Volume 19, Issue 9 | September 2009

Letter
- - Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans
    Alison H. Harrill
    Paul B. Watkins
    Stephen Su
    Pamela K. Ross
    David E. Harbourt
    Ioannis M. Stylianou Gary A. Boorman Mark W. Russo Richard S. Sackler Stephen C. Harris Philip C. Smith Raymond Tennant Molly Bogue Kenneth Paigen Christopher Harris
    ...[+10 authors]...,
    Tanupriya Contractor
    Timothy Wiltshire
    Ivan Rusyn
    David W. Threadgill
    First Published May 5, 2009
  - Mobile elements create structural variation: Analysis of a complete human genome
    Jinchuan Xing
    Yuhua Zhang
    Kyudong Han
    Abdel Halim Salem
    Shurjo K. Sen
    Chad D. Huff Qiong Zhou
    ...[+2 authors]...,
    Ewen F. Kirkness
    Samuel Levy
    Mark A. Batzer
    Lynn B. Jorde
    First Published May 13, 2009
Methods
- - Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
    Kevin Judd McKernan
    Heather E. Peckham
    Gina L. Costa
    Stephen F. McLaughlin
    Yutao Fu
    Eric F. Tsung Christopher R. Clouser Cisyla Duncan Jeffrey K. Ichikawa Clarence C. Lee Zheng Zhang Swati S. Ranade Eileen T. Dimalanta Fiona C. Hyland Tanya D. Sokolsky Lei Zhang Andrew Sheridan Haoning Fu Cynthia L. Hendrickson Bin Li Lev Kotler Jeremy R. Stuart Joel A. Malek Jonathan M. Manning Alena A. Antipova Damon S. Perez Michael P. Moore Kathleen C. Hayashibara Michael R. Lyons Robert E. Beaudoin Brittany E. Coleman Michael W. Laptewicz Adam E. Sannicandro Michael D. Rhodes Rajesh K. Gottimukkala Shan Yang Vineet Bafna Ali Bashir Andrew MacBride Can Alkan Jeffrey M. Kidd
    ...[+36 authors]...,
    Evan E. Eichler
    Martin G. Reese
    Francisco M. De La Vega
    Alan P. Blanchard
    First Published June 22, 2009
  - A probabilistic approach for SNP discovery in high-throughput human resequencing data
    Rose Hoberman
    Joana Dias
    Bing Ge
    Eef Harmsen
    Michael Mayhew
    Dominique J. Verlaan
    ...[+1 authors]...,
    Tony Kwan
    Ken Dewar
    Mathieu Blanchette
    Tomi Pastinen
    First Published July 15, 2009
  - Identification of deleterious mutations within three human genomes
    Sung Chun
    Justin C. Fay
    First Published July 14, 2009
  - Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations
    Sudhir Kumar
    Michael P. Suleski
    Glenn J. Markov
    Simon Lawrence
    Antonio Marco
    First Published June 22, 2009
  - Identification of rare cancer driver mutations by network reconstruction
    Ali Torkamani
    Nicholas J. Schork
    First Published July 2, 2009
  - A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease
    Heather C. Mefford
    Gregory M. Cooper
    Troy Zerr
    Joshua D. Smith
    Carl Baker
    Neil Shafer Erik C. Thorland
    ...[+2 authors]...,
    Cindy Skinner
    Charles E. Schwartz
    Deborah A. Nickerson
    Evan E. Eichler
    First Published June 8, 2009
  - Sensitive and accurate detection of copy number variants using read depth of coverage
    Seungtai Yoon
    Zhenyu Xuan
    Vladimir Makarov
    Kenny Ye
    Jonathan Sebat
    First Published August 5, 2009
  - High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
    Emily Hodges
    Andrew D. Smith
    Jude Kendall
    Zhenyu Xuan
    Kandasamy Ravi
    Michelle Rooks Michael Q. Zhang Kenny Ye Arindam Bhattacharjee Leonardo Brizuela
    ...[+5 authors]...,
    W. Richard McCombie
    Michael Wigler
    Gregory J. Hannon
    James B. Hicks
    First Published July 6, 2009
  - Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
    Jin Billy Li
    Yuan Gao
    John Aach
    Kun Zhang
    Gregory V. Kryukov
    Bin Xie Annika Ahlford Jung-Ki Yoon Abraham M. Rosenbaum
    ...[+4 authors]...,
    Alexander Wait Zaranek
    Emily LeProust
    Shamil R. Sunyaev
    George M. Church
    First Published June 12, 2009
  - Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing
    Daniel Summerer
    Haiguo Wu
    Bettina Haase
    Yang Cheng
    Nadine Schracke
    First Published July 28, 2009
Resource
- - The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group
    Sung-Min Ahn
    Tae-Hyung Kim
    Sunghoon Lee
    Deokhoon Kim
    Ho Ghang
    Dae-Soo Kim Byoung-Chul Kim Sang-Yoon Kim Woo-Yeon Kim Chulhong Kim Daeui Park Yong Seok Lee Sangsoo Kim Rohit Reja Sungwoong Jho Chang Geun Kim Ji-Young Cha
    ...[+12 authors]...,
    Kyung-Hee Kim
    Bonghee Lee
    Jong Bhak
    Seong-Jin Kim
    First Published May 26, 2009
  - JBrowse: A next-generation genome browser
    Mitchell E. Skinner
    Andrew V. Uzilov
    Lincoln D. Stein
    Christopher J. Mungall
    Ian H. Holmes
    First Published July 1, 2009
  - Circos: An information aesthetic for comparative genomics
    Martin Krzywinski
    Jacqueline Schein
    İnanç Birol
    Joseph Connors
    Randy Gascoyne
    First Published June 18, 2009
  - RazerS—fast read mapping with sensitivity control
    David Weese
    Anne-Katrin Emde
    Tobias Rausch
    Andreas Döring
    Knut Reinert
    First Published July 10, 2009
  - Fast model-based estimation of ancestry in unrelated individuals
    David H. Alexander
    John Novembre
    Kenneth Lange
    First Published July 31, 2009
  - The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine
    Leslie G. Biesecker
    James C. Mullikin
    Flavia M. Facio
    Clesson Turner
    Praveen F. Cherukuri
    Robert W. Blakesley Gerard G. Bouffard Peter S. Chines Pedro Cruz Nancy F. Hansen Jamie K. Teer Baishali Maskeri Alice C. Young Teri A. Manolio Alexander F. Wilson Toren Finkel Paul Hwang Andrew Arai Alan T. Remaley
    ...[+14 authors]...,
    Vandana Sachdev
    Robert Shamburek
    Richard O. Cannon
    Eric D. Green
    First Published July 14, 2009
  - Instrumenting the health care enterprise for discovery research in the genomic era
    Shawn Murphy
    Susanne Churchill
    Lynn Bry
    Henry Chueh
    Scott Weiss
    Ross Lazarus Qing Zeng Anil Dubey
    ...[+3 authors]...,
    Vivian Gainer
    Michael Mendis
    John Glaser
    Isaac Kohane
    First Published July 14, 2009
  - High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications
    Tamim H. Shaikh
    Xiaowu Gai
    Juan C. Perin
    Joseph T. Glessner
    Hongbo Xie
    Kevin Murphy Ryan O'Hara Tracy Casalunovo Laura K. Conlin Monica D'Arcy Edward C. Frackelton Elizabeth A. Geiger Chad Haldeman-Englert Marcin Imielinski Cecilia E. Kim Livija Medne Kiran Annaiah Jonathan P. Bradfield Elvira Dabaghyan Andrew Eckert Chioma C. Onyiah Svetlana Ostapenko F. George Otieno Erin Santa Julie L. Shaner Robert Skraban Ryan M. Smith Josephine Elia Elizabeth Goldmuntz Nancy B. Spinner Elaine H. Zackai Rosetta M. Chiavacci Robert Grundmeier
    ...[+28 authors]...,
    Eric F. Rappaport
    Struan F.A. Grant
    Peter S. White
    Hakon Hakonarson
    First Published July 10, 2009
Erratum
- - Erratum
    First Published September 1, 2009

Table of Contents

Volume 19, Issue 9 | September 2009

Letter

Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans

Mobile elements create structural variation: Analysis of a complete human genome

Methods

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

A probabilistic approach for SNP discovery in high-throughput human resequencing data

Identification of deleterious mutations within three human genomes

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

Identification of rare cancer driver mutations by network reconstruction

A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease

Sensitive and accurate detection of copy number variants using read depth of coverage

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations

Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing

Resource

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

JBrowse: A next-generation genome browser

Circos: An information aesthetic for comparative genomics

RazerS—fast read mapping with sensitivity control

Fast model-based estimation of ancestry in unrelated individuals

The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine

Instrumenting the health care enterprise for discovery research in the genomic era

High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications

Erratum

Erratum

Table of Contents

Volume 19, Issue 9 | September 2009

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Erratum