conclusions Our results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA.

وصف الملف: electronic resource

العلاقة: http://link.springer.com/article/10.1186/s12864-018-4572-6Test; https://doaj.org/toc/1471-2164Test

الوصول الحر: https://doaj.org/article/371d8d142e9f4e97baedf052bf07d0acTest

المؤلفون: Zeni Wu, Doratha A. Byrd, Yunhu Wan, Daniel Ansong, Joe‐Nat Clegg‐Lamptey, Beatrice Wiafe‐Addai, Lawrence Edusei, Ernest Adjei, Nicholas Titiloye, Florence Dedey, Francis Aitpillah, Joseph Oppong, Verna Vanderpuye, Ernest Osei‐Bonsu, Casey L. Dagnall, Kristine Jones, Amy Hutchinson, Belynda D. Hicks, Thomas U. Ahearn, Jianxin Shi, Rob Knight, Richard Biritwum, Joel Yarney, Seth Wiafe, Baffour Awuah, Kofi Nyarko, Jonine D. Figueroa, Rashmi Sinha, Montserrat Garcia‐Closas, Louise A. Brinton, Emily Vogtmann

المصدر: Wu, Z, Byrd, D A, Wan, Y, Ansong, D, Clegg-Lamptey, J-N, Wiafe-Addai, B, Edusei, L, Adjei, E, Titiloye, N, Dedey, F, Aitpillah, F, Oppong, J, Vanderpuye, V, Osei-Bonsu, E, Dagnall, C L, Jones, K, Hutchinson, A, Hicks, B D, Ahearn, T U, Shi, J, Knight, R, Biritwum, R, Yarney, J, Wiafe, S, Awuah, B, Nyarko, K, Figueroa, J D, Sinha, R, Garcia-Closas, M, Brinton, L A & Vogtmann, E 2022, ' The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study ', International Journal of Cancer . https://doi.org/10.1002/ijc.34145Test

مصطلحات موضوعية: Cancer Research, Microbiota, nonmalignant breast diseases, Breast Neoplasms, Ghana, Gastrointestinal Microbiome, Feces, Logistic Models, breast cancer, oral microbiome, Oncology, Case-Control Studies, RNA, Ribosomal, 16S, Humans, Female, Phylogeny, fecal microbiome

الوصف: The oral microbiome, like the fecal microbiome, may be related to breast cancer risk. Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana. A total of 881 women were included (369 breast cancers, 93 nonmalignant cases and 419 population-based controls). The V4 region of the 16S rRNA gene was sequenced from oral and fecal samples. Alpha-diversity (observed amplicon sequence variants [ASVs], Shannon index and Faith's Phylogenetic Diversity) and beta-diversity (Bray-Curtis, Jaccard and weighted and unweighted UniFrac) metrics were computed. MiRKAT and logistic regression models were used to investigate the case-control associations. Oral sample alpha-diversity was inversely associated with breast cancer and nonmalignant breast disease with odds ratios (95% CIs) per every 10 observed ASVs of 0.86 (0.83-0.89) and 0.79 (0.73-0.85), respectively, compared to controls. Beta-diversity was also associated with breast cancer and nonmalignant breast disease compared to controls (P ≤ .001). The relative abundances of Porphyromonas and Fusobacterium were lower for breast cancer cases compared to controls. Alpha-diversity and presence/relative abundance of specific genera from the oral and fecal microbiome were strongly correlated among breast cancer cases, but weakly correlated among controls. Particularly, the relative abundance of oral Porphyromonas was strongly, inversely correlated with fecal Bacteroides among breast cancer cases (r = -.37, P ≤ .001). Many oral microbial metrics were strongly associated with breast cancer and nonmalignant breast disease, and strongly correlated with fecal microbiome among breast cancer cases, but not controls.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::30328b3119434bf7291dd4b5e9d0d901Test
https://doi.org/10.1002/ijc.34145Test

المؤلفون: Sharon A. Savage, Stephen J. Chanock, Robert N. Hoover, Meredith Yeager, Laurie Burdett, Aurelie Vogt, Belynda D. Hicks, Joseph F. Boland, Neil E. Caporaso, Joseph F. Fraumeni, Sholom Wacholder, Margaret Tucker, Madison T. Weg, Natalie K. Wolf, Kelsie L. Becklin, George M. Otto, Lee Helman, Neyssa Marina, Donald A. Barkauskas, Sean Davis, David M. Thomas, Mandy L. Ballinger, Dina Halai, Maria Fernanda Amary, Roberto Tirabosco, Adrienne M. Flanagan, Katia Scotlandi, Piero Picci, Claudia Hattinger, Massimo Serra, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis, Fernando Lecanda, Luis Sierrasesúmaga, Ana Patiño-Garcia, Antonio S. Petrilli, Silvia Regina Caminada de Toledo, Chand Khanna, Richard Gorlick, Julie M. Gastier-Foster, Zhaoming Wang, David Largaespada, Orestis A. Panagiotou, Nathan Pankratz, Mitchell J. Machiela, Joy Gary, Paul S. Meltzer, Logan G. Spector, Branden S. Moriarity, Roelof Koster, Lisa Mirabello

الوصف: Top 30 loci associated with metastasis at diagnosis in the discovery set of 541 European osteosarcoma cases.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::09f795faca595e27bc4b967075eb3a07Test
https://doi.org/10.1158/2159-8290.22531533Test

المؤلفون: Sharon A. Savage, Stephen J. Chanock, Robert N. Hoover, Meredith Yeager, Laurie Burdett, Aurelie Vogt, Belynda D. Hicks, Joseph F. Boland, Neil E. Caporaso, Joseph F. Fraumeni, Sholom Wacholder, Margaret Tucker, Madison T. Weg, Natalie K. Wolf, Kelsie L. Becklin, George M. Otto, Lee Helman, Neyssa Marina, Donald A. Barkauskas, Sean Davis, David M. Thomas, Mandy L. Ballinger, Dina Halai, Maria Fernanda Amary, Roberto Tirabosco, Adrienne M. Flanagan, Katia Scotlandi, Piero Picci, Claudia Hattinger, Massimo Serra, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis, Fernando Lecanda, Luis Sierrasesúmaga, Ana Patiño-Garcia, Antonio S. Petrilli, Silvia Regina Caminada de Toledo, Chand Khanna, Richard Gorlick, Julie M. Gastier-Foster, Zhaoming Wang, David Largaespada, Orestis A. Panagiotou, Nathan Pankratz, Mitchell J. Machiela, Joy Gary, Paul S. Meltzer, Logan G. Spector, Branden S. Moriarity, Roelof Koster, Lisa Mirabello

الوصف: Relationship of variables to metastasis at diagnosis in the discovery set.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2a9a1b2ef77bb095791c86b743966fc3Test
https://doi.org/10.1158/2159-8290.22531536.v1Test

المؤلفون: Sharon A. Savage, Stephen J. Chanock, Robert N. Hoover, Meredith Yeager, Laurie Burdett, Aurelie Vogt, Belynda D. Hicks, Joseph F. Boland, Neil E. Caporaso, Joseph F. Fraumeni, Sholom Wacholder, Margaret Tucker, Madison T. Weg, Natalie K. Wolf, Kelsie L. Becklin, George M. Otto, Lee Helman, Neyssa Marina, Donald A. Barkauskas, Sean Davis, David M. Thomas, Mandy L. Ballinger, Dina Halai, Maria Fernanda Amary, Roberto Tirabosco, Adrienne M. Flanagan, Katia Scotlandi, Piero Picci, Claudia Hattinger, Massimo Serra, Nalan Gokgoz, Jay S. Wunder, Irene L. Andrulis, Fernando Lecanda, Luis Sierrasesúmaga, Ana Patiño-Garcia, Antonio S. Petrilli, Silvia Regina Caminada de Toledo, Chand Khanna, Richard Gorlick, Julie M. Gastier-Foster, Zhaoming Wang, David Largaespada, Orestis A. Panagiotou, Nathan Pankratz, Mitchell J. Machiela, Joy Gary, Paul S. Meltzer, Logan G. Spector, Branden S. Moriarity, Roelof Koster, Lisa Mirabello

الوصف: SNPs in the NFIB locus associated with metastasis at diagnosis with P{less than or equal to}1x10-5 in the discovery stage, and functionally annotated with information from the ENCODE and 1000 Genomes Project data.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0868cac5acb5964b729f531efe2c4eecTest
https://doi.org/10.1158/2159-8290.22531524.v1Test