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Additional file 4: Overlapping CpG regions partitioned by SOMNiBUS and bumphunter ranked by significance, stratified by chromosome

Additional file 2. Supplementaion Figures S1–S7.

Additional file 3: Nucleotide-level smoothed regional disease effect coefficients for all CpG regions identified by SOMNiBUS with p-value < 0.05 and identified by bumphunter with q-value < 0.05

Additional file 2: Nucleotide-level smoothed regional disease effect coefficients for all DMGs identified by SOMNiBUS

Additional file 5: Histogram of number of CpG sites per CpG region partitioned by bumphunter and SOMNiBUS

Purpose Hemoglobin A1c (HbA1c) is the accepted measure of effectiveness for type 1 diabetes therapies. We investigated preferences for measures of diabetes control in addition to HbA1c among adults with type 1 diabetes and caregivers of children with type 1 diabetes. Methods Using discrete-choice experiment methodology, surveys for adults with type 1 diabetes and caregivers presented choices between hypothetical treatments described by six attributes with varying levels: HbA1c, time in optimal glucose range, weekly number and severity of hypoglycemic and hyperglycemic events, additional disease management time, and additional treatment cost. Choice data were analyzed using random-parameters logit. Results A total of 300 adults with type 1 diabetes and 400 caregivers completed the survey. Adults and caregivers placed the most importance on reducing hypoglycemic and hyperglycemic events. For adults, avoiding 1–5 mild-to-moderate hypoglycemic events (glucose 54–69 mg/dL)/week was five times more important than being a half-point above target HbA1c. Avoiding 1–5 hyperglycemic events (glucose >180 mg/dL)/week was seven times more important than being a half-point above target HbA1c. Additional time in optimal glucose range was as important as a reduction greater than a half-point in HbA1c. Avoiding hyperglycemic and hypoglycemic events was more important than all other outcomes for caregivers of younger children. Caregivers of children >12 years placed relatively more weight on avoiding hypoglycemic events, Video Abstract Point your SmartPhone at the code above. If you have a QR code reader, the video abstract will appear. Or use: https://youtu.be/zPrBA6mK5hM

Background Combination chemotherapy has contributed to increased survival from Hodgkin disease (HD) and testicular cancer (TC). However, questions concerning the quality of spermatozoa after treatment have arisen. While studies have shown evidence of DNA damage and aneuploidy in spermatozoa years following anticancer treatment, the sperm epigenome has received little attention. Our objectives here were to determine the impact of HD and TC, as well as their treatments, on sperm DNA methylation. Semen samples were collected from community controls (CC) and from men undergoing treatment for HD or TC, both before initiation of chemotherapy and at multiple times post-treatment. Sperm DNA methylation was assessed using genome-wide and locus-specific approaches. Results Imprinted gene methylation was not affected in the sperm of HD or TC men, before or after treatment. Prior to treatment, using Illumina HumanMethylation450 BeadChip (450 K) arrays, a subset of 500 probes was able to distinguish sperm samples from TC, HD and CC subjects; differences between groups persisted post-treatment. Comparing altered sperm methylation between HD or TC patients versus CC men, twice as many sites were affected in TC versus HD men; for both groups, the most affected CpGs were hypomethylated. For TC patients, the promoter region of GDF2 contained the largest region of differential methylation. To assess alterations in DNA methylation over time/post-chemotherapy, serial samples from individual patients were compared. With restriction landmark genome scanning and 450 K array analyses, some patients who underwent chemotherapy showed increased alterations in DNA methylation, up to 2 to 3 years post-treatment, when compared to the CC cohort. Similarly, a higher-resolution human sperm-specific assay that includes assessment of environmentally sensitive regions, or “dynamic sites,” also demonstrated persistently altered sperm DNA methylation in cancer patients post-treatment and suggested preferential susceptibility of “dynamic” CpG sites. Conclusions Distinct sperm DNA methylation signatures were present pre-treatment in men with HD and TC and may help explain increases in birth defects reported in recent clinical studies. Epigenetic defects in spermatozoa of some cancer survivors were evident even up to 2 years post-treatment. Abnormalities in the sperm epigenome both pre- and post-chemotherapy may contribute to detrimental effects on future reproductive health.

This study aimed to elicit preferences for psoriasis treatment features and to test for preference heterogeneity across groups of respondents. A discrete-choice experiment was employed to elicit preferences of patients with plaque psoriasis in multiple countries. The survey instrument included a series of choice questions between three hypothetical treatments, each characterized by varying levels of six attributes (namely, lesion reduction, risk of impairing side effects, time to reach results, mode and frequency of administration, itching reduction, and side effects). Random parameters logit was used to model the data. Results were compared across a total of 18 subgroup sets. The data analysis from 1,123 respondents showed that, on average, respondents receive more utility gain from higher levels of lesion reduction and lower risks of impairing side effects than changes in other attributes included in the study. Systematic differences were detected for 13 sets; the most pronounced differences were observed based on disease severity, nail psoriasis, biologic experience, and quality-of-life scores. These many sources of preference heterogeneity identified by our analysis suggest that to improve patient satisfaction and, probably, adherence and persistence, clinicians should discuss options with patients when prescribing their treatment.