Additional file 2 of DNA methylation-based detection and prediction of cervical intraepithelial neoplasia grade 3 and invasive cervical cancer with the WID™-qCIN test

Additional file 2: Original data for calculations in the manuscript

Additional file 1: Figure S1. of The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer

Design of the nested case-control study based on the UKCTOCS Cohort. Figure S2. DMR discovery with Illumina 450 K methylation arrays. Figure S3. Pattern counts for informative regions. Figure S4. Pattern frequencies for the different regions analyzed in serum set 1 samples. Figure S5. Pattern frequencies for the different regions analyzed in serum set 2 samples. Figure S6. DNA methylation for regions #144, #204, and #228 according to OC stages. Figure S7. Coverage (number of reads) for the three different regions analyzed in serum set 3 samples. Figure S8. CA125 levels measured in NACT serum set samples. Figure S9. Pattern frequencies for the top three reactions measured in NACT serum set samples. Figure S10. Coverage (number of reads) for the top three reactions measured in NACT serum set samples. Figure S11. Average DNA amount extracted correlates with average UK temperature. Figure S12 The fraction (%) of small fragment (50–250 bp) DNA in the serum DNA preparation for 171 UKCTOCS samples analyzed in the study. Figure S13. Box plots comparing the average beta values for 450 k array probes within regions #204 and #228 between each normal (N), cancer (C) group, and white blood cell (WBC) data for OC and other 19 TCGA cancer types. (DOCX 3024 kb

Additional file 1: Figure S1. of Methylation patterns in serum DNA for early identification of disseminated breast cancer

Samples from the SUCCESS trial analyzed within this study. Figure S2. Samples from the UKCTOCS cohort analyzed within this study (nested case/control setting). Figure S3. Absolute pattern counts for all patterns detected in the region of marker EFC#93 in Serum Set 1 samples. Figure S4. Pattern frequency of EFC#93 serum DNAme in two prospectively independently collected cohorts. Figure S5. DNA amount per mL serum in the prospectively collected serum (Set 1 and 2), SUCCESS cohort, and UKCTOCS cohort. Figure S6. Pattern frequency for EFC#93 measured in SUCCESS serum set samples from women with no, 1–4 or ≥ 5 CTCs in the matched blood sample before (A) or after (B) chemotherapy. Figure S7. Impact of the presence (+ve, ≥ 1 cancer cell in blood sample) or absence (-ve) of CTCs on patient outcome. Figure S8. Impact of the presence (+ve, EFC#93 pattern frequency ≥ 0.00008) or absence (-ve) of serum DNA methylation in CTC + ve (≥1 cancer cell in pre-chemotherapy blood sample) or absence CTC-ve patients. Figure S9. Relapse-free and overall survival according to samples taken after chemotherapy. Figure S10. Relapse-free and overall survival according to samples taken after chemotherapy. Figure S11. Average serum DNA amount correlates with average UK temperature. Figure S12. Average serum DNA fragment size correlates with average UK temperature. Figure S13. Correlation of DNA fragment size and DNA amount. Figure S14. Overall survival of women whose samples were taken before and after chemotherapy and before anti-hormonal treatment in hormone receptor-negative and -positive SUCCESS participants. Figure S15. Overall survival of women whose samples were taken before and after chemotherapy and before anti-hormonal treatment in hormone receptor-negative and -positive SUCCESS participants. (PDF 2123 kb

Kostelec nad Černými lesy - A Guide-book for Teachers

Jako téma své diplomové práce jsem si vybrala zpracování vlastivědné příručky pro učitele prvního stupně základní školy o městě Kostelci nad Černými lesy. V Kostelci nad Černými lesy jsem prožila své dětství a stále se tam ráda vracím. Je to místo, které vnímám jako svůj domov, místo, kam patřím. Přestože mám již delší dobu bydliště jinde, vždy se těším na jeho poklidnou atmosféru. Ačkoli se jedná o malé městečko, jeho historie je bohatá a o pozoruhodnosti tu není nouze. Je to místo zasazené v překrásné krajině, která přímo vybízí toulkám a výletům. I proto toto město vyhledává stále více návštěvníků. Většina lidí však zná Kostelec nad Černými lesy jen ze školních diktátů, kdy si jako žáci při českém jazyce lámali hlavu nad psaním velkým písmen. Někteří vám tak ještě poví, že v okolí asi budou nějaké lesy, jak název napovídá. Kostelec by si ale určitě zasloužil více pozornosti, jelikož má co nabídnout. Možná je důvod i v tom, že toto město nebylo v poslední době předmětem zpracování žádné publikace. dispozici jsou informace pouze ve formě brožurek, které nebývají obsáhlé. Jediná rozsáhlejší kniha, která byla vydána příležitosti pětisetletého výročí povýšení Kostelce nad Černými lesy na městečko v roce 1989, je příliš ideologicky zatížena. Rozhodla jsem se, že využiji všech dostupných materiálů a podám..

Additional file 3: Table S1. of Methylation patterns in serum DNA for early identification of disseminated breast cancer

Coordinates and primers used to amplify the identified target regions using bisulfite sequencing. (PDF 578 kb

The WID-BC-index identifies women with primary poor prognostic breast cancer based on DNA methylation in cervical samples

Genetic and non-genetic factors contribute to breast cancer development. An epigenome-based signature capturing these components in easily accessible samples could identify women at risk. Here, we analyse the DNA methylome in 2,818 cervical, 357 and 227 matched buccal and blood samples respectively, and 42 breast tissue samples from women with and without breast cancer. Utilising cervical liquid-based cytology samples, we develop the DNA methylation-based Women's risk IDentification for Breast Cancer index (WID-BC-index) that identifies women with breast cancer with an AUROC (Area Under the Receiver Operator Characteristic) of 0.84 (95% CI: 0.80-0.88) and 0.81 (95% CI: 0.76-0.86) in internal and external validation sets, respectively. CpGs at progesterone receptor binding sites hypomethylated in normal breast tissue of women with breast cancer or in BRCA mutation carriers are also hypomethylated in cervical samples of women with poor prognostic breast cancer. Our data indicate that a systemic epigenetic programming defect is highly prevalent in women who develop breast cancer. Further studies validating the WID-BC-index may enable clinical implementation for monitoring breast cancer risk

La Vigie marocaine

12 mai 19371937/05/12 (A28,N9288)-1937/05/12

Additional file 7: of HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer

Ten-fold internal cross-validations to identify an optimal DNAme signature. Upper panel shows the total misclassification error (y-axis) as a function of the shrinkage threshold (x-axis) used. Lower panel shows the misclassification error for each phenotype (1 = low HOTAIR expression, 2 = high HOTAIR expression) as a function of the same shrinkage threshold. The optimal minimal classifier was found at a threshold of approximately 1.47, corresponding to a 67-CpG signature at an estimated false discovery rate (FDR) of approximately 0.17 (not shown). The FDR was estimated using a permutation scheme as implemented in the pamr R-package, and the relatively low FDR (only about 17 % of the 67 CpGs are expected to be false positives) demonstrates the presence of a genuine DNAme signal associated with HOTAIR expression. (PDF 13 kb