DNA sequence and analysis of human chromosome 8

Chad Nusbaum; Tarjei S. Mikkelsen; Michael C. Zody; Shuichi Asakawa; Stefan Taudien; Manuel Garber; Chinnappa D. Kodira; Mary G. Schueler; Atsushi Shimizu; Charles A. Whittaker; Jean L. Chang; Christina A. Cuomo; Ken Dewar; Michael G. FitzGerald; Xiaoping Yang; Nicole R. Allen; Scott Anderson; Teruyo Asakawa; Karin Blechschmidt; Toby Bloom; Mark L. Borowsky; Jonathan Butler; April Cook; Benjamin Corum; Kurt DeArellano; David DeCaprio; Kathleen T. Dooley; Lester Dorris; Reinhard Engels; Gernot Glöckner; Nabil Hafez; Daniel S. Hagopian; Jennifer L. Hall; Sabine K. Ishikawa; David B. Jaffe; Asha Kamat; Jun Kudoh; Rüdiger Lehmann; Tashi Lokitsang; Pendexter Macdonald; John E. Major; Charles D. Matthews; Evan Mauceli; Uwe Menzel; Atanas H. Mihalev; Shinsei Minoshima; Yuji Murayama; Jerome W. Naylor; Robert Nicol; Cindy Nguyen

doi:10.1038/nature04406

DNA sequence and analysis of human chromosome 8

Chad Nusbaum, Tarjei S. Mikkelsen, Michael C. Zody, Shuichi Asakawa, Stefan Taudien, Manuel Garber, Chinnappa D. Kodira, Mary G. Schueler, Atsushi Shimizu, Charles A. Whittaker, Jean L. Chang, Christina A. Cuomo, Ken Dewar, Michael G. FitzGerald, Xiaoping Yang, Nicole R. Allen, Scott Anderson, Teruyo Asakawa, Karin Blechschmidt, Toby BloomMark L. Borowsky, Jonathan Butler, April Cook, Benjamin Corum, Kurt DeArellano, David DeCaprio, Kathleen T. Dooley, Lester Dorris, Reinhard Engels, Gernot Glöckner, Nabil Hafez, Daniel S. Hagopian, Jennifer L. Hall, Sabine K. Ishikawa, David B. Jaffe, Asha Kamat, Jun Kudoh, Rüdiger Lehmann, Tashi Lokitsang, Pendexter Macdonald, John E. Major, Charles D. Matthews, Evan Mauceli, Uwe Menzel, Atanas H. Mihalev, Shinsei Minoshima, Yuji Murayama, Jerome W. Naylor, Robert Nicol, Cindy Nguyen

Medicine - Cardiology Division

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Abstract

The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome¹. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of ∼15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection² - these include the major defensin (DEF) gene cluster^3,4 and MCPH1^5,6, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.

Original language	English (US)
Pages (from-to)	331-335
Number of pages	5
Journal	Nature
Volume	439
Issue number	7074
DOIs	https://doi.org/10.1038/nature04406
State	Published - Jan 19 2006

Bibliographical note

Funding Information:
Acknowledgements We thank L. Gaffney for help with figures and tables; L. French and her group at the Sanger Institute for attempting fibre FISH analysis to size some clone gaps in the tiling path of chromosome 8; E. Eichler and X. She for sharing their data on segmental duplications; T. Furey for help with lists of genetic markers and placement of RefSeq genes; M. Kamal for assistance and advice with synteny analysis; and K. Lindblad-Toh for sharing data from the dog genome project. We also acknowledge the HUGO Gene Nomenclature Committee (S. Povey, chair) for assigning official gene symbols. We are deeply grateful to all the members, present and past, of the Genome Sequencing Platform of the Broad Institute (and Whitehead Center for Genome Research), Keio University School of Medicine and the Institute of Molecular Biology at Jena for their dedication and for the consistent high quality of their data that made this work possible. This work was supported by grants from the National Human Genome Research Institute, RIKEN, the ‘Research for the Future’ Program from the Japan Society for the Promotion of Science (JSPS), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), the Federal German Ministry of Education, Research and Technology, and the Thüringer Kultusministerium.

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Nusbaum, C., Mikkelsen, T. S., Zody, M. C., Asakawa, S., Taudien, S., Garber, M., Kodira, C. D., Schueler, M. G., Shimizu, A., Whittaker, C. A., Chang, J. L., Cuomo, C. A., Dewar, K., FitzGerald, M. G., Yang, X., Allen, N. R., Anderson, S., Asakawa, T., Blechschmidt, K., ... Nguyen, C. (2006). DNA sequence and analysis of human chromosome 8. Nature, 439(7074), 331-335. https://doi.org/10.1038/nature04406

Nusbaum, C, Mikkelsen, TS, Zody, MC, Asakawa, S, Taudien, S, Garber, M, Kodira, CD, Schueler, MG, Shimizu, A, Whittaker, CA, Chang, JL, Cuomo, CA, Dewar, K, FitzGerald, MG, Yang, X, Allen, NR, Anderson, S, Asakawa, T, Blechschmidt, K, Bloom, T, Borowsky, ML, Butler, J, Cook, A, Corum, B, DeArellano, K, DeCaprio, D, Dooley, KT, Dorris, L, Engels, R, Glöckner, G, Hafez, N, Hagopian, DS, Hall, JL, Ishikawa, SK, Jaffe, DB, Kamat, A, Kudoh, J, Lehmann, R, Lokitsang, T, Macdonald, P, Major, JE, Matthews, CD, Mauceli, E, Menzel, U, Mihalev, AH, Minoshima, S, Murayama, Y, Naylor, JW, Nicol, R & Nguyen, C 2006, 'DNA sequence and analysis of human chromosome 8', Nature, vol. 439, no. 7074, pp. 331-335. https://doi.org/10.1038/nature04406

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title = "DNA sequence and analysis of human chromosome 8",

abstract = "The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome1. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of ∼15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection2 - these include the major defensin (DEF) gene cluster3,4 and MCPH15,6, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.",

author = "Chad Nusbaum and Mikkelsen, {Tarjei S.} and Zody, {Michael C.} and Shuichi Asakawa and Stefan Taudien and Manuel Garber and Kodira, {Chinnappa D.} and Schueler, {Mary G.} and Atsushi Shimizu and Whittaker, {Charles A.} and Chang, {Jean L.} and Cuomo, {Christina A.} and Ken Dewar and FitzGerald, {Michael G.} and Xiaoping Yang and Allen, {Nicole R.} and Scott Anderson and Teruyo Asakawa and Karin Blechschmidt and Toby Bloom and Borowsky, {Mark L.} and Jonathan Butler and April Cook and Benjamin Corum and Kurt DeArellano and David DeCaprio and Dooley, {Kathleen T.} and Lester Dorris and Reinhard Engels and Gernot Gl{\"o}ckner and Nabil Hafez and Hagopian, {Daniel S.} and Hall, {Jennifer L.} and Ishikawa, {Sabine K.} and Jaffe, {David B.} and Asha Kamat and Jun Kudoh and R{\"u}diger Lehmann and Tashi Lokitsang and Pendexter Macdonald and Major, {John E.} and Matthews, {Charles D.} and Evan Mauceli and Uwe Menzel and Mihalev, {Atanas H.} and Shinsei Minoshima and Yuji Murayama and Naylor, {Jerome W.} and Robert Nicol and Cindy Nguyen",

note = "Funding Information: Acknowledgements We thank L. Gaffney for help with figures and tables; L. French and her group at the Sanger Institute for attempting fibre FISH analysis to size some clone gaps in the tiling path of chromosome 8; E. Eichler and X. She for sharing their data on segmental duplications; T. Furey for help with lists of genetic markers and placement of RefSeq genes; M. Kamal for assistance and advice with synteny analysis; and K. Lindblad-Toh for sharing data from the dog genome project. We also acknowledge the HUGO Gene Nomenclature Committee (S. Povey, chair) for assigning official gene symbols. We are deeply grateful to all the members, present and past, of the Genome Sequencing Platform of the Broad Institute (and Whitehead Center for Genome Research), Keio University School of Medicine and the Institute of Molecular Biology at Jena for their dedication and for the consistent high quality of their data that made this work possible. This work was supported by grants from the National Human Genome Research Institute, RIKEN, the {\textquoteleft}Research for the Future{\textquoteright} Program from the Japan Society for the Promotion of Science (JSPS), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), the Federal German Ministry of Education, Research and Technology, and the Th{\"u}ringer Kultusministerium.",

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doi = "10.1038/nature04406",

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T1 - DNA sequence and analysis of human chromosome 8

AU - Nusbaum, Chad

AU - Mikkelsen, Tarjei S.

AU - Zody, Michael C.

AU - Asakawa, Shuichi

AU - Taudien, Stefan

AU - Garber, Manuel

AU - Kodira, Chinnappa D.

AU - Schueler, Mary G.

AU - Shimizu, Atsushi

AU - Whittaker, Charles A.

AU - Chang, Jean L.

AU - Cuomo, Christina A.

AU - Dewar, Ken

AU - FitzGerald, Michael G.

AU - Yang, Xiaoping

AU - Allen, Nicole R.

AU - Anderson, Scott

AU - Asakawa, Teruyo

AU - Blechschmidt, Karin

AU - Bloom, Toby

AU - Borowsky, Mark L.

AU - Butler, Jonathan

AU - Cook, April

AU - Corum, Benjamin

AU - DeArellano, Kurt

AU - DeCaprio, David

AU - Dooley, Kathleen T.

AU - Dorris, Lester

AU - Engels, Reinhard

AU - Glöckner, Gernot

AU - Hafez, Nabil

AU - Hagopian, Daniel S.

AU - Hall, Jennifer L.

AU - Ishikawa, Sabine K.

AU - Jaffe, David B.

AU - Kamat, Asha

AU - Kudoh, Jun

AU - Lehmann, Rüdiger

AU - Lokitsang, Tashi

AU - Macdonald, Pendexter

AU - Major, John E.

AU - Matthews, Charles D.

AU - Mauceli, Evan

AU - Menzel, Uwe

AU - Mihalev, Atanas H.

AU - Minoshima, Shinsei

AU - Murayama, Yuji

AU - Naylor, Jerome W.

AU - Nicol, Robert

AU - Nguyen, Cindy

N1 - Funding Information: Acknowledgements We thank L. Gaffney for help with figures and tables; L. French and her group at the Sanger Institute for attempting fibre FISH analysis to size some clone gaps in the tiling path of chromosome 8; E. Eichler and X. She for sharing their data on segmental duplications; T. Furey for help with lists of genetic markers and placement of RefSeq genes; M. Kamal for assistance and advice with synteny analysis; and K. Lindblad-Toh for sharing data from the dog genome project. We also acknowledge the HUGO Gene Nomenclature Committee (S. Povey, chair) for assigning official gene symbols. We are deeply grateful to all the members, present and past, of the Genome Sequencing Platform of the Broad Institute (and Whitehead Center for Genome Research), Keio University School of Medicine and the Institute of Molecular Biology at Jena for their dedication and for the consistent high quality of their data that made this work possible. This work was supported by grants from the National Human Genome Research Institute, RIKEN, the ‘Research for the Future’ Program from the Japan Society for the Promotion of Science (JSPS), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), the Federal German Ministry of Education, Research and Technology, and the Thüringer Kultusministerium.

PY - 2006/1/19

Y1 - 2006/1/19

N2 - The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome1. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of ∼15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection2 - these include the major defensin (DEF) gene cluster3,4 and MCPH15,6, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.

AB - The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome1. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of ∼15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection2 - these include the major defensin (DEF) gene cluster3,4 and MCPH15,6, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.

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DNA sequence and analysis of human chromosome 8

Abstract

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