scholarly journals GBSmode: a pipeline for haplotype-aware analysis of genotyping-by-sequencing data

2021 ◽  
Author(s):  
Steven Andrew Yates ◽  
Bruno Studer
Keyword(s):  
Oryza Sativa L ◽  
Molecular Genetic ◽  
Genotyping By Sequencing ◽  
Molecular Genetic Analysis ◽  
Shotgun Sequencing ◽  
Biological Information ◽  
Genotyping Errors ◽  
Sequencing Data ◽  
Manihot Esculenta Crantz ◽  
F2 Population

BACKGROUND: Genotyping-by-sequencing (GBS) has revolutionised molecular genetic analysis. It enables simultaneous genotyping of thousands of DNA markers in the genome of any species. In contrast to whole-genome shotgun sequencing, GBS exploits a restriction enzyme to reduce genome complexity and directs the sequencing to begin at fixed digestion sites. However, currently used tools for the analysis of GBS data, such as SAMtools, often neglect the fundamental technical differences between GBS and shotgun sequencing. RESULTS: Here we present GBSmode, a dedicated pipeline to call DNA sequence variants using whole-read information from GBS data. It removes false positives by incorporating biological features such as the ploidy level and the number of possible alleles in the population under investigation. Comparison of GBSmode with SAMtools in an F2 population of rice (Oryza sativa L.) showed both identified a similar number of polymorphisms (13,449 and 14,445, respectively) with a high overlap (8,143). However, differences were found in the number of read misalignments (8.0% and 14.3% for GBSmode and SAMtools, respectively) and genotyping errors (5.0% and 8.3% for GBSmode and SAMtools, respectively). Further tests in a bi-parental F1 population of cassava (Manihot esculenta Crantz) showed GBSmode found 31,489 polymorphic loci, whereas the number was higher with SAMtools (43,860). However, this difference was mainly attributable to GBSmode rejecting 11,695 loci that were biologically not possible. CONCLUSIONS: This study shows that GBSmode is a versatile tool for the analysis of GBS data. Moreover, GBSmode was able to reduce genotyping errors arising from read misalignments by combining haplotype data with biological information. Whilst other tools may find more markers, GBSmode is designed for accuracy.

scholarly journals Molecular Genetic Analysis of Human Endometrial Mesenchymal Stem Cells That Survived Sublethal Heat Shock

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
A. E. Vinogradov ◽  
M. A. Shilina ◽  
O. V. Anatskaya ◽  
L. L. Alekseenko ◽  
I. I. Fridlyanskaya ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Heat Shock ◽  
Replicative Senescence ◽  
Molecular Genetic ◽  
Interaction Network ◽  
Molecular Genetic Analysis ◽  
Molecular Karyotyping ◽  
Sequencing Data ◽  
Oncogenic Signaling

High temperature is a critical environmental and personal factor. Although heat shock is a well-studied biological phenomenon, hyperthermia response of stem cells is poorly understood. Previously, we demonstrated that sublethal heat shock induced premature senescence in human endometrial mesenchymal stem cells (eMSC). This study aimed to investigate the fate of eMSC-survived sublethal heat shock (SHS) with special emphasis on their genetic stability and possible malignant transformation using methods of classic and molecular karyotyping, next-generation sequencing, and transcriptome functional analysis. G-banding revealed random chromosome breakages and aneuploidy in the SHS-treated eMSC. Molecular karyotyping found no genomic imbalance in these cells. Gene module and protein interaction network analysis of mRNA sequencing data showed that compared to untreated cells, SHS-survived progeny revealed some difference in gene expression. However, no hallmarks of cancer were found. Our data identified downregulation of oncogenic signaling, upregulation of tumor-suppressing and prosenescence signaling, induction of mismatch, and excision DNA repair. The common feature of heated eMSC is the silence of MYC, AKT1/PKB oncogenes, and hTERT telomerase. Overall, our data indicate that despite genetic instability, SHS-survived eMSC do not undergo transformation. After long-term cultivation, these cells like their unheated counterparts enter replicative senescence and die.

Molecular Genetic Analysis of QTLs for Ferulic Acid Content in Dried Straw of Rice (Oryza sativa L.)

2005 ◽  
Vol 43 (1-2) ◽  
pp. 25-34 ◽  
Author(s):  
Yanjun Dong ◽  
E. Tsuzuki ◽  
H. Kamiunten ◽  
Dongzhi Lin ◽  
H. Terao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Genetic Analysis ◽  
Ferulic Acid ◽  
Acid Content ◽  
Oryza Sativa L ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis

Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

2013 ◽  
Vol 20 (1-2) ◽  
pp. 1-8
Author(s):  
MM Rahman ◽  
L Rahman ◽  
SN Begum ◽  
F Nur
Keyword(s):  
Genetic Distance ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Polymorphic Loci ◽  
Rice Genotypes ◽  
High Level ◽  
Genetic Diversity Study ◽  
Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Nei’s genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 – 8, 2009

Diagnosis and Management of Cardiomyopathies – A Focus on Genetics, Cardiac Magnetic Resonance and Clinical Features

2011 ◽  
Vol 7 (3) ◽  
pp. 225
Author(s):  
Gianfranco Sinagra ◽  
Michele Moretti ◽  
Giancarlo Vitrella ◽  
Marco Merlo ◽  
Rossana Bussani ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Cardiac Magnetic Resonance ◽  
Magnetic Resonance ◽  
Imaging Techniques ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Routine Clinical Practice ◽  
Clinical Approach ◽  
Diagnosis And Management ◽  
Made In

In recent years, outstanding progress has been made in the diagnosis and treatment of cardiomyopathies. Genetics is emerging as a primary point in the diagnosis and management of these diseases. However, molecular genetic analyses are not yet included in routine clinical practice, mainly because of their elevated costs and execution time. A patient-based and patient-oriented clinical approach, coupled with new imaging techniques such as cardiac magnetic resonance, can be of great help in selecting patients for molecular genetic analysis and is crucial for a better characterisation of these diseases. This article will specifically address clinical, magnetic resonance and genetic aspects of the diagnosis and management of cardiomyopathies.

scholarly journals MOLECULAR GENETIC ANALYSIS OF THE DILUTE-SHORT EAR (d-se) REGION OF THE MOUSE

Genetics ◽  
1986 ◽  
Vol 112 (2) ◽  
pp. 321-342
Author(s):  
Eugene M Rinchik ◽  
Liane B Russell ◽  
Neal G Copeland ◽  
Nancy A Jenkins
Keyword(s):  
Physical Map ◽  
Leukemia Virus ◽  
Molecular Genetic ◽  
Break Point ◽  
Virus Genome ◽  
Molecular Genetic Analysis ◽  
Chromosome 9 ◽  
Genetic Complementation ◽  
Induced Mutations ◽  
Radiation Induced

ABSTRACT Genes of the dilute-short ear (d-se) region of mouse chromosome 9 comprise an array of loci important to the normal development of the animal. Over 200 spontaneous, chemically induced and radiation-induced mutations at these loci have been identified, making it one of the most genetically well-characterized regions of the mouse. Molecular analysis of this region has recently become feasible by the identification of a dilute mutation that was induced by integration of an ecotropic murine leukemia virus genome. Several unique sequence cellular DNA probes flanking this provirus have now been identified and used to investigate the organization of wild-type chromosomes and chromosomes with radiation-induced d-se region mutations. As expected, several of these mutations are associated with deletions, and, in general, the molecular and genetic complementation maps of these mutants are concordant. Furthermore, a deletion break-point fusion fragment has been identified and has been used to orient the physical map of the d-se region with respect to the genetic complementation map. These experiments provide important initial steps for analyzing this developmentally important region at the molecular level, as well as for studying in detail how a diverse group of mutagens acts on the mammalian germline.

scholarly journals Repeated molecular genetic analysis in Brugada syndrome revealed a novel disease-associated large deletion in the SCN5A gene

2016 ◽  
Vol 2 (3) ◽  
pp. 261-264 ◽  
Author(s):  
Anders Krogh Broendberg ◽  
Lisbeth Noerum Pedersen ◽  
Jens Cosedis Nielsen ◽  
Henrik Kjaerulf Jensen
Keyword(s):  
Genetic Analysis ◽  
Brugada Syndrome ◽  
Molecular Genetic ◽  
Large Deletion ◽  
Molecular Genetic Analysis ◽  
Scn5a Gene

scholarly journals Paternal Uniparental Isodisomy of Chromosome 2 in a Patient with CNGA3-Associated Autosomal Recessive Achromatopsia

2021 ◽  
Vol 22 (15) ◽  
pp. 7842
Author(s):  
Susanne Kohl ◽  
Britta Baumann ◽  
Francesca Dassie ◽  
Anja K. Mayer ◽  
Maria Solaki ◽  
...  
Keyword(s):  
Segregation Analysis ◽  
Molecular Genetic ◽  
Retinal Disease ◽  
Underlying Mechanism ◽  
Recurrence Risk ◽  
Molecular Genetic Analysis ◽  
Recessive Mutation ◽  
Chromosome 2 ◽  
Inherited Retinal Disease ◽  
Uniparental Isodisomy

Achromatopsia (ACHM) is a rare autosomal recessively inherited retinal disease characterized by congenital photophobia, nystagmus, low visual acuity, and absence of color vision. ACHM is genetically heterogeneous and can be caused by biallelic mutations in the genes CNGA3, CNGB3, GNAT2, PDE6C, PDE6H, or ATF6. We undertook molecular genetic analysis in a single female patient with a clinical diagnosis of ACHM and identified the homozygous variant c.778G>C;p.(D260H) in the CNGA3 gene. While segregation analysis in the father, as expected, identified the CNGA3 variant in a heterozygous state, it could not be displayed in the mother. Microsatellite marker analysis provided evidence that the homozygosity of the CNGA3 variant is due to partial or complete paternal uniparental isodisomy (UPD) of chromosome 2 in the patient. Apart from the ACHM phenotype, the patient was clinically unsuspicious and healthy. This is one of few examples proving UPD as the underlying mechanism for the clinical manifestation of a recessive mutation in a patient with inherited retinal disease. It also highlights the importance of segregation analysis in both parents of a given patient or especially in cases of homozygous recessive mutations, as UPD has significant implications for genetic counseling with a very low recurrence risk assessment in such families.

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