Resolving Breakpoints of Chromosomal Rearrangements at the Nucleotide Level Using Sanger Sequencing

2020 ◽  
Vol 108 (1) ◽  
Author(s):  
Katarena Nalbandian ◽  
Raul E. Piña‐Aguilar ◽  
Cynthia C. Morton
Keyword(s):  
Sanger Sequencing ◽  
Chromosomal Rearrangements ◽  
Nucleotide Level

scholarly journals Structural Chromosomal Rearrangements Require Nucleotide-Level Resolution: Lessons from Next-Generation Sequencing in Prenatal Diagnosis

2016 ◽  
Vol 99 (5) ◽  
pp. 1015-1033 ◽  
Author(s):  
Zehra Ordulu ◽  
Tammy Kammin ◽  
Harrison Brand ◽  
Vamsee Pillalamarri ◽  
Claire E. Redin ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Next Generation Sequencing ◽  
Chromosomal Rearrangements ◽  
Next Generation ◽  
Nucleotide Level ◽  
Generation Sequencing

scholarly journals Phenotypic interpretation of complex chromosomal rearrangements informed by nucleotide-level resolution and structural organization of chromatin

2018 ◽  
Vol 26 (3) ◽  
pp. 374-381 ◽  
Author(s):  
Cinthya J. Zepeda-Mendoza ◽  
Alexandra Bardon ◽  
Tammy Kammin ◽  
David J. Harris ◽  
Helen Cox ◽  
...  
Keyword(s):  
Structural Organization ◽  
Chromosomal Rearrangements ◽  
Nucleotide Level ◽  
Complex Chromosomal Rearrangements

Electron Microscopy and image analysis of nucleo-protein complexes

1994 ◽  
Vol 52 ◽  
pp. 88-89
Author(s):  
E. H. Egelman ◽  
X. Yu
Keyword(s):  
Electron Microscopy ◽  
Image Analysis ◽  
Normal Cell ◽  
Genetic Recombination ◽  
Protein Complexes ◽  
Chromosomal Rearrangements ◽  
Reca Protein ◽  
E Coli ◽  
Helical Polymer ◽  
Specific Protease

The RecA protein of E. coli has been shown to mediate genetic recombination, regulate its own synthesis, control the expression of other genes, act as a specific protease, form a helical polymer and have an ATPase activity, among other observed properties. The unusual filament formed by the RecA protein on DNA has not previously been shown to exist outside of bacteria. Within this filament, the 36 Å pitch of B-form DNA is extended to about 95 Å, the pitch of the RecA helix. We have now establishedthat similar nucleo-protein complexes are formed by bacteriophage and yeast proteins, and availableevidence suggests that this structure is universal across all of biology, including humans. Thus, understanding the function of the RecA protein will reveal basic mechanisms, in existence inall organisms, that are at the foundation of general genetic recombination and repair.Recombination at this moment is assuming an importance far greater than just pure biology. The association between chromosomal rearrangements and neoplasms has become stronger and stronger, and these rearrangements are most likely products of the recombinatory apparatus of the normal cell. Further, damage to DNA appears to be a major cause of cancer.

The experience of holding the cycles of assisted reproductive technology with defrost, a biopsy, genetic study and refreezing of embryos in patients with multiple unsuccessful implantations

2016 ◽  
pp. 166-170
Author(s):  
Y.V. Masliy ◽  
◽  
I.O. Sudoma ◽  
P.S. Mazur ◽  
D.A. Mykytenko ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Genetic Diagnosis ◽  
Morphological Characteristics ◽  
Implantation Rate ◽  
Ovarian Response ◽  
Reproductive Technologies ◽  
Comparative Genome Hybridization ◽  
Comparative Genome ◽  
Vitro Fertilization

The objective: to study the possibility of using frozen blastocysts for biopsy and genetic testing and performance measurement transfer euploeded 5–7-day-old embryos after thawing, biopsies, refreezing and thawing in patients with unsuccessful implantation. Patients and methods. The object of the study was the group of patients with repeated failure of implantation (4) in programs of auxiliary reproductive technologies (ART), subject to transfer to the uterus in total (i.e. in all the programs) for at least 6 good quality embryos based on morphological characteristics). All women had sufficient ovarian reserve. The patient was treated for infertility within the ART programs of the clinic of reproductive medicine "Nadiya" in the period from 2006 to 2016. The sample included couples who were not carriers of chromosomal rearrangements, without anomalies of the uterus (congenital and acquired: a doubling of the uterus, one-horned uterus, intrauterine membrane, synechia, submucous myoma of the uterus). All women had a positive ovarian response to controlled stimulation with gonadotropins (at least 7 oocytes) and a sufficient number of cryopreserved embryos. The first group (G1) included 64 women who trophectodermal a biopsy was performed on fresh blastocysts (in a loop controlled ovarian hyperstimulation). The second group (G2) were included 31 women who underwent thawing previously cryopreserved blastocysts trophectodermal re-biopsy and vitrification of blastocysts. Results. It was found that the performance of transfers euploid embryos that were vitrified, bioptrone and revitriphted, a little lower than those that were bioptrone fresh and vitrified only once. At the same time computationa genetic diagnosis previously vitrified blastocysts using comparative genome hybridization in patients with recurrent failed implantation allows to obtain a reasonable pregnancy rate (58%), implantation rate (33.3 %) and the birth of living children (45.1 %). Conclusion. Reprising biopropane embryos does not cause significant destructive impact and allows you to achieve pregnancy and birth of the alive child. Key words: in vitro fertilization, reusable unsuccessful implantation, a method of comparative genome hybridization, refreezing.

THE NUCLEAR FACTOR OF HEPATOCYTES 1β (HNF1β)–ASSOCIATED DISEASE. CLINIC, DIAGNOSTIC, TREATMENT (LITERATURE REVIEW AND CLINICAL OBSERVATION)

2019 ◽  
Vol 23 (2) ◽  
pp. 100-108
Author(s):  
S. V. Papizh ◽  
O. R. Piruzieva
Keyword(s):  
Sanger Sequencing ◽  
Clinical Observation ◽  
Liver Enzymes ◽  
Renal Ultrasound ◽  
Nuclear Factor ◽  
Hepatocyte Nuclear Factor ◽  
Renal Hypoplasia ◽  
Unilateral Renal Agenesis ◽  
Elevated Liver Enzymes ◽  
Medullary Nephrocalcinosis

Hepatocyte nuclear factor 1β (HNF1β)-associated disease is a rare autosomal dominant disease caused by various mutations in the HNF1β gene coding the hepatocyte nuclear factor 1β. HNF1β is a transcription factor that is critical for the development of kidney urogenital tract, pancreas, liver, brain, and parathyroid gland. Renal phenotype or HNF1β- nephropathy appeared to be extremely heterogenic: multicystic renal dysplasia, renal hypoplasia, unilateral renal agenesis, horseshoe kidney, atypical familial juvenile hyperuricemic nephropathy, urinary tract malformations and tubular dysfunction. Extrarenal phenotype of HNF1β-associated disease could be maturity-onset diabetes of the young (MODY), pancreatic atrophy and exocrine pancreatic dysfunction, elevated liver enzymes, neonatal cholestasis, congenital abnormalities of the genital tract, hyperparathyroidism, neurological symptoms. The multisystem phenotype makes clinical verification of the diagnosis extremely difficult. In this article, we present a clinical observation of a child with HNF1β – associated disease. The first clinical presentation of HNF1β-associated disease was ultrasound changes in the kidneys (hyperechogenic kidneys?), which were detected by prenatal ultrasonography in pregnancy. Renal ultrasound revealed polycystic kidney disease in the first days of life and bilateral medullary nephrocalcinosis by the age of three. The clinical examination showed a reduced renal function and developed Fanconi syndrome (glycosuria, low molecular proteinuria, hypophosphatemia, aminoaciduria, hyperuricosuria) in the first year of life. Also the child had a non-constant asymptomatic elevation of liver enzymes, hyperparathyroidism, osteoporosis. The diagnosis was confirmed by the results of next generation sequencing which revealed novel heterozygous mutation in exon 4 of the HNF1b gene (chr17: 36091813C>T), p.Cys273Tyr (c.818G>A). The identified mutation was validated by Sanger sequencing. Validation by Sanger sequencing did not reveal a chr17: 36091813C>T mutation in parents, which suggested the appearance of a mutation in the child de novo.

Quantitative Evaluation of Chromosomal Rearrangements in Primary Gene-Edited Human Stem Cells by Preclinical CAST-Seq

2020 ◽  
Author(s):  
Giandomenico Turchiano ◽  
Geoffroy Andrieux ◽  
Georges Blattner ◽  
Valentina Pennucci ◽  
Julia Klermund ◽  
...  
Keyword(s):  
Stem Cells ◽  
Quantitative Evaluation ◽  
Chromosomal Rearrangements ◽  
Human Stem Cells ◽  
Primary Gene

Rare Germline GLMN Variants Identified from Blue Rubber Bleb Nevus Syndrome Might Impact mTOR Signaling

2020 ◽  
Vol 22 (10) ◽  
pp. 675-682 ◽  
Author(s):  
Jie Yin ◽  
Zhongping Qin ◽  
Kai Wu ◽  
Yufei Zhu ◽  
Landian Hu ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Sanger Sequencing ◽  
Somatic Mutations ◽  
Venous Malformation ◽  
Underlying Disease ◽  
Mtor Signaling ◽  
Functional Effect ◽  
Germline Variants ◽  
Whole Exome

Backgrounds and Objective: Blue rubber bleb nevus syndrome (BRBN) or Bean syndrome is a rare Venous Malformation (VM)-associated disorder, which mostly affects the skin and gastrointestinal tract in early childhood. Somatic mutations in TEK have been identified from BRBN patients; however, the etiology of TEK mutation-negative patients of BRBN need further investigation. Method: Two unrelated sporadic BRBNs and one sporadic VM were firstly screened for any rare nonsilent mutation in TEK by Sanger sequencing and subsequently applied to whole-exome sequencing to identify underlying disease causative variants. Overexpression assay and immunoblotting were used to evaluate the functional effect of the candidate disease causative variants. Results: In the VM case, we identified the known causative somatic mutation in the TEK gene c.2740C>T (p.Leu914Phe). In the BRBN patients, we identified two rare germline variants in GLMN gene c.761C>G (p.Pro254Arg) and c.1630G>T(p.Glu544*). The GLMN-P254R-expressing and GLMN-E544X-expressing HUVECs exhibited increased phosphorylation of mTOR-Ser-2448 in comparison with GLMN-WTexpressing HUVECs in vitro. Conclusion: Our results demonstrated that rare germline variants in GLMN might contribute to the pathogenesis of BRBN. Moreover, abnormal mTOR signaling might be the pathogenesis mechanism underlying the dysfunction of GLMN protein.

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