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[No title available]

Blood cancer discovery

Beauchamp EM, Leventhal M, Bernard E, Hoppe ER, Todisco G, Creignou M, Gallì A, Castellano CA, McConkey M, Tarun A, Wong W, Schenone M, Stanclift C, Tanenbaum B, Malolepsza E, Nilsson B, Bick AG, Weinstock JS, Miller M, Niroula A, Dunford A, Taylor-Weiner A, Wood T, Barbera A, Anand S, Psaty BM, Desai P, Cho MH, Johnson AD, Loos R, MacArthur DG, Lek M, Neuberg DS, Lage K, Carr SA, Hellstrom-Lindberg E, Malcovati L, Papaemmanuil E, Stewart C, Getz G, Bradley RK, Jaiswal S, Ebert BL.
PMID: 34568833
Blood Cancer Discov. 2021 Sep;2(5):500-517. doi: 10.1158/2643-3230.BCD-20-0224. Epub 2021 Jul 14.

Clonal hematopoiesis results from somatic mutations in cancer driver genes in hematopoietic stem cells. We sought to identify novel drivers of clonal expansion using an unbiased analysis of sequencing data from 84,683 persons and identified common mutations in the...

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Beauchamp EM, Leventhal M, Bernard E, et al. . Blood Cancer Discov. 2021;2(5):500-517doi: 10.1158/2643-3230.BCD-20-0224.
Beauchamp, E. M., Leventhal, M., Bernard, E., Hoppe, E. R., Todisco, G., Creignou, M., Gallì, A., Castellano, C. A., McConkey, M., Tarun, A., Wong, W., Schenone, M., Stanclift, C., Tanenbaum, B., Malolepsza, E., Nilsson, B., Bick, A. G., Weinstock, J. S., Miller, M., Niroula, A., Dunford, A., Taylor-Weiner, A., Wood, T., Barbera, A., Anand, S., Psaty, B. M., Desai, P., Cho, M. H., Johnson, A. D., Loos, R., MacArthur, D. G., Lek, M., Neuberg, D. S., Lage, K., Carr, S. A., Hellstrom-Lindberg, E., Malcovati, L., Papaemmanuil, E., Stewart, C., Getz, G., Bradley, R. K., Jaiswal, S., & Ebert, B. L. (2021). . Blood cancer discovery, 2(5), 500-517. https://doi.org/10.1158/2643-3230.BCD-20-0224
Beauchamp, Ellen M, et al. "." Blood cancer discovery vol. 2,5 (2021): 500-517. doi: https://doi.org/10.1158/2643-3230.BCD-20-0224
Beauchamp EM, Leventhal M, Bernard E, Hoppe ER, Todisco G, Creignou M, Gallì A, Castellano CA, McConkey M, Tarun A, Wong W, Schenone M, Stanclift C, Tanenbaum B, Malolepsza E, Nilsson B, Bick AG, Weinstock JS, Miller M, Niroula A, Dunford A, Taylor-Weiner A, Wood T, Barbera A, Anand S, Psaty BM, Desai P, Cho MH, Johnson AD, Loos R, MacArthur DG, Lek M, Neuberg DS, Lage K, Carr SA, Hellstrom-Lindberg E, Malcovati L, Papaemmanuil E, Stewart C, Getz G, Bradley RK, Jaiswal S, Ebert BL. . Blood Cancer Discov. 2021 Sep;2(5):500-517. doi: 10.1158/2643-3230.BCD-20-0224. Epub 2021 Jul 14. PMID: 34568833; PMCID: PMC8462124.
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Accurate, scalable cohort variant calls using DeepVariant and GLnexus.

Bioinformatics (Oxford, England)

Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY.
PMID: 33399819
Bioinformatics. 2021 Jan 05; doi: 10.1093/bioinformatics/btaa1081. Epub 2021 Jan 05.

MOTIVATION: Population-scale sequenced cohorts are foundational resources for genetic analyses, but processing raw reads into analysis-ready cohort-level variants remains challenging.RESULTS: We introduce an open-source cohort-calling method that uses the highly-accurate caller DeepVariant and scalable merging tool GLnexus. Using callset...

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Yun T, Li H, Chang PC, et al. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Bioinformatics. 2021;doi: 10.1093/bioinformatics/btaa1081.
Yun, T., Li, H., Chang, P. C., Lin, M. F., Carroll, A., & McLean, C. Y. (2021). Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Bioinformatics (Oxford, England), . https://doi.org/10.1093/bioinformatics/btaa1081
Yun, Taedong, et al. "Accurate, scalable cohort variant calls using DeepVariant and GLnexus." Bioinformatics (Oxford, England) vol. (2021). doi: https://doi.org/10.1093/bioinformatics/btaa1081
Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Bioinformatics. 2021 Jan 05; doi: 10.1093/bioinformatics/btaa1081. Epub 2021 Jan 05. PMID: 33399819; PMCID: PMC8023681.
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[No title available]

Blood cancer discovery

Beauchamp EM, Leventhal M, Bernard E, Hoppe ER, Todisco G, Creignou M, Gallì A, Castellano CA, McConkey M, Tarun A, Wong W, Schenone M, Stanclift C, Tanenbaum B, Malolepsza E, Nilsson B, Bick AG, Weinstock JS, Miller M, Niroula A, Dunford A, Taylor-Weiner A, Wood T, Barbera A, Anand S, Psaty BM, Desai P, Cho MH, Johnson AD, Loos R, MacArthur DG, Lek M, Neuberg DS, Lage K, Carr SA, Hellstrom-Lindberg E, Malcovati L, Papaemmanuil E, Stewart C, Getz G, Bradley RK, Jaiswal S, Ebert BL.
PMID: 34568833
Blood Cancer Discov. 2021 Sep;2(5):500-517. doi: 10.1158/2643-3230.BCD-20-0224. Epub 2021 Jul 14.

Clonal hematopoiesis results from somatic mutations in cancer driver genes in hematopoietic stem cells. We sought to identify novel drivers of clonal expansion using an unbiased analysis of sequencing data from 84,683 persons and identified common mutations in the...

Cite
Beauchamp EM, Leventhal M, Bernard E, et al. . Blood Cancer Discov. 2021;2(5):500-517doi: 10.1158/2643-3230.BCD-20-0224.
Beauchamp, E. M., Leventhal, M., Bernard, E., Hoppe, E. R., Todisco, G., Creignou, M., Gallì, A., Castellano, C. A., McConkey, M., Tarun, A., Wong, W., Schenone, M., Stanclift, C., Tanenbaum, B., Malolepsza, E., Nilsson, B., Bick, A. G., Weinstock, J. S., Miller, M., Niroula, A., Dunford, A., Taylor-Weiner, A., Wood, T., Barbera, A., Anand, S., Psaty, B. M., Desai, P., Cho, M. H., Johnson, A. D., Loos, R., MacArthur, D. G., Lek, M., Neuberg, D. S., Lage, K., Carr, S. A., Hellstrom-Lindberg, E., Malcovati, L., Papaemmanuil, E., Stewart, C., Getz, G., Bradley, R. K., Jaiswal, S., & Ebert, B. L. (2021). . Blood cancer discovery, 2(5), 500-517. https://doi.org/10.1158/2643-3230.BCD-20-0224
Beauchamp, Ellen M, et al. "." Blood cancer discovery vol. 2,5 (2021): 500-517. doi: https://doi.org/10.1158/2643-3230.BCD-20-0224
Beauchamp EM, Leventhal M, Bernard E, Hoppe ER, Todisco G, Creignou M, Gallì A, Castellano CA, McConkey M, Tarun A, Wong W, Schenone M, Stanclift C, Tanenbaum B, Malolepsza E, Nilsson B, Bick AG, Weinstock JS, Miller M, Niroula A, Dunford A, Taylor-Weiner A, Wood T, Barbera A, Anand S, Psaty BM, Desai P, Cho MH, Johnson AD, Loos R, MacArthur DG, Lek M, Neuberg DS, Lage K, Carr SA, Hellstrom-Lindberg E, Malcovati L, Papaemmanuil E, Stewart C, Getz G, Bradley RK, Jaiswal S, Ebert BL. . Blood Cancer Discov. 2021 Sep;2(5):500-517. doi: 10.1158/2643-3230.BCD-20-0224. Epub 2021 Jul 14. PMID: 34568833; PMCID: PMC8462124.
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Correction to: Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium.

Diabetologia

Bien SA, Pankow JS, Haessler J, Lu Y, Pankratz N, Rohde RR, Tamuno A, Carlson CS, Schumacher FR, Bůžková P, Daviglus ML, Lim U, Fornage M, Fernandez-Rhodes L, Avilés-Santa L, Buyske S, Gross MD, Graff M, Isasi CR, Kuller LH, Manson JE, Matise TC, Prentice RL, Wilkens LR, Yoneyama S, Loos RJF, Hindorff LA, Le Marchand L, North KE, Haiman CA, Peters U, Kooperberg C.
PMID: 29038867
Diabetologia. 2017 Dec;60(12):2542-2543. doi: 10.1007/s00125-017-4476-z.

The authors regret that Yinchang Lu's name incorrectly included a middle initial in the author list. The details given in this erratum are correct.

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Bien SA, Pankow JS, Haessler J, et al. Correction to: Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium. Diabetologia. 2017;60(12):2542-2543doi: 10.1007/s00125-017-4476-z.
Bien, S. A., Pankow, J. S., Haessler, J., Lu, Y., Pankratz, N., Rohde, R. R., Tamuno, A., Carlson, C. S., Schumacher, F. R., Bůžková, P., Daviglus, M. L., Lim, U., Fornage, M., Fernandez-Rhodes, L., Avilés-Santa, L., Buyske, S., Gross, M. D., Graff, M., Isasi, C. R., Kuller, L. H., Manson, J. E., Matise, T. C., Prentice, R. L., Wilkens, L. R., Yoneyama, S., Loos, R. J. F., Hindorff, L. A., Le Marchand, L., North, K. E., Haiman, C. A., Peters, U., & Kooperberg, C. (2017). Correction to: Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium. Diabetologia, 60(12), 2542-2543. https://doi.org/10.1007/s00125-017-4476-z
Bien, Stephanie A, et al. "Correction to: Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium." Diabetologia vol. 60,12 (2017): 2542-2543. doi: https://doi.org/10.1007/s00125-017-4476-z
Bien SA, Pankow JS, Haessler J, Lu Y, Pankratz N, Rohde RR, Tamuno A, Carlson CS, Schumacher FR, Bůžková P, Daviglus ML, Lim U, Fornage M, Fernandez-Rhodes L, Avilés-Santa L, Buyske S, Gross MD, Graff M, Isasi CR, Kuller LH, Manson JE, Matise TC, Prentice RL, Wilkens LR, Yoneyama S, Loos RJF, Hindorff LA, Le Marchand L, North KE, Haiman CA, Peters U, Kooperberg C. Correction to: Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium. Diabetologia. 2017 Dec;60(12):2542-2543. doi: 10.1007/s00125-017-4476-z. PMID: 29038867; PMCID: PMC6145818.
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Genetics of Chronic Kidney Disease Stages Across Ancestries: The PAGE Study.

Frontiers in genetics

Lin BM, Nadkarni GN, Tao R, Graff M, Fornage M, Buyske S, Matise TC, Highland HM, Wilkens LR, Carlson CS, Park SL, Setiawan VW, Ambite JL, Heiss G, Boerwinkle E, Lin DY, Morris AP, Loos RJF, Kooperberg C, North KE, Wassel CL, Franceschini N.
PMID: 31178898
Front Genet. 2019 May 24;10:494. doi: 10.3389/fgene.2019.00494. eCollection 2019.

BACKGROUND: Chronic kidney disease (CKD) is common and disproportionally burdens United States ethnic minorities. Its genetic determinants may differ by disease severity and clinical stages. To uncover genetic factors associated CKD severity among high-risk ethnic groups, we performed genome-wide...

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Lin BM, Nadkarni GN, Tao R, et al. Genetics of Chronic Kidney Disease Stages Across Ancestries: The PAGE Study. Front Genet. 2019;10:494doi: 10.3389/fgene.2019.00494.
Lin, B. M., Nadkarni, G. N., Tao, R., Graff, M., Fornage, M., Buyske, S., Matise, T. C., Highland, H. M., Wilkens, L. R., Carlson, C. S., Park, S. L., Setiawan, V. W., Ambite, J. L., Heiss, G., Boerwinkle, E., Lin, D. Y., Morris, A. P., Loos, R. J. F., Kooperberg, C., North, K. E., Wassel, C. L., & Franceschini, N. (2019). Genetics of Chronic Kidney Disease Stages Across Ancestries: The PAGE Study. Frontiers in genetics, 10494. https://doi.org/10.3389/fgene.2019.00494
Lin, Bridget M, et al. "Genetics of Chronic Kidney Disease Stages Across Ancestries: The PAGE Study." Frontiers in genetics vol. 10 (2019): 494. doi: https://doi.org/10.3389/fgene.2019.00494
Lin BM, Nadkarni GN, Tao R, Graff M, Fornage M, Buyske S, Matise TC, Highland HM, Wilkens LR, Carlson CS, Park SL, Setiawan VW, Ambite JL, Heiss G, Boerwinkle E, Lin DY, Morris AP, Loos RJF, Kooperberg C, North KE, Wassel CL, Franceschini N. Genetics of Chronic Kidney Disease Stages Across Ancestries: The PAGE Study. Front Genet. 2019 May 24;10:494. doi: 10.3389/fgene.2019.00494. eCollection 2019. PMID: 31178898; PMCID: PMC6544117.
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CDH1 pathogenic variants and cancer risk in an unselected patient population.

Familial cancer

Bar-Mashiah A, Soper ER, Cullina S, Belbin GM, Kenny EE, Lucas AL, Abul-Husn NS.
PMID: 33886068
Fam Cancer. 2021 Apr 22; doi: 10.1007/s10689-021-00257-x. Epub 2021 Apr 22.

CDH1 pathogenic variants confer a markedly elevated lifetime risk of developing diffuse gastric cancer (DGC) and lobular breast cancer (LBC). The aim of this study was to evaluate the prevalence and clinical impact of CDH1 pathogenic variants in the...

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Bar-Mashiah A, Soper ER, Cullina S, et al. CDH1 pathogenic variants and cancer risk in an unselected patient population. Fam Cancer. 2021;doi: 10.1007/s10689-021-00257-x.
Bar-Mashiah, A., Soper, E. R., Cullina, S., Belbin, G. M., Kenny, E. E., Lucas, A. L., & Abul-Husn, N. S. (2021). CDH1 pathogenic variants and cancer risk in an unselected patient population. Familial cancer, . https://doi.org/10.1007/s10689-021-00257-x
Bar-Mashiah, Ariel, et al. "CDH1 pathogenic variants and cancer risk in an unselected patient population." Familial cancer vol. (2021). doi: https://doi.org/10.1007/s10689-021-00257-x
Bar-Mashiah A, Soper ER, Cullina S, Belbin GM, Kenny EE, Lucas AL, Abul-Husn NS. CDH1 pathogenic variants and cancer risk in an unselected patient population. Fam Cancer. 2021 Apr 22; doi: 10.1007/s10689-021-00257-x. Epub 2021 Apr 22. PMID: 33886068; PMCID: PMC8531152.
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Lynch Syndrome-Associated Variants and Cancer Rates in an Ancestrally Diverse Biobank.

JCO precision oncology

Rosenblum RE, Ang C, Suckiel SA, Soper ER, Sigireddi MR, Cullina S, Belbin GM, Lucas AL, Kenny EE, Abul-Husn NS.
PMID: 33283134
JCO Precis Oncol. 2020 Nov 23;4. doi: 10.1200/PO.20.00290. eCollection 2020.

PURPOSE: Limited data are available on the prevalence and clinical impact of Lynch syndrome (LS)-associated genomic variants in non-European ancestry populations. We identified and characterized individuals harboring LS-associated variants in the ancestrally diverse BioPATIENTS AND METHODS: Exome sequence data...

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Rosenblum RE, Ang C, Suckiel SA, et al. Lynch Syndrome-Associated Variants and Cancer Rates in an Ancestrally Diverse Biobank. JCO Precis Oncol. 2020;4doi: 10.1200/PO.20.00290.
Rosenblum, R. E., Ang, C., Suckiel, S. A., Soper, E. R., Sigireddi, M. R., Cullina, S., Belbin, G. M., Lucas, A. L., Kenny, E. E., & Abul-Husn, N. S. (2020). Lynch Syndrome-Associated Variants and Cancer Rates in an Ancestrally Diverse Biobank. JCO precision oncology, 4. https://doi.org/10.1200/PO.20.00290
Rosenblum, Rachel E, et al. "Lynch Syndrome-Associated Variants and Cancer Rates in an Ancestrally Diverse Biobank." JCO precision oncology vol. 4 (2020). doi: https://doi.org/10.1200/PO.20.00290
Rosenblum RE, Ang C, Suckiel SA, Soper ER, Sigireddi MR, Cullina S, Belbin GM, Lucas AL, Kenny EE, Abul-Husn NS. Lynch Syndrome-Associated Variants and Cancer Rates in an Ancestrally Diverse Biobank. JCO Precis Oncol. 2020 Nov 23;4. doi: 10.1200/PO.20.00290. eCollection 2020. PMID: 33283134; PMCID: PMC7713527.
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Complex patterns of direct and indirect association between the transcription Factor-7 like 2 gene, body mass index and type 2 diabetes diagnosis in adulthood in the Hispanic Community Health Study/Study of Latinos.

BMC obesity

Fernández-Rhodes L, Howard AG, Graff M, Isasi CR, Highland HM, Young KL, Parra E, Below JE, Qi Q, Kaplan RC, Justice AE, Papanicolaou G, Laurie CC, Grant SFA, Haiman C, Loos RJF, North KE.
PMID: 30305909
BMC Obes. 2018 Oct 02;5:26. doi: 10.1186/s40608-018-0200-x. eCollection 2018.

BACKGROUND: Genome-wide association studies have implicated the METHODS: Using 9031 Hispanic/Latino adults (21-76 years) with complete weight history and genetic data from the community-based Hispanic Community Health Study/Study of Latinos (HCHS/SOL, Baseline 2008-2011), we estimated the multivariable association between...

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Fernández-Rhodes L, Howard AG, Graff M, et al. Complex patterns of direct and indirect association between the transcription Factor-7 like 2 gene, body mass index and type 2 diabetes diagnosis in adulthood in the Hispanic Community Health Study/Study of Latinos. BMC Obes. 2018;5:26doi: 10.1186/s40608-018-0200-x.
Fernández-Rhodes, L., Howard, A. G., Graff, M., Isasi, C. R., Highland, H. M., Young, K. L., Parra, E., Below, J. E., Qi, Q., Kaplan, R. C., Justice, A. E., Papanicolaou, G., Laurie, C. C., Grant, S. F. A., Haiman, C., Loos, R. J. F., & North, K. E. (2018). Complex patterns of direct and indirect association between the transcription Factor-7 like 2 gene, body mass index and type 2 diabetes diagnosis in adulthood in the Hispanic Community Health Study/Study of Latinos. BMC obesity, 526. https://doi.org/10.1186/s40608-018-0200-x
Fernández-Rhodes, Lindsay, et al. "Complex patterns of direct and indirect association between the transcription Factor-7 like 2 gene, body mass index and type 2 diabetes diagnosis in adulthood in the Hispanic Community Health Study/Study of Latinos." BMC obesity vol. 5 (2018): 26. doi: https://doi.org/10.1186/s40608-018-0200-x
Fernández-Rhodes L, Howard AG, Graff M, Isasi CR, Highland HM, Young KL, Parra E, Below JE, Qi Q, Kaplan RC, Justice AE, Papanicolaou G, Laurie CC, Grant SFA, Haiman C, Loos RJF, North KE. Complex patterns of direct and indirect association between the transcription Factor-7 like 2 gene, body mass index and type 2 diabetes diagnosis in adulthood in the Hispanic Community Health Study/Study of Latinos. BMC Obes. 2018 Oct 02;5:26. doi: 10.1186/s40608-018-0200-x. eCollection 2018. PMID: 30305909; PMCID: PMC6167893.
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