Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells.
Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ∼100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.
Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA. bpeters@completegenomics.com
Brock A
BA
Peters
Bahram G
BG
Kermani
Andrew B
AB
Sparks
Oleg
O
Alferov
Peter
P
Hong
Andrei
A
Alexeev
Yuan
Y
Jiang
Fredrik
F
Dahl
Y Tom
YT
Tang
Juergen
J
Haas
Kimberly
K
Robasky
Alexander Wait
AW
Zaranek
Je-Hyuk
JH
Lee
Madeleine Price
MP
Ball
Joseph E
JE
Peterson
Helena
H
Perazich
George
G
Yeung
Jia
J
Liu
Linsu
L
Chen
Michael I
MI
Kennemer
Kaliprasad
K
Pothuraju
Karel
K
Konvicka
Mike
M
Tsoupko-Sitnikov
Krishna P
KP
Pant
Jessica C
JC
Ebert
Geoffrey B
GB
Nilsen
Jonathan
J
Baccash
Aaron L
AL
Halpern
George M
GM
Church
Radoje
R
Drmanac
D000483:Alleles; D002460:Cell Line; D005260:Female; D020868:Gene Silencing; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D009154:Mutation; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods* / Q000592:standards