Can I get cell lines for IGSR samples?


In almost all cases, cell lines are available. For most samples, cell lines are held at the Coriell Cell Repository. Samples from HGDP are available at CEPH.

Coriell hold detailed information on the 1000 Genomes Project populations and sample collection process.

Individual sample pages in the data portal include links to the repository where the cell line is available.

The main exception to the above is around 400 samples in the Gambian Genome Variation Project (GGVP), for which cell lines are not available.

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What was the source of the DNA for sequencing?


For the 1000 Genomes Project, the early samples were taken from the HapMap project and these all sourced their DNA from cell line cultures but some libraries were produced from blood.

The sample spreadsheet for the 1000 Genomes Project has annotation about the EBV coverage and the annotated sample source of the sequencing data in columns 59 and 60 of the 20130606_sample_info.txt

This spreadsheet gives the aligned coverage of EBV and then the annotation if Coriell stated the sample was sourced from blood. Please note some samples were sequenced both using sample from blood and LCL transformed cells but this data was not analysed independently so the EBV coverage will be high. Also some samples with very low EBV coverage (ie ~1x) may be from blood but just indicate an endogenous infection of EBV in the individual sampled.

For studies other than the 1000 Genomes Project, commonly the DNA is derived from cell lines as the original blood samples are limited. Further details, however, can be found by consulting the publications.

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