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Genomics Research

19:36 EST 9th December 2018 | BioPortfolio

Developing a Process for Returning Medically Actionable Genomic Variants to Latino Patients in a Federally Qualified Health Center.

To develop a process for returning medically actionable genomic variants to Latino patients receiving care in a Federally Qualified Health Center.

N6-Hydroxymethyladenine: a hydroxylation derivative of N6-methyladenine in genomic DNA of mammals.

In addition to DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC), DNA adenine methylation (N6-methyl-2'-deoxyadenosine, m6dA) is another DNA modification that has been discovered in eukaryotes. Recent studies demonstrated that the content and distribution of m6dA in genomic DNA of vertebrates and mammals exhibit dynamic regulation, indicating m6dA may function as a potential epigenetic ma...

Genomic Analysis and Prediction within a US Public Collaborative Winter Wheat Regional Testing Nursery.

The development of inexpensive, whole-genome profiling enables a transition to allele-based breeding using genomic prediction models. These models consider alleles shared between lines to predict phenotypes and select new lines based on estimated breeding values. This approach can leverage highly unbalanced datasets that are common to breeding programs. The Southern Regional Performance Nursery (S...

Genome-Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High-Quality Rice.

Rice ( L.) is one of the most important staple food crops in the world; however, there has recently been a shift in consumer demand for higher grain quality. Therefore, understanding the genetic architecture of grain quality has become a key objective of rice breeding programs. Genome-wide association studies (GWAS) using large diversity panels have successfully identified genomic regions associat...

Prospects and Challenges of Applied Genomic Selection-A New Paradigm in Breeding for Grain Yield in Bread Wheat.

Genomic selection (GS) has been promising for increasing genetic gains in several species. Therefore, we evaluated the potential integration of GS for grain yield (GY) in bread wheat ( L.) in CIMMYT's elite yield trial nurseries. We observed that the genomic prediction accuracies within nurseries (0.44 and 0.35) were substantially higher than across-nursery accuracies (0.15 and 0.05) for GY evalua...

Agnostic detection of genomic alterations by holistic DNA structural interrogation.

There is an established relationship between primary DNA sequence, secondary and tertiary chromatin structure, and transcriptional activity, suggesting that observed differences in one of these properties may reflect changes in the others. Here, we exploit these relationships to show that variations in DNA structure can be used to identify a wide range of genomic alterations in mammalian samples. ...

Blockchain-based platforms for genomic data sharing: a de-centralized approach in response to the governance problems?

Multivariate genomic predictions for age at puberty in tropically adapted beef heifers.

Heifers that have an earlier age at puberty often have greater lifetime productivity. Age at puberty is moderately heritable so selection should effectively reduce the number of days to puberty, and improve heifer productivity and profitability as a result. However, recording age at puberty is intensive, requiring repeat ovarian scanning to determine age at first corpus luteum (AGECL). Genomic sel...

Construction and characterization of ribonuclease H2 knockout NIH3T3 cells.

Ribonuclease H (RNase H) specifically hydrolyzes the 5'-phosphodiester bonds of the RNA of RNA/DNA hybrid. Both type 1 and 2 RNases H act on the RNA strand of the hybrid, while only type 2 acts on the single ribonucleotide embedded in DNA duplex. In this study, to explore the role of mammalian type 2 RNase H (RNase H2) in cells, we constructed the RNase H2 knockout NIH3T3 cells (KO cells) by CRISP...

Karyomapping for simultaneous genomic evaluation and aneuploidy screening of preimplantation bovine embryos: The first live-born calves.

In cattle breeding, the development of genomic selection strategies based on single nucleotide polymorphism (SNP) interrogation has led to improved rates of genetic gain. Additionally, the application of genomic selection to in-vitro produced (IVP) embryos is expected to bring further benefits thanks to the ability to test a greater number of individuals before establishing a pregnancy and to ensu...

Genetics and genomics of reproductive disorders in Canadian Holstein cattle.

In Canada, reproductive disorders known to affect the profitability of dairy cattle herds have been recorded by producers on a voluntary basis since 2007. Previous studies have shown the feasibility of using producer-recorded health data for genetic evaluations. Despite low heritability estimates and limited availability of phenotypic information, sufficient genetic variation has been observed for...

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.

The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays, which map the genome-wide locations of transcription factor binding sites, histone post-translational modifications and regions of chromatin accessible to endonuclease activity. Currently, the Cistrome DB contains approximately 47,000 ...

Description of grain weight distribution leading to genomic selection for grain-filling characteristics in rice.

Grain-filling ability is one of the factors that controls grain yield in rice (Oryza sativa L.). We developed a method for describing grain weight distribution, which is the probability density function of single grain weight in a panicle, using 128 Japanese rice varieties. With this method, we quantitively analyzed genotypic differences in grain-filling ability and used the grain weight distribut...

Genome-wide regulatory adaptation shapes population-level genomic landscapes in Heliconius.

cis-regulatory evolution is an important engine of organismal diversification. While recent studies have looked at genomic patterns of regulatory evolution between species, we still have a poor understanding of the magnitude and nature of regulatory variation within species. Here we examine the evolution of regulatory element activity over wing development in three Heliconius erato butterfly popul...

Evaluation for Genetic Disorders in the Absence of a Clinical Indication for Testing: Elective Genomic Testing.

The increasing quality and diminishing cost of next-generation sequencing has transformed our ability to interrogate large quantities of genetic information. This has led to a dramatic increase in the number of elective genomic tests performed. In this article elective test denotes a test that a patient chooses to undertake without a clinical indication. The variety of elective genomic testing opt...

A behavior-theoretic evaluation of values clarification on parental beliefs and intentions toward genomic sequencing for newborns.

Decision aids commonly include values clarification exercises to help people consider which aspects of a choice matter most to them, and to help them make decisions that are congruent with their personal values and preferences. Using a randomized online experiment, we examined the influence of values clarification on parental beliefs and intentions about having genomic sequencing for newborns. We ...

Miniaturization of tardigrades (water bears): Morphological and genomic perspectives.

Tardigrades form a monophyletic group of microscopic ecdysozoans best known for surviving extreme environmental conditions. Due to their key phylogenetic position as a subgroup of the Panarthropoda, understanding tardigrade biology is important for comparative studies with related groups like Arthropoda. Panarthropods - and Ecdysozoa as a whole - likely evolved from macroscopic ancestors, with sev...

Australians' perspectives on support around use of personal genomic testing: Findings from the Genioz study.

Personal genomic testing using direct-to-consumer and consumer-directed models, with or without involvement of healthcare providers, is increasing internationally, including in Australia. This study forms a sub-set of the Genioz study - Genomics: National Insights of Australians. We aimed to explore Australians' experiences with these types of tests, especially online DNA tests, and their views re...

SeQuiLa: An elastic, fast and scalable SQL-oriented solution for processing and querying genomic intervals.

Efficient processing of large-scale genomic datasets has recently become possible due to the application of 'big data' technologies in bioinformatics pipelines.We present SeQuiLa - a distributed, ANSI SQL compliant solution for speedy querying and processing of genomic intervals that is available as an Apache Spark package. Proposed range join strategy is significantly (~22x) faster than the defau...

Regulatory Genomic Data Cubism.

A regularly shaped grid is useful for analyzing data particularly at multilayer levels, where patterns can be visually represented and analytically compared-conceptually similar to Picasso's cubism. Here we introduce ATLAS, featuring a suite of spatially ordered maps designed for representation and comparison of patterns seen in regulatory genomic data. It produces a landscape learned from input d...

Loss of function of NF1 is a mechanism of acquired resistance to endocrine therapy in lobular breast cancer.

Invasive lobular carcinoma (ILC) as a disease entity distinct from invasive ductal carcinoma (IDC) has merited focused studies of the genomic landscape, but those to date are largely limited to the assessment of early-stage cancers. Given that genomic alterations may develop as acquired resistance to endocrine therapy, studies on refractory ILC are needed.

Genomic Prediction for Crossbred Performance using Metafounders.

Future genomic evaluation models to be used routinely in breeding programs for pigs and poultry need to be able to optimally use information of crossbred animals to predict breeding values for crossbred performance of purebred selection candidates. Important challenges in the commonly used single-step genomic best linear unbiased prediction (ssGBLUP) model, are the definition of relationships betw...

Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools.

The growing appetite of behavioral neuroscience for automated data production is prompting the need for new computational standards allowing improved interoperability, reproducibility, and shareability. We show here how these issues can be solved by repurposing existing genomic formats whose structure perfectly supports the handling of time series. This allows existing genomic analysis and visuali...

Return of secondary findings in genomic sequencing: Military implications.

Genomic sequencing has become a widely used tool in clinical and research settings in both civilian and military healthcare systems.

Circulating tumor DNA in advanced prostate cancer: transitioning from discovery to a clinically implemented test.

The genomic landscape of metastatic castration-resistant prostate cancer (mCRPC) differs from that of the primary tumor and is dynamic during tumor progression. The real-time and repeated characterization of this process via conventional solid tumor biopsies is challenging. Alternatively, circulating cell-free DNA (cfDNA) containing circulating tumor DNA (ctDNA) can be obtained from patient plasma...

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