Open Access Highly Accessed Research article

In depth comparison of an individual’s DNA and its lymphoblastoid cell line using whole genome sequencing

Dorothee Nickles1, Lohith Madireddy1, Shan Yang2, Pouya Khankhanian1, Steve Lincoln2, Stephen L Hauser1, Jorge R Oksenberg1 and Sergio E Baranzini1*

Author Affiliations

1 Department of Neurology, University of California San Francisco, 513 Parnassus Ave, Room S-256, San Francisco, CA, 94143-0435, USA

2 Complete Genomics, Inc, Mountain View, CA, USA

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BMC Genomics 2012, 13:477  doi:10.1186/1471-2164-13-477

Published: 14 September 2012

Additional files

Additional file 1:

High resolution karyotype of cell line. The cell line exhibits a normal karyotype.

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Additional file 2:

Comparison with previously published whole exome/genome datasets. Comparison of a number of sequencing characteristics with previously published genomes/exomes.

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Additional file 3:

Number of chromosomal rearrangements in both genomes. Information on all high confidence junctions identified per genome and the number of unique junctions, specifying the number of junctions with a frequency of less than or equal to 75% (i.e. seen in less than or exactly 75% of all genomes sequenced by CGI at the time) and the percentage of inter-chromosomal rearrangements.

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Additional file 4:

Chromosomal rearrangements that were only reported for the genomic DNA sample. This file contains details on the chromosomal rearrangements (junctions) unique to the genomic DNA sample.

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Additional file 5:

Chromosomal rearrangements that were only reported for the cell line sample. This file contains details on the chromosomal rearrangements (junctions) unique to the cell line sample.

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Additional file 6:

Copy number variation (CNV) differences between genomic and cell line DNA. Copy number variation (CNV) differences between genomic and cell line DNA.

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Additional file 7:

Analysis strategy and overall differences found between the two sequenced genomes.A. Workflow of the genome analysis. Besides various data files and software tools provided by Complete Genomics (blue), Bioconductor packages and R (green) were used for analysis. B. Gross comparison statistics as output from cgatools calldiff SuperlocusStats. “Identical” sequences are sequences that are fully called and identical in both genomes. “Consistent” sequences are not fully called, but what is called is identical in both genomes. “Only C” and “Only G” denote variants only found in cell line and genomic DNA, respectively. At “mismatch” positions, the two genomes are different from each other and different from the reference. “Phase-mismatch” means that even though the two genomes have the same alleles, the phase of the alleles differ. The two genomes don’t have any “ploidy mismatches” because genomes are from the same male person (with one X and one Y chromosome).

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Additional file 8:

Distribution of filtered variants across the genome. All variants passing a SomaticScore cut-off of 0.5 in the CT (outer circle) and GT analysis (inner circle) are plotted, respectively. SNPs are displayed in orange, insertions in blue, substitutions in green and deletion in yellow.

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Additional file 9:

Filtered SNPs unique to the cell line targeting gene loci containing a coding sequence. Filtered SNPs unique to the cell line targeting gene loci containing a coding sequence.

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Additional file 10:

Protocol for the creation of lymphoblastoid cell line. The detailed protocol that was used to create the lymphoblastoid cell line that was studied. (DOCX 136 kb)

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Additional file 11:

Quality of the DNA sent for sequencing. 400 ng of DNA were loaded per lane on a 1% agarose gel. Marker: 1 kB DNA ladder (New England Biolabs, Ipswich, MA). No DNA degradation was detectable. Samples were run on the same gel, but on opposite sides.

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