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BMC Genomics Jul 2015Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases....
BACKGROUND
Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of several modern layer chicken lines from diverse breeds.
RESULTS
To reduce the error rates seen in InDel detection, this study used the consensus set from two InDel-calling packages: SAMtools and Dindel, as well as stringent post-filtering criteria. By analysing sequence data from 163 chickens from 11 commercial and 5 experimental layer lines, this study detected about 883 K high quality consensus InDels with 93% validation rate and an average density of 0.78 InDels/kb over the genome. Certain chromosomes, viz, GGAZ, 16, 22 and 25 showed very low densities of InDels whereas the highest rate was observed on GGA6. In spite of the higher recombination rates on microchromosomes, the InDel density on these chromosomes was generally lower relative to macrochromosomes possibly due to their higher gene density. About 43-87% of the InDels were found to be fixed within each line. The majority of detected InDels (86%) were 1-5 bases and about 63% were non-repetitive in nature while the rest were tandem repeats of various motif types. Functional annotation identified 613 frameshift, 465 non-frameshift and 10 stop-gain/loss InDels. Apart from the frameshift and stopgain/loss InDels that are expected to affect the translation of protein sequences and their biological activity, 33% of the non-frameshift were predicted as evolutionary intolerant with potential impact on protein functions. Moreover, about 2.5% of the InDels coincided with the most-conserved elements previously mapped on the chicken genome and are likely to define functional elements. InDels potentially affecting protein function were found to be enriched for certain gene-classes e.g. those associated with cell proliferation, chromosome and Golgi organization, spermatogenesis, and muscle contraction.
CONCLUSIONS
The large catalogue of InDels presented in this study along with their associated information such as functional annotation, estimated allele frequency, etc. are expected to serve as a rich resource for application in future research and breeding in the chicken.
Topics: Amino Acid Sequence; Animals; Chickens; Genome; INDEL Mutation; Polymorphism, Single Nucleotide; Sequence Deletion
PubMed: 26227840
DOI: 10.1186/s12864-015-1711-1 -
Methods in Molecular Biology (Clifton,... 2018We describe a method for gamma-irradiation of mature maize seeds to generate mutants with opaque endosperm and reduced kernel fill phenotypes. We also describe methods...
We describe a method for gamma-irradiation of mature maize seeds to generate mutants with opaque endosperm and reduced kernel fill phenotypes. We also describe methods for mapping mutants and identifying causal gene mutations. Using this method, a population of 1788M2 families and 47 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes was developed. For molecular characterization of the mutants, we utilized a novel functional genomics platform that combines separate Bulked Segregant RNA and exome sequencing data sets (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. We also describe the use of exome capture sequencing of F2 mutant and normal pools to perform mapping and candidate gene identification without the need for separate RNA-seq (BSEx-seq). To exemplify the utility of the deletion mutants for functional genomics and provide proof-of-concept for the bioinformatics platform, we summarize the identification of the causative deletion in two mutants. Mutant 937, which was characterized by BSREx-seq, harbors a 6203-bp in-frame deletion covering six exons within the Opaque-1 gene on chromosome 4. Preliminary investigation of opaque mutant 1486 with BSEx-seq shows a tight mapping interval and associated deletion on chromosome 10.
Topics: Chromosome Mapping; Chromosomes, Plant; High-Throughput Nucleotide Sequencing; Mutagenesis; Mutation; Phenotype; Plant Proteins; RNA, Plant; Sequence Analysis, DNA; Sequence Deletion; Zea mays
PubMed: 28986905
DOI: 10.1007/978-1-4939-7315-6_5 -
Proceedings of the National Academy of... Jun 2021Mammalian cells equalize X-linked dosages between the male (XY) and female (XX) sexes by silencing one X chromosome in the female sex. This process, known as "X...
Mammalian cells equalize X-linked dosages between the male (XY) and female (XX) sexes by silencing one X chromosome in the female sex. This process, known as "X chromosome inactivation" (XCI), requires a master switch within the X inactivation center (). The spans several hundred kilobases in the mouse and includes a number of regulatory noncoding genes that produce functional transcripts. Over three decades, transgenic and deletional analyses have demonstrated both the necessity and sufficiency of the to induce XCI, including the steps of X chromosome counting, choice, and initiation of whole-chromosome silencing. One recent study, however, reported that deleting the noncoding sequences of the surprisingly had no effect for XCI and attributed a sufficiency to drive counting to the coding gene, Here, we revisit the question by creating independent deletion cell lines. Multiple independent clones carrying heterozygous deletions of the display an inability to up-regulate Xist expression, consistent with a counting defect. This defect is rescued by a second site mutation in occurring , bypassing the defect in counting. These findings reaffirm the essential nature of noncoding elements for the initiation of XCI.
Topics: Alleles; Animals; Cell Death; Cell Line; Female; Mice; Mouse Embryonic Stem Cells; Sequence Deletion; X Chromosome Inactivation
PubMed: 34161282
DOI: 10.1073/pnas.2102683118 -
The Annals of Otology, Rhinology, and... Nov 2023About 80% of congenital hearing loss cases have genetic causes, often autosomal recessive and non-syndromic. Autosomal Recessive Non-syndromic hearing loss is... (Review)
Review
BACKGROUND
About 80% of congenital hearing loss cases have genetic causes, often autosomal recessive and non-syndromic. Autosomal Recessive Non-syndromic hearing loss is characterized by extreme genetic heterogeneity.
OBJECTIVES
To report a case of congenital hearing loss with novel homozygous deletion in GRXCR1 gene.
METHODS
Case reports and review of literatures.
RESULTS
In this study, the proband was a 32-year-old woman seeking pre-marriage genetic counseling with non-syndromic congenital hearing loss. An owing negative test for GJB2 mutations, she underwent exome sequencing, unveiling a novel homozygous exon 2 deletion of the gene. This mutation was confirmed in her affected mother and sibling by PCR and Quantitative Real-Time PCR.
CONCLUSION
We identified a novel gene mutation related to congenital hearing loss in a family. Our study highlights the efficiency of exome sequencing in discovering gene mutations in cases of diseases with genetic heterogeneity.
Topics: Humans; Female; Adult; Connexins; Connexin 26; Homozygote; Sequence Deletion; Deafness; Hearing Loss, Sensorineural; Mutation; Exons; Pedigree
PubMed: 37009772
DOI: 10.1177/00034894231161866 -
PloS One 2018All-trans retinoic acid (ATRA) and arsenic trioxide (ATO) are essential for acute promyelocytic leukemia (APL) treatment. It has been reported that mutations in PML-RARA...
All-trans retinoic acid (ATRA) and arsenic trioxide (ATO) are essential for acute promyelocytic leukemia (APL) treatment. It has been reported that mutations in PML-RARA confer resistance to ATRA and ATO, and are associated with poor prognosis. Although most PML-RARA mutations were point mutations, we identified a novel seven amino acid deletion mutation (p.K227_T233del) in the RARA region of PML-RARA in a refractory APL patient. Here, we analyzed the evolution of the mutated clone and demonstrated the resistance of the mutated clone to retinoic acid (RA). Mutation analysis of PML-RARA was performed using samples from a chemotherapy- and ATRA-resistant APL patient, and the frequencies of mutated PML-RARA transcript were analyzed by targeted deep sequencing. To clarify the biological significance of the identified PML-RARA mutations, we analyzed the ATRA-induced differentiation and PML nuclear body formation in mutant PML-RARA-transduced HL-60 cells. At molecular relapse, the p.K227_T233del deletion and the p.R217S point-mutation in the RARA region of PML-RARA were identified, and their frequencies increased after re-induction therapy with another type of retinoiec acid (RA), tamibarotene. In deletion PML-RARA-transduced cells, the CD11b expression levels and NBT reducing ability were significantly decreased compared with control cells and the formation of PML nuclear bodies was rarely observed after RA treatment. These results indicate that this deletion mutation was closely associated with the disease progression during RA treatment.
Topics: CD11b Antigen; Cell Line, Tumor; Disease Progression; Down-Regulation; Drug Resistance, Neoplasm; Female; Gene Expression Regulation, Neoplastic; HL-60 Cells; Humans; Leukemia, Promyelocytic, Acute; Mutation; Oncogene Proteins, Fusion; Point Mutation; Sequence Deletion; Tretinoin
PubMed: 30289902
DOI: 10.1371/journal.pone.0204850 -
Zhonghua Er Ke Za Zhi = Chinese Journal... Apr 2018To investigate the spectrum of mutations in families with benign familial neonatal-infantile epilepsy (BFNIE) . Clinical data and peripheral blood DNA samples of all...
To investigate the spectrum of mutations in families with benign familial neonatal-infantile epilepsy (BFNIE) . Clinical data and peripheral blood DNA samples of all BFNIE probands and their family members were collected from Peking University First Hospital between December 2012 and April 2016. Clinical phenotypes of affected members were analyzed. Genomic DNA was extracted from peripheral blood samples with standard protoco1. Mutations in PRRT2 were screened using Sanger sequencing. For families that PRRT2 mutations were not detected by Sanger sequencing, candidate gene mutations were further screened by next-generation sequencing for epilepsy. A total of 7 families were collected. Of the 30 affected members, 15 were male and 15 were female. The age of epilepsy onset was from 2 days to 6 months. Genetic testing led to the identification of gene mutations in all families. One family had the PRRT2 hotspot mutation (c.649dupC). Three families had missense SCN2A mutations (c.2674G>A/p.V892I, c.2872A>G/p.M958V, and c.2627A>G/p.N876S) . Both c.2872A>G/p.M958V and c.2627A>G/p.N876S were novel SCN2A mutations. Three families had KCNQ2 mutations. Two of them had missense mutations (c.958G>A/p.V320I and c.998G>A/p.R333Q) . The KCNQ2 mutation c.958G>A/p.V320I was novel. One family had a gene deletion of KCNQ2, which also extended to the adjacent gene, CHRNA4; and the deletion involved all the exons of KCNQ2 and CHRNA4. Mutations in KCNQ2, SCN2A, and PRRT2 are genetic causes of BFNIE in Chinese families. The detection rate for gene mutations is high in BFNIE families. KCNQ2 and SCN2A mutations are common in BFNIE families. SCN2A mutations (c.2872A>G/p.M958V and c.2627A>G/p.N876S) and KCNQ2 mutation (c.958G>A/p.V320I) are novel mutations.
Topics: Asian People; Epilepsy, Benign Neonatal; Exons; Family; Female; Gene Deletion; Genetic Testing; High-Throughput Nucleotide Sequencing; Humans; Male; Membrane Proteins; Mutation, Missense; Nerve Tissue Proteins; Pedigree; Phenotype; Sequence Deletion
PubMed: 29614566
DOI: 10.3760/cma.j.issn.0578-1310.2018.04.006 -
Brain & Development Nov 2017Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder. Over 95% of SMA patients have homozygous deletions of the SMA-causative gene, SMN1. Thus,...
BACKGROUND
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder. Over 95% of SMA patients have homozygous deletions of the SMA-causative gene, SMN1. Thus, SMA carriers are usually diagnosed based on SMN1 copy number, with one copy indicating SMA carrier status. However, two SMN1 copies do not always exclude carrier status. In this study, we identified SMA carriers with two SMN1 copies.
SUBJECTS AND METHODS
From 33 families, 65 parents of genetically confirmed SMA patients were tested to determine SMA carrier status. Molecular genetic analyses, including multiplex ligation-dependent probe amplification (MLPA) assay, were performed using blood samples from family members.
RESULTS
Of the 65 parents, three parents from three families had two SMN1 copies. Accordingly, the frequency of carriers with two SMN1 copies was 4.6%. Two of these families were further studied. Patient 1 was homozygous for SMN1 deletion. Patient 1's mother had two SMN1 copies on one chromosome, with deletion of SMN1 on the other chromosome ([2+0] genotype). Patient 1 inherited SMN1-deleted chromosomes from both parents. Patient 2 was compound heterozygous for two SMN1 mutations: whole-gene deletion and intragenic missense mutation, c.826T>C (p.Tyr276His). Patient 2's father had two SMN1 copies with the same intragenic mutation in one copy ([1+1] genotype, intragenic mutation). Patient 2 inherited the chromosome with an SMN1 mutation from the father and SMN1-deleted chromosome from the mother.
CONCLUSION
SMA carriers with two SMN1 copies may be rare, but its possibility should be taken into consideration in carrier testing and counseling for SMA families or population-based carrier screening.
Topics: Adult; DNA Copy Number Variations; Family; Female; Gene Deletion; Genetic Carrier Screening; Genetic Counseling; Homozygote; Humans; Male; Middle Aged; Multiplex Polymerase Chain Reaction; Muscular Atrophy, Spinal; Mutation; Pedigree; Sequence Deletion; Survival of Motor Neuron 1 Protein
PubMed: 28676237
DOI: 10.1016/j.braindev.2017.06.002 -
BMC Nephrology Feb 2018It has been reported that mutations in arginine vasopressin type 2 receptor (AVPR2) cause congenital X-linked nephrogenic diabetes insipidus (NDI). However, only a few...
BACKGROUND
It has been reported that mutations in arginine vasopressin type 2 receptor (AVPR2) cause congenital X-linked nephrogenic diabetes insipidus (NDI). However, only a few cases of AVPR2 deletion have been documented in China.
METHODS
An NDI pedigree was included in this study, including the proband and his mother. All NDI patients had polyuria, polydipsia, and growth retardation. PCR mapping, long range PCR and sanger sequencing were used to identify genetic causes of NDI.
RESULTS
A novel 22,110 bp deletion comprising AVPR2 and ARH4GAP4 genes was identified by PCR mapping, long range PCR and sanger sequencing. The deletion happened perhaps due to the 4-bp homologous sequence (TTTT) at the junctions of both 5' and 3' breakpoints. The gross deletion co-segregates with NDI. After analyzing available data of putative clinical signs of AVPR2 and ARH4GAP4 deletion, we reconsider the potential role of AVPR2 deletion in short stature.
CONCLUSIONS
We identified a novel 22.1-kb deletion leading to X-linked NDI in a Chinese pedigree, which would increase the current knowledge in AVPR2 mutation.
Topics: Adolescent; Asian People; Chromosome Breakpoints; Diabetes Insipidus, Nephrogenic; Female; GTPase-Activating Proteins; Gene Deletion; Humans; Male; Mutation; Pedigree; Receptors, Vasopressin; Sequence Deletion
PubMed: 29394883
DOI: 10.1186/s12882-018-0825-5 -
Experimental Gerontology Jan 2015Mitochondrial DNA (mtDNA) deletion mutations are proposed contributors to aging-related muscle fiber loss and atrophy, but evidence of a causal role for these mutations...
Mitochondrial DNA (mtDNA) deletion mutations are proposed contributors to aging-related muscle fiber loss and atrophy, but evidence of a causal role for these mutations in muscle aging is lacking. Elucidating the etiology of in vivo mtDNA deletion mutations will help to better understand and test the possible roles of these mutations in aging. The implication of mtDNA mutations in aging is based on the susceptibility of mtDNA to oxidative damage by reactive oxygen species (ROS) due to residing in mitochondria, the primary source of endogenous ROS. Cells possess many pathways for neutralizing ROSs, including a variety of superoxide dismutases (SOD). Mice lacking CuZnSOD (Sod1(-/-) mice) have high levels of oxidative damage in many tissues including skeletal muscle and are a model for testing the role of oxidative damage in the formation of mtDNA deletion mutations. The increased DNA oxidative damage in Sod1(-/-) mice is associated with increased mtDNA deletion mutations in a variety of tissues, but skeletal muscle mtDNA mutations have not been reported. We hypothesized that a life-long absence of mouse muscle CuZnSOD would increase mtDNA deletion mutation frequency and focal accumulation of these mutations in aging mouse skeletal muscle. Focal accumulations of mtDNA deletion mutations were detected by histochemical staining for cytochrome c oxidase (cytOX) activity and detection of cytOX-negative fibers, a marker of focal mtDNA mutation accumulation, within approximately 20,000 muscle fibers through a distance of 1000μm. Total DNA was extracted from intervening unstained sections and mtDNA deletion mutation frequency was measured by a droplet digital PCR. Droplet digital PCR quantification of mtDNA deletion mutations showed no difference in mtDNA deletion mutation frequency in Sod1(-/-) mouse muscle compared to wild-type mice and we observed no significant increase in the number of cytOX-negative muscle fibers, in Sod1(-/-) mice compared to wild-type mice. These data demonstrate that not all changes in cellular oxidative stress are linked to mtDNA deletion mutations and shift the focus to other etiologies for these mutations that need to be clarified to better test their possible role in aging.
Topics: Aging; Animals; DNA, Mitochondrial; Electron Transport Complex IV; Mice; Muscle, Skeletal; Sequence Deletion; Superoxide Dismutase
PubMed: 25449857
DOI: 10.1016/j.exger.2014.11.012 -
Virulence Dec 2022It was noticed that the mortality rate of SARS-CoV-2 infection experienced a significant declination in the early stage of the epidemic. We suspect that the sharp...
It was noticed that the mortality rate of SARS-CoV-2 infection experienced a significant declination in the early stage of the epidemic. We suspect that the sharp deterioration of virus toxicity is related to the deletion of the untranslated region (UTR) of the virus genome. It was found that the genome length of SARS-CoV-2 engaged a significant truncation due to UTR deletion after a mega-sequence analysis. Sequence similarity analysis further indicated that short UTR strains originated from its long UTR ancestors after an irreversible deletion. A good correlation was discovered between genome length and mortality, which demonstrated that the deletion of the virus UTR significantly affected the toxicity of the virus. This correlation was further confirmed in a significance analysis of the genetic influence on the clinical outcomes. The viral genome length of hospitalized patients was significantly more extensive than that of asymptomatic patients. In contrast, the viral genome length of asymptomatic was considerably longer than that of ordinary patients with symptoms. A genome-level mutation scanning was performed to systematically evaluate the influence of mutations at each position on virulence. The results indicated that UTR deletion was the primary driving force in alternating virus virulence in the early evolution. In the end, we proposed a mathematical model to explain why this UTR deletion was not continuous.
Topics: Base Sequence; COVID-19; Genome, Viral; Humans; SARS-CoV-2; Sequence Deletion; Untranslated Regions
PubMed: 36217240
DOI: 10.1080/21505594.2022.2132059