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1. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Mallick, S, Li, H, Lipson, M, Mathieson, I, Gymrek, M, Racimo, F, Zhao, M, Chennagiri, N, Nordenfelt, S, Tandon, A, Skoglund, P, Lazaridis, I, Sankararaman, S, Fu, Q, Rohland, N, Renaud, G, Erlich, Y, Willems, T, Gallo, C, Spence, JP, Song, YS, Poletti, G, Balloux, F, van Driem, G, de Knijff, P, Romero, IG, Jha, AR, Behar, DM, Bravi, CM, Capelli, C, Hervig, T, Moreno-Estrada, A, Posukh, OL, Balanovska, E, Balanovsky, O, Karachanak-Yankova, S, Sahakyan, H, Toncheva, D, Yepiskoposyan, L, Tyler-Smith, C, Xue, Y, Abdullah, MS, Ruiz-Linares, A, Beall, CM, Di Rienzo, A, Jeong, C, Starikovskaya, EB, Metspalu, E, Parik, J, Villems, R, Henn, BM, Hodoglugil, U, Mahley, R, Sajantila, A, Stamatoyannopoulos, G, Wee, JTS, Khusainova, R, Khusnutdinova, E, Litvinov, S, Ayodo, G, Comas, D, Hammer, MF, Kivisild, T, Klitz, W, Winkler, CA, Labuda, D, Bamshad, M, Jorde, LB, Tishkoff, SA, Watkins, WS, Metspalu, M, Dryomov, S, Sukernik, R, Singh, L, Thangaraj, K, Paeaebo, S, Kelso, J, Patterson, N, Reich, D, Mallick, S, Li, H, Lipson, M, Mathieson, I, Gymrek, M, Racimo, F, Zhao, M, Chennagiri, N, Nordenfelt, S, Tandon, A, Skoglund, P, Lazaridis, I, Sankararaman, S, Fu, Q, Rohland, N, Renaud, G, Erlich, Y, Willems, T, Gallo, C, Spence, JP, Song, YS, Poletti, G, Balloux, F, van Driem, G, de Knijff, P, Romero, IG, Jha, AR, Behar, DM, Bravi, CM, Capelli, C, Hervig, T, Moreno-Estrada, A, Posukh, OL, Balanovska, E, Balanovsky, O, Karachanak-Yankova, S, Sahakyan, H, Toncheva, D, Yepiskoposyan, L, Tyler-Smith, C, Xue, Y, Abdullah, MS, Ruiz-Linares, A, Beall, CM, Di Rienzo, A, Jeong, C, Starikovskaya, EB, Metspalu, E, Parik, J, Villems, R, Henn, BM, Hodoglugil, U, Mahley, R, Sajantila, A, Stamatoyannopoulos, G, Wee, JTS, Khusainova, R, Khusnutdinova, E, Litvinov, S, Ayodo, G, Comas, D, Hammer, MF, Kivisild, T, Klitz, W, Winkler, CA, Labuda, D, Bamshad, M, Jorde, LB, Tishkoff, SA, Watkins, WS, Metspalu, M, Dryomov, S, Sukernik, R, Singh, L, Thangaraj, K, Paeaebo, S, Kelso, J, Patterson, N, and Reich, D

Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Published
2016

2. Correction: Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry.

Author

Viollet, L, Glusman, G, Murphy, KJ, Newcomb, TM, Reyna, SP, Sweney, M, Nelson, B, Andermann, F, Andermann, E, Acsadi, G, Barbano, RL, Brown, C, Brunkow, ME, Chugani, HT, Cheyette, SR, Collins, A, DeBrosse, SD, Galas, D, Friedman, J, Hood, L, Huff, C, Jorde, LB, King, MD, LaSalle, B, Leventer, RJ, Lewelt, AJ, Massart, MB, Mérida, MR, Ptáček, LJ, Roach, JC, Rust, RS, Renault, F, Sanger, TD, Sotero de Menezes, MA, Tennyson, R, Uldall, P, Zhang, Y, Zupanc, M, Xin, W, Silver, K, Swoboda, KJ, Viollet, L, Glusman, G, Murphy, KJ, Newcomb, TM, Reyna, SP, Sweney, M, Nelson, B, Andermann, F, Andermann, E, Acsadi, G, Barbano, RL, Brown, C, Brunkow, ME, Chugani, HT, Cheyette, SR, Collins, A, DeBrosse, SD, Galas, D, Friedman, J, Hood, L, Huff, C, Jorde, LB, King, MD, LaSalle, B, Leventer, RJ, Lewelt, AJ, Massart, MB, Mérida, MR, Ptáček, LJ, Roach, JC, Rust, RS, Renault, F, Sanger, TD, Sotero de Menezes, MA, Tennyson, R, Uldall, P, Zhang, Y, Zupanc, M, Xin, W, Silver, K, and Swoboda, KJ

Published
2015

3. Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry

Author

Zhou, F, Viollet, L, Glusman, G, Murphy, KJ, Newcomb, TM, Reyna, SP, Sweney, M, Nelson, B, Andermann, F, Andermann, E, Acsadi, G, Barbano, RL, Brown, C, Brunkow, ME, Chugani, HT, Cheyette, SR, Collins, A, DeBrosse, SD, Galas, D, Friedman, J, Hood, L, Huff, C, Jorde, LB, King, MD, LaSalle, B, Leventer, RJ, Lewelt, AJ, Massart, MB, Merida, MR, Ptacek, LJ, Roach, JC, Rust, RS, Renault, F, Sanger, TD, de Menezes, MAS, Tennyson, R, Uldall, P, Zhang, Y, Zupanc, M, Xin, W, Silver, K, Swoboda, KJ, Zhou, F, Viollet, L, Glusman, G, Murphy, KJ, Newcomb, TM, Reyna, SP, Sweney, M, Nelson, B, Andermann, F, Andermann, E, Acsadi, G, Barbano, RL, Brown, C, Brunkow, ME, Chugani, HT, Cheyette, SR, Collins, A, DeBrosse, SD, Galas, D, Friedman, J, Hood, L, Huff, C, Jorde, LB, King, MD, LaSalle, B, Leventer, RJ, Lewelt, AJ, Massart, MB, Merida, MR, Ptacek, LJ, Roach, JC, Rust, RS, Renault, F, Sanger, TD, de Menezes, MAS, Tennyson, R, Uldall, P, Zhang, Y, Zupanc, M, Xin, W, Silver, K, and Swoboda, KJ

Abstract

Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers' questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clusteredin exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K(26%) and 11 had G947R (8%) mutations [corrected].Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.

Published
2015

4. Alternating hemiplegia of childhood: Retrospective genetic study and genotype-phenotype correlations in 187 subjects from the US AHCF registry

Author

Viollet, L, Glusman, G, Murphy, KJ, Newcomb, TM, Reyna, SP, Sweney, M, Nelson, B, Andermann, F, Andermann, E, Acsadi, G, Barbano, RL, Brown, C, Brunkow, ME, Chugani, HT, Cheyette, SR, Collins, A, DeBrosse, SD, Galas, D, Friedman, J, Hood, L, Huff, C, Jorde, LB, King, MD, LaSalle, B, Leventer, RJ, Lewelt, AJ, Massart, MB, Mérida, MR, Ptáček, LJ, Roach, JC, Rust, RS, Renault, F, Sanger, TD, De Menezes, MAS, Tennyson, R, Uldall, P, Zhang, Y, Zupanc, M, Xin, W, Silver, K, Swoboda, KJ, Viollet, L, Glusman, G, Murphy, KJ, Newcomb, TM, Reyna, SP, Sweney, M, Nelson, B, Andermann, F, Andermann, E, Acsadi, G, Barbano, RL, Brown, C, Brunkow, ME, Chugani, HT, Cheyette, SR, Collins, A, DeBrosse, SD, Galas, D, Friedman, J, Hood, L, Huff, C, Jorde, LB, King, MD, LaSalle, B, Leventer, RJ, Lewelt, AJ, Massart, MB, Mérida, MR, Ptáček, LJ, Roach, JC, Rust, RS, Renault, F, Sanger, TD, De Menezes, MAS, Tennyson, R, Uldall, P, Zhang, Y, Zupanc, M, Xin, W, Silver, K, and Swoboda, KJ

Abstract

Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers' questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clustered in exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K (26%) and 11 had G937R (8%) mutations. Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.

Published
2015

5. Alternating hemiplegia of childhood: Retrospective genetic study and genotype-phenotype correlations in 187 subjects from the US AHCF registry

Author

Viollet, L, Glusman, G, Murphy, KJ, Newcomb, TM, Reyna, SP, Sweney, M, Nelson, B, Andermann, F, Andermann, E, Acsadi, G, Barbano, RL, Brown, C, Brunkow, ME, Chugani, HT, Cheyette, SR, Collins, A, DeBrosse, SD, Galas, D, Friedman, J, Hood, L, Huff, C, Jorde, LB, King, MD, LaSalle, B, Leventer, RJ, Lewelt, AJ, Massart, MB, Mérida, MR, Ptáček, LJ, Roach, JC, Rust, RS, Renault, F, Sanger, TD, De Menezes, MAS, Tennyson, R, Uldall, P, Zhang, Y, Zupanc, M, Xin, W, Silver, K, Swoboda, KJ, Viollet, L, Glusman, G, Murphy, KJ, Newcomb, TM, Reyna, SP, Sweney, M, Nelson, B, Andermann, F, Andermann, E, Acsadi, G, Barbano, RL, Brown, C, Brunkow, ME, Chugani, HT, Cheyette, SR, Collins, A, DeBrosse, SD, Galas, D, Friedman, J, Hood, L, Huff, C, Jorde, LB, King, MD, LaSalle, B, Leventer, RJ, Lewelt, AJ, Massart, MB, Mérida, MR, Ptáček, LJ, Roach, JC, Rust, RS, Renault, F, Sanger, TD, De Menezes, MAS, Tennyson, R, Uldall, P, Zhang, Y, Zupanc, M, Xin, W, Silver, K, and Swoboda, KJ

Abstract

Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers' questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clustered in exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K (26%) and 11 had G937R (8%) mutations. Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.

Published
2015

6. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood

Author

Heinzen, EL, Swoboda, KJ, Hitomi, Y, Gurrieri, F, Nicole, S, de Vries, B, Tiziano, FD, Fontaine, B, Walley, NM, Heavin, S, Panagiotakaki, E, Fiori, S, Abiusi, E, Di Pietro, L, Sweney, MT, Newcomb, TM, Viollet, L, Huff, C, Jorde, LB, Reyna, SP, Murphy, KJ, Shianna, KV, Gumbs, CE, Little, L, Silver, K, Ptacek, LJ, Haan, J, Ferrari, MD, Bye, AM, Herkes, GK, Whitelaw, CM, Webb, D, Lynch, BJ, Uldall, P, King, MD, Scheffer, IE, Neri, G, Arzimanoglou, A, van den Maagdenberg, AMJM, Sisodiya, SM, Mikati, MA, Goldstein, DB, Heinzen, EL, Swoboda, KJ, Hitomi, Y, Gurrieri, F, Nicole, S, de Vries, B, Tiziano, FD, Fontaine, B, Walley, NM, Heavin, S, Panagiotakaki, E, Fiori, S, Abiusi, E, Di Pietro, L, Sweney, MT, Newcomb, TM, Viollet, L, Huff, C, Jorde, LB, Reyna, SP, Murphy, KJ, Shianna, KV, Gumbs, CE, Little, L, Silver, K, Ptacek, LJ, Haan, J, Ferrari, MD, Bye, AM, Herkes, GK, Whitelaw, CM, Webb, D, Lynch, BJ, Uldall, P, King, MD, Scheffer, IE, Neri, G, Arzimanoglou, A, van den Maagdenberg, AMJM, Sisodiya, SM, Mikati, MA, and Goldstein, DB

Abstract

Alternating hemiplegia of childhood (AHC) is a rare, severe neurodevelopmental syndrome characterized by recurrent hemiplegic episodes and distinct neurological manifestations. AHC is usually a sporadic disorder and has unknown etiology. We used exome sequencing of seven patients with AHC and their unaffected parents to identify de novo nonsynonymous mutations in ATP1A3 in all seven individuals. In a subsequent sequence analysis of ATP1A3 in 98 other patients with AHC, we found that ATP1A3 mutations were likely to be responsible for at least 74% of the cases; we also identified one inherited mutation in a case of familial AHC. Notably, most AHC cases are caused by one of seven recurrent ATP1A3 mutations, one of which was observed in 36 patients. Unlike ATP1A3 mutations that cause rapid-onset dystonia-parkinsonism, AHC-causing mutations in this gene caused consistent reductions in ATPase activity without affecting the level of protein expression. This work identifies de novo ATP1A3 mutations as the primary cause of AHC and offers insight into disease pathophysiology by expanding the spectrum of phenotypes associated with mutations in ATP1A3.

Published
2012

7. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood.

Author

Heinzen, El, Swoboda, Kj, Hitomi, Y, Gurrieri, Fiorella, Tiziano, Francesco Danilo, Nicole, S, Fontaine, B, De Vries, B, Walley, Nm, Heavin, S, Panagiotakaki, E, Koelewijn, S, Kamphorst, J, Geilenkirchen, M, Pelzer, N, Laan, L, Haan, J, Ferrari, Mirella, Van Den Maagdenberg, A, Fiori, S, Abiusi, E, Di Pietro, Lorena, Sweney, Mt, Newcomb, Tm, Viollet, L, Huff, C, Jorde, Lb, Reyna, Sp, Murphy, Kj, Shianna, Kv, Gumbs, Ce, Little, L, Silver, K, Ptáček, Lj, Herke, S Gk, Whitelaw, Cm, Webb, D, Lynch, Bj, Uldall, P, King, Md, Scheffer, Ie, Neri, Giovanni, Arzimanoglou, A, Sisodiya, Sm, Mikati, Ma, Goldstein, Db, Gurrieri, Fiorella (ORCID:0000-0002-6775-5972), Tiziano, Francesco Danilo (ORCID:0000-0002-5545-6158), Di Pietro, Lorena (ORCID:0000-0001-5723-2169), Heinzen, El, Swoboda, Kj, Hitomi, Y, Gurrieri, Fiorella, Tiziano, Francesco Danilo, Nicole, S, Fontaine, B, De Vries, B, Walley, Nm, Heavin, S, Panagiotakaki, E, Koelewijn, S, Kamphorst, J, Geilenkirchen, M, Pelzer, N, Laan, L, Haan, J, Ferrari, Mirella, Van Den Maagdenberg, A, Fiori, S, Abiusi, E, Di Pietro, Lorena, Sweney, Mt, Newcomb, Tm, Viollet, L, Huff, C, Jorde, Lb, Reyna, Sp, Murphy, Kj, Shianna, Kv, Gumbs, Ce, Little, L, Silver, K, Ptáček, Lj, Herke, S Gk, Whitelaw, Cm, Webb, D, Lynch, Bj, Uldall, P, King, Md, Scheffer, Ie, Neri, Giovanni, Arzimanoglou, A, Sisodiya, Sm, Mikati, Ma, Goldstein, Db, Gurrieri, Fiorella (ORCID:0000-0002-6775-5972), Tiziano, Francesco Danilo (ORCID:0000-0002-5545-6158), and Di Pietro, Lorena (ORCID:0000-0001-5723-2169)

Abstract

Alternating hemiplegia of childhood (AHC) is a rare, severe neurodevelopmental syndrome characterized by recurrent hemiplegic episodes and distinct neurological manifestations. AHC is usually a sporadic disorder and has unknown etiology. We used exome sequencing of seven patients with AHC and their unaffected parents to identify de novo nonsynonymous mutations in ATP1A3 in all seven individuals. In a subsequent sequence analysis of ATP1A3 in 98 other patients with AHC, we found that ATP1A3 mutations were likely to be responsible for at least 74% of the cases; we also identified one inherited mutation in a case of familial AHC. Notably, most AHC cases are caused by one of seven recurrent ATP1A3 mutations, one of which was observed in 36 patients. Unlike ATP1A3 mutations that cause rapid-onset dystonia-parkinsonism, AHC-causing mutations in this gene caused consistent reductions in ATPase activity without affecting the level of protein expression. This work identifies de novo ATP1A3 mutations as the primary cause of AHC and offers insight into disease pathophysiology by expanding the spectrum of phenotypes associated with mutations in ATP1A3.

Published
2012

8. The International HapMap Project

Author

Gibbs, RA, Belmont, JW, Hardenbol, P., Willis, TD, Yu, FL, Yang, HM, Ch'ang, LY, Huang, W., Liu, B., Shen, Y., Tam, PKH, Foster, MW, Jasperse, M., Knoppers, BM, Kwok, PY, Licinio, J., Long, JC, Marshall, PA, Ossorio, PN, Wang, VO, Rotimi, CN, Tsui, LC, Royal, CDM, Spallone, P., Terry, SF, Lander, ES, Lai, EH, Nickerson, DA, Abecasis, GR, Altshuler, D., Bentley, DR, Boehnke, M., Waye, MMY, Cardon, LR, Daly, MJ, Deloukas, P., Douglas, JA, Gabriel, SB, Hudson, RR, Hudson, TJ, Kruglyak, L., Nakamura, Y., Wong, JTF, Nussbaum, RL, Schaffner, SF, Sherry, ST, Stein, LD, Tanaka, T., Zeng, CQ, Zhang, QR, Chee, MS, Galver, LM, Kruglyak, S., Murray, SS, Oliphant, AR, Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, MS, Verner, A., Duan, SH, Lind, DL, Miller, RD, Rice, JP, Saccone, NL, Taillon-Miller, P., Xiao, M., Sekine, A., Sorimachi, K., Tanaka, Y., Tsunoda, T., Yoshino, E., Hunt, S., Powell, D., Qiu, RZ, Ken, A., Dunston, GM, Kato, K., Niikawa, N., Clayton, EW, Watkin, J., Sodergren, E., Weinstock, GM, Wilson, RK, Fulton, LL, Rogers, J., Birren, BW, Han, H., Wang, HG, Godbout, M., Wallenburg, JC, L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, AL, Collins, FS, Brooks, LD, McEwen, JE, Guyer, MS, Jordan, E., Peterson, JL, Spiegel, J., Sung, LM, Zacharia, LF, Kennedy, K., Dunn, MG, Seabrook, R., Shillito, M., Skene, B., Stewart, JG, Valle, DL, Jorde, LB, Chakravarti, A., Cho, MK, Duster, T., Gibbs, RA, Belmont, JW, Hardenbol, P., Willis, TD, Yu, FL, Yang, HM, Ch'ang, LY, Huang, W., Liu, B., Shen, Y., Tam, PKH, Foster, MW, Jasperse, M., Knoppers, BM, Kwok, PY, Licinio, J., Long, JC, Marshall, PA, Ossorio, PN, Wang, VO, Rotimi, CN, Tsui, LC, Royal, CDM, Spallone, P., Terry, SF, Lander, ES, Lai, EH, Nickerson, DA, Abecasis, GR, Altshuler, D., Bentley, DR, Boehnke, M., Waye, MMY, Cardon, LR, Daly, MJ, Deloukas, P., Douglas, JA, Gabriel, SB, Hudson, RR, Hudson, TJ, Kruglyak, L., Nakamura, Y., Wong, JTF, Nussbaum, RL, Schaffner, SF, Sherry, ST, Stein, LD, Tanaka, T., Zeng, CQ, Zhang, QR, Chee, MS, Galver, LM, Kruglyak, S., Murray, SS, Oliphant, AR, Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, MS, Verner, A., Duan, SH, Lind, DL, Miller, RD, Rice, JP, Saccone, NL, Taillon-Miller, P., Xiao, M., Sekine, A., Sorimachi, K., Tanaka, Y., Tsunoda, T., Yoshino, E., Hunt, S., Powell, D., Qiu, RZ, Ken, A., Dunston, GM, Kato, K., Niikawa, N., Clayton, EW, Watkin, J., Sodergren, E., Weinstock, GM, Wilson, RK, Fulton, LL, Rogers, J., Birren, BW, Han, H., Wang, HG, Godbout, M., Wallenburg, JC, L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, AL, Collins, FS, Brooks, LD, McEwen, JE, Guyer, MS, Jordan, E., Peterson, JL, Spiegel, J., Sung, LM, Zacharia, LF, Kennedy, K., Dunn, MG, Seabrook, R., Shillito, M., Skene, B., Stewart, JG, Valle, DL, Jorde, LB, Chakravarti, A., Cho, MK, and Duster, T.

Published
2003

9. The International HapMap Project

Author

Gibbs, RA, Belmont, JW, Hardenbol, P., Willis, TD, Yu, FL, Yang, HM, Ch'ang, LY, Huang, W., Liu, B., Shen, Y., Tam, PKH, Foster, MW, Jasperse, M., Knoppers, BM, Kwok, PY, Licinio, J., Long, JC, Marshall, PA, Ossorio, PN, Wang, VO, Rotimi, CN, Tsui, LC, Royal, CDM, Spallone, P., Terry, SF, Lander, ES, Lai, EH, Nickerson, DA, Abecasis, GR, Altshuler, D., Bentley, DR, Boehnke, M., Waye, MMY, Cardon, LR, Daly, MJ, Deloukas, P., Douglas, JA, Gabriel, SB, Hudson, RR, Hudson, TJ, Kruglyak, L., Nakamura, Y., Wong, JTF, Nussbaum, RL, Schaffner, SF, Sherry, ST, Stein, LD, Tanaka, T., Zeng, CQ, Zhang, QR, Chee, MS, Galver, LM, Kruglyak, S., Murray, SS, Oliphant, AR, Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, MS, Verner, A., Duan, SH, Lind, DL, Miller, RD, Rice, JP, Saccone, NL, Taillon-Miller, P., Xiao, M., Sekine, A., Sorimachi, K., Tanaka, Y., Tsunoda, T., Yoshino, E., Hunt, S., Powell, D., Qiu, RZ, Ken, A., Dunston, GM, Kato, K., Niikawa, N., Clayton, EW, Watkin, J., Sodergren, E., Weinstock, GM, Wilson, RK, Fulton, LL, Rogers, J., Birren, BW, Han, H., Wang, HG, Godbout, M., Wallenburg, JC, L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, AL, Collins, FS, Brooks, LD, McEwen, JE, Guyer, MS, Jordan, E., Peterson, JL, Spiegel, J., Sung, LM, Zacharia, LF, Kennedy, K., Dunn, MG, Seabrook, R., Shillito, M., Skene, B., Stewart, JG, Valle, DL, Jorde, LB, Chakravarti, A., Cho, MK, Duster, T., Gibbs, RA, Belmont, JW, Hardenbol, P., Willis, TD, Yu, FL, Yang, HM, Ch'ang, LY, Huang, W., Liu, B., Shen, Y., Tam, PKH, Foster, MW, Jasperse, M., Knoppers, BM, Kwok, PY, Licinio, J., Long, JC, Marshall, PA, Ossorio, PN, Wang, VO, Rotimi, CN, Tsui, LC, Royal, CDM, Spallone, P., Terry, SF, Lander, ES, Lai, EH, Nickerson, DA, Abecasis, GR, Altshuler, D., Bentley, DR, Boehnke, M., Waye, MMY, Cardon, LR, Daly, MJ, Deloukas, P., Douglas, JA, Gabriel, SB, Hudson, RR, Hudson, TJ, Kruglyak, L., Nakamura, Y., Wong, JTF, Nussbaum, RL, Schaffner, SF, Sherry, ST, Stein, LD, Tanaka, T., Zeng, CQ, Zhang, QR, Chee, MS, Galver, LM, Kruglyak, S., Murray, SS, Oliphant, AR, Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, MS, Verner, A., Duan, SH, Lind, DL, Miller, RD, Rice, JP, Saccone, NL, Taillon-Miller, P., Xiao, M., Sekine, A., Sorimachi, K., Tanaka, Y., Tsunoda, T., Yoshino, E., Hunt, S., Powell, D., Qiu, RZ, Ken, A., Dunston, GM, Kato, K., Niikawa, N., Clayton, EW, Watkin, J., Sodergren, E., Weinstock, GM, Wilson, RK, Fulton, LL, Rogers, J., Birren, BW, Han, H., Wang, HG, Godbout, M., Wallenburg, JC, L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, AL, Collins, FS, Brooks, LD, McEwen, JE, Guyer, MS, Jordan, E., Peterson, JL, Spiegel, J., Sung, LM, Zacharia, LF, Kennedy, K., Dunn, MG, Seabrook, R., Shillito, M., Skene, B., Stewart, JG, Valle, DL, Jorde, LB, Chakravarti, A., Cho, MK, and Duster, T.

Published
2003

10. The International HapMap Project

Author

Gibbs, RA, Belmont, JW, Hardenbol, P., Willis, TD, Yu, FL, Yang, HM, Ch'ang, LY, Huang, W., Liu, B., Shen, Y., Tam, PKH, Foster, MW, Jasperse, M., Knoppers, BM, Kwok, PY, Licinio, J., Long, JC, Marshall, PA, Ossorio, PN, Wang, VO, Rotimi, CN, Tsui, LC, Royal, CDM, Spallone, P., Terry, SF, Lander, ES, Lai, EH, Nickerson, DA, Abecasis, GR, Altshuler, D., Bentley, DR, Boehnke, M., Waye, MMY, Cardon, LR, Daly, MJ, Deloukas, P., Douglas, JA, Gabriel, SB, Hudson, RR, Hudson, TJ, Kruglyak, L., Nakamura, Y., Wong, JTF, Nussbaum, RL, Schaffner, SF, Sherry, ST, Stein, LD, Tanaka, T., Zeng, CQ, Zhang, QR, Chee, MS, Galver, LM, Kruglyak, S., Murray, SS, Oliphant, AR, Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, MS, Verner, A., Duan, SH, Lind, DL, Miller, RD, Rice, JP, Saccone, NL, Taillon-Miller, P., Xiao, M., Sekine, A., Sorimachi, K., Tanaka, Y., Tsunoda, T., Yoshino, E., Hunt, S., Powell, D., Qiu, RZ, Ken, A., Dunston, GM, Kato, K., Niikawa, N., Clayton, EW, Watkin, J., Sodergren, E., Weinstock, GM, Wilson, RK, Fulton, LL, Rogers, J., Birren, BW, Han, H., Wang, HG, Godbout, M., Wallenburg, JC, L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, AL, Collins, FS, Brooks, LD, McEwen, JE, Guyer, MS, Jordan, E., Peterson, JL, Spiegel, J., Sung, LM, Zacharia, LF, Kennedy, K., Dunn, MG, Seabrook, R., Shillito, M., Skene, B., Stewart, JG, Valle, DL, Jorde, LB, Chakravarti, A., Cho, MK, Duster, T., Gibbs, RA, Belmont, JW, Hardenbol, P., Willis, TD, Yu, FL, Yang, HM, Ch'ang, LY, Huang, W., Liu, B., Shen, Y., Tam, PKH, Foster, MW, Jasperse, M., Knoppers, BM, Kwok, PY, Licinio, J., Long, JC, Marshall, PA, Ossorio, PN, Wang, VO, Rotimi, CN, Tsui, LC, Royal, CDM, Spallone, P., Terry, SF, Lander, ES, Lai, EH, Nickerson, DA, Abecasis, GR, Altshuler, D., Bentley, DR, Boehnke, M., Waye, MMY, Cardon, LR, Daly, MJ, Deloukas, P., Douglas, JA, Gabriel, SB, Hudson, RR, Hudson, TJ, Kruglyak, L., Nakamura, Y., Wong, JTF, Nussbaum, RL, Schaffner, SF, Sherry, ST, Stein, LD, Tanaka, T., Zeng, CQ, Zhang, QR, Chee, MS, Galver, LM, Kruglyak, S., Murray, SS, Oliphant, AR, Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Phillips, MS, Verner, A., Duan, SH, Lind, DL, Miller, RD, Rice, JP, Saccone, NL, Taillon-Miller, P., Xiao, M., Sekine, A., Sorimachi, K., Tanaka, Y., Tsunoda, T., Yoshino, E., Hunt, S., Powell, D., Qiu, RZ, Ken, A., Dunston, GM, Kato, K., Niikawa, N., Clayton, EW, Watkin, J., Sodergren, E., Weinstock, GM, Wilson, RK, Fulton, LL, Rogers, J., Birren, BW, Han, H., Wang, HG, Godbout, M., Wallenburg, JC, L'Archeveque, P., Bellemare, G., Todani, K., Fujita, T., Tanaka, S., Holden, AL, Collins, FS, Brooks, LD, McEwen, JE, Guyer, MS, Jordan, E., Peterson, JL, Spiegel, J., Sung, LM, Zacharia, LF, Kennedy, K., Dunn, MG, Seabrook, R., Shillito, M., Skene, B., Stewart, JG, Valle, DL, Jorde, LB, Chakravarti, A., Cho, MK, and Duster, T.

Published
2003

13. The spectrum of mutations in TBX3: Genotype phenotype relationship in ulnar-mammary syndrome

Author

UCL, Bamshad, M, Le, T, Watkins, WS, Dixon, ME, Kramer, BE, Roeder, AD, Carey, JC, Root, S, Schinzel, A, Van Maldergem, L., Gardner, RJM, Lin, RC, Seidman, CE, Seidman, JG, Wallerstein, R, Moran, E, Sutphen, R, Campbell, CE, Jorde, LB, UCL, Bamshad, M, Le, T, Watkins, WS, Dixon, ME, Kramer, BE, Roeder, AD, Carey, JC, Root, S, Schinzel, A, Van Maldergem, L., Gardner, RJM, Lin, RC, Seidman, CE, Seidman, JG, Wallerstein, R, Moran, E, Sutphen, R, Campbell, CE, and Jorde, LB

Abstract

Ulnar-mammary syndrome (UMS) is a pleiotropic disorder affecting limb, apocrine-gland, tooth, hair, and genital development. Mutations that disrupt the DNA-binding-domain of the T-box gene, TBX3, have been demonstrated-to cause UMS. However, the 3' terminus of the open reading frame(ORF) of TBX3 was not identified, and mutations were detected in only two families with UMS. Furthermore, no substantial homology outside the T-box was found among TBX3 and its orthologues. The subsequent cloning of new TBX3 cDNAs allowed us to complete the characterization of TBX3 and to identify alternatively transcribed TBX3 transcripts, including one that interrupts the T-box. The complete ORF of TBX3 is predicted to encode a 723-residue protein, of which 255 amino acids are encoded by newly identified exons. Comparison of other T-box genes to TBX3 indicates regions of substantial homology outside the DNA-binding domain. Novel mutations have been found in all-of eight newly reported families with UMS, including five mutations downstream of the region encoding the T-box. This suggests that a domain(s) outside the T-box is highly conserved and important for the function of TBX3. We found no obvious phenotypic differences between those who have missense mutations and those who have deletions or frameshifts.

Published
1999

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