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

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. A new DNA analysis method termed long fragment read technology is described, and the approach is used to determine parental haplotypes and to sequence human genomes cost-effectively and accurately from only 10 to 20 cells. Many of the hoped-for advances in the field of personalized medicine are dependent on the development of low-cost genome-sequencing technology that combines clinical accuracy with the ability to describe the context (the genetic haplotype) in which variants occur on an individual chromosome. The technique described here, termed long-fragment read technology, is similar to that used to sequence long single DNA molecules, but without DNA cloning or chromosome separation. The authors demonstrate the potential of this approach by generating seven accurate human genome sequences, as well as haplotype data, from samples containing just 10–20 cells. This advance shows that it should be possible to achieve clinical quality and scale in personal genome sequencing of microbiopsies and circulating cancer cells.