scholarly journals Identification of functional genetic variation in exome sequence analysis

2011 ◽  
Vol 5 (S9) ◽  
Author(s):  
Andrew Jaffe ◽  
Genevieve Wojcik ◽  
Audrey Chu ◽  
Asieh Golozar ◽  
Ankit Maroo ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Sequence Analysis ◽  
Functional Genetic Variation ◽  
Exome Sequence

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Functional genetic variation in the Rev-Erbαpathway and lithium response in the treatment of bipolar disorder

2011 ◽  
Vol 10 (8) ◽  
pp. 852-861 ◽  
Author(s):  
M. J. McCarthy ◽  
C. M. Nievergelt ◽  
T. Shekhtman ◽  
D. F. Kripke ◽  
D. K. Welsh ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Genetic Variation ◽  
Functional Genetic Variation ◽  
Lithium Response

scholarly journals The crucial role of genome-wide genetic variation in conservation

2021 ◽  
Vol 118 (48) ◽  
pp. e2104642118
Author(s):  
Marty Kardos ◽  
Ellie E. Armstrong ◽  
Sarah W. Fitzpatrick ◽  
Samantha Hauser ◽  
Philip W. Hedrick ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Environmental Changes ◽  
Population Viability ◽  
Adaptive Potential ◽  
Biodiversity Crisis ◽  
Genome Wide ◽  
Simulation Based ◽  
Functional Genetic Variation

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.

scholarly journals Functional Genetic Variation in NFKBIA and Susceptibility to Childhood Asthma, Bronchiolitis, and Bronchopulmonary Dysplasia

2013 ◽  
Vol 190 (8) ◽  
pp. 3949-3958 ◽  
Author(s):  
Salman Ali ◽  
Aaron F. Hirschfeld ◽  
Matthew L. Mayer ◽  
Edgardo S. Fortuno ◽  
Nathan Corbett ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Bronchopulmonary Dysplasia ◽  
Childhood Asthma ◽  
Functional Genetic Variation

scholarly journals Novel COL11A2 Pathogenic Variants in a Child with Autosomal Recessive Otospondylomegaepiphyseal Dysplasia: A Review of the Literature

2019 ◽  
Vol 09 (02) ◽  
pp. 117-120
Author(s):  
Pavalan Selvam ◽  
Shekhar Singh ◽  
Angita Jain ◽  
Herjot Atwal ◽  
Paldeep S. Atwal
Keyword(s):  
Sequence Analysis ◽  
Autosomal Recessive ◽  
Autosomal Dominant ◽  
Review Of The Literature ◽  
Pathogenic Variants ◽  
Phenotypic Spectrum ◽  
Whole Exome ◽  
The Family ◽  
Type Xi Collagen ◽  
Exome Sequence

AbstractOtospondylomegaepiphyseal dysplasia (OSMED) is an inherited autosomal dominant and recessive skeletal dysplasia caused by both heterozygous and homozygous pathogenic variants in COL11A2 encoding the α2(XI) collagen chains, a part of type XI collagen. Here, we describe a 2-year-old girl presenting from birth with a phenotype suggestive of OSMED. On whole exome sequence analysis of the family via commercially available methods, we detected two novel heterozygous pathogenic variants in the proband. In addition, we reviewed the phenotype of autosomal recessive OSMED cases with COL11A2 pathogenic variants reported to date and quantitatively highlighted the phenotypic spectrum.

scholarly journals Natural selection and functional genetic variation in the p53 pathway

2011 ◽  
Vol 20 (8) ◽  
pp. 1502-1508 ◽  
Author(s):  
Lara Sucheston ◽  
David B. Witonsky ◽  
Darcie Hastings ◽  
Ozlem Yildiz ◽  
Vanessa J. Clark ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
P53 Pathway ◽  
Functional Genetic Variation
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