Sharing dog exome/genome variant and phenotype data in Varda and LOVD3 - Peter Taschner

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We hypothesize that efficient sharing of genetic variants and phenotype data from other species may help overcoming the main hurdle in current whole exome (WES) and whole genome sequencing (WGS) studies aimed at cracking rare disease: finding sufficient evidence to prove causality. Roughly, studies give a yield of 1/3 proven causality, 1/3 likely causality and 1/3 unresolved cases. Obviously, using other world-wide resources to find additional positive or negative evidence for candidate variants remaining might improve overall yield. An important obstacle here is that information from other organisms is often not easy to find and access in an interoperable manner. Furthermore, lack of standards and metadata may interfere with reuse of data. Reference protein sequences from other organisms are already used to predict amino acid conservation scores [1, 2]. These might be improved if protein variants in individual races of certain species could be included in the calculations. When these variants would be annotated with the frequency and their functional effects, this information would be even more valuable. Variants causing disease in animals are currently stored in Online Mendelian Inheritance in Animals (OMIA, http://omia.angis.org.au/). For several species, including dogs, the research community has partially adopted standards resembling HGNC and HGVS nomenclature. Further standardization may contribute to data from other species becoming more FAIR (Findable, Accessible, Interoperable, and Re-usable) (FAIR data, http://www.dtls.nl/fair-data/). As a first step, we have established instances of the variant frequency database Varda (Dog Varda, http://varda.generade.nl) and the LOVD3 gene variant database platform [3] for the dog (Dog LOVD, http://databases. generade.nl/dog/). We demonstrate that variants from VCF files can be stored and annotated with their frequency in Varda. Information about the functional effects of variants and the resulting phenotypes in individual animals can be stored in the Canis familiaris LOVD. We hope that this example will be followed by research and diagnostic centers world-wide for the dog and other species. [1] PolyPhen-2, PMID:20354512, http://genetics.bwh.harvard.edu/pph2/ [2] SIFT, PMID:11337480, http://sift.bii.a-star.edu.sg/ [3] LOVD, Leiden Open-source Variation Database, PMID:21520333, http://www.LOVD.nl

Science

Sharing dog exome/genome
variant and phenotype data
in Varda and LOVD3
Human Variome Project Meeting, Paris, June 2, 2016
Peter Taschner
taschner@generade.nl

Serious health problems: inbreeding
Hereditary disorders in pedigree dog breeds
Selection reduces genetic diversity
Small genetic basis: founder effects
Exome / genome sequencing:
Selection of dogs to maintain genetic diversity and reduce carrier load
Variants in disease-causing genes: candidate genes for human disease
Dog variants: evidence for causal variants in human patients?
2
Why share dog data?

Nature 438: 803 (2005)
Genetic bottleneck: loss of variation

5
5 dogs per breed
Panel 96 markers
Variation between 85 dog breeds

OMIA
http://omia.angis.org.au
672 dog traits/disorders
201 causative variant known
378 disease models

OMIA: dog CLN6
c.829C>T p.(Trp277Arg)
Reference sequence?
More information in
causal variant tables

Monarch database: dog CLN6
https://monarchinitiative.org/disease/OMIA:001443-9615

Dog exome capture kit design
Raw read data in SRA
No variant details provided
No dbSNP submissions

11
Clinical exome sequencing
Varda
Re-analyze raw dog data
VCF variant file
Annotate using VEP
Import into Varda
Import filtered set into LOVD

12
Varda – dog variant frequencies
https://varda.generade.nl/aule/
DMD gene
Other tools available for dogs:
Mutalyzer:
Name Checker
Position Converter
Mapping database for dog and mouse

13
Variant Effect Predictor
Canine gene symbols follow HGNC systematics
Variants described in HGVS format
Challenges:
Many predicted transcripts and gene models
LOVD uses human-oriented resources
Adaptation/manual intervention necessary
http://databases.generade.nl/dog

14
Acknowledgments
Bioinformatics, UAS Leiden
Thomas Olivier
Koen van Diemen
Rosa Hegi
Olga Veth
Bo Blanckenburg
Floyd Wittink
LUMC, Human Genetics
Ivo Fokkema
Martijn Vermaat
LUMC, Sequence Analysis Support Core
Wibowo Arindrarto
University Gent
Bart Broeckx
OMIA
Frank Nicholas
Varda dog: https://varda.generade.nl/aule/
Dog LOVD: http://databases.generade.nl/dog

Exome sequencing has emerged as an economical way of focusing DNA sequencing efforts on the most functionally understood regions of the genome. Pre-capture pooling, where one bait library is used to pull down the exonic regions of several pooled samples simultaneously is a further financial improvement. However, rare alleles in the pool might not be able to attract baits at the same rate as reference conform sequences can, and may hence be underrepresented. We investigated this potential issue by sequencing a hapmap family (4 individuals) using the pre-capture protocol from Illumina and Nimblegen. We did not observe clear evidence that heterozygote variants are missed but noted a trend for indels to be imbalanced. Our findings do not provide clear evidence to rule out allelic imbalance or bias having an impact on research findings, this may be especially critical for low cellular cancer tissue where rare alleles are more ubiquitous.

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Since volcanic activity was first discovered on Io from Voyager images in 1979, changes on Io’s surface have been monitored from both spacecraft and ground-based telescopes. Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images show that a plume deposit from a powerful eruption at Pillan Patera has covered part of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive optics at visible wavelengths.

如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样

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原版纸张【微信：741003700 】【(uvic毕业证书)维多利亚大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma 1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700 留信网认证的作用: 1:该专业认证可证明留学生真实身份 2:同时对留学生所学专业登记给予评定 3:国家专业人才认证中心颁发入库证书 4:这个认证书并且可以归档倒地方 5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息 6:个人职称评审加20分 7:个人信誉贷款加10分 8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才

ESR spectroscopy in liquid food and beverages.pptx

PRIYANKA PATEL

With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.

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KrushnaDarade1

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Salas, V. (2024) "John of St. Thomas (Poinsot) on the Science of Sacred Theol...

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I Introduction II Subalternation and Theology III Theology and Dogmatic Declarations IV The Mixed Principles of Theology V Virtual Revelation: The Unity of Theology VI Theology as a Natural Science VII Theology’s Certitude VIII Conclusion Notes Bibliography All the contents are fully attributable to the author, Doctor Victor Salas. Should you wish to get this text republished, get in touch with the author or the editorial committee of the Studia Poinsotiana. Insofar as possible, we will be happy to broker your contact.

The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx

MAGOTI ERNEST

Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024). Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).

Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...

Ana Luísa Pinho

Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.

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Sharing dog exome/genome variant and phenotype data in Varda and LOVD3 - Peter Taschner

1. Sharing dog exome/genome variant and phenotype data in Varda and LOVD3 Human Variome Project Meeting, Paris, June 2, 2016 Peter Taschner taschner@generade.nl

2. Serious health problems: inbreeding Hereditary disorders in pedigree dog breeds Selection reduces genetic diversity Small genetic basis: founder effects Exome / genome sequencing: Selection of dogs to maintain genetic diversity and reduce carrier load Variants in disease-causing genes: candidate genes for human disease Dog variants: evidence for causal variants in human patients? 2 Why share dog data?

3. Dog genome CanFam3.1 CanFam1.0

4. Nature 438: 803 (2005) Genetic bottleneck: loss of variation

5. 5 5 dogs per breed Panel 96 markers Variation between 85 dog breeds

6. DNA passport dog - Healthy carrier www.genoscoper.com - Screening known variants - Determine and maintain population dynamics Extension: DNA-profile for verification of: - Parenthood - Pedigree

7. OMIA http://omia.angis.org.au 672 dog traits/disorders 201 causative variant known 378 disease models

8. OMIA: dog CLN6 c.829C>T p.(Trp277Arg) Reference sequence? More information in causal variant tables

9. Monarch database: dog CLN6 https://monarchinitiative.org/disease/OMIA:001443-9615

10. Dog exome capture kit design Raw read data in SRA No variant details provided No dbSNP submissions

11. 11 Clinical exome sequencing Varda Re-analyze raw dog data VCF variant file Annotate using VEP Import into Varda Import filtered set into LOVD

12. 12 Varda – dog variant frequencies https://varda.generade.nl/aule/ DMD gene Other tools available for dogs: Mutalyzer: Name Checker Position Converter Mapping database for dog and mouse

13. 13 Variant Effect Predictor Canine gene symbols follow HGNC systematics Variants described in HGVS format Challenges: Many predicted transcripts and gene models LOVD uses human-oriented resources Adaptation/manual intervention necessary http://databases.generade.nl/dog

14. 14 Acknowledgments Bioinformatics, UAS Leiden Thomas Olivier Koen van Diemen Rosa Hegi Olga Veth Bo Blanckenburg Floyd Wittink LUMC, Human Genetics Ivo Fokkema Martijn Vermaat LUMC, Sequence Analysis Support Core Wibowo Arindrarto University Gent Bart Broeckx OMIA Frank Nicholas Varda dog: https://varda.generade.nl/aule/ Dog LOVD: http://databases.generade.nl/dog

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