RT-PCR results for <i>BRCA1</i> c.4484G>C(p.Arg1495Thr) and <i>BRCA2:</i>c.7828G>A (p.Val2610Met).

<p><i>M</i> - 100bp DNA marker (New England Biolabs). A) <i>BRCA2</i>:c.7828G>A (p.Val2610Met). Lane 1: RT-PCR products from variant carrier derived cycloheximide treated LCL. Lane 2–7: Cycloheximide treated LCLs from unaffected female controls. There is no evidence for a predicted loss of 149bp from exon 17 as a result of a <i>de novo</i> donor site. The Δexon 18 (540bp) and Δexon 17/18 (369bp) are detected in the variant carrier and all but one control samples. B) <i>BRCA1</i> c.4484G>C(p.Arg1495Thr). Lane 1: RT-PCR products from whole blood derived RNA from the variant carrier showing the Δexon 14 and Δexon 14/15 splicing aberration. Lane 2: RT-PCR carried out on whole blood derived RNA from an unaffected female control (collection and extraction methods as per the variant carrier). Lane 3–7: Cycloheximide treated LCLs from unaffected female controls.</p

BRCA1 RING-domain variants with reported loss of function on the basis of <i>in-vitro</i> functional assays and/or (likely) clinically significant from multifactorial likelihood analysis.

*<p>p.Met18Thr, p.Cys61Gly and p.Cys64Gly are also shown to have abrogated function using mouse embryonic stem cell assays <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086836#pone.0086836-Bouwman1" target="_blank">[44]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086836#pone.0086836-Chang1" target="_blank">[49]</a>. (No other variants listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086836#pone-0086836-t003" target="_blank">Table 3</a> were assayed using this method).</p

Bioinformatic splice prediction scores^* and <i>in-vitro</i> splicing assay results.

*<p>Bracketed percentages refer to the difference between variant and wild-type scores as a proportion of the wild-type score. NSC, no sites created (no scores provided by bioinformatic program output). Positive values for HSF matrices and MaxEntScan represent an increased likelihood of creating a <i>de novo</i> site when compared with the wild-type sequence where the variant occurs. Negative values represent a decreased likelihood. Positive values for ESEfinder represent an increase in strength for the enhancer motif as a result of the variant. The proximal consensus site is taken as the donor or acceptor site of the exon in which the variant occurs. Variant scores for NNsplice are for splice sites created by the variant, except for <i>BRCA1</i>:c.4484G>C (p.Arg1495Thr) for which the variant score is for the consensus splice junction in the presence of the variant.</p

Classification of <i>BRCA1</i> and <i>BRCA2</i> variants on the basis of multifactorial and splicing information.

<p>Classifications for multifactorial likelihood as described in Plon et al. (3) and splicing as described in Spurdle et al. (32). Frequency data from 1000 Genomes and EVS datasets is available for a subset of the variants studied (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086836#pone.0086836.s002" target="_blank">Table S2</a>). Information used to determine tumor pathology LRs was as follows: <i>BRCA1</i>c.122A>G(p.His41Arg) - one ER-positive Grade 3 tumor; <i>BRCA2</i> variants c.440A>G (p.Gln147Arg) and c.1514T>C (p.Ile505Thr) - tubule formation present in <10% of tumor; <i>BRCA2</i>:c.5278T>G (p.Ser1760Ala) – tubule formation in >75% tumor.</p

Characteristics of 15 high-risk breast cancer families selected for exome sequencing.

a<p>Breast cancer (BC), ovarian cancer (OC), bilat. (bilateral). Age of diagnosis shown in parentheses.</p>b<p>Other cancer types observed in family branch with apparent breast cancer risk (multiple cases shown in parentheses).</p

<i>FANCC</i> and <i>BLM</i> mutations identified in familial breast cancer pedigrees.

<p>Males and females are represented by squares and circles, respectively. Arrows indicate individuals who underwent whole exome sequencing (families 1–3) or were the index case in subsequent mutation analysis (<i>FANCC</i> p.Asp23fs, p.Leu554Pro and p.Arg185Gln and <i>BLM</i> p.Arg899* families). Cancer-affected individuals are represented with the following symbols: breast cancer, top right quadrant filled in; bilateral breast cancer, top half; ovarian cancer, bottom left quadrant; or other cancers as indicated, centre circle. Mutation status is indicated with either the family specific mutation or wildtype (wt) under each tested individual. Age at cancer diagnosis or year of birth (b.) where known is shown for all mutation carriers. Breast cancer (BC), ovarian cancer (OC), acute leukaemia (AL), colorectal cancer (CRC), haematological malignancy (type unspecified) (Haem.), kidney cancer (KC), liver cancer (LivC), melanoma (Mel.), pancreatic cancer (PaC), prostate cancer (PrC), skin non-melanoma (Non-mel.) stomach cancer (SC), testicular cancer (TestC). Mutations indicated in parentheses indicate untested obligate carriers. Family 2 contains an individual (indicated by #) for whom mutation status is inferred assuming that non-paternity or gonadal mosaicism have not occurred.</p

Supplementary Data from Weight is More Informative than Body Mass Index for Predicting Postmenopausal Breast Cancer Risk: Prospective Family Study Cohort (ProF-SC)

Supplementary Data from Weight is More Informative than Body Mass Index for Predicting Postmenopausal Breast Cancer Risk: Prospective Family Study Cohort (ProF-SC

Targeting MDM4 as a Novel Therapeutic Approach in Prostate Cancer Independent of p53 Status

Metastatic prostate cancer is a lethal disease in patients incapable of responding to therapeutic interventions. Invasive prostate cancer spread is caused by failure of the normal anti-cancer defense systems that are controlled by the tumour suppressor protein, p53. Upon mutation, p53 malfunctions. Therapeutic strategies to directly re-empower the growth-restrictive capacities of p53 in cancers have largely been unsuccessful, frequently because of a failure to discriminate responses in diseased and healthy tissues. Our studies sought alternative prostate cancer drivers, intending to uncover new treatment targets. We discovered the oncogenic potency of MDM4 in prostate cancer cells, both in the presence and absence of p53 and also its mutation. We uncovered that sustained depletion of MDM4 is growth inhibitory in prostate cancer cells, involving either apoptosis or senescence, depending on the cell and genetic context. We identified that the potency of MDM4 targeting could be potentiated in prostate cancers with mutant p53 through the addition of a first-in-class small molecule drug that was selected as a p53 reactivator and has the capacity to elevate oxidative stress in cancer cells to drive their death

Targeting MDM4 as a Novel Therapeutic Approach in Prostate Cancer Independent of p53 Status

Metastatic prostate cancer is a lethal disease in patients incapable of responding to therapeutic interventions. Invasive prostate cancer spread is caused by failure of the normal anti-cancer defense systems that are controlled by the tumour suppressor protein, p53. Upon mutation, p53 malfunctions. Therapeutic strategies to directly re-empower the growth-restrictive capacities of p53 in cancers have largely been unsuccessful, frequently because of a failure to discriminate responses in diseased and healthy tissues. Our studies sought alternative prostate cancer drivers, intending to uncover new treatment targets. We discovered the oncogenic potency of MDM4 in prostate cancer cells, both in the presence and absence of p53 and also its mutation. We uncovered that sustained depletion of MDM4 is growth inhibitory in prostate cancer cells, involving either apoptosis or senescence, depending on the cell and genetic context. We identified that the potency of MDM4 targeting could be potentiated in prostate cancers with mutant p53 through the addition of a first-in-class small molecule drug that was selected as a p53 reactivator and has the capacity to elevate oxidative stress in cancer cells to drive their death

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer