Dissertation (Ph.D.)--University of South Florida, 2008. / Includes vita. Also available online. Includes bibliographical references (leaves 93-111).

Le macrosatellite RNU2 est constitué de répétitions en tandem d'une unité de 6,1 kb. Largement étudié pendant les années 1980 et 1990, il est maintenant oublié des études pan-génomiques du fait de son absence du génome de référence. J'ai dans un premier temps finement caractérisé ce macrosatellite, en réalisant un assemblage in silico de la région génomique, en développant un code-barres pour la technique de peignage moléculaire et en analysant les données du projet 1000 Génomes. J'ai ainsi validé la localisation du locus RNU2 124 kb en amont de BRCA1, et affiné les données de polymorphisme en montrant que le nombre allélique de copies pouvait varier entre 5 et 82 chez 42 individus. J'ai tiré profit de sa localisation au sein d'un large bloc de déséquilibre de liaison pour définir le taux de mutation de ce macrosatellite à l'origine du nombre important d'allèles identifiables au sein de la population générale. Compte tenu de sa proximité avec BRCA1 et de son fort taux de polymorphisme, j'ai étudié le nombre global de copies du CNV dans 2 cohortes de cas de cancer du sein et témoins associés. J'ai montré que le nombre global de copies est significativement plus élevé chez les cas que chez les témoins. Ce travail suggère que le nombre de copies du macrosatellite RNU2 pourrait être impliqué dans la prédisposition génétique au cancer du sein, impliquant ainsi pour la première fois un CNV dans un mécanisme d'inactivation d'un gène de prédisposition au cancer

Les femmes porteuses d'une mutation du gène BRCA1 ou BRCA2 ont un risque de cancer du sein (CS) très élevé dont les estimations varient beaucoup d'une étude à l'autre. L'objectif principal de cette étude est de mieux estimer le risque de CS associé aux gènes BRCA1/2 en tenant compte de la variabilité des mutations et des facteurs " environnementaux/style de vie " et de leur éventuelle interaction. Nous avons analysé les données de la cohorte GENEPSO composée de femmes porteuses d'une mutation du gène BRCA1 ou BRCA2 à l'aide d'un modèle de Cox pondéré. L'analyse des facteurs de risque gynéco-obstétrique et de " style de vie " a permis de mettre en évidence une association entre le risque de CS et les radiations ionisantes, la consommation de tabac, l'indice de masse corporelle, l'âge aux premières règles, la parité, les interruptions de grossesse, la contraception orale, la ménopause et les traitements hormonaux substitutifs. Cette étude confirme l'existence d'une zone centrale à moindre risque de CS dans les gènes BRCA1/2 et de décrire une nouvelle région à haut risque située dans la région 3' du gène BRCA2. Cette étude montre également une interaction entre la localisation des mutations et la parité ainsi que la ménopause. Cette étude montre l'importance de la prise en compte simultanée des facteurs de risque " non génétiques " et de la localisation des mutations dans les gènes BRCA1/2 dans l'estimation des risques de CS. Si nos résultats sont confirmés sur de plus larges données, cette étude pourrait aider ces femmes dans le choix du type de stratégie de surveillance ou de prévention le mieux adapté à leur situation.

Abstract The purpose of this study was to develop a hypothetical model of genetic counseling for male hereditary breast cancer mutation (BRCA1/2) carriers. The methodological approach involved mixed methods. The aim of the first phase was to describe male BRCA1/2 mutation carriers’ genetic counseling, experiences and needs for developing genetic counseling. Quantitative data were acquired using a patient counseling questionnaire (n=35) based on consecutive sampling, whereas theme-based interviews (n=31) were conducted as a qualitative approach. In the second phase, the theme-based interview data were used to describe males’ experiences after identification as BRCA1/2 mutation carriers and effects of identification as a carrier on their lives (n=31). The data were analyzed using descriptive statistics and inductive content analysis. The results of the study were combined into a model describing genetic counseling for male BRCA1/2 mutation carriers. Based on the quantitative data, the genetic counseling was evaluated as good. Psychosocial support was insufficient. According to the qualitative data, there was lack of noticing individual wishes and needs during the genetic counseling process. Operational conditions of departments of clinical genetics and genetic healthcare professionals’ readiness to provide gentic counseling were varied. Identification as a BRCA1/2 mutation carrier caused varied emotional reactions associated with identification as a carrier, hereditary transmission of the mutation, cancer risks and possibility of developing cancer. However, the duration of the reactions varied. Identification as a carrier had effects on male carriers’ health and social wellbeing. According to the hypothetical model, genetic counseling was based on the backgrounds and individual needs of the male BRCA1/2 mutation carriers, which was implemented with appropriate operational conditions. It included sufficient psychological support, which genetics healthcare professionals had professional responsibility for implementing. The information study provided can be used to broaden the knowledge base of nursing science in clinical genetics. The information may also be utilized in continued nursing education. / Tiivistelmä Tutkimuksen tarkoituksena oli kehittää periytyvän rintasyöpäalttiusmutaation (BRCA1/2) kantajamiesten hypoteettinen perinnöllisyysneuvontamalli. Tutkimuksessa käytettiin monimenetelmämetodologiaa. Ensimmäisessä vaiheessa kuvattiin BRCA1/2-alttiusmutaation kantajamiesten perinnöllisyysneuvontaa, perinnöllisyysneuvontakokemuksia ja kehittämistarpeita. Aineisto kerättiin kokonaisotannalla kvantitatiivisesti Potilasohjaus-kyselylomakkeella (n=35) ja kvalitatiivisesti teemahaastatteluilla (n=31). Toisessa vaiheessa kuvattiin ensimmäisessä vaiheessa kerätyllä haastatteluaineistolla kantajamiesten kokemuksia alttiusmutaation kantajuudesta ja kantajuuden vaikutuksista elämään (n=31). Tutkimuksen aineistot analysoitiin tilastollisin menetelmin ja induktiivisella sisällönanalyysillä. Tutkimuksen tulosten perusteella muodostettiin BRCA1/2-alttiusmutaation kantajamiesten perinnöllisyysneuvontamalli. Kvantitatiivisen tutkimuksen perusteella perinnöllisyysneuvonta arvioitiin hyväksi. Psykososiaalisen tuen saaminen oli vähäistä. Kvalitatiivisen tutkimuksen mukaan kantajamiesten yksilöllisten toiveiden ja tarpeiden huomioiminen perinnöllisyysneuvontaprosessin aikana oli puutteellista. Kliinisen genetiikan yksiköiden toimintaedellytyksissä ja perinnöllisyysneuvonnan antajien ohjausvalmiuksissa oli vaihtelevuutta. BRCA1/2-alttiusmutaation kantajuus aiheutti kantajamiehille eriasteisia ja -kestoisia emotionaalisia tunteita, jotka liittyivät kantajuuteen, alttiusmutaation periytymiseen, syöpäriskiin ja syöpään sairastumiseen. Kantajuudella oli lisäksi vaikutusta kantajamiesten terveydelliseen ja sosiaaliseen hyvinvointiin. Periytyvän rintasyöpäalttiusgeenin hypoteettisen mallin perusteella perinnöllisyysneuvonta oli BRCA1/2-alttiusmutaation kantajamiehen taustatilanteeseen ja yksilölliseen tarpeeseen perustuva neuvonta, joka oli toteutettu asianmukaisin toimintaedellytyksin. Se sisälsi riittävästi psykososiaalista tukea ja sen antajalla oli ammatillinen vastuu perinnöllisyysneuvonnan toteuttamisesta. Tutkimuksessa tuotetun tiedon avulla lisätään hoitotieteellistä tietoperustaa perinnöllisyyslääketieteen alueelle. Tietoa voidaan hyödyntää myös hoitotyön täydennyskoulutuksessa.

Abstract Approximately 5–10% of all breast cancer cases are estimated to result from a hereditary predisposition to the disease. Currently no more than 25–30% of these familial cases can be explained by mutations in the known susceptibility genes, BRCA1 and BRCA2 being the major ones. Additional predisposing genes are therefore likely to be discovered. This study evaluates whether germline alterations in three BRCA1-associated genes, BACH1 (i.e. BRIP1/FANCJ), BARD1 and TOPBP1, contribute to familial breast cancer. Altogether 214 Finnish patients having breast and/or ovarian cancer were analysed for germline mutations in the BACH1 gene. Nine alterations were observed, four of which located in the protein-encoding region. The previously unidentified Pro1034Leu was considered a possible cancer-associated alteration as it appeared with two-fold higher frequency among cancer cases compared to controls. All the other observed alterations were classified as harmless polymorphisms. Mutation analysis of the BARD1 gene among 126 Finnish patients having family history of breast and/or ovarian cancer revealed seven alterations in the protein-encoding region. The Cys557Ser alteration was seen at an elevated frequency among familial cancer cases compared to controls (p = 0.005, odds ratio [OR] 4.2, 95% confidence interval [CI] 1.7–10.7). The other alterations appeared to be harmless polymorphisms. To evaluate further the possible effect of Cys557Ser on cancer risk, a large case-control study was performed, consisting of 3,956 cancer patients from the Nordic countries. The highest prevalence of Cys557Ser was found among breast and ovarian cancer patients from BRCA1/BRCA2 mutation-negative families (p < 0.001, OR 2.6, 95% CI 1.7–4.0). In contrast, no significant association with male breast cancer, ovarian, colorectal or prostate cancer was observed. The current study is the first evaluating the role of TOPBP1 mutations in familial cancer predisposition. The analysis of 125 Finnish patients having breast and/or ovarian cancer revealed one putative pathogenic alteration. The commonly occurring Arg309Cys allele was observed at a significantly higher frequency among familial cancer cases compared to controls (p = 0.002, OR 2.4, 95% CI 1.3–4.2). The other 18 alterations observed were classified as harmless polymorphisms.

Abstract In Western countries, breast and ovarian cancer are among the most frequent malignancies affecting women. Approximately 5–10% of the cases in the general population have been suggested to be attributed to inherited disease susceptibility. BRCA1 and BRCA2 are the main genes associated with predisposition to breast and ovarian cancer. Mutations in these two genes explain a major part of the families displaying a large number of early-onset breast and/or ovarian cancers, but at least one third of the cases appear to be influenced by other, as yet unidentified genes. Therefore, it is likely that defects in other cancer predisposing genes, perhaps associated with lower disease penetrance and action in a polygenic context, will also be discovered. In the present study, the contribution of germline mutations in putative breast and/or ovarian cancer susceptibility genes, based on their biological function, has been investigated in Finnish breast cancer families. The role of large genomic deletions or other rearrangements in the BRCA1 and BRCA2 genes was evaluated by Southern blot analysis, and mutation analysis of TP53, RAD51, the BRC repeats of BRCA2, and 53BP1 was performed by conformation sensitive gel electrophoresis and DNA sequencing. Germline TP53 mutations were searched for in 108 Finnish breast cancer families without BRCA1 or BRCA2 alterations. In this study, the pathogenic TP53 germline mutation, Arg248Gln, was identified in only one family. This family showed a strong family history of breast cancer and other cancers also fulfilling the criteria for Li-Fraumeni-like syndrome. Germline TP53 mutations are expected to be found in cancer families with clinical features seen in Li-Fraumeni or Li-Fraumeni-like syndromes. In this study, large deletions in BRCA1 and BRCA2 were not observed in 82 breast and/or ovarian cancer families. Likewise, no disease-related aberrations were detected in RAD51, the BRC repeats of BRCA2 or 53BP1 in the 126 breast and/or ovarian cancer families studied. The obtained results were validated by comparing to the occurrence in 288–300 female cancer-free control individuals. These results do not support the hypothesis that alterations in these particular genomic regions play a significant role in breast cancer predisposition in Finland. Thus, there are still genes to be discovered to explain the molecular background of breast cancer.

Purpose: This study assessed effectiveness of five tools recommended by the US Preventive Services Task Force (USPSTF), designed to help primary care clinicians determine which unaffected patients to refer to genetics specialists for breast cancer risk assessment based on concerning family history. Design: This descriptive secondary analysis included 85 women aged 40-74. All participants had a first-degree female relative previously diagnosed with breast cancer who also had uninformative negative BRCA1/2 tests. Methods: Each pedigree was evaluated using the five tools including the Family History Screen-7 (FHS-7), Pedigree Assessment Tool (PAT), Manchester Scoring System, Referral Screening Tool (RST), and Ontario-Family History Assessment Tool (Ontario-FHAT). All five tools were applied to each study participant. Sensitivity, specificity, positive predictive value, and negative predictive value were calculated to describe each tool’s ability to identify women with elevated risk as calculated by the Claus model. Receiver operating curves (ROC) were also plotted. Differences between areas under the curve (AUCs) for all possible pairs of tools were estimated through logistic regression to assess for differences in tool performance. Results: Claus calculations identified 14 women out of 85 whose lifetime risk of breast cancer was elevated at > 15%. Only two tools, the Ontario-FHAT and FHS-7, identified all 14 women with elevated risk, a sensitivity of 100%. The FHS-7 tool flagged all 85 participants, meaning its specificity was zero. The Ontario-FHAT flagged 59 participants as needing referral (specificity 36.2%) and had a negative predictive value (NPV) of 100%, indicating that if a woman was not found to need a referral to a genetics professional, it is likely she did not have an elevated lifetime risk of developing breast cancer. AUC values were not significantly different between tools (all p values > .05), and thus were not helpful in discriminating between the tools. Conclusion: In this population, the Ontario-FHAT out-performed other tools in terms of sensitivity and negative predictive value; however, low specificity and positive predictive value must be balanced against these findings. Thus, the Ontario-FHAT can help determine which women would benefit from referral to a genetics specialist.

Genetic test results have important implications for close family members. Indeterminate negative results are the most common outcome of BRCA1/2 mutation testing. Little is known about family members' understanding of indeterminate negative BRCA1/2 test results. The purpose of this qualitative descriptive study was to investigate how daughters and sisters received and understood genetic test results as shared by their mothers or sisters. Participants included 81 women aged 40-74 with mothers or sisters previously diagnosed with breast cancer and who received indeterminate negative BRCA1/2 test results. Participants had never been diagnosed with breast cancer nor received their own genetic testing or counseling. This IRB approved study utilized semi-structured interviews administered via telephone. The research team developed descriptive codes, and NVIVO software was used during qualitative analysis. Participants reported low amounts of information shared with them. Most women described test results as negative and incorrectly interpreted the test to mean there was no genetic component to the pattern of cancer in their families. Only 7 of 81 women accurately described test results consistent with the meaning of an indeterminate negative result — meaning a genetic cause for cancer in their family could still exist. Our findings demonstrate that indeterminate negative genetic test results are not well understood by family members. Lack of understanding may lead to an inability to effectively communicate results to primary care providers and missed opportunities for prevention, screening and further genetic testing. We recommend providing family members letters they can share with their own primary care providers whenever genetic testing is performed.

No description available.

The breast cancer susceptibility protein, BRCA1, is a tumor suppressor that helps maintain genomic integrity. Changes in BRCA1 that effect DNA repair processes can fuel cancer induction. The Kelly lab, at the Virginia Tech Carilion Research Institute, has recently developed a new methodology that employs silicon nitride (SiN) microchips to isolate BRCA1 assemblies from the nuclear material of breast cancer cells. These microchips are coated with adaptor proteins that include antibodies against target proteins of interest. The adaptor proteins are added in sequential steps to the coated microchips, followed by an aliquot of sample containing the protein of interest, such as BRCA1. The Kelly lab, partnered with Protochips Inc., developed these devices as a robust, tunable platform to monitor molecular processes, and refer to them as 'Cryo-SiN' in cryo-Electron Microscopy (EM) imaging. We are currently using Cryo-SiN to recruit BRCA1 protein assemblies to the microchip surface under mild conditions, while simultaneously preparing them for cryogenic preservation and EM imaging. This strategy presents a viable alternative to antibody affinity columns that require stringent elution steps to obtain protein complexes from the column. Another advantage of the microchip strategy is that it requires only a 30-minute nuclear extraction, a 60-minute enrichment procedure, and a 5-minute microchip capture step--a total of 95 minutes from initially lysing the cells to plunge-freezing the EM specimens. Therefore, these novel approaches represent a major departure from classical separation procedures that often require days to complete, during which time active protein assemblies can readily dissociate or become inactive. Overall, our use of BRCA1-specific microchips may reveal changes in the BRCA1 architecture during various stages of cancer progression--a major gap in knowledge that persists in cancer research. / M. S.