cell line  (ATCC)

Journal:

Article Title: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping

doi: 10.1101/gr.5402306

Figure Lengend Snippet: Analyzing heterogeneous tumor samples. DNA from a tumor cell line was mixed with matched normal DNA at ratios of 0%, 25%, 50%, 75%, and 100% and analyzed on the Human-1 (109K) BeadChip. The genome profile of chromosome 13 is shown as an example. (A) No aberrations are seen in the sample containing 100% normal gDNA. (B) No discernable differences in the log R ratio are seen in a sample composed of 75% normal and 25% tumor. It is also difficult to determine if there are any changes in the allelic frequency. (C) At 50% normal and 50% tumor DNA, deflections in the log R ratio appear. Changes in the AF are also seen, although it is difficult to establish the nature of each aberration. At these levels, an allelic duplication event and allelic LOH bear resemblance to each other. (D) At 25% normal and 75% tumor gDNA, the nature of each type of aberration becomes more apparent. For example, the large decrease in the log R ratio in the center of the plot denotes a potential region with a deletion, which was not easily discernable in C. (E) The genoplot from a pure (100%) tumor sample. A homozygous deletion can be seen in the center of the plot, visualized by a decrease in the log R ratio. (F) A region exhibiting LOH is observed on chromosome 3 in a paired colon tumor patient sample analyzed on the HumanHap300 BeadChip. A decrease in the log R ratio indicates a loss of copy number. The AF is divided into two populations(∼0.33 and ∼0.67), suggesting that this sample contains ∼67% normal cells. The blue line shown for all log R ratio profiles indicates a 250-kb and a 100-kb moving median for the Human-1 and HumanHap300 BeadChips, respectively.

Article Snippet: To evaluate the differences between single and paired sample modes, we used paired breast tumor cell lines obtained from ATCC (CRL-2325D, CRL-2324D).

Techniques:

Journal:

Article Title: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping

doi: 10.1101/gr.5402306

Figure Lengend Snippet: Paired versus single sample analysis. Varying starting inputs of DNA (10 ng and 750 ng) from a paired breast tumor cell line were hybridized to a multisample BeadChip containing a subset of loci (∼33,000) from the HumanHap300 product. In addition, Phi29 was used to amplify 10 ng of gDNA, and 750 ng of this amplified product was used in the initial whole-genome amplification step. Overall, we find that the effect of different inputs of gDNA on the resulting genomic profiles is ameliorated by paired-sample analysis. (A) In the single sample mode, the variability (standard deviation) in the log R ratio is shown as gray dots for Phi29-amplified gDNA, 10 ng of input DNA, and 750 ng of input gDNA (from top to bottom). (B) In the paired-sample mode, the variation in the log R ratio across chromosome 8 is reduced for the same samples. For reference, the AF for the tumor sample is shown on the bottom left and the |Allele Freq subject-reference| for the same tumor sample with paired analysis is shown on the bottom right. Using paired-sample analysis, the allele frequency difference between normal and tumor genotypes is very distinct. Where applicable, a 500-kb moving median was used (blue line).

Article Snippet: To evaluate the differences between single and paired sample modes, we used paired breast tumor cell lines obtained from ATCC (CRL-2325D, CRL-2324D).

Techniques: Amplification, Whole Genome Amplification, Standard Deviation