DNA Methylation Arrays as Surrogate Measures of Cell mixture Distribution

There has been a long-standing need in biomedical research for a method that quantifies the normally mixed composition of leukocytes beyond what is possible by simple histological or flow cytometric assessments. The latter is restricted by the labile nature of protein epitopes, requirements for cell processing, and timely cell analysis. In a diverse array of diseases and following numerous immune-toxic exposures, leukocyte composition will critically inform the underlying immuno-biology to most chronic medical conditions. Emerging research demonstrates that DNA methylation is responsible for cellular differentiation, and when measured in whole peripheral blood, serves to distinguish cancer cases from controls

Note and Comment

Safeguarding the Criminal Defendant - Every now and then a new attack is made somewhere in the United States upon the rule prohibiting comment before the jury upon the fact that the defendant in a criminal case has not testified as a witness in his own behalf. At the present time an effort of this kind is being made in the Michigan legislature, and the introduction of the bill drew quite a little storm of protest from the State press as a dangerous inroad upon our ancient guarantees of personal liberty and security. In fact, however, it directly touches nothing more ancient than a statutory privilege which dates from the year i86i. By the Public Acts of that year the disability of parties to actions to testify as witnesses in this State was removed, but it was expressly provided that defendants in criminal cases could not be compelled to testify, but might do so or not at their own pleasure. (Act No. 125, §2). In 1881 an amendment to this statute was passed providing, as to the defendant in a criminal case, that his neglect to testify shall not create any presumption against him, nor shall the court permit any reference or comment to be made to or upon such neglect. (Pub. Acts, 188I, No. 245). And this is the form it retains in the Judicature Act. (Ch. 17, §64)

Breast Cancer DNA Methylation Profiles Are Associated with Tumor Size and Alcohol and Folate Intake

Although tumor size and lymph node involvement are the current cornerstones of breast cancer prognosis, they have not been extensively explored in relation to tumor methylation attributes in conjunction with other tumor and patient dietary and hormonal characteristics. Using primary breast tumors from 162 (AJCC stage I–IV) women from the Kaiser Division of Research Pathways Study and the Illumina GoldenGate methylation bead-array platform, we measured 1,413 autosomal CpG loci associated with 773 cancer-related genes and validated select CpG loci with Sequenom EpiTYPER. Tumor grade, size, estrogen and progesterone receptor status, and triple negative status were significantly (Q-values <0.05) associated with altered methylation of 209, 74, 183, 69, and 130 loci, respectively. Unsupervised clustering, using a recursively partitioned mixture model (RPMM), of all autosomal CpG loci revealed eight distinct methylation classes. Methylation class membership was significantly associated with patient race (P<0.02) and tumor size (P<0.001) in univariate tests. Using multinomial logistic regression to adjust for potential confounders, patient age and tumor size, as well as known disease risk factors of alcohol intake and total dietary folate, were all significantly (P<0.0001) associated with methylation class membership. Breast cancer prognostic characteristics and risk-related exposures appear to be associated with gene-specific tumor methylation, as well as overall methylation patterns

DNA methylation arrays as surrogate measures of cell mixture distribution

Background: There has been a long-standing need in biomedical research for a method that quantifies the normally mixed composition of leukocytes beyond what is possible by simple histological or flow cytometric assessments. The latter is restricted by the labile nature of protein epitopes, requirements for cell processing, and timely cell analysis. In a diverse array of diseases and following numerous immune-toxic exposures, leukocyte composition will critically inform the underlying immuno-biology to most chronic medical conditions. Emerging research demonstrates that DNA methylation is responsible for cellular differentiation, and when measured in whole peripheral blood, serves to distinguish cancer cases from controls. Results: Here we present a method, similar to regression calibration, for inferring changes in the distribution of white blood cells between different subpopulations (e. g. cases and controls) using DNA methylation signatures, in combination with a previously obtained external validation set consisting of signatures from purified leukocyte samples. We validate the fundamental idea in a cell mixture reconstruction experiment, then demonstrate our method on DNA methylation data sets from several studies, including data from a Head and Neck Squamous Cell Carcinoma (HNSCC) study and an ovarian cancer study. Our method produces results consistent with prior biological findings, thereby validating the approach. Conclusions: Our method, in combination with an appropriate external validation set, promises new opportunities for large-scale immunological studies of both disease states and noxious exposures.Keywords: Down syndrome, Absolute counts, Variable analysis, Lung cancer, Measurement error, Peripheral blood, Stem cells, Gene expression, T lymphocyte subsets, Ovarian cance

Note and Comment

Safeguarding the Criminal Defendant - Every now and then a new attack is made somewhere in the United States upon the rule prohibiting comment before the jury upon the fact that the defendant in a criminal case has not testified as a witness in his own behalf. At the present time an effort of this kind is being made in the Michigan legislature, and the introduction of the bill drew quite a little storm of protest from the State press as a dangerous inroad upon our ancient guarantees of personal liberty and security. In fact, however, it directly touches nothing more ancient than a statutory privilege which dates from the year i86i. By the Public Acts of that year the disability of parties to actions to testify as witnesses in this State was removed, but it was expressly provided that defendants in criminal cases could not be compelled to testify, but might do so or not at their own pleasure. (Act No. 125, §2). In 1881 an amendment to this statute was passed providing, as to the defendant in a criminal case, that his neglect to testify shall not create any presumption against him, nor shall the court permit any reference or comment to be made to or upon such neglect. (Pub. Acts, 188I, No. 245). And this is the form it retains in the Judicature Act. (Ch. 17, §64)

Enlarged leukocyte referent libraries can explain additional variance in blood-based epigenome-wide association studies

AIM: We examined whether variation in blood-based epigenome-wide association studies could be more completely explained by augmenting existing reference DNA methylation libraries. MATERIALS & METHODS: We compared existing and enhanced libraries in predicting variability in three publicly available 450K methylation datasets that collected whole-blood samples. Models were fit separately to each CpG site and used to estimate the additional variability when adjustments for cell composition were made with each library. RESULTS: Calculation of the mean difference in the CpG-specific residual sums of squares error between models for an arthritis, aging and metabolic syndrome dataset, indicated that an enhanced library explained significantly more variation across all three datasets (p < 10(-3)). CONCLUSION: Pathologically important immune cell subtypes can explain important variability in epigenome-wide association studies done in blood

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

International audienc

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

International audienc