Archive for the ‘Genomic Analysis of EKG Electrophysiology Genomics’ Category

scPopCorn: A New Computational Method for Subpopulation Detection and their Comparative Analysis Across Single-Cell Experiments

Reporter and Curator: Dr. Sudipta Saha, Ph.D.


4.2.5   scPopCorn: A New Computational Method for Subpopulation Detection and their Comparative Analysis Across Single-Cell Experiments, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 4: Single Cell Genomics

Present day technological advances have facilitated unprecedented opportunities for studying biological systems at single-cell level resolution. For example, single-cell RNA sequencing (scRNA-seq) enables the measurement of transcriptomic information of thousands of individual cells in one experiment. Analyses of such data provide information that was not accessible using bulk sequencing, which can only assess average properties of cell populations. Single-cell measurements, however, can capture the heterogeneity of a population of cells. In particular, single-cell studies allow for the identification of novel cell types, states, and dynamics.

One of the most prominent uses of the scRNA-seq technology is the identification of subpopulations of cells present in a sample and comparing such subpopulations across samples. Such information is crucial for understanding the heterogeneity of cells in a sample and for comparative analysis of samples from different conditions, tissues, and species. A frequently used approach is to cluster every dataset separately, inspect marker genes for each cluster, and compare these clusters in an attempt to determine which cell types were shared between samples. This approach, however, relies on the existence of predefined or clearly identifiable marker genes and their consistent measurement across subpopulations.

Although the aligned data can then be clustered to reveal subpopulations and their correspondence, solving the subpopulation-mapping problem by performing global alignment first and clustering second overlooks the original information about subpopulations existing in each experiment. In contrast, an approach addressing this problem directly might represent a more suitable solution. So, keeping this in mind the researchers developed a computational method, single-cell subpopulations comparison (scPopCorn), that allows for comparative analysis of two or more single-cell populations.

The performance of scPopCorn was tested in three distinct settings. First, its potential was demonstrated in identifying and aligning subpopulations from single-cell data from human and mouse pancreatic single-cell data. Next, scPopCorn was applied to the task of aligning biological replicates of mouse kidney single-cell data. scPopCorn achieved the best performance over the previously published tools. Finally, it was applied to compare populations of cells from cancer and healthy brain tissues, revealing the relation of neoplastic cells to neural cells and astrocytes. Consequently, as a result of this integrative approach, scPopCorn provides a powerful tool for comparative analysis of single-cell populations.

This scPopCorn is basically a computational method for the identification of subpopulations of cells present within individual single-cell experiments and mapping of these subpopulations across these experiments. Different from other approaches, scPopCorn performs the tasks of population identification and mapping simultaneously by optimizing a function that combines both objectives. When applied to complex biological data, scPopCorn outperforms previous methods. However, it should be kept in mind that scPopCorn assumes the input single-cell data to consist of separable subpopulations and it is not designed to perform a comparative analysis of single cell trajectories datasets that do not fulfill this constraint.

Several innovations developed in this work contributed to the performance of scPopCorn. First, unifying the above-mentioned tasks into a single problem statement allowed for integrating the signal from different experiments while identifying subpopulations within each experiment. Such an incorporation aids the reduction of biological and experimental noise. The researchers believe that the ideas introduced in scPopCorn not only enabled the design of a highly accurate identification of subpopulations and mapping approach, but can also provide a stepping stone for other tools to interrogate the relationships between single cell experiments.







Read Full Post »

Clever experiment: GWAS of 500 time points in an EKG – The genetic makeup of the electrocardiogram

Reporter: Aviva Lev-Ari, PhD, RN

The genetic makeup of the electrocardiogram

Niek VerweijJan-Walter BenjaminsMichael P. MorleyYordi van de VegteAlexander TeumerTeresa TrenkwalderWibke ReinhardThomas P. CappolaPim van der Harst


Since its original description in 1893 by Willem van Einthoven, the electrocardiogram (ECG) has been instrumental in the recognition of a wide array of cardiac disorders1,2. Although many electrocardiographic patterns have been well described, the underlying biology is incompletely understood. Genetic associations of particular features of the ECG have been identified by genome wide studies. This snapshot approach only provides fragmented information of the underlying genetic makeup of the ECG. Here, we follow the effects of individual genetic variants through the complete cardiac cycle the ECG represents. We found that genetic variants have unique morphological signatures not identified by previous analyses. By exploiting identified abberations of these morphological signatures, we show that novel genetic loci can be identified for cardiac disorders. Our results demonstrate how an integrated approach to analyse high-dimensional data can further our understanding of the ECG, adding to the earlier undertaken snapshot analyses of individual ECG components. We anticipate that our comprehensive resource will fuel in silico explorations of the biological mechanisms underlying cardiac traits and disorders represented on the ECG. For example, known disease causing variants can be used to identify novel morphological ECG signatures, which in turn can be utilized to prioritize genetic variants or genes for functional validation. Furthermore, the ECG plays a major role in the development of drugs, a genetic assessment of the entire ECG can drive such developments.



made available under a CC-BY-ND 4.0 International license.

Read Full Post »

%d bloggers like this: