Patient and cell line characteristics: diagnosis, karyotype and <i>EVI1</i> FISH and RT-qPCR results.

<p>Bold formatting indicates the 3q26 rearrangement.</p>*<p>AML = acute myeloid leukemia and MDS = myelodysplastic syndrome.</p>†<p>The chromosomal aberration implicating the <i>EVI1</i> locus is indicated with bold formatting.</p>‡<p>Positive for <i>EVI1</i> FISH/qRT-PCR = +and negative for <i>EVI1</i> FISH/qRT-PCR = −.</p

Array CGH results of chromosome 7 deletions.

<p>Bold formatting indicates deletions on the 7q arm.</p>*<p>Based upon the UCSC genome browser (<a href="http://genome.ucsc.edu/cgi-bin/hgGateway" target="_blank">http://genome.ucsc.edu/cgi-bin/hgGateway</a>, NCBI Build 36.1).</p>†<p>Between brackets is the total number of genes residing in the deleted area.</p>‡<p>Homozygous deletion.</p

Overview of deletions in cell lines and patients.

<p>Chromosome view of chromosome 7 deletions in the cell lines Kasumi-3, MUTZ-3 and UCSD-AML1 and in cases 2, 3 and 9. Deletions are indicated using grey bars.</p

Array CGH profile of chromosome 7 (141 Mb–153 Mb) for Kasumi-3, MUTZ-3 and UCSD-AML1.

<p>A) Array CGH profile of Kasumi-3, B) MUTZ-3 and C) UCSD-AML1 indicating the 0.39 Mb SRO on 7q35 and the 1.33 Mb SRO on chromosome bands 7q35–q36. Log₂-ratios of the clones are depicted by vertical dots corresponding to the respective genomic position (NCBI build 36). Deletions are shown in red. The SROs are indicated with a purple box. The bottom of the figure shows the genomic position with an indication of known CNVs as present in the Database of Genomic Variants (<a href="http://projects.tcag.ca/variation/" target="_blank">http://projects.tcag.ca/variation/</a>). Regions of segmental duplication are displayed using black and grey boxes indicating identical genomic regions. A screenshot of the UCSC Genome Browser (NCBI build 36, <a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>) shows an overview of the known RefSeq genes in the 1.33 Mb critical region.</p

Genes located in the 1.33 Mb SRO on 7q35−q36.

<p>Genes located in the 1.33 Mb SRO on 7q35−q36.</p

Name and position of FISH probes.

*<p>UCSC genome browser database (<a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>).</p

Additional file 1: of Increased chromosomal radiosensitivity in asymptomatic carriers of a heterozygous BRCA1 mutation

Primers. The primer sequences (both forward and reverse). (PDF 29 kb

Phenotypic impact of observed genetic variants in the <i>PSIP1</i> coding region.

<p>Box-plots showing the association of individual observed SNPs in the coding region with CD4 decline (top), average log viral load (middle) and LEDGF/p75 mRNA expression (bottom).The data are combined for Africans and Caucasians. SNPs not in accordance with Hardy-Weinberg law (rs35678110) were excluded. In case of insufficient data to create a boxplot (limited amount of data points) a bar representing the mean of the values is shown.</p

Patient characteristics.

<p>Overview of the patient characteristics, divided for Ghent and RIS cohort and per ethnicity (Africans, Caucasians). The number of patients per subcategory is presented for sex, ethnicity, disease progression groups and current antiretroviral treatment.</p><p>IQR = interquartile range; N = number; LTNP = long-term non-progressor; ART = antiretroviral treatment.</p

Observed genetic variants in the <i>PSIP1</i> non-coding region.

†<p>signifies variants not in accordance with Hardy Weinberg law.</p>§<p>signifies p<0.001, after Bonferroni correction.</p><p>Overview of the observed SNPs in the <i>PSIP1</i> non-coding region. Both expected and observed minor allele frequencies (MAF) are shown per ethnicity.</p><p>HGVS = Human Genomic Variation Society; SNP = single nucleotide polymorphism; MAF = minor allele frequency; NA = not assessed; rs = referenced SNP id number; ss = submitted SNP id number.</p