22 results on '"Onofrio, R"'
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2. Evolution of interface singularities in shallow water equations with variable bottom topography
- Author
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Camassa, R, D'Onofrio, R, Falqui, G, Ortenzi, G, Pedroni, M, Camassa R., D'Onofrio R., Falqui G., Ortenzi G., Pedroni M., Camassa, R, D'Onofrio, R, Falqui, G, Ortenzi, G, Pedroni, M, Camassa R., D'Onofrio R., Falqui G., Ortenzi G., and Pedroni M.
- Abstract
Wave front propagation with nontrivial bottom topography is studied within the formalism of hyperbolic long wave models. Evolution of nonsmooth initial data is examined, and, in particular, the splitting of singular points and their short time behavior is described. In the opposite limit of longer times, the local analysis of wave fronts is used to estimate the gradient catastrophe formation and how this is influenced by the topography. The limiting cases when the free surface intersects the bottom boundary, belonging to the so-called “physical” and “nonphysical” vacuum classes, are examined. Solutions expressed by power series in the spatial variable lead to a hierarchy of ordinary differential equations for the time-dependent series coefficients, which are shown to reveal basic differences between the two vacuum cases: for nonphysical vacuums, the equations of the hierarchy are recursive and linear past the first two pairs, whereas for physical vacuums, the hierarchy is nonrecursive, fully coupled, and nonlinear. The former case may admit solutions that are free of singularities for nonzero time intervals, whereas the latter is shown to develop nonstandard velocity shocks instantaneously. Polynomial bottom topographies simplify the hierarchy, as they contribute only a finite number of inhomogeneous forcing terms to the equations in the recursion relations. However, we show that truncation to finite-dimensional systems and polynomial solutions is in general only possible for the case of a quadratic bottom profile. In this case, the system's evolution can reduce to, and is completely described by, a low-dimensional dynamical system for the time-dependent coefficients. This system encapsulates all the nonlinear properties of the solution for general power series initial data, and, in particular, governs the loss of regularity in finite times at the dry point. For the special case of parabolic bottom topographies, an exact, self-similar solution class is introduced an
- Published
- 2022
3. Evolution of interface singularities in shallow water equations with variable bottom topography
- Author
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Camassa, R, D'Onofrio, R, Falqui, G, Ortenzi, G, Pedroni, M, Camassa R., D'Onofrio R., Falqui G., Ortenzi G., Pedroni M., Camassa, R, D'Onofrio, R, Falqui, G, Ortenzi, G, Pedroni, M, Camassa R., D'Onofrio R., Falqui G., Ortenzi G., and Pedroni M.
- Abstract
Wave front propagation with nontrivial bottom topography is studied within the formalism of hyperbolic long wave models. Evolution of nonsmooth initial data is examined, and, in particular, the splitting of singular points and their short time behavior is described. In the opposite limit of longer times, the local analysis of wave fronts is used to estimate the gradient catastrophe formation and how this is influenced by the topography. The limiting cases when the free surface intersects the bottom boundary, belonging to the so-called “physical” and “nonphysical” vacuum classes, are examined. Solutions expressed by power series in the spatial variable lead to a hierarchy of ordinary differential equations for the time-dependent series coefficients, which are shown to reveal basic differences between the two vacuum cases: for nonphysical vacuums, the equations of the hierarchy are recursive and linear past the first two pairs, whereas for physical vacuums, the hierarchy is nonrecursive, fully coupled, and nonlinear. The former case may admit solutions that are free of singularities for nonzero time intervals, whereas the latter is shown to develop nonstandard velocity shocks instantaneously. Polynomial bottom topographies simplify the hierarchy, as they contribute only a finite number of inhomogeneous forcing terms to the equations in the recursion relations. However, we show that truncation to finite-dimensional systems and polynomial solutions is in general only possible for the case of a quadratic bottom profile. In this case, the system's evolution can reduce to, and is completely described by, a low-dimensional dynamical system for the time-dependent coefficients. This system encapsulates all the nonlinear properties of the solution for general power series initial data, and, in particular, governs the loss of regularity in finite times at the dry point. For the special case of parabolic bottom topographies, an exact, self-similar solution class is introduced an
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- 2022
4. Solutions and singularities of the semigeostrophic equations via the geometry of Lagrangian submanifolds
- Author
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D’Onofrio, R, Ortenzi, G, Roulstone, I, Rubtsov, V, D’Onofrio, Roberto, Ortenzi, Giovanni, Roulstone, Ian, Rubtsov, Volodya, D’Onofrio, R, Ortenzi, G, Roulstone, I, Rubtsov, V, D’Onofrio, Roberto, Ortenzi, Giovanni, Roulstone, Ian, and Rubtsov, Volodya
- Abstract
By using Monge-Ampère geometry, we study the singular structure of a class of nonlinear Monge-Ampère equations in three dimensions, arising in geophysical fluid dynamics. We extend seminal earlier work on Monge-Ampère geometry by examining the role of an induced metric on Lagrangian submanifolds of the cotangent bundle. In particular, we show that the signature of the metric serves as a classification of the Monge-Ampère equation, while singularities and elliptic-hyperbolic transitions are revealed by degeneracies of the metric. The theory is illustrated by application to an example solution of the semigeostrophic equations.
- Published
- 2023
5. Efficient computation of collisional $\ell$-mixing rate coefficients in astrophysical plasmas
- Author
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Vrinceanu, D., Onofrio, R., Oonk, J. B. R., Salas, P., Sadeghpour, H. R., Vrinceanu, D., Onofrio, R., Oonk, J. B. R., Salas, P., and Sadeghpour, H. R.
- Abstract
We present analytical expressions for direct evaluation of $\ell$-mixing rate coefficients in proton-excited hydrogen atom collisions and describe a software package for efficient numerical evaluation of the collisional rate coefficients. Comparisons between rate coefficients calculated with various levels of approximation are discussed, highlighting their range of validity. These rate coefficients are benchmarked via radio recombination lines for hydrogen, evaluating the corresponding departure coefficients from local thermal equilibrium.
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- 2019
- Full Text
- View/download PDF
6. Efficient computation of collisional $\ell$-mixing rate coefficients in astrophysical plasmas
- Author
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Vrinceanu, D., Onofrio, R., Oonk, J. B. R., Salas, P., Sadeghpour, H. R., Vrinceanu, D., Onofrio, R., Oonk, J. B. R., Salas, P., and Sadeghpour, H. R.
- Abstract
We present analytical expressions for direct evaluation of $\ell$-mixing rate coefficients in proton-excited hydrogen atom collisions and describe a software package for efficient numerical evaluation of the collisional rate coefficients. Comparisons between rate coefficients calculated with various levels of approximation are discussed, highlighting their range of validity. These rate coefficients are benchmarked via radio recombination lines for hydrogen, evaluating the corresponding departure coefficients from local thermal equilibrium.
- Published
- 2019
- Full Text
- View/download PDF
7. Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.
- Author
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Flannick, J, Fuchsberger, C, Mahajan, A, Teslovich, TM, Agarwala, V, Gaulton, KJ, Caulkins, L, Koesterer, R, Ma, C, Moutsianas, L, McCarthy, DJ, Rivas, MA, Perry, JRB, Sim, X, Blackwell, TW, Robertson, NR, Rayner, NW, Cingolani, P, Locke, AE, Tajes, JF, Highland, HM, Dupuis, J, Chines, PS, Lindgren, CM, Hartl, C, Jackson, AU, Chen, H, Huyghe, JR, van de Bunt, M, Pearson, RD, Kumar, A, Mueller-Nurasyid, M, Grarup, N, Stringham, HM, Gamazon, ER, Lee, J, Chen, Y, Scott, RA, Below, JE, Chen, P, Huang, J, Go, MJ, Stitzel, ML, Pasko, D, Parker, SCJ, Varga, TV, Green, T, Beer, NL, Day-Williams, AG, Ferreira, T, Fingerlin, T, Horikoshi, M, Hu, C, Huh, I, Ikram, MK, Kim, B-J, Kim, Y, Kim, YJ, Kwon, M-S, Lee, S, Lin, K-H, Maxwell, TJ, Nagai, Y, Wang, X, Welch, RP, Yoon, J, Zhang, W, Barzilai, N, Voight, BF, Han, B-G, Jenkinson, CP, Kuulasmaa, T, Kuusisto, J, Manning, A, Ng, MCY, Palmer, ND, Balkau, B, Stancakova, A, Abboud, HE, Boeing, H, Giedraitis, V, Prabhakaran, D, Gottesman, O, Scott, J, Carey, J, Kwan, P, Grant, G, Smith, JD, Neale, BM, Purcell, S, Butterworth, AS, Howson, JMM, Lee, HM, Lu, Y, Kwak, S-H, Zhao, W, Danesh, J, Lam, VKL, Park, KS, Saleheen, D, So, WY, Tam, CHT, Afzal, U, Aguilar, D, Arya, R, Aung, T, Chan, E, Navarro, C, Cheng, C-Y, Palli, D, Correa, A, Curran, JE, Rybin, D, Farook, VS, Fowler, SP, Freedman, BI, Griswold, M, Hale, DE, Hicks, PJ, Khor, C-C, Kumar, S, Lehne, B, Thuillier, D, Lim, WY, Liu, J, Loh, M, Musani, SK, Puppala, S, Scott, WR, Yengo, L, Tan, S-T, Taylor, HA, Thameem, F, Wilson, G, Wong, TY, Njolstad, PR, Levy, JC, Mangino, M, Bonnycastle, LL, Schwarzmayr, T, Fadista, J, Surdulescu, GL, Herder, C, Groves, CJ, Wieland, T, Bork-Jensen, J, Brandslund, I, Christensen, C, Koistinen, HA, Doney, ASF, Kinnunen, L, Esko, T, Farmer, AJ, Hakaste, L, Hodgkiss, D, Kravic, J, Lyssenko, V, Hollensted, M, Jorgensen, ME, Jorgensen, T, Ladenvall, C, Justesen, JM, Karajamaki, A, Kriebel, J, Rathmann, W, Lannfelt, L, Lauritzen, T, Narisu, N, Linneberg, A, Melander, O, Milani, L, Neville, M, Orho-Melander, M, Qi, L, Qi, Q, Roden, M, Rolandsson, O, Swift, A, Rosengren, AH, Stirrups, K, Wood, AR, Mihailov, E, Blancher, C, Carneiro, MO, Maguire, J, Poplin, R, Shakir, K, Fennell, T, DePristo, M, de Angelis, MH, Deloukas, P, Gjesing, AP, Jun, G, Nilsson, PM, Murphy, J, Onofrio, R, Thorand, B, Hansen, T, Meisinger, C, Hu, FB, Isomaa, B, Karpe, F, Liang, L, Peters, A, Huth, C, O'Rahilly, SP, Palmer, CNA, Pedersen, O, Rauramaa, R, Tuomilehto, J, Salomaa, V, Watanabe, RM, Syvanen, A-C, Bergman, RN, Bharadwaj, D, Bottinger, EP, Cho, YS, Chandak, GR, Chan, JC, Chia, KS, Daly, MJ, Ebrahim, SB, Langenberg, C, Elliott, P, Jablonski, KA, Lehman, DM, Jia, W, Ma, RCW, Pollin, TI, Sandhu, M, Tandon, N, Froguel, P, Barroso, I, Teo, YY, Zeggini, E, Loos, RJF, Small, KS, Ried, JS, DeFronzo, RA, Grallert, H, Glaser, B, Metspalu, A, Wareham, NJ, Walker, M, Banks, E, Gieger, C, Ingelsson, E, Im, HK, Illig, T, Franks, PW, Buck, G, Trakalo, J, Buck, D, Prokopenko, I, Magi, R, Lind, L, Farjoun, Y, Owen, KR, Gloyn, AL, Strauch, K, Tuomi, T, Kooner, JS, Lee, J-Y, Park, T, Donnelly, P, Morris, AD, Hattersley, AT, Bowden, DW, Collins, FS, Atzmon, G, Chambers, JC, Spector, TD, Laakso, M, Strom, TM, Bell, GI, Blangero, J, Duggirala, R, Tai, E, McVean, G, Hanis, CL, Wilson, JG, Seielstad, M, Frayling, TM, Meigs, JB, Cox, NJ, Sladek, R, Lander, ES, Gabriel, S, Mohlke, KL, Meitinger, T, Groop, L, Abecasis, G, Scott, LJ, Morris, AP, Kang, HM, Altshuler, D, Burtt, NP, Florez, JC, Boehnke, M, McCarthy, MI, Flannick, J, Fuchsberger, C, Mahajan, A, Teslovich, TM, Agarwala, V, Gaulton, KJ, Caulkins, L, Koesterer, R, Ma, C, Moutsianas, L, McCarthy, DJ, Rivas, MA, Perry, JRB, Sim, X, Blackwell, TW, Robertson, NR, Rayner, NW, Cingolani, P, Locke, AE, Tajes, JF, Highland, HM, Dupuis, J, Chines, PS, Lindgren, CM, Hartl, C, Jackson, AU, Chen, H, Huyghe, JR, van de Bunt, M, Pearson, RD, Kumar, A, Mueller-Nurasyid, M, Grarup, N, Stringham, HM, Gamazon, ER, Lee, J, Chen, Y, Scott, RA, Below, JE, Chen, P, Huang, J, Go, MJ, Stitzel, ML, Pasko, D, Parker, SCJ, Varga, TV, Green, T, Beer, NL, Day-Williams, AG, Ferreira, T, Fingerlin, T, Horikoshi, M, Hu, C, Huh, I, Ikram, MK, Kim, B-J, Kim, Y, Kim, YJ, Kwon, M-S, Lee, S, Lin, K-H, Maxwell, TJ, Nagai, Y, Wang, X, Welch, RP, Yoon, J, Zhang, W, Barzilai, N, Voight, BF, Han, B-G, Jenkinson, CP, Kuulasmaa, T, Kuusisto, J, Manning, A, Ng, MCY, Palmer, ND, Balkau, B, Stancakova, A, Abboud, HE, Boeing, H, Giedraitis, V, Prabhakaran, D, Gottesman, O, Scott, J, Carey, J, Kwan, P, Grant, G, Smith, JD, Neale, BM, Purcell, S, Butterworth, AS, Howson, JMM, Lee, HM, Lu, Y, Kwak, S-H, Zhao, W, Danesh, J, Lam, VKL, Park, KS, Saleheen, D, So, WY, Tam, CHT, Afzal, U, Aguilar, D, Arya, R, Aung, T, Chan, E, Navarro, C, Cheng, C-Y, Palli, D, Correa, A, Curran, JE, Rybin, D, Farook, VS, Fowler, SP, Freedman, BI, Griswold, M, Hale, DE, Hicks, PJ, Khor, C-C, Kumar, S, Lehne, B, Thuillier, D, Lim, WY, Liu, J, Loh, M, Musani, SK, Puppala, S, Scott, WR, Yengo, L, Tan, S-T, Taylor, HA, Thameem, F, Wilson, G, Wong, TY, Njolstad, PR, Levy, JC, Mangino, M, Bonnycastle, LL, Schwarzmayr, T, Fadista, J, Surdulescu, GL, Herder, C, Groves, CJ, Wieland, T, Bork-Jensen, J, Brandslund, I, Christensen, C, Koistinen, HA, Doney, ASF, Kinnunen, L, Esko, T, Farmer, AJ, Hakaste, L, Hodgkiss, D, Kravic, J, Lyssenko, V, Hollensted, M, Jorgensen, ME, Jorgensen, T, Ladenvall, C, Justesen, JM, Karajamaki, A, Kriebel, J, Rathmann, W, Lannfelt, L, Lauritzen, T, Narisu, N, Linneberg, A, Melander, O, Milani, L, Neville, M, Orho-Melander, M, Qi, L, Qi, Q, Roden, M, Rolandsson, O, Swift, A, Rosengren, AH, Stirrups, K, Wood, AR, Mihailov, E, Blancher, C, Carneiro, MO, Maguire, J, Poplin, R, Shakir, K, Fennell, T, DePristo, M, de Angelis, MH, Deloukas, P, Gjesing, AP, Jun, G, Nilsson, PM, Murphy, J, Onofrio, R, Thorand, B, Hansen, T, Meisinger, C, Hu, FB, Isomaa, B, Karpe, F, Liang, L, Peters, A, Huth, C, O'Rahilly, SP, Palmer, CNA, Pedersen, O, Rauramaa, R, Tuomilehto, J, Salomaa, V, Watanabe, RM, Syvanen, A-C, Bergman, RN, Bharadwaj, D, Bottinger, EP, Cho, YS, Chandak, GR, Chan, JC, Chia, KS, Daly, MJ, Ebrahim, SB, Langenberg, C, Elliott, P, Jablonski, KA, Lehman, DM, Jia, W, Ma, RCW, Pollin, TI, Sandhu, M, Tandon, N, Froguel, P, Barroso, I, Teo, YY, Zeggini, E, Loos, RJF, Small, KS, Ried, JS, DeFronzo, RA, Grallert, H, Glaser, B, Metspalu, A, Wareham, NJ, Walker, M, Banks, E, Gieger, C, Ingelsson, E, Im, HK, Illig, T, Franks, PW, Buck, G, Trakalo, J, Buck, D, Prokopenko, I, Magi, R, Lind, L, Farjoun, Y, Owen, KR, Gloyn, AL, Strauch, K, Tuomi, T, Kooner, JS, Lee, J-Y, Park, T, Donnelly, P, Morris, AD, Hattersley, AT, Bowden, DW, Collins, FS, Atzmon, G, Chambers, JC, Spector, TD, Laakso, M, Strom, TM, Bell, GI, Blangero, J, Duggirala, R, Tai, E, McVean, G, Hanis, CL, Wilson, JG, Seielstad, M, Frayling, TM, Meigs, JB, Cox, NJ, Sladek, R, Lander, ES, Gabriel, S, Mohlke, KL, Meitinger, T, Groop, L, Abecasis, G, Scott, LJ, Morris, AP, Kang, HM, Altshuler, D, Burtt, NP, Florez, JC, Boehnke, M, and McCarthy, MI
- Abstract
This corrects the article DOI: 10.1038/sdata.2017.179.
- Published
- 2018
8. On the treatment of $\ell$-changing proton-hydrogen Rydberg atom collisions
- Author
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Vrinceanu, D., Onofrio, R., Sadeghpour, H. R., Vrinceanu, D., Onofrio, R., and Sadeghpour, H. R.
- Abstract
Energy-conserving, angular momentum-changing collisions between protons and highly excited Rydberg hydrogen atoms are important for precise understanding of atomic recombination at the photon decoupling era, and the elemental abundance after primordial nucleosynthesis. Early approaches to $\ell$-changing collisions used perturbation theory for only dipole-allowed ($\Delta \ell=\pm 1$) transitions. An exact non-perturbative quantum mechanical treatment is possible, but it comes at computational cost for highly excited Rydberg states. In this note we show how to obtain a semi-classical limit that is accurate and simple, and develop further physical insights afforded by the non-perturbative quantum mechanical treatment.
- Published
- 2017
- Full Text
- View/download PDF
9. Data Descriptor: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
- Author
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Flannick, J, Fuchsberger, C, Mahajan, A, Teslovich, TM, Agarwala, V, Gaulton, KJ, Caulkins, L, Koesterer, R, Ma, C, Moutsianas, L, McCarthy, DJ, Rivas, MA, Perry, JRB, Sim, X, Blackwell, TW, Robertson, NR, Rayner, NW, Cingolani, P, Locke, AE, Tajes, JF, Highland, HM, Dupuis, J, Chines, PS, Lindgren, CM, Hartl, C, Jackson, AU, Chen, H, Huyghe, JR, De Bunt, MV, Pearson, RD, Kumar, A, Muller-Nurasyid, M, Grarup, N, Stringham, HM, Gamazon, ER, Lee, J, Chen, Y, Scott, RA, Below, JE, Chen, P, Huang, J, Go, MJ, Stitzel, ML, Pasko, D, Parker, SCJ, Varga, TV, Green, T, Beer, NL, Day-Williams, AG, Ferreira, T, Fingerlin, T, Horikoshi, M, Hu, C, Huh, I, Ikram, MK, Kim, B-J, Kim, Y, Kim, YJ, Kwon, M-S, Lee, S, Lin, K-H, Maxwell, TJ, Nagai, Y, Wang, X, Welch, RP, Yoon, J, Zhang, W, Barzilai, N, Voight, BF, Han, B-G, Jenkinson, CP, Kuulasmaa, T, Kuusisto, J, Manning, A, Ng, MCY, Palmer, ND, Balkau, B, Stancakova, A, Abboud, HE, Boeing, H, Giedraitis, V, Prabhakaran, D, Gottesman, O, Scott, J, Carey, J, Kwan, P, Grant, G, Smith, JD, Neale, BM, Purcell, S, Butterworth, AS, Howson, JMM, Lee, HM, Lu, Y, Kwak, S-H, Zhao, W, Danesh, J, Lam, VKL, Park, KS, Saleheen, D, So, WY, Tam, CHT, Afzal, U, Aguilar, D, Arya, R, Aung, T, Chan, E, Navarro, C, Cheng, C-Y, Palli, D, Correa, A, Curran, JE, Rybin, D, Farook, VS, Fowler, SP, Freedman, BI, Griswold, M, Hale, DE, Hicks, PJ, Khor, C-C, Kumar, S, Lehne, B, Thuillier, D, Lim, WY, Liu, J, Loh, M, Musani, SK, Puppala, S, Scott, WR, Yengo, L, Tan, S-T, Taylor, HA, Thameem, F, Wilson, G, Wong, TY, Njolstad, PR, Levy, JC, Mangino, M, Bonnycastle, LL, Schwarzmayr, T, Fadista, J, Surdulescu, GL, Herder, C, Groves, CJ, Wieland, T, Bork-Jensen, J, Brandslund, I, Christensen, C, Koistinen, HA, Doney, ASF, Kinnunen, L, Esko, T, Farmer, AJ, Hakaste, L, Hodgkiss, D, Kravic, J, Lyssenko, V, Hollensted, M, Jorgensen, ME, Jorgensen, T, Ladenvall, C, Justesen, JM, Karajamaki, A, Kriebel, J, Rathmann, W, Lannfelt, L, Lauritzen, T, Narisu, N, Linneberg, A, Melander, O, Milani, L, Neville, M, Orho-Melander, M, Qi, L, Qi, Q, Roden, M, Rolandsson, O, Swift, A, Rosengren, AH, Stirrups, K, Wood, AR, Mihailov, E, Blancher, C, Carneiro, MO, Maguire, J, Poplin, R, Shakir, K, Fennell, T, DePristo, M, De Angelis, MH, Deloukas, P, Gjesing, AP, Jun, G, Nilsson, PM, Murphy, J, Onofrio, R, Thorand, B, Hansen, T, Meisinger, C, Hu, FB, Isomaa, B, Karpe, F, Liang, L, Peters, A, Huth, C, O'Rahilly, SP, Palmer, CNA, Pedersen, O, Rauramaa, R, Tuomilehto, J, Salomaa, V, Watanabe, RM, Syvanen, A-C, Bergman, RN, Bharadwaj, D, Bottinger, EP, Cho, YS, Chandak, GR, Chan, JC, Chia, KS, Daly, MJ, Ebrahim, SB, Langenberg, C, Elliott, P, Jablonski, KA, Lehman, DM, Jia, W, Ma, RC, Pollin, TI, Sandhu, M, Tandon, N, Froguel, P, Barroso, I, Teo, YY, Zeggini, E, Loos, RJF, Small, KS, Ried, JS, DeFronzo, RA, Grallert, H, Glaser, B, Metspalu, A, Wareham, NJ, Walker, M, Banks, E, Gieger, C, Ingelsson, E, Im, HK, Illig, T, Franks, PW, Buck, G, Trakalo, J, Buck, D, Prokopenko, I, Magi, R, Lind, L, Farjoun, Y, Owen, KR, Gloyn, AL, Strauch, K, Tuomi, T, Kooner, JS, Lee, J-Y, Park, T, Donnelly, P, Morris, AD, Hattersley, AT, Bowden, DW, Collins, FS, Atzmon, G, Chambers, JC, Spector, TD, Laakso, M, Strom, TM, Bell, GI, Blangero, J, Duggirala, R, Tai, E, McVean, G, Hanis, CL, Wilson, JG, Seielstad, M, Frayling, TM, Meigs, JB, Cox, NJ, Sladek, R, Lander, ES, Gabriel, S, Mohlke, KL, Meitinger, T, Groop, L, Abecasis, G, Scott, LJ, Morris, AP, Kang, HM, Altshuler, D, Burtt, NP, Florez, JC, Boehnke, M, McCarthy, MI, Flannick, J, Fuchsberger, C, Mahajan, A, Teslovich, TM, Agarwala, V, Gaulton, KJ, Caulkins, L, Koesterer, R, Ma, C, Moutsianas, L, McCarthy, DJ, Rivas, MA, Perry, JRB, Sim, X, Blackwell, TW, Robertson, NR, Rayner, NW, Cingolani, P, Locke, AE, Tajes, JF, Highland, HM, Dupuis, J, Chines, PS, Lindgren, CM, Hartl, C, Jackson, AU, Chen, H, Huyghe, JR, De Bunt, MV, Pearson, RD, Kumar, A, Muller-Nurasyid, M, Grarup, N, Stringham, HM, Gamazon, ER, Lee, J, Chen, Y, Scott, RA, Below, JE, Chen, P, Huang, J, Go, MJ, Stitzel, ML, Pasko, D, Parker, SCJ, Varga, TV, Green, T, Beer, NL, Day-Williams, AG, Ferreira, T, Fingerlin, T, Horikoshi, M, Hu, C, Huh, I, Ikram, MK, Kim, B-J, Kim, Y, Kim, YJ, Kwon, M-S, Lee, S, Lin, K-H, Maxwell, TJ, Nagai, Y, Wang, X, Welch, RP, Yoon, J, Zhang, W, Barzilai, N, Voight, BF, Han, B-G, Jenkinson, CP, Kuulasmaa, T, Kuusisto, J, Manning, A, Ng, MCY, Palmer, ND, Balkau, B, Stancakova, A, Abboud, HE, Boeing, H, Giedraitis, V, Prabhakaran, D, Gottesman, O, Scott, J, Carey, J, Kwan, P, Grant, G, Smith, JD, Neale, BM, Purcell, S, Butterworth, AS, Howson, JMM, Lee, HM, Lu, Y, Kwak, S-H, Zhao, W, Danesh, J, Lam, VKL, Park, KS, Saleheen, D, So, WY, Tam, CHT, Afzal, U, Aguilar, D, Arya, R, Aung, T, Chan, E, Navarro, C, Cheng, C-Y, Palli, D, Correa, A, Curran, JE, Rybin, D, Farook, VS, Fowler, SP, Freedman, BI, Griswold, M, Hale, DE, Hicks, PJ, Khor, C-C, Kumar, S, Lehne, B, Thuillier, D, Lim, WY, Liu, J, Loh, M, Musani, SK, Puppala, S, Scott, WR, Yengo, L, Tan, S-T, Taylor, HA, Thameem, F, Wilson, G, Wong, TY, Njolstad, PR, Levy, JC, Mangino, M, Bonnycastle, LL, Schwarzmayr, T, Fadista, J, Surdulescu, GL, Herder, C, Groves, CJ, Wieland, T, Bork-Jensen, J, Brandslund, I, Christensen, C, Koistinen, HA, Doney, ASF, Kinnunen, L, Esko, T, Farmer, AJ, Hakaste, L, Hodgkiss, D, Kravic, J, Lyssenko, V, Hollensted, M, Jorgensen, ME, Jorgensen, T, Ladenvall, C, Justesen, JM, Karajamaki, A, Kriebel, J, Rathmann, W, Lannfelt, L, Lauritzen, T, Narisu, N, Linneberg, A, Melander, O, Milani, L, Neville, M, Orho-Melander, M, Qi, L, Qi, Q, Roden, M, Rolandsson, O, Swift, A, Rosengren, AH, Stirrups, K, Wood, AR, Mihailov, E, Blancher, C, Carneiro, MO, Maguire, J, Poplin, R, Shakir, K, Fennell, T, DePristo, M, De Angelis, MH, Deloukas, P, Gjesing, AP, Jun, G, Nilsson, PM, Murphy, J, Onofrio, R, Thorand, B, Hansen, T, Meisinger, C, Hu, FB, Isomaa, B, Karpe, F, Liang, L, Peters, A, Huth, C, O'Rahilly, SP, Palmer, CNA, Pedersen, O, Rauramaa, R, Tuomilehto, J, Salomaa, V, Watanabe, RM, Syvanen, A-C, Bergman, RN, Bharadwaj, D, Bottinger, EP, Cho, YS, Chandak, GR, Chan, JC, Chia, KS, Daly, MJ, Ebrahim, SB, Langenberg, C, Elliott, P, Jablonski, KA, Lehman, DM, Jia, W, Ma, RC, Pollin, TI, Sandhu, M, Tandon, N, Froguel, P, Barroso, I, Teo, YY, Zeggini, E, Loos, RJF, Small, KS, Ried, JS, DeFronzo, RA, Grallert, H, Glaser, B, Metspalu, A, Wareham, NJ, Walker, M, Banks, E, Gieger, C, Ingelsson, E, Im, HK, Illig, T, Franks, PW, Buck, G, Trakalo, J, Buck, D, Prokopenko, I, Magi, R, Lind, L, Farjoun, Y, Owen, KR, Gloyn, AL, Strauch, K, Tuomi, T, Kooner, JS, Lee, J-Y, Park, T, Donnelly, P, Morris, AD, Hattersley, AT, Bowden, DW, Collins, FS, Atzmon, G, Chambers, JC, Spector, TD, Laakso, M, Strom, TM, Bell, GI, Blangero, J, Duggirala, R, Tai, E, McVean, G, Hanis, CL, Wilson, JG, Seielstad, M, Frayling, TM, Meigs, JB, Cox, NJ, Sladek, R, Lander, ES, Gabriel, S, Mohlke, KL, Meitinger, T, Groop, L, Abecasis, G, Scott, LJ, Morris, AP, Kang, HM, Altshuler, D, Burtt, NP, Florez, JC, Boehnke, M, and McCarthy, MI
- Abstract
To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.
- Published
- 2017
10. On the treatment of $\ell$-changing proton-hydrogen Rydberg atom collisions
- Author
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Vrinceanu, D., Onofrio, R., Sadeghpour, H. R., Vrinceanu, D., Onofrio, R., and Sadeghpour, H. R.
- Abstract
Energy-conserving, angular momentum-changing collisions between protons and highly excited Rydberg hydrogen atoms are important for precise understanding of atomic recombination at the photon decoupling era, and the elemental abundance after primordial nucleosynthesis. Early approaches to $\ell$-changing collisions used perturbation theory for only dipole-allowed ($\Delta \ell=\pm 1$) transitions. An exact non-perturbative quantum mechanical treatment is possible, but it comes at computational cost for highly excited Rydberg states. In this note we show how to obtain a semi-classical limit that is accurate and simple, and develop further physical insights afforded by the non-perturbative quantum mechanical treatment.
- Published
- 2017
- Full Text
- View/download PDF
11. Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network
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Collisson, E., Campbell, J., Brooks, A., Berger, A., Lee, W., Chmielecki, J., Beer, D., Cope, L., Creighton, C., Danilova, L., Ding, L., Getz, G., Hammerman, P., Hayes, D., Hernandez, B., Herman, J., Heymach, J., Jurisica, I., Kucherlapati, R., Kwiatkowski, D., Ladanyi, M., Robertson, G., Schultz, N., Shen, R., Sinha, R., Sougnez, C., Tsao, M., Travis, W., Weinstein, J., Wigle, D., Wilkerson, M., Chu, A., Cherniack, A., Hadjipanayis, A., Rosenberg, M., Weisenberger, D., Laird, P., Radenbaugh, A., Ma, S., Stuart, J., Byers, L., Baylin, S., Govindan, R., Meyerson, M., Gabriel, S., Cibulskis, K., Kim, J., Stewart, C., Lichtenstein, L., Lander, E., Lawrence, M., Getz, E., Fulton, R., Fulton, L., McLellan, M., Wilson, R., Ye, K., Fronick, C., Maher, C., Miller, C., Wendl, M., Cabanski, C., Mardis, E., Wheeler, D., Balasundaram, M., Butterfield, Y., Carlsen, R., Chuah, E., Dhalla, N., Guin, R., Hirst, C., Lee, D., Li, H., Mayo, M., Moore, R., Mungall, A., Schein, J., Sipahimalani, P., Tam, A., Varhol, Richard, Robertson, A., Wye, N., Thiessen, N., Holt, R., Jones, S., Marra, M., Imielinski, M., Onofrio, R., Hodis, E., Zack, T., Helman, E., Collisson, E., Campbell, J., Brooks, A., Berger, A., Lee, W., Chmielecki, J., Beer, D., Cope, L., Creighton, C., Danilova, L., Ding, L., Getz, G., Hammerman, P., Hayes, D., Hernandez, B., Herman, J., Heymach, J., Jurisica, I., Kucherlapati, R., Kwiatkowski, D., Ladanyi, M., Robertson, G., Schultz, N., Shen, R., Sinha, R., Sougnez, C., Tsao, M., Travis, W., Weinstein, J., Wigle, D., Wilkerson, M., Chu, A., Cherniack, A., Hadjipanayis, A., Rosenberg, M., Weisenberger, D., Laird, P., Radenbaugh, A., Ma, S., Stuart, J., Byers, L., Baylin, S., Govindan, R., Meyerson, M., Gabriel, S., Cibulskis, K., Kim, J., Stewart, C., Lichtenstein, L., Lander, E., Lawrence, M., Getz, E., Fulton, R., Fulton, L., McLellan, M., Wilson, R., Ye, K., Fronick, C., Maher, C., Miller, C., Wendl, M., Cabanski, C., Mardis, E., Wheeler, D., Balasundaram, M., Butterfield, Y., Carlsen, R., Chuah, E., Dhalla, N., Guin, R., Hirst, C., Lee, D., Li, H., Mayo, M., Moore, R., Mungall, A., Schein, J., Sipahimalani, P., Tam, A., Varhol, Richard, Robertson, A., Wye, N., Thiessen, N., Holt, R., Jones, S., Marra, M., Imielinski, M., Onofrio, R., Hodis, E., Zack, T., and Helman, E.
- Abstract
Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.
- Published
- 2014
12. Comprehensivemolecular characterization of clear cell renal cell carcinoma
- Author
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Creighton, C., Morgan, M., Gunaratne, P., Wheeler, D., Gibbs, R., Robertson, A., Chu, A., Beroukhim, R., Cibulskis, K., Signoretti, S., Vandin, F., Wu, H., Raphael, B., Verhaak, R., Tamboli, P., Torres-Garcia, W., Akbani, R., Weinstein, J., Reuter, V., Hsieh, J., Brannon, A., Hakimi, A., Jacobsen, A., Ciriello, G., Reva, B., Ricketts, C., Linehan, W., Stuart, J., Rathmell, W., Shen, H., Laird, P., Muzny, D., Davis, C., Xi, L., Chang, K., Kakkar, N., Trevino, L., Benton, S., Reid, J., Morton, D., Doddapaneni, H., Han, Y., Lewis, L., Dinh, H., Kovar, C., Zhu, Y., Santibanez, J., Wang, M., Hale, W., Kalra, D., Getz, G., Lawrence, M., Sougnez, C., Carter, S., Sivachenko, A., Lichtenstein, L., Stewart, C., Voet, D., Fisher, S., Gabriel, S., Lander, E., Schumacher, S., Tabak, B., Saksena, G., Onofrio, R., Cherniack, A., Gentry, J., Ardlie, K., Meyerson, M., Chun, H., Mungall, A., Sipahimalani, P., Stoll, D., Ally, A., Balasundaram, M., Butterfield, Y., Carlsen, R., Carter, C., Chuah, E., Coope, R., Dhalla, N., Gorski, S., Guin, R., Hirst, C., Hirst, M., Holt, R., Lebovitz, C., Lee, D., Li, H., Mayo, M., Moore, R., Pleasance, E., Plettner, P., Schein, J., Shafiei, A., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Wye, N., Zhao, Y., Birol, I., Jones, S., Marra, M., Auman, J., Tan, D., Jones, C., Hoadley, K., Mieczkowski, P., Mose, L., Jefferys, S., Topal, M., Liquori, C., Turman, Y., Shi, Y., Waring, S., Buda, E., Walsh, J., Wu, J., Bodenheimer, T., Hoyle, A., Simons, J., Soloway, M., Balu, S., Parker, J., Hayes, D., Perou, C., Kucherlapati, R., Park, P., Triche, T., Weisenberger, D., Lai, P., Bootwalla, M., Maglinte, D., Mahurkar, S., Berman, B., Van den Berg, D., Cope, L., Baylin, S., Noble, M., DiCara, D., Zhang, H., Cho, J., Heiman, D., Gehlenborg, N., Mallard, W., Lin, P., Frazer, S., Stojanov, P., Liu, Y., Zhou, L., Kim, J., Chin, L., Benz, C., Yau, C., Reynolds, S., Shmulevich, I., Vegesna, R., Kim, H., Zhang, W., Cogdell, D., Jonasch, E., Ding, Z., Lu, Y., Zhang, N., Unruh, A., Casasent, T., Wakefield, C., Tsavachidou, D., Mills, G., Schultz, N., Antipin, Y., Gao, J., Cerami, E., Gross, B., Aksoy, B., Sinha, R., Weinhold, N., Sumer, S., Taylor, B., Shen, R., Ostrovnaya, I., Berger, M., Ladanyi, M., Sander, C., Fei, S., Stout, A., Spellman, P., Rubin, D., Liu, T., Sam, N., Paull, E., Carlin, D., Goldstein, T., Waltman, P., Ellrott, K., Zhu, J., Haussler, D., Xiao, W., Shelton, C., Gardner, J., Penny, R., Sherman, M., Mallery, D., Morris, S., Paulauskis, J., Burnett, K., Shelton, T., Kaelin, W., Choueiri, T., Atkins, M., Curley, E., Tickoo, S., Thorne, L., Boice, L., Huang, M., Fisher, J., Vocke, C., Peterson, J., Worrell, R., Merino, M., Schmidt, L., Czerniak, B., Aldape, K., Wood, C., Boyd, J., Weaver, J., Iacocca, M., Petrelli, N., Witkin, G., Brown, J., Czerwinski, C., Huelsenbeck-Dill, L., Rabeno, B., Myers, J., Morrison, C., Bergsten, J., Eckman, J., Harr, J., Smith, C., Tucker, K., Zach, L., Bshara, W., Gaudioso, C., Dhir, R., Maranchie, J., Nelson, J., Parwani, A., Potapova, O., Fedosenko, K., Cheville, J., Thompson, R., Mosquera, J., Rubin, M., Blute, M., Pihl, T., Jensen, M., Sfeir, R., Kahn, A., Kothiyal, P., Snyder, E., Pontius, J., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D., Nicholls, M., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P., Alonso, S., Sanbhadti, R., Barletta, S., Pot, D., Sheth, M., Demchok, J., Davidsen, T., Wang, Z., Yang, L., Tarnuzzer, R., Zhang, J., Eley, G., Ferguson, M., Shaw, K., Guyer, M., Ozenberger, B., Sofia, H., Creighton, C., Morgan, M., Gunaratne, P., Wheeler, D., Gibbs, R., Robertson, A., Chu, A., Beroukhim, R., Cibulskis, K., Signoretti, S., Vandin, F., Wu, H., Raphael, B., Verhaak, R., Tamboli, P., Torres-Garcia, W., Akbani, R., Weinstein, J., Reuter, V., Hsieh, J., Brannon, A., Hakimi, A., Jacobsen, A., Ciriello, G., Reva, B., Ricketts, C., Linehan, W., Stuart, J., Rathmell, W., Shen, H., Laird, P., Muzny, D., Davis, C., Xi, L., Chang, K., Kakkar, N., Trevino, L., Benton, S., Reid, J., Morton, D., Doddapaneni, H., Han, Y., Lewis, L., Dinh, H., Kovar, C., Zhu, Y., Santibanez, J., Wang, M., Hale, W., Kalra, D., Getz, G., Lawrence, M., Sougnez, C., Carter, S., Sivachenko, A., Lichtenstein, L., Stewart, C., Voet, D., Fisher, S., Gabriel, S., Lander, E., Schumacher, S., Tabak, B., Saksena, G., Onofrio, R., Cherniack, A., Gentry, J., Ardlie, K., Meyerson, M., Chun, H., Mungall, A., Sipahimalani, P., Stoll, D., Ally, A., Balasundaram, M., Butterfield, Y., Carlsen, R., Carter, C., Chuah, E., Coope, R., Dhalla, N., Gorski, S., Guin, R., Hirst, C., Hirst, M., Holt, R., Lebovitz, C., Lee, D., Li, H., Mayo, M., Moore, R., Pleasance, E., Plettner, P., Schein, J., Shafiei, A., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Wye, N., Zhao, Y., Birol, I., Jones, S., Marra, M., Auman, J., Tan, D., Jones, C., Hoadley, K., Mieczkowski, P., Mose, L., Jefferys, S., Topal, M., Liquori, C., Turman, Y., Shi, Y., Waring, S., Buda, E., Walsh, J., Wu, J., Bodenheimer, T., Hoyle, A., Simons, J., Soloway, M., Balu, S., Parker, J., Hayes, D., Perou, C., Kucherlapati, R., Park, P., Triche, T., Weisenberger, D., Lai, P., Bootwalla, M., Maglinte, D., Mahurkar, S., Berman, B., Van den Berg, D., Cope, L., Baylin, S., Noble, M., DiCara, D., Zhang, H., Cho, J., Heiman, D., Gehlenborg, N., Mallard, W., Lin, P., Frazer, S., Stojanov, P., Liu, Y., Zhou, L., Kim, J., Chin, L., Benz, C., Yau, C., Reynolds, S., Shmulevich, I., Vegesna, R., Kim, H., Zhang, W., Cogdell, D., Jonasch, E., Ding, Z., Lu, Y., Zhang, N., Unruh, A., Casasent, T., Wakefield, C., Tsavachidou, D., Mills, G., Schultz, N., Antipin, Y., Gao, J., Cerami, E., Gross, B., Aksoy, B., Sinha, R., Weinhold, N., Sumer, S., Taylor, B., Shen, R., Ostrovnaya, I., Berger, M., Ladanyi, M., Sander, C., Fei, S., Stout, A., Spellman, P., Rubin, D., Liu, T., Sam, N., Paull, E., Carlin, D., Goldstein, T., Waltman, P., Ellrott, K., Zhu, J., Haussler, D., Xiao, W., Shelton, C., Gardner, J., Penny, R., Sherman, M., Mallery, D., Morris, S., Paulauskis, J., Burnett, K., Shelton, T., Kaelin, W., Choueiri, T., Atkins, M., Curley, E., Tickoo, S., Thorne, L., Boice, L., Huang, M., Fisher, J., Vocke, C., Peterson, J., Worrell, R., Merino, M., Schmidt, L., Czerniak, B., Aldape, K., Wood, C., Boyd, J., Weaver, J., Iacocca, M., Petrelli, N., Witkin, G., Brown, J., Czerwinski, C., Huelsenbeck-Dill, L., Rabeno, B., Myers, J., Morrison, C., Bergsten, J., Eckman, J., Harr, J., Smith, C., Tucker, K., Zach, L., Bshara, W., Gaudioso, C., Dhir, R., Maranchie, J., Nelson, J., Parwani, A., Potapova, O., Fedosenko, K., Cheville, J., Thompson, R., Mosquera, J., Rubin, M., Blute, M., Pihl, T., Jensen, M., Sfeir, R., Kahn, A., Kothiyal, P., Snyder, E., Pontius, J., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D., Nicholls, M., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P., Alonso, S., Sanbhadti, R., Barletta, S., Pot, D., Sheth, M., Demchok, J., Davidsen, T., Wang, Z., Yang, L., Tarnuzzer, R., Zhang, J., Eley, G., Ferguson, M., Shaw, K., Guyer, M., Ozenberger, B., and Sofia, H.
- Abstract
Genetic changes underlying clear cell renal cell carcinoma(ccRCC) include alterations in genes controlling cellularoxygen sensing (for example, VHL) and the maintenance of chromatin states (for example, PBRM1). We surveyed more than 400 tumours using different genomic platforms and identified 19 significantly mutated genes. The PI(3)K/AKT pathway was recurrently mutated, suggesting this pathway as a potential therapeutic target. Widespread DNA hypomethylation was associated with mutation of the H3K36 methyltransferase SETD2, and integrative analysis suggested that mutations involving the SWI/SNF chromatin remodelling complex (PBRM1, ARID1A, SMARCA4) could have far-reaching effects on other pathways. Aggressive cancers demonstrated evidence of a metabolic shift, involving downregulation of genes involved in the TCA cycle, decreasedAMPK and PTEN protein levels, upregulation of the pentose phosphate pathway and the glutamine transporter genes, increased acetyl-CoA carboxylase protein, and altered promoter methylation of miR-21 (also known as MIR21) and GRB10. Remodelling cellular metabolism thus constitutes a recurrent pattern in ccRCC that correlates with tumour stage and severity and offers new views on the opportunities for disease treatment. © 2013 Macmillan Publishers Limited. All rights reserved.
- Published
- 2013
13. Integrated genomic characterization of endometrial carcinoma
- Author
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Getz, G., Gabriel, S., Cibulskis, K., Lander, E., Sivachenko, A., Sougnez, C., Lawrence, M., Kandoth, C., Dooling, D., Fulton, R., Fulton, L., Kalicki-Veizer, J., McLellan, M., O'Laughlin, M., Schmidt, H., Wilson, R., Ye, K., Li, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H., Dhalla, N., Guin, R., Hirst, C., Holt, R., Jones, S., Lee, D., Li, H., Marra, M., Mayo, M., Moore, R., Mungall, A., Plettner, P., Schein, J., Sipahimalani, P., Tam, A., Varhol, Richard, Gordon Robertson, A., Cherniack, A., Pashtan, I., Saksena, G., Onofrio, R., Schumacher, S., Tabak, B., Carter, S., Hernandez, B., Gentry, J., Salvesen, H., Ardlie, K., Winckler, W., Beroukhim, R., Meyerson, M., Hadjipanayis, A., Lee, S., Mahadeshwar, H., Park, P., Protopopov, A., Ren, X., Seth, S., Song, X., Tang, J., Xi, R., Yang, L., Dong, Z., Kucherlapati, R., Chin, L., Zhang, J., Todd Auman, J., Balu, S., Bodenheimer, T., Buda, E., Neil Hayes, D., Hoyle, A., Jefferys, S., Jones, C., Meng, S., Mieczkowski, P., Mose, L., Parker, J., Perou, C., Getz, G., Gabriel, S., Cibulskis, K., Lander, E., Sivachenko, A., Sougnez, C., Lawrence, M., Kandoth, C., Dooling, D., Fulton, R., Fulton, L., Kalicki-Veizer, J., McLellan, M., O'Laughlin, M., Schmidt, H., Wilson, R., Ye, K., Li, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H., Dhalla, N., Guin, R., Hirst, C., Holt, R., Jones, S., Lee, D., Li, H., Marra, M., Mayo, M., Moore, R., Mungall, A., Plettner, P., Schein, J., Sipahimalani, P., Tam, A., Varhol, Richard, Gordon Robertson, A., Cherniack, A., Pashtan, I., Saksena, G., Onofrio, R., Schumacher, S., Tabak, B., Carter, S., Hernandez, B., Gentry, J., Salvesen, H., Ardlie, K., Winckler, W., Beroukhim, R., Meyerson, M., Hadjipanayis, A., Lee, S., Mahadeshwar, H., Park, P., Protopopov, A., Ren, X., Seth, S., Song, X., Tang, J., Xi, R., Yang, L., Dong, Z., Kucherlapati, R., Chin, L., Zhang, J., Todd Auman, J., Balu, S., Bodenheimer, T., Buda, E., Neil Hayes, D., Hoyle, A., Jefferys, S., Jones, C., Meng, S., Mieczkowski, P., Mose, L., Parker, J., and Perou, C.
- Abstract
We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array-and sequencing-based technologies. Uterine serous tumours and ~25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours. © 2013 Macmillan Publishers Limited. All rights reserved.
- Published
- 2013
14. Angular momentum changing transitions in proton-Rydberg atom collisions
- Author
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Vrinceanu, D., Onofrio, R., Sadeghpour, H. R., Vrinceanu, D., Onofrio, R., and Sadeghpour, H. R.
- Abstract
Collisions between electrically charged particles and neutral atoms are central for understanding the dynamics of neutral gases and plasmas in a variety of physical situaziones of terrestrial and astronomical interest. Specifically, redistribution of angular momentum states within the degenerate shell of highly excited Rydberg atoms occurs efficiently in distant collisions with ions. This process is crucial in establishing the validity of the local thermal equilibrium assumption and may also play a role in determining a precise ionization fraction in primordial recombination. We provide an accurate expression for the non-perturbative rate coefficient of collsions between protons and H(n_l) ending in a final state H(n_l'), with n being the principal quantum number and l,l' the initial and final angular momentum quantum numbers, respectively. The validity of this result is confirmed by results of classical trajectory Monte Carlo simulations. Previous results, obtained by Pengelly and Seaton only for dipole-allowed transitions, l--->l+-1, overestimate the l-changing collisional rate approximately by a factor of six, and the physical origin of this overestimation is discussed., Comment: 19 pages, 3 figures
- Published
- 2012
- Full Text
- View/download PDF
15. Angular momentum changing transitions in proton-Rydberg atom collisions
- Author
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Vrinceanu, D., Onofrio, R., Sadeghpour, H. R., Vrinceanu, D., Onofrio, R., and Sadeghpour, H. R.
- Abstract
Collisions between electrically charged particles and neutral atoms are central for understanding the dynamics of neutral gases and plasmas in a variety of physical situaziones of terrestrial and astronomical interest. Specifically, redistribution of angular momentum states within the degenerate shell of highly excited Rydberg atoms occurs efficiently in distant collisions with ions. This process is crucial in establishing the validity of the local thermal equilibrium assumption and may also play a role in determining a precise ionization fraction in primordial recombination. We provide an accurate expression for the non-perturbative rate coefficient of collsions between protons and H(n_l) ending in a final state H(n_l'), with n being the principal quantum number and l,l' the initial and final angular momentum quantum numbers, respectively. The validity of this result is confirmed by results of classical trajectory Monte Carlo simulations. Previous results, obtained by Pengelly and Seaton only for dipole-allowed transitions, l--->l+-1, overestimate the l-changing collisional rate approximately by a factor of six, and the physical origin of this overestimation is discussed., Comment: 19 pages, 3 figures
- Published
- 2012
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16. Comprehensive molecular portraits of human breast tumours
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Koboldt, D., Fulton, R., McLellan, M., Schmidt, H., Kalicki-Veizer, J., McMichael, J., Fulton, L., Dooling, D., Ding, L., Mardis, E., Wilson, R., Ally, A., Balasundaram, M., Butterfield, Y., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H., Coope, R., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Mungall, A., Pleasance, E., Robertson, A., Schein, J., Shafiei, A., Sipahimalani, P., Slobodan, J., Stoll, D., Tam, A., Thiessen, N., Varhol, Richard, Wye, N., Zeng, T., Zhao, Y., Birol, I., Jones, S., Marra, M., Cherniack, A., Saksena, G., Onofrio, R., Pho, N., Carter, S., Schumacher, S., Tabak, B., Hernandez, B., Gentry, J., Nguyen, H., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Getz, G., Gabriel, S., Meyerson, M., Chin, L., Kucherlapati, R., Hoadley, K., Auman, J., Fan, C., Turman, Y., Shi, Y., Li, L., Topal, M., He, X., Chao, H., Prat, A., Silva, G., Iglesia, M., Koboldt, D., Fulton, R., McLellan, M., Schmidt, H., Kalicki-Veizer, J., McMichael, J., Fulton, L., Dooling, D., Ding, L., Mardis, E., Wilson, R., Ally, A., Balasundaram, M., Butterfield, Y., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H., Coope, R., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Mungall, A., Pleasance, E., Robertson, A., Schein, J., Shafiei, A., Sipahimalani, P., Slobodan, J., Stoll, D., Tam, A., Thiessen, N., Varhol, Richard, Wye, N., Zeng, T., Zhao, Y., Birol, I., Jones, S., Marra, M., Cherniack, A., Saksena, G., Onofrio, R., Pho, N., Carter, S., Schumacher, S., Tabak, B., Hernandez, B., Gentry, J., Nguyen, H., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Getz, G., Gabriel, S., Meyerson, M., Chin, L., Kucherlapati, R., Hoadley, K., Auman, J., Fan, C., Turman, Y., Shi, Y., Li, L., Topal, M., He, X., Chao, H., Prat, A., Silva, G., and Iglesia, M.
- Abstract
We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at.10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the luminal A subtype. We identified two novel protein-expression-defined subgroups, possibly produced by stromal/microenvironmental elements, and integrated analyses identified specific signalling pathways dominant in each molecular subtype including a HER2/phosphorylated HER2/EGFR/phosphorylated EGFR signature within the HER2-enriched expression subtype. Comparison of basal-like breast tumours with high-grade serous ovarian tumours showed many molecular commonalities, indicating a related aetiology and similar therapeutic opportunities. The biological finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biological subtypes of breast cancer. © 2012 Macmillan Publishers Limited. All rights reserved.
- Published
- 2012
17. Comprehensive molecular characterization of human colon and rectal cancer
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Muzny, D., Bainbridge, M., Chang, K., Dinh, H., Drummond, J., Fowler, G., Kovar, C., Lewis, L., Morgan, M., Newsham, I., Reid, J., Santibanez, J., Shinbrot, E., Trevino, L., Wu, Y., Wang, M., Gunaratne, P., Donehower, L., Creighton, C., Wheeler, D., Gibbs, R., Lawrence, M., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E., Gabriel, S., Ding, L., Fulton, R., Koboldt, D., Wylie, T., Walker, J., Dooling, D., Fulton, L., Delehaunty, K., Fronick, C., Demeter, R., Mardis, E., Wilson, R., Chu, A., Chun, H., Mungall, A., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y., Chuah, E., Coope, R., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Schein, J., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Zeng, T., Zhao, Y., Jones, S., Marra, M., Bass, A., Ramos, A., Saksena, G., Cherniack, A., Schumacher, S., Tabak, B., Carter, S., Pho, N., Nguyen, H., Onofrio, R., Crenshaw, A., Ardlie, K., Muzny, D., Bainbridge, M., Chang, K., Dinh, H., Drummond, J., Fowler, G., Kovar, C., Lewis, L., Morgan, M., Newsham, I., Reid, J., Santibanez, J., Shinbrot, E., Trevino, L., Wu, Y., Wang, M., Gunaratne, P., Donehower, L., Creighton, C., Wheeler, D., Gibbs, R., Lawrence, M., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E., Gabriel, S., Ding, L., Fulton, R., Koboldt, D., Wylie, T., Walker, J., Dooling, D., Fulton, L., Delehaunty, K., Fronick, C., Demeter, R., Mardis, E., Wilson, R., Chu, A., Chun, H., Mungall, A., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y., Chuah, E., Coope, R., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Schein, J., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Zeng, T., Zhao, Y., Jones, S., Marra, M., Bass, A., Ramos, A., Saksena, G., Cherniack, A., Schumacher, S., Tabak, B., Carter, S., Pho, N., Nguyen, H., Onofrio, R., Crenshaw, A., and Ardlie, K.
- Abstract
To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase µ (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression. © 2012 Macmillan Publishers Limited. All rights reserved.
- Published
- 2012
18. Comprehensive genomic characterization of squamous cell lung cancers
- Author
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Hammerman, P., Voet, D., Lawrence, M., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E., Gabriel, S., Getz, G., Imielinski, M., Helman, E., Hernandez, B., Pho, N., Meyerson, M., Chu, A., Hye-Chun, J., Mungall, A., Pleasance, E., Robertson, A., Sipahimalani, P., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y., Chuah, E., Coope, R., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Mungall, K., Nip, K., Olshen, A., Schein, J., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Zeng, T., Zhao, Y., Jones, S., Marra, M., Saksena, G., Cherniack, A., Schumacher, S., Tabak, B., Carter, S., Nguyen, H., Onofrio, R., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Protopopov, A., Zhang, J., Hadjipanayis, A., Lee, S., Xi, R., Yang, L., Ren, X., Zhang, H., Shukla, S., Chen, P., Haseley, P., Lee, E., Chin, L., Hammerman, P., Voet, D., Lawrence, M., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E., Gabriel, S., Getz, G., Imielinski, M., Helman, E., Hernandez, B., Pho, N., Meyerson, M., Chu, A., Hye-Chun, J., Mungall, A., Pleasance, E., Robertson, A., Sipahimalani, P., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y., Chuah, E., Coope, R., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Mungall, K., Nip, K., Olshen, A., Schein, J., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Zeng, T., Zhao, Y., Jones, S., Marra, M., Saksena, G., Cherniack, A., Schumacher, S., Tabak, B., Carter, S., Nguyen, H., Onofrio, R., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Protopopov, A., Zhang, J., Hadjipanayis, A., Lee, S., Xi, R., Yang, L., Ren, X., Zhang, H., Shukla, S., Chen, P., Haseley, P., Lee, E., and Chin, L.
- Abstract
Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers. © 2012 Macmillan Publishers Limited. All rights reserved.
- Published
- 2012
19. Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse
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Wade, C. M., Giulotto, E., Sigurdsson, Snaevar, Zoli, M., Gnerre, S., Imsland, Freyja, Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., Bloecker, H., Distl, O., Edgar, R. C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J. N., Penedo, M. C. T., Raison, J. M., Sharpe, T., Vogel, J., Andersson, Leif, Antczak, D. F., Biagi, T., Binns, M. M., Chowdhary, B. P., Coleman, S. J., Della Valle, G., Fryc, S., Guerin, G., Hasegawa, T., Hill, E. W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J. R., Murray, J., Nergadze, S. G., Onofrio, R., Pedroni, S., Piras, M. F., Raudsepp, T., Rocchi, M., Roed, K. H., Ryder, O. A., Searle, S., Skow, L., Swinburne, J. E., Syvänen, A. C., Tozaki, T., Valberg, S. J., Vaudin, M., White, J. R., Zody, Michael C., Lander, E. S., Lindblad-Toh, Kerstin, Wade, C. M., Giulotto, E., Sigurdsson, Snaevar, Zoli, M., Gnerre, S., Imsland, Freyja, Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., Bloecker, H., Distl, O., Edgar, R. C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J. N., Penedo, M. C. T., Raison, J. M., Sharpe, T., Vogel, J., Andersson, Leif, Antczak, D. F., Biagi, T., Binns, M. M., Chowdhary, B. P., Coleman, S. J., Della Valle, G., Fryc, S., Guerin, G., Hasegawa, T., Hill, E. W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J. R., Murray, J., Nergadze, S. G., Onofrio, R., Pedroni, S., Piras, M. F., Raudsepp, T., Rocchi, M., Roed, K. H., Ryder, O. A., Searle, S., Skow, L., Swinburne, J. E., Syvänen, A. C., Tozaki, T., Valberg, S. J., Vaudin, M., White, J. R., Zody, Michael C., Lander, E. S., and Lindblad-Toh, Kerstin
- Abstract
We report a high-quality draft sequence of the genome of the horse ( Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.
- Published
- 2009
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20. Reply to 'Comment on 'Anomalies in electrostatic calibrations for the measurement of the Casimir force in a sphere-plane geometry''
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Kim, W. J., Brown-Hayes, M., Dalvit, D. A. R., Brownell, J. H., Onofrio, R., Kim, W. J., Brown-Hayes, M., Dalvit, D. A. R., Brownell, J. H., and Onofrio, R.
- Abstract
In a recent Comment, Decca et al. [Phys. Rev. A 79, 026101 (2009); arXiv:0809.3576] discussed the origin of the anomalies recently reported by us in Phys. Rev. A 78, 036102(R) (2008); arXiv:0812.0028 . Here we restate our view, corroborated by their considerations, that quantitative geometrical and electrostatic characterizations of the conducting surfaces (a topic not discussed explicitly in the literature until very recently) are critical for the assessment of precision and accuracy of the demonstration of the Casimir force and for deriving meaningful limits on the existence of Yukawian components possibly superimposed to the Newtonian gravitational interaction., Comment: Reply to Comment posted as arXiv:0809.3576, requested from Phys. Rev. A on December 3, 2008, accepted January 20, 2009
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- 2009
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21. On electrostatic and Casimir force measurements between conducting surfaces in a sphere-plane configuration
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Kim, W. J., Brown-Hayes, M., Dalvit, D. A. R., Brownell, J. H., Onofrio, R., Kim, W. J., Brown-Hayes, M., Dalvit, D. A. R., Brownell, J. H., and Onofrio, R.
- Abstract
We report on measurements of forces acting between two conducting surfaces in a spherical-plane configuration in the 35 nm-1 micrometer separation range. The measurements are obtained by performing electrostatic calibrations followed by a residual analysis after subtracting the electrostatic-dependent component. We find in all runs optimal fitting of the calibrations for exponents smaller than the one predicted by electrostatics for an ideal sphere-plane geometry. We also find that the external bias potential necessary to minimize the electrostatic contribution depends on the sphere-plane distance. In spite of these anomalies, by implementing a parametrixation-dependent subtraction of the electrostatic contribution we have found evidence for short-distance attractive forces of magnitude comparable to the expected Casimir-Lifshitz force. We finally discuss the relevance of our findings in the more general context of Casimir-Lifshitz force measurements, with particular regard to the critical issues of the electrical and geometrical characterization of the involved surfaces., Comment: 22 pages, 15 figures
- Published
- 2008
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22. Anomalies in electrostatic calibrations for the measurement of the Casimir force in a sphere-plane geometry
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Kim, W. J., Brown-Hayes, M., Dalvit, D. A. R., Brownell, J. H., Onofrio, R., Kim, W. J., Brown-Hayes, M., Dalvit, D. A. R., Brownell, J. H., and Onofrio, R.
- Abstract
We have performed precision electrostatic calibrations in the sphere-plane geometry and observed anomalous behavior. Namely, the scaling exponent of the electrostatic signal with distance was found to be smaller than expected on the basis of the pure Coulombian contribution and the residual potential found to be distance dependent. We argue that these findings affect the accuracy of the electrostatic calibrations and invite reanalysis of previous determinations of the Casimir force., Comment: 4 pages, 4 figures
- Published
- 2008
- Full Text
- View/download PDF
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