Trending Papers in genetics
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A person's genes indicate if they are likely to respond to a specific antidepressant drug
From Paper: Genome-wide association studies of antidepressant class response and treatment-resistant depression
Authors:
Qingqin S. Li, Chao Tian, David HindsPublished: Oct 2020
- The results identified several genetic markers potentially associated with TRD and with antidepressant treatment response in a large population of individuals using self-reported outcomes
- This study was identified novel genetic variants associated with response to classes of antidepressant therapy to improve our understanding of a potential genetic basis of antidepressant treatment response and to differentiate TRD from non-TRD (NTRD)
Submitted by Patrick Joyce
Insights into human genetic variation and population history from 929 diverse genomes
Authors:
Bergström, Anders, et alPublished: Jun 2019
- Overall the authors identified 67.3 million single nucleotide polymorphisms, 8.8 million small insertions or deletions (indels), and 40,736 copy number variants. This includes hundreds of thousands of variants that had not been discovered by previous sequencing efforts, but which are common in one or more population
- The results reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions
Retrieved from biorxiv
In children, gene expression within peripheral blood is associated with emotional and behavioral profiles
From Paper: Gene co-expression networks in peripheral blood capture dimensional measures of emotional and behavioral problems from the Child Behavior Checklist (CBCL)
Published: Sep 2020
- MANBA has been implicated as a druggable gene and may offer a new avenue for ADHD treatment
- Expression of MANBA, a gene that encodes a lysosomal enzyme called mannosidase beta, was found in our study to be significantly positively associated with the CBCL attention problems scale
Submitted by Patrick Joyce
Using epigenetics to reconstruct the anatomy of an extinct species of humans
From Paper: Reconstructing Denisovan Anatomy Using DNA Methylation Maps
Authors:
Gokhman, David, et alPublished: Sep 2019
- This system was tested by reconstructing the known anatomy of Neanderthal and chimp profiles based on their hypermethylated genes
- The phenotype of methylation-based downregulation was inferred from known loss-of-function phenotypes
Submitted by Patrick Joyce
The coding capacity of SARS-CoV-2
Abstract SARS-CoV-2 is a coronavirus responsible for the COVID-19 pandemic. In order to understand its pathogenicity, antigenic potential and to develop diagnostic and therapeutic tools, it is essential to portray the full repertoire of its expressed proteins. The SARS-CoV-2 coding capacity map is currently based on computational predictions and relies on homology to other coronaviruses. Since coronaviruses differ in their protein array, especially in the variety of accessory proteins, it is crucial to characterize the specific collection of SARS-CoV-2 translated open reading frames (ORF)s in an unbiased and open-ended manner. Utilizing a suit of ribosome profiling techniques, we present a high-resolution map of the SARS-CoV-2 coding regions, allowing us to accurately quantify the expression of canonical viral ORFs and to identify 23 novel unannotated viral ORFs. These ORFs include several in-frame internal ORFs lying within existing ORFs, resulting in N-terminally truncated products, as well as internal out-of-frame ORFs, which generate novel polypeptides. Finally, we detected a prominent initiation at a CUG codon located in the 5’UTR. Although this codon is shared by all SARS-CoV-2 transcripts, the initiation was specific to the genomic RNA, indicating that the genomic RNA harbors unique features that may affect ribosome engagement. Overall, our work reveals the full coding capacity of SARS-CoV-2 genome, providing a rich resource, which will form the basis of future functional studies and diagnostic efforts.
Submitted by Patrick Joyce
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Genetic Engineering of Lipid Biosynthesis in Seeds
Published: Jun 2013
The demand for vegetable oils, including those derived from crucifer (Brassicaceae) species, has been increasing rapidly over recent years for use in both food and industrial applications. In order to meet these demands, biotechnological approaches will almost certainly be a necessity to generate crops with improved lipid traits. In addition to the clear need to increase the seed oil content of crucifer species, there has also been growing interest in generating transgenic lines that display improved compositions of fatty acids and non-acyl lipids, including carotenoids and tocochromanols, for enhanced nutritional or industrial applicability. Fortunately, knowledge concerning oilseed metabolism and lipid biosynthesis are accumulating at a rapid pace, which is enabling attempts to genetically engineer crucifer species with enhanced oil content and quality. This chapter outlines the various attempts and successes in this field to date.
Submitted by xue pan
Haplotype-phased common marmoset embryonic stem cells for genome editing using CRISPR/Cas9
Authors:
Zhou, Bo, et alPublished: Jul 2018
Due to anatomical and physiological similarities to humans, the common marmoset (Callithrix jacchus), a non-human primate, is an ideal organism for the study of many human diseases. Researchers are currently leveraging genome-editing technologies such as CRISPR/Cas9 to genetically engineer marmosets for the in vivo biomedical modeling of human neuropsychiatric and neurodegenerative diseases. Several marmoset embryonic stem cell (ESC) lines and induced pluripotent stem cell (iPSC) lines established for these purposes are now available and being distributed to various research institutions. The genome characterization of these cell lines can greatly reinforce these transgenic efforts and serve as a valuable resource in many ways. For example, knowing the genomic sequence variants and haplotype phasing information for a particular marmoset cell line allows for the better control of off-target effects in CRISPR/Cas9 experiments and also the ability to make allele-specific edits. It also provides the genomic contexts required for the accurate interpretation of functional genomics data. Here, we performed whole-genome characterization in a haplotype-resolved manner for marmoset ESC line cj367 from the Wisconsin National Primate Research Center. This is the first haplotype-resolved analysis of a marmoset genome and the first whole-genome characterization of any marmoset ESC line. We identified and phased single-nucleotide variants (SNVs) and Indels across the genome. By leveraging this haplotype information, we then compiled a list of cj367 ESC allele-specific CRISPR targeting sites. Furthermore, we demonstrated successful Cas9 Endonuclease Dead (dCas9) expression and targeted localization in cj367 as well as sustained pluripotency after dCas9 transfection by teratoma assay. Lastly, we show that these ESCs can be directly induced into functional neurons in a rapid, single-step process. Our study provides a valuable set of genomic resources for primate transgenics in this post-genome era.
Retrieved from biorxiv
NAD modulates DNA methylation and cell differentiation
- NAD+ treated cells exhibit significant morphological and phenotypical changes that correspond to myeloid differentiation
- Impairment of DNMT1 enzymatic activity by NAD-promoted ADP-ribosylation, leads to demethylation and transcriptional activation of CEBPA gene
Submitted by Patrick Joyce
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Rationales, design and recruitment of the Taizhou Longitudinal Study
Published: Jul 2009
Background: Rapid economic growth in China in the past decades has been accompanied by dramatic changes in lifestyle and environmental exposures. The burdens of non-communicable diseases, such as cardiovascular diseases, diabetes and cancer, have also increased substantially.Methods/design: We initiated a large prospective cohort–the Taizhou Longitudinal Study–in Taizhou (a medium-size city in China) to explore the environmental and genetic risk factors for common non-communicable diseases. The sample size of the cohort will be at least 100,000 adultsaged 30–80 years drawn from the general residents of the districts of Hailin, Gaogang, and Taixing (sample frame, 1.8 million) of Taizhou. A three-stage stratified sampling method will be applied.Baseline investigations include interviewer-administered questionnaire, anthropometric measurements, and collection of buccal mucosal cells and blood specimens. DNA will be extracted for genetic studies and serum samples will be used for biochemical examinations. A follow-upsurvey will be conducted every three years to obtain information on disease occurrence and information on selected lifestyle exposures. Study participants will be followed-up indefinitely by using a chronic disease register system for morbidity and cause-specific mortality. Information onnon-fatal events will be obtained for certain major categories of disease (e.g., cancer, stroke, myocardial infarction) through established registry systems.Discussion: The Taizhou Longitudinal Study will provide a good basis for exploring the roles of many important environmental factors (especially those concomitant with the economic transformation in China) for common chronic diseases, solely or via interaction with genetic factors.
Submitted by Patrick Joyce
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Experimental Alzheimers blood test performed better than MRI brain scans, was as good as PET scans, and was nearly as accurate as autopsies in diagnosing the disease
From Paper: Discriminative Accuracy of Plasma Phospho-tau217 for Alzheimer Disease vs Other Neurodegenerative Disorders
Published: Jul 2020
- The Arizona part of the study included 81 patients who had donated their brains upon death. Researchers were able to show that blood testing while they were alive closely matched evidence of disease during autopsies.
- The Colombia part of the study included patients with a rare gene that virtually destines them to develop Alzheimer's at a young age, typically in their 40s. In those with the gene, p-tau217 blood levels started to rise 20 years before symptoms, which means the test could distinguish between those with and without the mutation in people as young as 25.
Submitted by Angela Meng
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