The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes

Gigascience. 2016 Oct 11;5(1):42. doi: 10.1186/s13742-016-0148-z.


Background: Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information.

Findings: As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data.

Conclusions: These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

Keywords: Complete genomics; Haplotypes; LFR; Long fragment read; PGP; Personal Genome Project; Whole genome sequencing.

MeSH terms

  • DNA / blood
  • Genome, Human*
  • Haplotypes
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*


  • DNA