Genome position and gene amplification

Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells

Expression profiling of 12 methotrexate resistant colonies with amplification of *

Unsupervised hierarchical clustering (Pearson) of genes with variable expression across the data set (SD ≥ 0.3) and present in >75% of samples (3,931 genes). Methotrexate resistant colonies represent four different integration sites, indicated by the shaded boxes below the dendrogram. Comparison of expression of target genes in the two clusters. The median absolute logratio change in expression of target genes in the right cluster compared to the left cluster is significantly higher than a similar comparison using 1,000 sets of 380 randomly selected genes (= 2.2e-16).<p><b>Copyright information:</b></p><p>Taken from "Genome position and gene amplification"</p><p>Genome Biology 2007;8(6):R120-R120.</p><p>Published online 21 Jun 2007</p><p>PMCID:PMC2394771.</p><p></p

Amplicons formed by two genomic regions, initially located on the different chromosomes

Chromosome 8 and 9 copy number profiles showing amplification on 9q and 8q. Organization of the amplicon. CTD-3145B15 (red) maps to the 9q telomere near the * insertion site and RP11-237F24 (green) to the region of amplification on chromosome 8 shown in (b). The chromosome 9 signals appear to flank the chromosome 8 material on this chromosome. Amplification of the region around * is indicated by the large hybridization signal from CTD-3145B15. The amplified DNA was determined to be located on chromosome 9 by hybridization of RP11-62H18 to 9pter (not shown). Thus, material from 9qter appears to be amplified on chromosome 9 and additional copies of material from the chromosome 9 amplicon are present on a separate chromosome together with amplified DNA from chromosome 8. Copy number profiles of chromosomes 19 (d) and 8 (e). Organization of the amplicon. RP11-691H23 (red) maps near the * integration site on chromosome 19 and RP11-175H20 (green) is one of the clones from the amplicon on chromosome 8 shown in (e). The chromosome 19 signals appear to flank a number of copies of chromosome 8, which could be as many as eight copies, since the CGH logratio = ~2. Two additional copies of RP11-691H23, mapping near * on chromosome 19, were also present on chromosome 19 (data not shown). Thus, amplified DNA near the * integration site is present and independently amplified on two chromosomes. 1M-42_9 CGH profile (chromosome 8) showing the * amplicon and its organization as determined by FISH. BAC clone RP11-91O11 (red) maps near the * integration site and is co-amplified with the distal part of chromosome 8 (RP11-237F24, green). The chromosomal region between the two co-amplified regions was lost. 1M-42_2 CGH profile (chromosome 8) and FISH analysis showing that the two regions of chromosome 8 were amplified as two independent amplicons on different chromosomes.<p><b>Copyright information:</b></p><p>Taken from "Genome position and gene amplification"</p><p>http://genomebiology.com/2007/8/6/R120</p><p>Genome Biology 2007;8(6):R120-R120.</p><p>Published online 21 Jun 2007</p><p>PMCID:PMC2394771.</p><p></p

Expression of genes mapping to the amplicon from methotrexate resistant colony 1M-89 6

Chromosome 19 copy number profile at approximately 1.4 Mb resolution (HumArray3.0) shows four discrete regions of amplification. Chromosome 19 copy number profile from the 32K BAC genome tiling path array in the amplified region showing the four regions of amplification detected on the lower resolution array and an additional small region distal to the others. The regions, ranging in size from 0.2 to 1.2 Mb, were amplified together in some cells as double minutes, while in others the amplified DNA was integrated into different chromosomes and present as a homogeneously staining region. Both copies of chromosome 19 were retained without rearrangement. As all regions are included together on the double minutes, their formation may have occurred by joining of broken pieces of DNA subsequent to resolution of stalled replication forks [63]. Expression levels of genes mapping to the five amplified regions plotted according to position on the human genome sequence. Expression levels are shown as the logratios of the signal intensities after hybridization of Cy3 labeled cDNA from the methotrexate resistant colony and Cy5 labeled cDNA from the untreated parent 1M-89 as reference. Shown is the list of genes in genomic order that map to the amplified regions according to the RefSeq database [64]. Genes that are expressed in this cell line with or without exposure to methotrexate are labeled in black and expression levels denoted by black dots. Genes present on the array, but not expressed in untreated or resistant cells, are colored by dark gray and represented by dots of the same color with zero change in expression. Genes not present on the array are listed in the upper line in light gray. Genes with logfold change >0.8 are indicated with an asterisk.<p><b>Copyright information:</b></p><p>Taken from "Genome position and gene amplification"</p><p>Genome Biology 2007;8(6):R120-R120.</p><p>Published online 21 Jun 2007</p><p>PMCID:PMC2394771.</p><p></p

Recurrent amplicon boundaries in 1M-42 methotrexate resistant clones and fragile sites

Chromosome 8 copy number profiles at approximately 1.4 Mb resolution. The vertical lines indicate the region from 99 to 105 Mb on chromosome 8 shown for hybridization of these same DNAs to the 32K genome tiling array.<p><b>Copyright information:</b></p><p>Taken from "Genome position and gene amplification"</p><p>Genome Biology 2007;8(6):R120-R120.</p><p>Published online 21 Jun 2007</p><p>PMCID:PMC2394771.</p><p></p

Parental * integration sites and copy number aberrations in methotrexate resistant colonies

Copy number profile of cell line HCT116+chr3 and positions of 13 * integrations. This near-diploid cell line is characterized by partial chromosomal gains on chromosomes 3, 8, 10, 12, 16, losses on chromosomes 4, 16 and 10 and homozygous deletion on chromosome 16. Shown are the logratios on BAC clones ordered according to genome position (UCSC Genome Browser, May 2004 freeze). Arrows indicate the positions of integration of one copy of * as mapped by inverse PCR to the human genome sequence. Heatmap representation of copy number changes detected by array CGH in 82 methotrexate resistant colonies from 12 different insertion sites. Each column represents one resistant colony. Resistant colonies from each * integration site were clustered according to their copy number changes. Positions of the insertion sites are indicated by the arrowheads. Individual BAC clones are shown as rows and ordered according to their genome position (UCSC Genome Browser, May 2004 freeze). Copy number losses are indicated in red, gains in green and amplifications as yellow dots.<p><b>Copyright information:</b></p><p>Taken from "Genome position and gene amplification"</p><p>Genome Biology 2007;8(6):R120-R120.</p><p>Published online 21 Jun 2007</p><p>PMCID:PMC2394771.</p><p></p