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Data released on October 10, 2016

Supporting data for "The Whole Genome Sequences and Experimentally Phased Haplotypes of over 100 Personal Genomes"

Agarwal, M, R; Ball, M, P; Barua, N; Carnevali, P; Chin, R; Church, G, M; Ciotlos, S; Clegg, T; Connelly, A; Drmanac, R; Estep, P, W; Mao, Q; Nguyen, S; Peters, B, A; Vandewege, W; Zaranek, A, W; Zhang, R, Y (2016): Supporting data for "The Whole Genome Sequences and Experimentally Phased Haplotypes of over 100 Personal Genomes" GigaScience Database. http://dx.doi.org/10.5524/100242 RIS BibTeX Text

Since the completion of the Human Genome Project in 2003 it has been estimated that over 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 as such are missing an important aspect of genome biology. In addition, much of the genomic data generated is not available to the public and lacks phenotypic information.
As part of the Personal Genome Project (PGP), 184 participants’ blood samples were collected and processed with Complete Genomics’ Long Fragment Read (LFR) technology. Here we report the results for the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X of 114 of these samples. This level of coverage is approximately 3 fold higher than the read coverage applied to most whole human genome assemblies and was done to ensure the highest quality results. Currently only 114 genomes from this data set are freely available on GigaDB and are associated with rich phenotypic data provided in this manuscript. It is our expectation that all 184 participants’ genomes will be made freely available in the near future, as soon as the individuals concerned have reviewed their own genomes prior to release in accordance with the PGP agreement.
Twenty genomes were sequenced at least two times using independently made LFR barcoded libraries for reproducibility analyses. Additionally, 7 genomes were also sequenced using Complete Genomics’ standard non-barcoded library process.
These genomes represent a unique source of haplotype and phenotype data for the scientific community. In addition, we report 2.6 million high quality rare variants not previously identified in dbSNP or Phase 3 1000 Genomes Project (1KG) data. The data presented here should help expand our understanding of the human genome evolution and functioning.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-016-0148-z

Additional information:

http://personalgenomes.org/

https://my.pgp-hms.org/

Accessions (data not in GigaDB):

dbGaP: phs000905.v1.p1

Keywords:

Long Fragment Read LFR Complete Genomics Personal Genome Project PGP WGS Haplotypes 

Genomic

http://gigadb.org/images/data/cropped/100242.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
hu01F73B9606HumanhumanHomo sapiens Age:21-29
Sex:Female
Ethnicity:White
...
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hu02C8E39606HumanhumanHomo sapiens Age:50-59
Sex:Female
Ethnicity:White
...
+
hu03E3D29606HumanhumanHomo sapiens Age:30-39
Sex:Male
Ethnicity:White
...
+
hu0486D69606HumanhumanHomo sapiens Age:50-59
Sex:Male
Ethnicity:White
...
+
hu04D9CD9606HumanhumanHomo sapiens Age:21-29
Sex:Male
Ethnicity:White
...
+
hu066C789606HumanhumanHomo sapiens Age:30-39
Sex:Female
Ethnicity:White
...
+
hu085B6D9606HumanhumanHomo sapiens Age:30-39
Sex:Female
Ethnicity:White
...
+
hu093F8B9606HumanhumanHomo sapiens Age:50-59
Sex:Female
Ethnicity:White
...
+
hu0BCA459606HumanhumanHomo sapiens Age:50-59
Sex:Male
Ethnicity:White
...
+
hu0E7AAF9606HumanhumanHomo sapiens Age:21-29
Sex:Female
Ethnicity:White
...
+
Displaying 1-10 of 183 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
hu646527archiveUNKNOWN39.73 GB2016-09-02
huEAE6C8archiveUNKNOWN39.55 GB2016-09-02
hu66D0AAarchiveUNKNOWN37.71 GB2016-09-02
hu02C8E3archiveUNKNOWN37.93 GB2016-09-02
hu6EDC7EarchiveUNKNOWN38.81 GB2016-09-02
hu904B18archiveUNKNOWN37.21 GB2016-09-02
hu4C20BCarchiveUNKNOWN37.85 GB2016-09-02
hu83BC6AarchiveUNKNOWN37.01 GB2016-09-02
hu87C6A9archiveUNKNOWN38.14 GB2016-09-02
hu0E7AAFarchiveUNKNOWN38.65 GB2016-09-02
Displaying 1-10 of 116 File(s).

History:

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