MD Edge ObGyn
Targeted sequencing panel IDs Lynch syndrome in women with/at risk for endometrial cancer

A targeted next-generation sequencing panel rapidly identifies both germline and somatic Lynch syndrome pathogenic mutations in women with – or at risk for – endometrial cancer, according to findings in a prospective patient cohort. more »

Optimizing de novo genome assembly from PCR-amplified metagenomes

Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated… more »

Use of a Targeted Lynch Syndrome Next Generation Sequencing Panel in Women at Risk for or With Endometrial Cancer [32M]

Women with endometrial cancer should be screened for Lynch syndrome (LS), a hereditary cancer syndrome caused by germline mutations in DNA mismatch repair (MMR) genes. This information directly affects immediate clinical management including future risk reducing/surveillance strategies for patients and at-risk family members. It is currently unclear how best to provide molecular screening… more »

Robust single-cell DNA methylome profiling with snmC-seq2

Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications of the method have been impeded by the modest quality of sequencing libraries. more »

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL

Cancer evolution is fueled by epigenetic as well as genetic diversity. In chronic lymphocytic leukemia (CLL), intra-tumoral DNA methylation (DNAme) heterogeneity empowers evolution. more »

Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study

Next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) supports blood-based genomic profiling but is not yet routinely implemented in the setting of a phase I trials clinic. more »

Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development

Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. However, recent work also shows that key molecular aspects of human END regulation differ even from rodents. more »

mRNA reprogramming of T8993G Leigh’s syndrome fibroblast cells to create induced pluripotent stem cell models for mitochondrial disorders

Early molecular and developmental events impacting many incurable mitochondrial disorders are not fully understood and require generation of relevant patient and disease-specific stem cell models. In this study, we focus on the ability of a non-viral and integration-free reprogramming method for deriving clinical-grade iPSCs specific to Leigh’s syndrome (LS), a fatal neurodegenerative mitochondrial disorder of infants. more »

The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight

What to expect after a year in space

Space is the final frontier for understanding how extreme environments affect human physiology. Following twin astronauts, one of which spent a year-long mission on the International Space Station, Garrett-Bakelman et al. examined molecular and physiological traits that may be affected by time in space (see the Perspective by Löbrich and Jeggo). more »

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Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation

Genome-wide association studies in obesity have identified a large number of non-coding loci located near genes expressed in the central nervous system. However, due to the difficulties in isolating and characterizing specific neuronal subpopulations, few obesity-associated single-nucleotide polymorphisms have been functionally characterized. more »

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. more »

Soil microbial responses to drought and exotic plants shift carbon metabolism

Significant gaps in our understanding of how global change drivers interact to affect the resistance and functioning of microbial communities hinders our ability to model ecosystem responses and feedbacks to co-occurring global stressors. more »

Unlocking a mechanism of lineage determination in the development of primary cancers using genomics.

Researchers are performing WGS and WES to identify immune cell cytokines that act on oncogenically transforming hepatocyctesand their epigenetic regulation.  more »

The highest peaking calling, sensitivity, and specificity values recorded for ChIP-Seq.

Seven methods designed for low input DNA/ChIP-seq sample preparation  (Accel-NGS 2S, Bowman-method, HTML-PCR, SeqPlex, DNA SMART, TELP, and ThruPLEX) were performed on five replicates of 1 ng and 0.1 ng input.  more »