<i>RB1</i> allelic imbalance in family F5.

<p>The normalized SNaPshot cDNA ratio between the mutant and the wild type alleles are indicated below each carrier individual with corresponding SNaPshot results. The c.1981C>T/p.Arg661Trp mutant allele “T” is indicated in green and the wild type allele “C” is indicated in blue. Dotted symbols: unaffected carriers; half-blackened symbols: unilateral Rb.</p

Family F7 segregating the <i>RB1</i> c.1981C>T/p.Arg661Trp mutation.

<p>Genotype is provided for tested members as m/n for heterozygous carriers and n/n for homozygous wild-type. OC indicates obligate carriers. Blackened symbols: bilateral Rb; half-blackened symbols: unilateral Rb; dotted symbols: unaffected carriers; dashed symbols: deceased.</p

Methylation analyses of <i>RB1</i> CpG islands using methylation array.

<p>X axis represents the position on chromosome 13. Y axis represents overall methylation level. CpG106 localizing in <i>RB1</i> promoter is shown in green, CpG42 is shown in pink and CpG85 is shown in blue. For each sample, multiple CpGs are located within an island and each dot represents a single result. A: Normal retina. CpG85 showing approximately 50% of methylation. B: Tumor sample. CpG85 displaying a hypermethylated profile.</p

Expression imbalance in 20 carriers of the c.1981C>T/p.Arg661Trp mutation.

<p>Transmission in family F5 is detailed <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005888#pgen.1005888.g003" target="_blank">Fig 3</a>. First degree relatives are indicated for the other families. See text for ratio calculation. (*) See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005888#pgen.1005888.g003" target="_blank">Fig 3</a>.</p

Description of variants predicted as deleterious by SIFT and as probably damaging by Polyphen.

<p>Ref.: Reference allele</p><p>Alt.: Alternative allele</p><p>Freq.: Minor allele frequency observed in our data</p><p>a. a. change: amino acid change</p><p>Description of variants predicted as deleterious by SIFT and as probably damaging by Polyphen.</p

Description of variants observed but unknown in MITOMAP.

<p>Pos.: position on mitochondrial genome</p><p>Ref.: Reference allele</p><p>Alt.: Alternative allele</p><p>Description of variants observed but unknown in MITOMAP.</p

Inclusion categories of selected index cases.

<p>Inclusion categories of selected index cases.</p

Additional file 1: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers

Table S1. Genomic regions showing copy number loss or loss/LOH in at least 70% of ATM-associated tumours. (XLSX 70 kb

Additional file 3: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers

Table S2. Comparison of genes altered at the copy number level between ATM-associated tumours and tumours from TCGA. (XLSX 13 kb

Associations between SNPs in 9p22.2 with ovarian cancer risk for <i>BRCA1</i> and <i>BRCA2</i> mutation carriers.

<p>In each plot, the purple diamond corresponds to the strongest associated SNP and the colour code indicates the linkage disequilibrium with respect to this variant. Horizontal lines indicate the -log₁₀ p-value such that the SNPs above the line are the potential causal ones. This set was defined based on a likelihood ratio for a particular SNP as being less or equal than 100, relative to the most likely variant and r²>0.1. (A) <i>BRCA1</i> mutation carriers, (B) <i>BRCA2</i> mutation carriers.</p