Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

Brock A. Peters (), Bahram G. Kermani, Andrew B. Sparks, Oleg Alferov, Peter Hong, Andrei Alexeev, Yuan Jiang, Fredrik Dahl, Y. Tom Tang, Juergen Haas, Kimberly Robasky, Alexander Wait Zaranek, Je-Hyuk Lee, Madeleine Price Ball, Joseph E. Peterson, Helena Perazich, George Yeung, Jia Liu, Linsu Chen, Michael I. Kennemer, Kaliprasad Pothuraju, Karel Konvicka, Mike Tsoupko-Sitnikov, Krishna P. Pant, Jessica C. Ebert, Geoffrey B. Nilsen, Jonathan Baccash, Aaron L. Halpern, George M. Church and Radoje Drmanac ()
Additional contact information
Brock A. Peters: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Bahram G. Kermani: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Andrew B. Sparks: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Oleg Alferov: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Peter Hong: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Andrei Alexeev: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Yuan Jiang: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Fredrik Dahl: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Y. Tom Tang: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Juergen Haas: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Kimberly Robasky: Harvard Medical School
Alexander Wait Zaranek: Harvard Medical School
Je-Hyuk Lee: Harvard Medical School
Madeleine Price Ball: Harvard Medical School
Joseph E. Peterson: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Helena Perazich: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
George Yeung: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Jia Liu: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Linsu Chen: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Michael I. Kennemer: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Kaliprasad Pothuraju: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Karel Konvicka: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Mike Tsoupko-Sitnikov: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Krishna P. Pant: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Jessica C. Ebert: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Geoffrey B. Nilsen: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Jonathan Baccash: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
Aaron L. Halpern: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA
George M. Church: Harvard Medical School
Radoje Drmanac: Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA

Nature, 2012, vol. 487, issue 7406, 190-195

Abstract: Abstract 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.

Date: 2012
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DOI: 10.1038/nature11236

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