Genetic structure and pathogenicity of populations of Phytophthora infestans from organic potato crops in France, Norway, Switzerland and the United Kingdom

Genetic variation and pathogenicity of Pbytophthora infestans isolates collected from organic potato crops of the susceptible cv. Bintje and the moderately resistant cv. Sante were assessed in France, Norway, and the United Kingdom in 2001 and in Switzerland in 2001 and 2002. Population structures differed considerably between the four P. infestans populations. Those from France, Switzerland and the UK were mainly clonal populations showing restricted levels of genetic diversity, whilst those from Norway were mixed A1 and A2 mating type populations with high levels of genetic diversity, suggesting periodical sexual reproduction. Isolates collected from cv. Bintje were on average more aggressive than or comparable to isolates from cv. Sante. Race complexity varied considerably between the regional P. infestans populations, with isolates from France and Switzerland showing the highest number of virulence factors. In all pathogen samples but the French, isolates collected from cv. Sante were more complex than isolates collected from cv. Bintje. No directional selection towards increased aggressiveness towards the more resistant cultivar Sante was observed. This suggests that there is no shift towards increased levels of pathogenicity in P. infestans populations following the large-scale introduction of more resistant potato varieties in organic production systems in Europe

Age-Related Somatic Structural Changes in the Nuclear Genome of Human Blood Cells

Structural variations are among the most frequent interindividual genetic differences in the human genome. The frequency and distribution of de novo somatic structural variants in normal cells is, however, poorly explored. Using age-stratified cohorts of 318 monozygotic (MZ) twins and 296 single-born subjects, we describe age-related accumulation of copy-number variation in the nuclear genomes in vivo and frequency changes for both megabase- and kilobase-range variants. Megabase-range aberrations were found in 3.4% (9 of 264) of subjects ≥60 years old; these subjects included 78 MZ twin pairs and 108 single-born individuals. No such findings were observed in 81 MZ pairs or 180 single-born subjects who were ≤55 years old. Recurrent region- and gene-specific mutations, mostly deletions, were observed. Longitudinal analyses of 43 subjects whose data were collected 7–19 years apart suggest considerable variation in the rate of accumulation of clones carrying structural changes. Furthermore, the longitudinal analysis of individuals with structural aberrations suggests that there is a natural self-removal of aberrant cell clones from peripheral blood. In three healthy subjects, we detected somatic aberrations characteristic of patients with myelodysplastic syndrome. The recurrent rearrangements uncovered here are candidates for common age-related defects in human blood cells. We anticipate that extension of these results will allow determination of the genetic age of different somatic-cell lineages and estimation of possible individual differences between genetic and chronological age. Our work might also help to explain the cause of an age-related reduction in the number of cell clones in the blood; such a reduction is one of the hallmarks of immunosenescence

Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer

Sporadic breast cancer (SBC) is a common disease without robust means of early risk prediction in the population. We studied 282 females with SBC, focusing on copy number aberrations in cancer-free breast tissue (uninvolved margin, UM) outside the primary tumor (PT). In total, 1162 UMs (1-14 per breast) were studied. Comparative analysis between UM(s), PT(s), and blood/skin from the same patient as a control is the core of the study design. We identified 108 patients with at least one aberrant UM, representing 38.3% of cases. Gains in gene copy number were the principal type of mutations in microscopically normal breast cells, suggesting that oncogenic activation of genes via increased gene copy number is a predominant mechanism for initiation of SBC pathogenesis. The gain of ERBB2, with overexpression of HER2 protein, was the most common aberration in normal cells. Five additional growth factor receptor genes (EGFR, FGFR1, IGF1R, LIFR, and NGFR) also showed recurrent gains, and these were occasionally present in combination with the gain of ERBB2. All the aberrations found in the normal breast cells were previously described in cancer literature, suggesting their causative, driving role in pathogenesis of SBC. We demonstrate that analysis of normal cells from cancer patients leads to identification of signatures that may increase risk of SBC and our results could influence the choice of surgical intervention to remove all predisposing cells. Early detection of copy number gains suggesting a predisposition toward cancer development, long before detectable tumors are formed, is a key to the anticipated shift into a preventive paradigm of personalized medicine for breast cancer.De 2 första författarna delar förstaförfattarskapet.</p

Graphical summary of variation in a presumptive regulatory VNTR containing region.

<p>Panel <b>A</b> shows an overview of approximately 2 Mb locus on 21q, around four genes encoding functionally related receptors; <i>IFNAR2</i>, <i>IL10Rβ</i>, <i>IFNAR1</i> and <i>IFNGR2</i>. Panel <b>B</b> is zooming on the position of the hypervariable region (HVR, red box), which is located approximately 4 kb upstream from the transcription start site of the <i>IFNAR1</i> gene and is flanked by CpG-islands (green boxes). The last three and the first three exons of <i>IL10Rβ</i>, and <i>IFNAR1</i>, respectively, are shown as grey boxes. Panel <b>C</b> is showing the size and position of HVR according to the most common allele (HVR1098, see below panel D) in relation to the CpG island. Positions of PCR and sequencing primers used in the analysis of the locus are also displayed. Yellow boxes indicate the position of the non-repetitive anchor 1 (A1) and anchor 2 (A2) sequences, that are immediately flanking the repeated segments and were used for alignments of sequence reads. Panel <b>D</b> shows a summary of eight HVR-alleles from the studied samples, which were identified based on Sanger sequencing results of PCR fragments sub-cloned in plasmids. The displayed alleles are ordered from longest to shortest according to size from anchor 1 (A1) to anchor 2 (A2) sequences. Summary of sizes for all 14 different HVR-alleles is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067752#pone-0067752-t001" target="_blank">Table 1</a>. Sizes of fragments (in base pairs) are given between non-repetitive A1 and A2 sequences and between primers p1 and p8, which were used for PCR amplification from genomic DNA. Asterisk (*) indicates the most frequent allele (HVR1098), which is in agreement with the reference sequence according to NCBI sequence build 36.3. The allele frequency shown here is taking into account only the nine alleles, where the entire sequence could be unequivocally determined using Sanger sequencing. The most common variation encompasses the variable number of 32 base pair segments; i.e. indel 2, indel 3, indel 4, and indel 5. The latter indel 5 is composed of 6 repeated 32 base pair segments (HVR1066). However, there are also indels containing shorther segments; e.g. indel 1, indel 6 and indel 7. Panel <b>E</b> illustrates the positions of two of the four probes from Illumina beadchips, which are aligned onto the NCBI reference sequence for this locus (top sequence with an asterisk, representing HVR1098). The two probes shown here are from Illumina 610 SNP array; cnvi0010761 (green) and cnvi0010759 (blue). All four Illumina probes from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067752#pone-0067752-g001" target="_blank">Figure 1</a>, which were used for initial identification of variation in this region are located within hypervariable region. As shown here for two of these four probes, the probeA sequences (as called by Illumina and used for capturing of genomic DNA on beadchips) are shifted only by two bases. The core 32 bp repeat motif is shown in brackets.</p

Size and distribution of 14 HVR-alleles identified by sequencing and gel electrophoresis.

<p>The •/× indicate that the size of the allele was determined by both agarose gel images and sequencing, whereas filled circles (•) denote that the allele size was estimated from agarose gel images.</p><p>The two most common alleles (HVR1098 and HVR1700) are highlighted in bold and underlined text.</p><p>The sample indicated by a single asterisk (*) are from breast cancer patients. BL, PT and UM indicate peripheral blood DNA, primary breast tumor and healthy morphologically normal breast tissue from a patient affected with breast cancer, respectively.</p><p>The samples indicated by two asterisks (**) are monozygotic twin pairs.</p