YFull: Articles (720) | SEARCH (Samples) |
Feder,J., Blech,I., Ovadia,O., Amar,S., Wainstein,J., Raz,I., Dadon,S., Arking,D.E., Glaser,B. and Mishmar,D.
BMC Genomics 9, 198 (2008)
Publication Status: Online-Only
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Friedlaender,J., Schurr,T., Gentz,F., Koki,G., Friedlaender,F., Horvat,G., Babb,P., Cerchio,S., Kaestle,F., Schanfield,M., Deka,R., Yanagihara,R. and Merriwether,D.A.
Mol. Biol. Evol. 22 (6), 1506-1517 (2005)
Erratum:[Mol Biol Evol. 2005 Nov;22(11):2313]
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Zaragoza,M.V., Brandon,M.C., Diegoli,M., Arbustini,E. and Wallace,D.C.
Eur. J. Hum. Genet. (2010) In press
Publication Status: Available-Online prior to print
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Loo,J.H., Trejaut,J.A., Yen,J.C., Chen,Z.S., Lee,C.L. and Lin,M.
BMC Genet. 12, 21 (2011)
Publication Status: Online-Only
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Fregel,R., Pestano,J., Arnay,M., Cabrera,V.M., Larruga,J.M. and Gonzalez,A.M.
Eur. J. Hum. Genet. 17 (10), 1314-1324 (2009)
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Gonzalez,A.M., Garcia,O., Larruga,J.M. and Cabrera,V.M.
BMC Genomics 7, 124 (2006)
Publication Status: Online-Only
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Thangaraj,K., Chaubey,G., Singh,V.K., Vanniarajan,A., Thanseem,I., Reddy,A.G. and Singh,L.
BMC Genomics 7, 151 (2006)
Publication Status: Online-Only
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Soini,H.K., Vaisanen,A., Karppa,M., Hinttala,R., Kytovuori,L., Moilanen,J.S., Uusimaa,J. and Majamaa,K.
BMC Med. Genet. 18 (1), 14 (2017)
Publication Status: Online-Only
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Gonzalez,A.M., Larruga,J.M., Abu-Amero,K.K., Shi,Y., Pestano,J. and Cabrera,V.M.
BMC Genomics 8 (1), 223 (2007)
Publication Status: Available-Online prior to print
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Lopez-Gallardo,E., Emperador,S., Hernandez-Ainsa,C., Montoya,J., Bayona-Bafaluy,M.P. and Ruiz-Pesini,E.
Food Chem. Toxicol. 120, 89-97 (2018)
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Peng,M.S., Quang,H.H., Dang,K.P., Trieu,A.V., Wang,H.W., Yao,Y.G., Kong,Q.P. and Zhang,Y.P.
Mol. Biol. Evol. 27 (10), 2417-2430 (2010)
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Tian,J.Y., Wang,H.W., Li,Y.C., Zhang,W., Yao,Y.G., van Straten,J., Richards,M.B. and Kong,Q.P.
Sci Rep 5, 8377 (2015)
Publication Status: Online-Only
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Maasz,A., Komlosi,K., Hadzsiev,K., Szabo,Z., Willems,P.J., Gerlinger,I., Kosztolanyi,G., Mehes,K. and Melegh,B.
Curr. Med. Chem. 15 (13), 1257-1262 (2008)
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Sylvester,C., Krishna,M.S., Rao,J.S. and Chandrasekar,A.
Genetica 146 (4-5), 383-389 (2018)
Erratum:[Genetica. 2018 Sep 10;:. PMID: 30203139]
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Zhang,A.M., Bandelt,H.J., Jia,X., Zhang,W., Li,S., Yu,D., Wang,D., Zhuang,X.Y., Zhang,Q. and Yao,Y.G.
PLoS ONE 6 (10), E26511 (2011)
Publication Status: Online-Only
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Palanichamy,M.G., Zhang,C.L., Mitra,B., Malyarchuk,B., Derenko,M., Chaudhuri,T.K. and Zhang,Y.P.
BMC Evol. Biol. 10 (1), 304 (2010)
Publication Status: Online-Only
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Ghelli,A., Porcelli,A.M., Zanna,C., Vidoni,S., Mattioli,S., Barbieri,A., Iommarini,L., Pala,M., Achilli,A., Torroni,A., Rugolo,M. and Carelli,V.
PLoS ONE 4 (11), E7922 (2009)
Publication Status: Online-Only
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Verny,C., Guegen,N., Desquiret,V., Chevrollier,A., Prundean,A., Dubas,F., Cassereau,J., Ferre,M., Amati-Bonneau,P., Bonneau,D., Reynier,P. and Procaccio,V.
Mitochondrion 11 (1), 70-75 (2011)
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Hill,C., Soares,P., Mormina,M., Macaulay,V., Meehan,W., Blackburn,J., Clarke,D., Raja,J.M., Ismail,P., Bulbeck,D., Oppenheimer,S. and Richards,M.
Mol. Biol. Evol. 23 (12), 2480-2491 (2006)
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Zhang,A.M., Jia,X., Guo,X., Zhang,Q. and Yao,Y.G.
J Transl Med 10, 43 (2012)
Publication Status: Online-Only
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Yu,D., Jia,X., Zhang,A.M., Guo,X., Zhang,Y.P., Zhang,Q. and Yao,Y.G.
Neurogenetics 11 (3), 349-356 (2010)
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Benazzi,S., Slon,V., Talamo,S., Negrino,F., Peresani,M., Bailey,S.E., Sawyer,S., Panetta,D., Vicino,G., Starnini,E., Mannino,M.A., Salvadori,P.A., Meyer,M., Paabo,S. and Hublin,J.-J.
Science (2015) In press
Publication Status: Available-Online prior to print
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Palanichamy,M.G., Mitra,B., Debnath,M., Agrawal,S., Chaudhuri,T.K. and Zhang,Y.P.
PLoS ONE 9 (10), E109331 (2014)
Publication Status: Online-Only
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Bi,R., Zhang,A.M., Zhang,W., Kong,Q.P., Wu,B.L., Yang,X.H., Wang,D., Zou,Y., Zhang,Y.P. and Yao,Y.G.
Hum. Mutat. 31 (5), 538-543 (2010)
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Janssen,G.M., Neu,A., 't Hart,L.M., van de Sande,C.M. and Antonie Maassen,J.
Exp. Clin. Endocrinol. Diabetes 114 (4), 168-174 (2006)
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Morris,A.G., Heinze,A., Chan,E.K., Smith,A.B. and Hayes,V.M.
Genome Biol Evol 6 (10), 2647-2653 (2014)
Publication Status: Online-Only
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Elango,S., Govindaraj,P., Vishwanadha,V.P., Reddy,A.G., Tamang,R., Muthusami,U., Kunnoth,S., Koyilil,V.K., Lakshman,M., Shanmugasundharam,N., Singh,L. and Thangaraj,K.
Mitochondrion 11 (6), 878-885 (2011)
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Abu-Amero,K.K., Larruga,J.M., Cabrera,V.M. and Gonzalez,A.M.
BMC Evol. Biol. 8, 45 (2008)
Publication Status: Online-Only
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Pereira,L., Cerny,V., Cerezo,M., Silva,N.M., Hajek,M., Vasikova,A., Kujanova,M., Brdicka,R. and Salas,A.
Eur. J. Hum. Genet. 18 (8), 915-923 (2010)
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Delgado-Sanchez,R., Zarate-Moysen,A., Monsalvo-Reyes,A., Herrero,M.D., Ruiz-Pesini,E., Lopez-Perez,M., Montoya,J. and Montiel-Sosa,J.F.
Rev Neurol 44 (1), 18-22 (2007)
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Fehren-Schmitz,L., Jarman,C.L., Harkins,K.M., Kayser,M., Popp,B.N. and Skoglund,P.
Curr. Biol. (2017) In press
Publication Status: Available-Online prior to print
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Zsurka,G., Hampel,K.G., Kudina,T., Kornblum,C., Kraytsberg,Y., Elger,C.E., Khrapko,K. and Kunz,W.S.
Am. J. Hum. Genet. 80 (2), 298-305 (2007)
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Zsurka,G., Hampel,K.G., Nelson,I., Jardel,C., Mirandola,S.R., Sassen,R., Kornblum,C., Marcorelles,P., Lavoue,S., Lombes,A. and Kunz,W.S.
Neurology 74 (6), 507-512 (2010)
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Carossa,V., Ghelli,A., Tropeano,C.V., Valentino,M.L., Iommarini,L., Maresca,A., Caporali,L., La Morgia,C., Liguori,R., Barboni,P., Carbonelli,M., Rizzo,G., Tonon,C., Lodi,R., Martinuzzi,A., De Nardo,V., Rugolo,M., Ferretti,L., Gandini,F., Pala,M., Achilli,A., Olivieri,A., Torroni,A. and Carelli,V.
Hum. Mutat. 35 (8), 954-958 (2014)
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Yang,J., Zhu,Y., Tong,Y., Zhang,Z., Chen,L., Chen,S., Cao,Z., Liu,C., Xu,J. and Ma,X.
Mitochondrion 9 (4), 273-278 (2009)
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Zhang,A.M., Jia,X., Yao,Y.G. and Zhang,Q.
Biochem. Biophys. Res. Commun. 376 (1), 221-224 (2008)
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Mitochondrial DNA haplogroup B5 confers genetic susceptibility to Alzheimer's disease in Han Chinese
Bi,R., Zhang,W., Yu,D., Li,X., Wang,H.Z., Hu,Q.X., Zhang,C., Lu,W., Ni,J., Fang,Y., Li,T. and Yao,Y.G.
Neurobiol. Aging (2014) In press
Publication Status: Available-Online prior to print
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Guillet,V., Chevrollier,A., Cassereau,J., Letournel,F., Gueguen,N., Richard,L., Desquiret,V., Verny,C., Procaccio,V., Amati-Bonneau,P., Reynier,P. and Bonneau,D.
Mitochondrion 10 (2), 115-124 (2010)
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Dancause,K.N., Chan,C.W., Arunotai,N.H. and Lum,J.K.
J. Hum. Genet. 54 (2), 86-93 (2009)
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Malhi,R.S., Cybulski,J.S., Tito,R.Y., Johnson,J., Harry,H. and Dan,C.
Am. J. Phys. Anthropol. 141 (3), 494-497 (2010)
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Alvarez-Iglesias,V., Mosquera-Miguel,A., Cerezo,M., Quintans,B., Zarrabeitia,M.T., Cusco,I., Lareu,M.V., Garcia,O., Perez-Jurado,L., Carracedo,A. and Salas,A.
PLoS ONE 4 (4), E5112 (2009)
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Ricaut,F.X., Razafindrazaka,H., Cox,M.P., Dugoujon,J.M., Guitard,E., Sambo,C., Mormina,M., Mirazon-Lahr,M., Ludes,B. and Crubezy,E.
BMC Genomics 10, 605 (2009)
Publication Status: Online-Only
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Perli,E., Giordano,C., Tuppen,H.A., Montopoli,M., Montanari,A., Orlandi,M., Pisano,A., Catanzaro,D., Caparrotta,L., Musumeci,B., Autore,C., Morea,V., Di Micco,P., Campese,A.F., Leopizzi,M., Gallo,P., Francisci,S., Frontali,L., Taylor,R.W. and d'Amati,G.
Hum. Mol. Genet. (2011) In press
Publication Status: Available-Online prior to print
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Ancora,M., Orsini,M., Colosimo,A., Marcacci,M., Russo,V., De Santo,M., D'Aurora,M., Stuppia,L., Barboni,B., Camma,C. and Gatta,V.
Mitochondrial DNA A DNA MappSeq Anal, 1-2 (2016) In press
Publication Status: Available-Online prior to print
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Gianoarli,L., Luiselli,D., Crivello,A.M., Lang,M., Ferraretti,A.P., De Fanti,S., Magli,M.C. and Romeo,G.
PLoS ONE 9 (7), E102182 (2014)
Publication Status: Online-Only
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Ennafaa,H., Cabrera,V.M., Abu-Amero,K.K., Gonzalez,A.M., Amor,M.B., Bouhaha,R., Dzimiri,N., Elgaaied,A.B. and Larruga,J.M.
BMC Genet. 10, 8 (2009)
Publication Status: Online-Only
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Guo,H., Zhuang,X.Y., Zhang,A.M., Zhang,W., Yuan,Y., Guo,L., Yu,D., Liu,J., Yang,D.K. and Yao,Y.G.
Biochim. Biophys. Acta 1822 (10), 1535-1543 (2012)
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Guo,L., Yuan,Y. and Bi,R.
Biochem. Biophys. Res. Commun. (2016) In press
Publication Status: Available-Online prior to print
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La Morgia,C., Caporali,L., Gandini,F., Olivieri,A., Toni,F., Nassetti,S., Brunetto,D., Stipa,C., Scaduto,C., Parmeggiani,A., Tonon,C., Lodi,R., Torroni,A. and Carelli,V.
BMC Neurol 14 (1), 116 (2014)
Publication Status: Available-Online prior to print
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De Fanti,S., Barbieri,C., Sarno,S., Sevini,F., Vianello,D., Tamm,E., Metspalu,E., van Oven,M., Hubner,A., Sazzini,M., Franceschi,C., Pettener,D. and Luiselli,D.
PLoS ONE 10 (12), E0144391 (2015)
Publication Status: Online-Only
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van de Loosdrecht,M., Bouzouggar,A., Humphrey,L., Posth,C., Barton,N., Aximu-Petri,A., Nickel,B., Nagel,S., Talbi,E.H., El Hajraoui,M.A., Amzazi,S., Hublin,J.J., Paabo,S., Schiffels,S., Meyer,M., Haak,W., Jeong,C. and Krause,J.
Science (2018) In press
Publication Status: Available-Online prior to print
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de Saint Pierre,M., Gandini,F., Perego,U.A., Bodner,M., Gomez-Carballa,A., Corach,D., Angerhofer,N., Woodward,S.R., Semino,O., Salas,A., Parson,W., Moraga,M., Achilli,A., Torroni,A. and Olivieri,A.
PLoS ONE 7 (12), E51311 (2012)
Publication Status: Online-Only
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Brisighelli,F., Capelli,C., Alvarez-Iglesias,V., Onofri,V., Paoli,G., Tofanelli,S., Carracedo,A., Pascali,V.L. and Salas,A.
Eur. J. Hum. Genet. 17 (5), 693-696 (2009)
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Li,Y.C., Wang,H.W., Tian,J.Y., Liu,L.N., Yang,L.Q., Zhu,C.L., Wu,S.F., Kong,Q.P. and Zhang,Y.P.
Sci Rep 5, 9473 (2015)
Publication Status: Online-Only
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van der Walt,E.M., Smuts,I., Taylor,R.W., Elson,J.L., Turnbull,D.M., Louw,R. and van der Westhuizen,F.H.
Eur. J. Hum. Genet. 20 (6), 650-656 (2012)
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Li,H., Bi,R., Fan,Y., Wu,Y., Tang,Y., Li,Z., He,Y., Zhou,J., Tang,J., Chen,X. and Yao,Y.G.
Mol. Neurobiol. 54 (6), 4343-4352 (2017)
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Fehren-Schmitz,L., Llamas,B., Lindauer,S., Tomasto-Cagigao,E., Kuzminsky,S., Rohland,N., Santos,F.R., Kaulicke,P., Valverde,G., Richards,S.M., Nordenfelt,S., Seidenberg,V., Mallick,S., Cooper,A., Reich,D. and Haak,W.
PLoS ONE 10 (6), E0127141 (2015)
Publication Status: Online-Only
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Komiyama,T., Ogura,A., Hirokawa,T., Zhijing,M., Kamiguchi,H., Asai,S., Miyachi,H. and Kobayashi,H.
Int J Mol Sci 18 (1), E12 (2016)
DOI:10.3390/ijms18010012 Publication Status: Online-Only
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Kilinc,G.M., Kashuba,N., Yaka,R., Sumer,A.P., Yuncu,E., Shergin,D., Ivanov,G.L., Kichigin,D., Pestereva,K., Volkov,D., Mandryka,P., Kharinskii,A., Tishkin,A., Ineshin,E., Kovychev,E., Stepanov,A., Alekseev,A., Fedoseeva,S.A., Somel,M., Jakobsson,M., Krzewinska,M., Stora,J. and Gotherstrom,A.
Sci Rep 8 (1), 8969 (2018)
Publication Status: Online-Only
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Arnason,U., Gullberg,A., Janke,A. and Kullberg,M.
Mol. Phylogenet. Evol. 45 (3), 863-874 (2007)
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Broushaki,F., Thomas,M.G., Link,V., Lopez,S., van Dorp,L., Kirsanow,K., Hofmanova,Z., Diekmann,Y., Cassidy,L.M., Diez-Del-Molino,D., Kousathanas,A., Sell,C., Robson,H.K., Martiniano,R., Blocher,J., Scheu,A., Kreutzer,S., Bollongino,R., Bobo,D., Davudi,H., Munoz,O., Currat,M., Abdi,K., Biglari,F., Craig,O.E., Bradley,D.G., Shennan,S., Veeramah,K.R., Mashkour,M., Wegmann,D., Hellenthal,G. and Burger,J.
Science, eaaf7943 (2016) In press
Publication Status: Available-Online prior to print
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Aure,K., Dubourg,O., Jardel,C., Clarysse,L., Sternberg,D., Fournier,E., Laforet,P., Streichenberger,N., Petiot,P., Gervais-Bernard,H., Vial,C., Bedat-Millet,A.L., Drouin-Garraud,V., Bouillaud,F., Vandier,C., Fontaine,B. and Lombes,A.
Neurology 81 (21), 1810-1818 (2013)
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Khan,N.A., Govindaraj,P., Jyothi,V., Meena,A.K. and Thangaraj,K.
Mol. Vis. 19, 1282-1289 (2013)
Publication Status: Online-Only
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Modi,A., Tassi,F., Susca,R.R., Vai,S., Rizzi,E., Bellis,G., Luglie,C., Gonzalez Fortes,G., Lari,M., Barbujani,G., Caramelli,D. and Ghirotto,S.
Sci Rep 7, 42869 (2017)
Publication Status: Online-Only
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Yamada,M., Emmanuele,V., Sanchez-Quintero,M.J., Sun,B., Lallos,G., Paull,D., Zimmer,M., Pagett,S., Prosser,R.W., Sauer,M.V., Hirano,M. and Egli,D.
Cell Stem Cell (2016) In press
Publication Status: Available-Online prior to print
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Yao,Y.G., Kong,Q.P., Salas,A. and Bandelt,H.J.
J. Med. Genet. 45 (12), 769-772 (2008)
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La Morgia,C., Achilli,A., Iommarini,L., Barboni,P., Pala,M., Olivieri,A., Zanna,C., Vidoni,S., Tonon,C., Lodi,R., Vetrugno,R., Mostacci,B., Liguori,R., Carroccia,R., Montagna,P., Rugolo,M., Torroni,A. and Carelli,V.
Neurology 70 (10), 762-770 (2008)
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Steinberg,K.M., Schneider,V.A., Graves-Lindsay,T.A., Fulton,R.S., Agarwala,R., Huddleston,J., Shiryev,S.A., Morgulis,A., Surti,U., Warren,W.C., Church,D.M., Eichler,E.E. and Wilson,R.K.
Genome Res. 24 (12), 2066-2076 (2014)
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Cold Spring Harb. Symp. Quant. Biol. 51 (PT 1), 103-114 (1986)
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Hum. Mol. Genet. 1 (2), 140 (1992)
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Zhang,A.M., Jia,X., Bi,R., Salas,A., Li,S., Xiao,X., Wang,P., Guo,X., Kong,Q.P., Zhang,Q. and Yao,Y.G.
PLoS ONE 6 (11), E27750 (2011)
Publication Status: Online-Only
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Cerny,V., Fernandes,V., Costa,M.D., Hajek,M., Mulligan,C.J. and Pereira,L.
BMC Evol. Biol. 9, 63 (2009)
Publication Status: Online-Only
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Arnason,U., Xu,X. and Gullberg,A.
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Zhang,A.M., Zou,Y., Guo,X., Jia,X., Zhang,Q. and Yao,Y.G.
Biochem. Biophys. Res. Commun. 386 (2), 392-395 (2009)
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Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs
Horai,S., Hayasaka,K., Kondo,R., Tsugane,K. and Takahata,N.
Proc. Natl. Acad. Sci. U.S.A. 92 (2), 532-536 (1995)
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Desquiret-Dumas,V., Gueguen,N., Barth,M., Chevrollier,A., Hancock,S., Wallace,D.C., Amati-Bonneau,P., Henrion,D., Bonneau,D., Reynier,P. and Procaccio,V.
Biochim. Biophys. Acta 1822 (6), 1019-1029 (2012)
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Fregel,R., Ordonez,A.C., Santana-Cabrera,J., Cabrera,V.M., Velasco-Vazquez,J., Alberto,V., Moreno-Benitez,M.A., Delgado-Darias,T., Rodriguez-Rodriguez,A., Hernandez,J.C., Pais,J., Gonzalez-Montelongo,R., Lorenzo-Salazar,J.M., Flores,C., Cruz-de-Mercadal,M.C., Alvarez-Rodriguez,N., Shapiro,B., Arnay,M. and Bustamante,C.D.
PLoS ONE 14 (3), e0209125 (2019)
Publication Status: Online-Only
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Gloria González-Fortes, Eppie R. Jones, Emma Lightfoot, Clive Bonsall, Catalin Lazar, Aurora Grandal-d’Anglade, María Dolores Garralda, Labib Drak, Veronika Siska, Angela Simalcsik, Adina Boroneanţ, Juan Ramón Vidal Romaní, Marcos Vaqueiro Rodríguez, Pablo Arias, Ron Pinhasi, Andrea Manica, Michael Hofreiter
The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin, who largely replaced the local Mesolithic hunter-gatherers. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.1× to 4.1× coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.7× and 5.3×) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stable-isotope analysis of this sample suggests a mixed terrestrial/aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization.
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Helena Malmström, Torsten Günther, Emma M. Svensson, Anna Juras, Magdalena Fraser, Arielle R. Munters, Łukasz Pospieszny, Mari Tõrv, Jonathan Lindström, Anders Götherström, Jan Storå and Mattias Jakobsson
The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330–1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26–3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial ‘Bergsgraven’. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic–Caspian steppe herders, as well as smaller components originating from hunter–gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.
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Michael Waas, Doron Yacobi, Leon Kull, Vadim Urasin, Gregory Magoon, Wim Penninx, Adam Brown and Ines Nogueiro
This article aims at researching the evolution of J-Z640 using an interdisciplinary approach in order to clarify the leading historical and anthropological events that shaped this particular branch of the human Y chromosome. We compiled a STR (short tandem repeat) and SNP (single nucleotide polymorphism) dataset of 145 known or predicted J-Z640 samples among the customers of Family Tree DNA and Full Genomes Corporation, as well as publicly available samples. Amongst these, we analyzed the results of 41 samples that had undergone Next-Generation Sequencing (NGS) and 32 samples that had undergone SNP testing using Sanger Sequencing. From this data, we constructed a J-Z640 phylogenetic tree that was dated using the method. Our data revealed that Haplogroup J-Z640 is a Y chromosome lineage found most notably, in several minority groups within the Near East such as the Samaritans, Druze, Armenians and Jews. J-Z640 originated during the Bronze Age, most likely in the Levant. During the Bronze Age the haplogroup rapidly expanded with multiple ancient branches surviving to the present, evidencing population growth. Further population expansion, and contraction, was also observed in later periods. Based on its geographic dispersal and age of the haplogroup and its subclades, the founder population most likely belonged to Canaanites found in the Levant. Following the collapse of the late Bronze age system, from the Iron Age onwards there followed a period of “differentiation by culture”, with many of the ancient branches surviving to the present separated along ethno-religious lines.
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Lingling Shi, Yunfei Guo, Chengliang Dong, John Huddleston, Hui Yang, Xiaolu Han, Aisi Fu, Quan Li, Na Li, Siyi Gong, Katherine E. Lintner, Qiong Ding, Zou Wang, Jiang Hu, Depeng Wang, Feng Wang, Lin Wang, Gholson J. Lyon, Yongtao Guan, Yufeng Shen, Oleg V. Evgrafov, James A. Knowles, Francoise Thibaud-Nissen, Valerie Schneider, Chack-Yung Yu, Libing Zhou, Evan E. Eichler, Kwok-Fai So & Kai Wang
Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arrays and generate a de novo assembly of 2.93 Gb (contig N50: 8.3 Mb, scaffold N50: 22.0 Mb, including 39.3 Mb N-bases), together with 206 Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8 Mb of HX1-specific sequences, including 4.1 Mb that are not present in previously reported Asian genomes. Furthermore, long-read sequencing of the transcriptome reveals novel spliced genes that are not annotated in GENCODE and are missed by short-read RNA-Seq. Our results imply that improved characterization of genome functional variation may require the use of a range of genomic technologies on diverse human populations.
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Jeong-Sun Seo, Arang Rhie, Junsoo Kim, Sangjin Lee, Min-Hwan Sohn, Chang-Uk Kim, Alex Hastie, Han Cao, Ji-Young Yun, Jihye Kim, Junho Kuk, Gun Hwa Park, Juhyeok Kim, Hanna Ryu, Jongbum Kim, Mira Roh, Jeonghun Baek, Michael W. Hunkapiller, Jonas Korlach, Jong-Yeon Shin & Changhoon Kim
Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing2, next-generation mapping3, microfluidics-based linked reads4, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.
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Klunk,J., Duggan,A.T., Redfern,R., Gamble,J., Boldsen,J.L., Golding,G.B., Walter,B.S., Eaton,K., Stangroom,J., Rouillard,J.M., Devault,A., DeWitte,S.N. and Poinar,H.N.
Am. J. Phys. Anthropol. (2019) In press
Publication Status: Available-Online prior to print
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Zhao,D., Ding,Y., Lin,H., Chen,X., Shen,W., Gao,M., Wei,Q., Zhou,S., Liu,X. and He,N.
AIDS Res. Hum. Retroviruses (2019) In press
Publication Status: Available-Online prior to print
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Modi,A., Nesheva,D., Sarno,S., Vai,S., Karachanak-Yankova,S., Luiselli,D., Pilli,E., Lari,M., Vergata,C., Yordanov,Y., Dimitrova,D., Kalcev,P., Staneva,R., Antonova,O., Hadjidekova,S., Galabov,A., Toncheva,D. and Caramelli,D.
Sci Rep 9 (1), 5412 (2019)
Publication Status: Online-Only
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Wood,M.R., Sturk-Andreaggi,K., Ring,J.D., Huber,N., Bodner,M., Crawford,M.H., Parson,W. and Marshall,C.
Forensic Sci Int Genet 43, 102143 (2019)
Publication Status: Available-Online prior to print
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Derenko,M., Denisova,G., Malyarchuk,B., Hovhannisyan,A., Khachatryan,Z., Hrechdakian,P., Litvinov,A. and Yepiskoposyan,L.
Mol. Genet. Genomics (2019) In press
Publication Status: Available-Online prior to print
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Keatley,K., Stromei-Cleroux,S., Wiltshire,T., Rajala,N., Burton,G., Holt,W.V., Littlewood,D.T.J., Briscoe,A.G., Jung,J., Ashkan,K., Heales,S.J., Pilkington,G.J., Meunier,B., McGeehan,J.E., Hargreaves,I.P. and McGeehan,R.E.
Int J Mol Sci 20 (13), E3364 (2019)
Publication Status: Online-Only
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Kiiskila,J., Moilanen,J.S., Kytovuori,L., Niemi,A.K. and Majamaa,K.
BMC Genomics 20 (1), 784 (2019)
Publication Status: Online-Only
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Chan,E.K.F., Timmermann,A., Baldi,B.F., Moore,A.E., Lyons,R.J., Lee,S.S., Kalsbeek,A.M.F., Petersen,D.C., Rautenbach,H., Fortsch,H.E.A., Bornman,M.S.R. and Hayes,V.M.
Nature 575, 185-189 (2019)
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Li,M., DeRosa,K.L., Mann,H., Spathis,R., Roome,A., Castellanos,D., Gowen,K., de Smet,T.S., Echard,J., Casey,K., Shamoon-Pour,M., Garruto,R.M. and Lum,K.
Am. J. Phys. Anthropol. (2020) In press
Publication Status: Available-Online prior to print
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