title: The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Mao
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.
authors.forename: Serban
authors.initials: S
authors.lastname: Ciotlos
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.
authors.forename: Rebecca Yu
authors.initials: RY
authors.lastname: Zhang
authors.affiliation: Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.|PersonalGenomes.org, 423 Brookline Avenue, #323, Boston, MA, 02215, USA.
authors.forename: Madeleine P
authors.initials: MP
authors.lastname: Ball
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Chin
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.
authors.forename: Paolo
authors.initials: P
authors.lastname: Carnevali
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.
authors.forename: Nina
authors.initials: N
authors.lastname: Barua
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.
authors.forename: Staci
authors.initials: S
authors.lastname: Nguyen
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.
authors.forename: Misha R
authors.initials: MR
authors.lastname: Agarwal
authors.affiliation: Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.|Curoverse Inc., 212 Elm St, 3rd Floor, Somerville, MA, 02144, USA.
authors.forename: Tom
authors.initials: T
authors.lastname: Clegg
authors.affiliation: Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.|Curoverse Inc., 212 Elm St, 3rd Floor, Somerville, MA, 02144, USA.
authors.forename: Abram
authors.initials: A
authors.lastname: Connelly
authors.affiliation: Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.|Curoverse Inc., 212 Elm St, 3rd Floor, Somerville, MA, 02144, USA.
authors.forename: Ward
authors.initials: W
authors.lastname: Vandewege
authors.affiliation: Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.|Curoverse Inc., 212 Elm St, 3rd Floor, Somerville, MA, 02144, USA.
authors.forename: Alexander Wait
authors.initials: AW
authors.lastname: Zaranek
authors.affiliation: Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
authors.forename: Preston W
authors.initials: PW
authors.lastname: Estep
authors.affiliation: Harvard Personal Genome Project, Harvard Medical School, NRB 238, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA.|BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Radoje
authors.initials: R
authors.lastname: Drmanac
authors.affiliation: Complete Genomics, Inc., 2071 Stierlin Ct., Mountain View, CA, 94043, USA. bpeters@completegenomics.com.|BGI-Shenzhen, Shenzhen, 518083, China. bpeters@completegenomics.com.
authors.forename: Brock A
authors.initials: BA
authors.lastname: Peters
mesh_terms: D004247:DNA / Q000097:blood; D015894:Genome, Human; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA
keywords: Complete genomics; Haplotypes; LFR; Long fragment read; PGP; Personal Genome Project; Whole genome sequencing