Accurate whole human genome sequencing using reversible terminator chemistry.
DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.
Bentley
David R
DR
Illumina Cambridge Ltd. (Formerly Solexa Ltd), Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK. dbentley@illumina.com
Balasubramanian
Shankar
S
Swerdlow
Harold P
HP
Smith
Geoffrey P
GP
Milton
John
J
Brown
Clive G
CG
Hall
Kevin P
KP
Evers
Dirk J
DJ
Barnes
Colin L
CL
Bignell
Helen R
HR
Boutell
Jonathan M
JM
Bryant
Jason
J
Carter
Richard J
RJ
Keira Cheetham
R
R
Cox
Anthony J
AJ
Ellis
Darren J
DJ
Flatbush
Michael R
MR
Gormley
Niall A
NA
Humphray
Sean J
SJ
Irving
Leslie J
LJ
Karbelashvili
Mirian S
MS
Kirk
Scott M
SM
Li
Heng
H
Liu
Xiaohai
X
Maisinger
Klaus S
KS
Murray
Lisa J
LJ
Obradovic
Bojan
B
Ost
Tobias
T
Parkinson
Michael L
ML
Pratt
Mark R
MR
Rasolonjatovo
Isabelle M J
IM
Reed
Mark T
MT
Rigatti
Roberto
R
Rodighiero
Chiara
C
Ross
Mark T
MT
Sabot
Andrea
A
Sankar
Subramanian V
SV
Scally
Aylwyn
A
Schroth
Gary P
GP
Smith
Mark E
ME
Smith
Vincent P
VP
Spiridou
Anastassia
A
Torrance
Peta E
PE
Tzonev
Svilen S
SS
Vermaas
Eric H
EH
Walter
Klaudia
K
Wu
Xiaolin
X
Zhang
Lu
L
Alam
Mohammed D
MD
Anastasi
Carole
C
Aniebo
Ify C
IC
Bailey
David M D
DM
Bancarz
Iain R
IR
Banerjee
Saibal
S
Barbour
Selena G
SG
Baybayan
Primo A
PA
Benoit
Vincent A
VA
Benson
Kevin F
KF
Bevis
Claire
C
Black
Phillip J
PJ
Boodhun
Asha
A
Brennan
Joe S
JS
Bridgham
John A
JA
Brown
Rob C
RC
Brown
Andrew A
AA
Buermann
Dale H
DH
Bundu
Abass A
AA
Burrows
James C
JC
Carter
Nigel P
NP
Castillo
Nestor
N
Chiara E Catenazzi
Maria
M
Chang
Simon
S
Neil Cooley
R
R
Crake
Natasha R
NR
Dada
Olubunmi O
OO
Diakoumakos
Konstantinos D
KD
Dominguez-Fernandez
Belen
B
Earnshaw
David J
DJ
Egbujor
Ugonna C
UC
Elmore
David W
DW
Etchin
Sergey S
SS
Ewan
Mark R
MR
Fedurco
Milan
M
Fraser
Louise J
LJ
Fuentes Fajardo
Karin V
KV
Scott Furey
W
W
George
David
D
Gietzen
Kimberley J
KJ
Goddard
Colin P
CP
Golda
George S
GS
Granieri
Philip A
PA
Green
David E
DE
Gustafson
David L
DL
Hansen
Nancy F
NF
Harnish
Kevin
K
Haudenschild
Christian D
CD
Heyer
Narinder I
NI
Hims
Matthew M
MM
Ho
Johnny T
JT
Horgan
Adrian M
AM
Hoschler
Katya
K
Hurwitz
Steve
S
Ivanov
Denis V
DV
Johnson
Maria Q
MQ
James
Terena
T
Huw Jones
T A
TA
Kang
Gyoung-Dong
GD
Kerelska
Tzvetana H
TH
Kersey
Alan D
AD
Khrebtukova
Irina
I
Kindwall
Alex P
AP
Kingsbury
Zoya
Z
Kokko-Gonzales
Paula I
PI
Kumar
Anil
A
Laurent
Marc A
MA
Lawley
Cynthia T
CT
Lee
Sarah E
SE
Lee
Xavier
X
Liao
Arnold K
AK
Loch
Jennifer A
JA
Lok
Mitch
M
Luo
Shujun
S
Mammen
Radhika M
RM
Martin
John W
JW
McCauley
Patrick G
PG
McNitt
Paul
P
Mehta
Parul
P
Moon
Keith W
KW
Mullens
Joe W
JW
Newington
Taksina
T
Ning
Zemin
Z
Ling Ng
Bee
B
Novo
Sonia M
SM
O'Neill
Michael J
MJ
Osborne
Mark A
MA
Osnowski
Andrew
A
Ostadan
Omead
O
Paraschos
Lambros L
LL
Pickering
Lea
L
Pike
Andrew C
AC
Pike
Alger C
AC
Chris Pinkard
D
D
Pliskin
Daniel P
DP
Podhasky
Joe
J
Quijano
Victor J
VJ
Raczy
Come
C
Rae
Vicki H
VH
Rawlings
Stephen R
SR
Chiva Rodriguez
Ana
A
Roe
Phyllida M
PM
Rogers
John
J
Rogert Bacigalupo
Maria C
MC
Romanov
Nikolai
N
Romieu
Anthony
A
Roth
Rithy K
RK
Rourke
Natalie J
NJ
Ruediger
Silke T
ST
Rusman
Eli
E
Sanches-Kuiper
Raquel M
RM
Schenker
Martin R
MR
Seoane
Josefina M
JM
Shaw
Richard J
RJ
Shiver
Mitch K
MK
Short
Steven W
SW
Sizto
Ning L
NL
Sluis
Johannes P
JP
Smith
Melanie A
MA
Ernest Sohna Sohna
Jean
J
Spence
Eric J
EJ
Stevens
Kim
K
Sutton
Neil
N
Szajkowski
Lukasz
L
Tregidgo
Carolyn L
CL
Turcatti
Gerardo
G
Vandevondele
Stephanie
S
Verhovsky
Yuli
Y
Virk
Selene M
SM
Wakelin
Suzanne
S
Walcott
Gregory C
GC
Wang
Jingwen
J
Worsley
Graham J
GJ
Yan
Juying
J
Yau
Ling
L
Zuerlein
Mike
M
Rogers
Jane
J
Mullikin
James C
JC
Hurles
Matthew E
ME
McCooke
Nick J
NJ
West
John S
JS
Oaks
Frank L
FL
Lundberg
Peter L
PL
Klenerman
David
D
Durbin
Richard
R
Smith
Anthony J
AJ
D041321:Chromosomes, Human, X / Q000235:genetics; D016384:Consensus Sequence / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics / Q000191:economics / Q000379:methods*; D005838:Genotype; D006801:Humans; D008297:Male; D009549:Nigeria; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*