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PubMed Journals Articles About "GHEP ISFG Collaborative Study Genetic Variation Autosomal Indels" RSS

01:56 EST 19th November 2018 | BioPortfolio

GHEP ISFG Collaborative Study Genetic Variation Autosomal Indels PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest GHEP ISFG Collaborative Study Genetic Variation Autosomal Indels articles that have been published worldwide.

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Showing "GHEP ISFG collaborative study genetic variation autosomal indels" PubMed Articles 1–25 of 66,000+

GHEP-ISFG collaborative exercise on mixture profiles (GHEP-MIX06). Reporting conclusions: Results and evaluation.

One of the main goals of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the field of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise o...


Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation.

X-chromosome inactivation (XCI), i.e., the inactivation of one of the female X chromosomes, restores equal expression of X-chromosomal genes between females and males. However, ~10% of genes show variable degrees of escape from XCI between females, although little is known about the causes of variable XCI. Using a discovery data-set of 1867 females and 1398 males and a replication sample of 3351 females, we show that genetic variation at three autosomal loci is associated with female-specific changes in X-c...

Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test.

Short insertions, deletions (INDELs) and larger structural variants have been increasingly employed in genetic association studies, but few improvements over SNP-based association have been reported. In order to understand why this might be the case, we analysed two publicly available datasets and observed that 63% of INDELs called in A. thaliana and 64% in D. melanogaster populations are misrepresented as multiple alleles with different functional annotations, i.e. where the same underlying variant is repr...


Preimplantation genetic diagnosis for infertile males with autosomal dominant polycystic kidney disease.

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common genetic renal diseases, which may cause oligoasthenospermia and azoospermia and result in male infertility. This study aimed to analyze the outcomes of preimplantation genetic diagnosis (PGD) in male patients with ADPKD-induced infertility.

An empirical study of collaborative capacity evaluation and scheduling optimization for a CPD project.

In a collaborative product design project, reasonable resource allocation can shorten the development cycle and reduce cost. Team capacity evaluation and a task-team scheduling model are presented. A collaborative team capacity model is constructed, and a 2-tuple linguistic method is used to evaluate the capacity of collaborative teams. Next, the matching degree between design task and collaborative team is defined. A collaborative product design scheduling model considering task-team matching is developed....

Immune diversity sheds light on missing variation in worldwide genetic diversity panels.

Defining worldwide human genetic variation is a critical step to reveal how genome plasticity contributes to disease. Yet, there is currently no metric to assess the representativeness and completeness of current and widely used data on genetic variation. We show here that Human Leukocyte Antigen (HLA) genes can serve as such metric as they are both the most polymorphic and the most studied genetic system. As a test case, we investigated the 1,000 Genomes Project panel. Using high-accuracy in silico HLA typ...

Evolutionary potential varies across populations and traits in the neotropical oak Quercus oleoides.

Heritable variation in polygenic (quantitative) traits is critical for adaptive evolution and is especially important in this era of rapid climate change. In this study, we examined the levels of quantitative genetic variation of populations of the tropical tree Quercus oleoides Cham. and Schlect. for a suite of traits related to resource use and drought resistance. We tested whether quantitative genetic variation differed across traits, populations and watering treatments. We also tested potential evolutio...

SLCO1B1 genetic variation and hormone therapy in menopausal women.

Response to menopausal hormone therapy (MHT) shows individual variation. SLCO1B1 encodes the OATP1B1 transporter expressed in the liver that transports many endogenous substances, including estrone sulfate, from the blood into hepatocytes. This study evaluated the relationship between genetic variation in SLCO1B1 and response to MHT in women enrolled in the Kronos Early Estrogen Prevention Study (KEEPS) at Mayo Clinic, Rochester, MN.

Neutral theory, microbial practice: challenges in bacterial population genetics.

Kimura's outstanding contributions to population genetics included many elegant theoretical results on the vagaries of alleles in populations. Once polymorphism data showed extensive variation in natural populations, these results led naturally to the Neutral Theory. In this article, I'll depart from some of these results to focus on four major open problems in microbial population genetics with direct implications to the study of molecular evolution: the lack of neutral polymorphism, the modeling of geneti...

Comparison of INDEL Calling Tools with Simulation Data and Real Short-Read Data.

Insertions and deletions (INDELs) comprise a significant proportion of human genetic variation, and recent papers have revealed that many human diseases may be attributable to INDELs. With the development of next-generation sequencing (NGS) technology, many statistical/computational tools have been developed for calling INDELs. However, there are differences among those tools, and comparisons among them have been limited. In order to better understand these inter-tool differences, five popular and publicly ...

Genome-wide association study of developmental dysplasia of the hip identifies an association with .

Developmental dysplasia of the hip (DDH) is the most common skeletal developmental disease. However, its genetic architecture is poorly understood. We conduct the largest DDH genome-wide association study to date and replicate our findings in independent cohorts. We find the heritable component of DDH attributable to common genetic variants to be 55% and distributed equally across the autosomal and X-chromosomes. We identify replicating evidence for association between promoter variation and DDH (rs143384,...

Ancestry analysis in rural Brazilian populations of African descent.

Rural communities comprise around 20% of Caribbean and South American populations, but are under-represented in autosomal marker databases. That deficiency is problematic for forensic genetics, as it relies on accurate descriptions of genetic variation and population structure. Brazilian populations were shaped by an intense, complex and heterogeneous process of admixture encompassing mainly Amerindians, Sub-Saharan Africans and Europeans. Quilombos are Brazilian populations with significant African descent...

Validation of a Long-Read PCR Assay for Sensitive Detection and Sizing of C9orf72 Hexanucleotide Repeat Expansions.

A hexanucleotide GGGGCC repeat expansion in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). Accurate determination and quantitation of the repeat length is critical in both clinical and research settings. However, due to the complexity of the C9orf72 expansion with high GC content, large size of repeats, and high rate of insertion/deletions (indels) and sequence variations in the flanking regions, molecular genetic analysis of the locus ...

CC002/Unc females are mouse models of exercise-induced paradoxical fat response.

Exercise results in beneficial health outcomes and protects against a variety of chronic diseases. However, U.S. exercise guidelines recommend identical exercise programs for everyone, despite individual variation in responses to these programs, including paradoxical fat gain. Experimental models of exercise-induced paradoxical outcomes may enable the dissection of underlying physiological mechanisms as well as the evaluation of potential interventions. Whereas several studies have identified individual mic...

Whole genome deep sequencing revealed host impact on population structure, variation and evolution of Rice stripe virus.

High-throughput deep sequencing and variant detection showed that variations of Rice stripe virus (RSV) populations obtained from small brown planthopper-transmitted rice plants and sap-inoculated N. benthamiana plants were single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels). The SNPs were more uniform across RSV genome, but InDels occurred mainly in the intergenic regions (IRs) and in the 5' or 3' noncoding regions. There were no clear patterns of InDels, although the inserted sequences...

Genetic basis of thermal plasticity variation in Drosophila melanogaster body size.

Body size is a quantitative trait that is closely associated to fitness and under the control of both genetic and environmental factors. While developmental plasticity for this and other traits is heritable and under selection, little is known about the genetic basis for variation in plasticity that can provide the raw material for its evolution. We quantified genetic variation for body size plasticity in Drosophila melanogaster by measuring thorax and abdomen length of females reared at two temperatures fr...

Allele frequencies of 15 autosomal STRs in Chinese Nakhi and Yi populations.

Genetic characterization of ethnically and geographically diverse populations via short tandem repeats (STRs) is relevant to various fundamental and applied areas of forensic genetics, population studies, and even molecular anthropology. In the present study, genetic polymorphisms of 15 autosomal STR loci were firstly obtained from 918 individuals (495 Nakhis and 423 Yis) residing in the foothills of the Himalayas. The cumulative powers of discrimination and probabilities of exclusion in the two studied eth...

Whole-genome sequencing reveals a recurrent missense mutation in the Connexin 46 (GJA3) gene causing autosomal-dominant lamellar cataract.

Congenital cataract, opacification of the ocular lens, is clinically and genetically a heterogeneous childhood disease. In this study we aimed to identify the underlying genetic cause of isolated autosomal-dominant lamellar cataract in a multi-generation English family.

Global Variations and Challenges With Tubercular Uveitis in the Collaborative Ocular Tuberculosis Study.

The aim of this study was to examine regional variation management practices and outcomes for tubercular uveitis (TBU).

Genetic analysis of 15 autosomal STRs in Yousafzai population of Pakistan.

Yousafzai is a Pushto-speaking Pathan tribe inhabiting the northern province of Pakistan who claim to be descendants of the prophet Yousaf (Joseph). Forensic and genetic parameters were determined for 203 genetically unrelated individuals on 15 autosomal STRs. D2S1338 was the most discriminating locus whereas TPOX was the least. The combined matching probability (CMP) for all loci was 1.52458 × 10 while combined power of discrimination (CPD) and combined power of exclusion (CPE) was 0.99999999999999999...

Autosomal dominant retinitis pigmentosa with macular involvement associated with a disease haplotype that included a novel PRPH2 variant (p.Cys250Gly).

It is known that PRPH2 variants appear to be rare causes of retinitis pigmentosa (RP) in the Japanese population. The purpose of this study was to describe clinical and genetic features in autosomal dominant RP (adRP) patients with a novel disease-causing variant in the PRHP2 gene.

Genetic diversity in the endangered terrestrial orchid Cypripedium japonicum in East Asia: Insights into population history and implications for conservation.

Little is known about levels and patterns of genetic diversity for the entire range of endangered orchids native to China, Korea, and Japan. In this study, we focus on Cypripedium japonicum and suggest three hypotheses: 1) that genetic drift has been a primary evolutionary force; 2) that populations in central and western China harbor higher levels of genetic variation relative to those from eastern China; and 3) that C. japonicum in China maintains the highest genetic variation among the three countries. U...

dbCID: a manually curated resource for exploring the driver indels in human cancer.

While recent advances in next-generation sequencing technologies have enabled the creation of a multitude of databases in cancer genomic research, there is no comprehensive database focusing on the annotation of driver indels (insertions and deletions) yet. Therefore, we have developed the database of Cancer driver InDels (dbCID), which is a collection of known coding indels that likely to be engaged in cancer development, progression or therapy. dbCID contains experimentally supported and putative driver i...

Mutations in Known Disease Genes Account for the Majority of Autosomal Recessive Retinal Dystrophies.

Retinal dystrophies (RD) are hereditary blinding eye conditions that are highly variable in their clinical presentation. The remarkable genetic heterogeneity that characterizes RD was a major challenge in establishing the molecular diagnosis in these patients until the recent advent of next-generation sequencing. It remains unclear, however, what percentage of autosomal recessive RD remain undiagnosed when all established RD genes are sequenced. We enrolled 75 families in which RD segregates in an apparentl...

Genetic ancestry of patients with porphyria cutanea tarda in a country with mixed races: a cross-sectional study (Rio de Janeiro - Brazil).

Porphyria cutanea tarda has a complex etiology with genetic factors not completely elucidated. The miscegenation of the Brazilian population has important implications in the predisposition to diseases. There are no studies concerning the genetic ancestry of patients with porphyria cutanea tarda from a mixed population. Thirty patients living in Rio de Janeiro with sporadic porphyria cutanea tarda were studied for the genetic ancestry through informative markers - INDELS. There was a significant predominanc...


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