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The sequence and analysis of duplication-rich human chromosome 16

Author

Listed:
  • Joel Martin

    (DOE Joint Genome Institute)

  • Cliff Han

    (Los Alamos National Laboratory)

  • Laurie A. Gordon

    (DOE Joint Genome Institute)

  • Astrid Terry

    (DOE Joint Genome Institute)

  • Shyam Prabhakar

    (Lawrence Berkeley National Laboratory)

  • Xinwei She

    (University of Washington)

  • Gary Xie

    (DOE Joint Genome Institute
    Los Alamos National Laboratory)

  • Uffe Hellsten

    (DOE Joint Genome Institute)

  • Yee Man Chan

    (Stanford University School of Medicine)

  • Michael Altherr

    (DOE Joint Genome Institute
    Los Alamos National Laboratory)

  • Olivier Couronne

    (Lawrence Berkeley National Laboratory)

  • Andrea Aerts

    (DOE Joint Genome Institute)

  • Eva Bajorek

    (Stanford University School of Medicine)

  • Stacey Black

    (Stanford University School of Medicine)

  • Heather Blumer

    (Los Alamos National Laboratory)

  • Elbert Branscomb

    (DOE Joint Genome Institute
    Lawrence Livermore National Laboratory)

  • Nancy C. Brown

    (Los Alamos National Laboratory)

  • William J. Bruno

    (Los Alamos National Laboratory)

  • Judith M. Buckingham

    (Los Alamos National Laboratory)

  • David F. Callen

    (Los Alamos National Laboratory)

  • Connie S. Campbell

    (Los Alamos National Laboratory)

  • Mary L. Campbell

    (Los Alamos National Laboratory)

  • Evelyn W. Campbell

    (Los Alamos National Laboratory)

  • Chenier Caoile

    (Stanford University School of Medicine)

  • Jean F. Challacombe

    (Los Alamos National Laboratory)

  • Leslie A. Chasteen

    (Los Alamos National Laboratory)

  • Olga Chertkov

    (Los Alamos National Laboratory)

  • Han C. Chi

    (Los Alamos National Laboratory)

  • Mari Christensen

    (Lawrence Livermore National Laboratory)

  • Lynn M. Clark

    (Los Alamos National Laboratory)

  • Judith D. Cohn

    (Los Alamos National Laboratory)

  • Mirian Denys

    (Stanford University School of Medicine)

  • John C. Detter

    (DOE Joint Genome Institute)

  • Mark Dickson

    (Stanford University School of Medicine)

  • Mira Dimitrijevic-Bussod

    (Los Alamos National Laboratory)

  • Julio Escobar

    (Stanford University School of Medicine)

  • Joseph J. Fawcett

    (Los Alamos National Laboratory)

  • Dave Flowers

    (Stanford University School of Medicine)

  • Dea Fotopulos

    (Stanford University School of Medicine)

  • Tijana Glavina

    (DOE Joint Genome Institute)

  • Maria Gomez

    (Stanford University School of Medicine)

  • Eidelyn Gonzales

    (Stanford University School of Medicine)

  • David Goodstein

    (DOE Joint Genome Institute)

  • Lynne A. Goodwin

    (Los Alamos National Laboratory)

  • Deborah L. Grady

    (Los Alamos National Laboratory)

  • Igor Grigoriev

    (DOE Joint Genome Institute)

  • Matthew Groza

    (Lawrence Livermore National Laboratory)

  • Nancy Hammon

    (DOE Joint Genome Institute)

  • Trevor Hawkins

    (DOE Joint Genome Institute)

  • Lauren Haydu

    (Stanford University School of Medicine)

  • Carl E. Hildebrand

    (Los Alamos National Laboratory)

  • Wayne Huang

    (DOE Joint Genome Institute)

  • Sanjay Israni

    (DOE Joint Genome Institute)

  • Jamie Jett

    (DOE Joint Genome Institute)

  • Phillip B. Jewett

    (Los Alamos National Laboratory)

  • Kristen Kadner

    (DOE Joint Genome Institute)

  • Heather Kimball

    (DOE Joint Genome Institute)

  • Arthur Kobayashi

    (DOE Joint Genome Institute
    Lawrence Livermore National Laboratory)

  • Marie-Claude Krawczyk

    (Los Alamos National Laboratory)

  • Tina Leyba

    (Los Alamos National Laboratory)

  • Jonathan L. Longmire

    (Los Alamos National Laboratory)

  • Frederick Lopez

    (Stanford University School of Medicine)

  • Yunian Lou

    (DOE Joint Genome Institute)

  • Steve Lowry

    (DOE Joint Genome Institute)

  • Thom Ludeman

    (Los Alamos National Laboratory)

  • Chitra F. Manohar

    (Lawrence Livermore National Laboratory)

  • Graham A. Mark

    (Los Alamos National Laboratory)

  • Kimberly L. McMurray

    (Los Alamos National Laboratory)

  • Linda J. Meincke

    (Los Alamos National Laboratory)

  • Jenna Morgan

    (DOE Joint Genome Institute)

  • Robert K. Moyzis

    (Los Alamos National Laboratory)

  • Mark O. Mundt

    (Los Alamos National Laboratory)

  • A. Christine Munk

    (Los Alamos National Laboratory)

  • Richard D. Nandkeshwar

    (Lawrence Livermore National Laboratory)

  • Sam Pitluck

    (DOE Joint Genome Institute)

  • Martin Pollard

    (DOE Joint Genome Institute)

  • Paul Predki

    (DOE Joint Genome Institute)

  • Beverly Parson-Quintana

    (Los Alamos National Laboratory)

  • Lucia Ramirez

    (Stanford University School of Medicine)

  • Sam Rash

    (DOE Joint Genome Institute)

  • James Retterer

    (Stanford University School of Medicine)

  • Darryl O. Ricke

    (Los Alamos National Laboratory)

  • Donna L. Robinson

    (Los Alamos National Laboratory)

  • Alex Rodriguez

    (Stanford University School of Medicine)

  • Asaf Salamov

    (DOE Joint Genome Institute)

  • Elizabeth H. Saunders

    (Los Alamos National Laboratory)

  • Duncan Scott

    (DOE Joint Genome Institute)

  • Timothy Shough

    (Los Alamos National Laboratory)

  • Raymond L. Stallings

    (Los Alamos National Laboratory)

  • Malinda Stalvey

    (Los Alamos National Laboratory)

  • Robert D. Sutherland

    (Los Alamos National Laboratory)

  • Roxanne Tapia

    (Los Alamos National Laboratory)

  • Judith G. Tesmer

    (Los Alamos National Laboratory)

  • Nina Thayer

    (DOE Joint Genome Institute
    Los Alamos National Laboratory)

  • Linda S. Thompson

    (Los Alamos National Laboratory)

  • Hope Tice

    (DOE Joint Genome Institute)

  • David C. Torney

    (Los Alamos National Laboratory)

  • Mary Tran-Gyamfi

    (DOE Joint Genome Institute)

  • Ming Tsai

    (Stanford University School of Medicine)

  • Levy E. Ulanovsky

    (Los Alamos National Laboratory)

  • Anna Ustaszewska

    (DOE Joint Genome Institute)

  • Nu Vo

    (Stanford University School of Medicine)

  • P. Scott White

    (Los Alamos National Laboratory)

  • Albert L. Williams

    (Los Alamos National Laboratory)

  • Patricia L. Wills

    (Los Alamos National Laboratory)

  • Jung-Rung Wu

    (Los Alamos National Laboratory)

  • Kevin Wu

    (Stanford University School of Medicine)

  • Joan Yang

    (Stanford University School of Medicine)

  • Pieter DeJong

    (Children's Hospital Oakland)

  • David Bruce

    (Los Alamos National Laboratory)

  • Norman A. Doggett

    (Los Alamos National Laboratory)

  • Larry Deaven

    (Los Alamos National Laboratory)

  • Jeremy Schmutz

    (Stanford University School of Medicine)

  • Jane Grimwood

    (Stanford University School of Medicine)

  • Paul Richardson

    (DOE Joint Genome Institute)

  • Daniel S. Rokhsar

    (DOE Joint Genome Institute)

  • Evan E. Eichler

    (University of Washington)

  • Paul Gilna

    (Los Alamos National Laboratory)

  • Susan M. Lucas

    (DOE Joint Genome Institute)

  • Richard M. Myers

    (Stanford University School of Medicine)

  • Edward M. Rubin

    (DOE Joint Genome Institute
    Lawrence Berkeley National Laboratory)

  • Len A. Pennacchio

    (DOE Joint Genome Institute
    Lawrence Berkeley National Laboratory)

Abstract

Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.

Suggested Citation

  • Joel Martin & Cliff Han & Laurie A. Gordon & Astrid Terry & Shyam Prabhakar & Xinwei She & Gary Xie & Uffe Hellsten & Yee Man Chan & Michael Altherr & Olivier Couronne & Andrea Aerts & Eva Bajorek & S, 2004. "The sequence and analysis of duplication-rich human chromosome 16," Nature, Nature, vol. 432(7020), pages 988-994, December.
    • Handle: RePEc:nat:nature:v:432:y:2004:i:7020:d:10.1038_nature03187
    DOI: 10.1038/nature03187
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