IBD mapping of founder mutations in recurrent regions of LOH.

<p>This diagram illustrates the principles underlying our method. A founder mutation (red star on the schematic diagram of chromosomes) spreads through a population within a chromosome fragment (in red) inherited from the ancestral founder (A). Due to crossing-overs (dashed lines) between homologous chromosomes at meiosis, this chromosome fragment is shortened over generations, such that mutation carriers (indicated in red) eventually harbor only a short identical by descent (IBD) haplotype around the mutant gene (B). In addition, the wild-type counterpart of germline mutations is frequently lost by LOH in tumors, such that the founder mutation typically lies within a minimal region of LOH (C). As a result, the founder mutation is located within a haplotype conserved in each mutation carrier (peak IBD score), in the minimal region of LOH (D).</p

Power to detect conserved haplotypes as a function of haplotype length and prevalence.

<p>Power to detect conserved haplotypes as a function of haplotype length and prevalence.</p

Power analysis with simulated data.

<p>The performance of FounderTracker was assessed under various conditions, by comparison with the DASH method. The ability of each method to detect conserved haplotypes was established as a function of haplotype length (1 to 5 cM) and prevalence (2 to 10% of the samples). For each condition, the mean ROC curve was established by applying each method to 100 simulated datasets.</p

Detection of a long conserved haplotype around <i>SDHD</i> gene in two paragangliomas.

<p>(A) LOH analysis revealed 10 chromosome arms with LOH frequency >20% in our set of 30 pheochromocytomas and paragangliomas (top). These regions were analyzed using FounderTracker to detect conserved haplotypes, revealing a single significant region on chromosome arm 11q (bottom). (B) Visualization of the significant region identified on chromosome 11 with the Integrative Genomics Viewer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035897#pone.0035897-Robinson1" target="_blank">[44]</a>. The IBD score is represented as a blue line above tumor haplotypes. Haplotypes are represented as series of blue and yellow vertical lines, corresponding to SNPs with respectively “A” and “B” genotype, according to Illumina nomenclature. The significant region detected by FounderTracker corresponds to the long haplotype that is identical in tumors HS_048 and HS_158, and results in a high IBD score for this segment. This region contains 32 genes, including <i>SDHD</i> (indicated in red).</p

Haplotype inference from tumor SNP profiles.

<p>Genotypes can be inferred from SNP array data, with the B allele frequency (BAF), which characterizes the fluorescence ratio between the A and B alleles at each locus: <i>BAF = B/</i>(<i>A+B</i>). In constitutive DNA, each SNP is present as two alleles. The genotype of each SNP (AA, AB, or BB) can thus be determined from the BAF (0, 0.5 or 1, respectively), but not the haplotype of each chromosome. By contrast, if one of the two copies has been lost by LOH in the tumor, the tumor SNP profile directly reflects the haplotype of the chromosome that is retained in the tumor. If paired constitutive and tumor DNA samples are available, the haplotype of the lost chromosome can be reconstructed by comparing the two profiles.</p

ROC analysis of the <i>BRCA2</i> signature in the validation set.

<p>Each tumor was given a score that was a weighted sum of the mean centered gene expression levels for each gene in the signature. The validation set contained 19 <i>BRCA2</i> and 12 <i>BRCAX</i> tumors. The AUC was 0.76.</p

<i>BRCA2</i> signature genes.

<p>Footnote. t: moderated t-statistic for 66 genes that best discriminate between <i>BRCA2</i> and <i>BRCAX</i> tumors. p: p-value after Benjamini Hochberg correction (all genes had an unadjusted p-value <0.0001).</p

GSEA for loss of chromosomal bands.

<p>Footnote. The genes column shows the number of genes used to score the band. The nominal, FDR and FWER p-values were all <0.001. ES, enrichment score; NES normalized enrichment score.</p

FISH with probes in the region of common deletion on chromosomes 13 and 14.

<p>Footnote. The table shows the percentage of nuclei with less than the modal ploidy or with ploidy = 1 for both the centromeric and the deletion probes. Tumours A-M were not characterized by CGH.</p

Cumulative rates of gain and loss for tumors analyzed by CGH (red, 4 <i>BRCA2</i>-mutant tumors; black, 24 <i>BRCAX</i> tumors).

<p>A, All chromosomes; B, Chromosome 13; C, Chromosome 14. Each vertical line in B & C corresponds to an individual BAC probe. When the red line reaches −1, all of the tumors showed loss for that probe.</p