Array-based molecular karyotyping in 115 VATER/VACTERL and VATER/VACTERL-like patients identifies disease-causing copy number variations

2017 ◽  
Vol 109 (13) ◽  
pp. 1063-1069 ◽  
Author(s):  
Rong Zhang ◽  
Florian Marsch ◽  
Franziska Kause ◽  
Franziska Degenhardt ◽  
Eeberhard Schmiedeke ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Variations ◽  
Molecular Karyotyping

scholarly journals Lessons Learned from CNV Analysis of Major Birth Defects

2020 ◽  
Vol 21 (21) ◽  
pp. 8247
Author(s):  
Alina Christine Hilger ◽  
Gabriel Clemens Dworschak ◽  
Heiko Martin Reutter
Keyword(s):  
Birth Defects ◽  
Copy Number ◽  
Congenital Malformations ◽  
De Novo ◽  
Copy Number Variations ◽  
Lessons Learned ◽  
Organ System ◽  
Molecular Karyotyping ◽  
The Past ◽  
Single Organ

The treatment of major birth defects are key concerns for child health. Hitherto, for the majority of birth defects, the underlying cause remains unknown, likely to be heterogeneous. The implicated mortality and/or reduced fecundity in major birth defects suggest a significant fraction of mutational de novo events among the affected individuals. With the advent of systematic array-based molecular karyotyping, larger cohorts of affected individuals have been screened over the past decade. This review discusses the identification of disease-causing copy-number variations (CNVs) among individuals with different congenital malformations. It highlights the differences in findings depending on the respective congenital malformation. It looks at the differences in findings of CNV analysis in non-isolated complex congenital malformations, associated with central nervous system malformations or intellectual disabilities, compared to isolated single organ-system malformations. We propose that the more complex an organ system is, and the more genes involved during embryonic development, the more likely it is that mutational de novo events, comprising CNVs, will confer to the expression of birth defects of this organ system.

scholarly journals Chromosomal abnormalities and copy number variations in children with idiopathic mental illness

2019 ◽  
pp. 80-81
Author(s):  
O. S. Kurinnaia ◽  
I. Y. Iourov ◽  
S. G. Vorsanova
Keyword(s):  
Mental Illness ◽  
Mental Disorders ◽  
Copy Number ◽  
Genetic Factors ◽  
Chromosomal Abnormalities ◽  
Copy Number Variations ◽  
Molecular Karyotyping ◽  
Correct Data

Genetic factors of mental illness are generally recognized. Here, it is shown that molecular karyotyping in combination with original bioinformatics methods offers the opportunity for effective uncovering genomic pathology, which may provide correct data on genetic factors for mental disorders in children.

scholarly journals Array-based comparative genomic hybridization (ARRAY-CGH) in analysis of chromosomalaberrations and CNV in blighted ovum pregnancies

2013 ◽  
Vol 62 (2) ◽  
pp. 117-125 ◽  
Author(s):  
Igor Nikolayevich Lebedev ◽  
Anna Aleksandrovna Kashevarova ◽  
Nikolay Alekseyevich Skryabin ◽  
Tatyana Vladimirovna Nikitina ◽  
Mariya Yevgenyevna Lopatkina ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Copy Number ◽  
Array Cgh ◽  
Copy Number Variations ◽  
Molecular Karyotyping ◽  
Comparative Genomic ◽  
Comparative Genomic Hybridization Array ◽  
Molecular Cytogenetic ◽  
Clinical Cytogenetics ◽  
Blighted Ovum

Application of modern molecular cytogenetic technologies in research and clinical practice provides unprecedented possibilities for high resolution molecular karyotyping in different areas of clinical cytogenetics. In this study the oligonucleotide-based array-CGH data about unbalanced chromosomal aberrations and copy number variations (CNV) in blighted ovum pregnancies are presented. Analysis of genes content of involved chromosomal regions was done. Scopes, perspectives and limitations of aCGH application into analysis of early pregnancy losses are discussed.

scholarly journals Benign, pathogenic and copy number variations of unknown clinical significance in patients with congenital malformations and developmental delay

2017 ◽  
Vol 20 (1) ◽  
pp. 5-12 ◽  
Author(s):  
M Mihaylova ◽  
R Staneva ◽  
D Toncheva ◽  
M Pancheva ◽  
S Hadjidekova
Keyword(s):  
Developmental Delay ◽  
Clinical Significance ◽  
High Frequency ◽  
Copy Number ◽  
Congenital Malformations ◽  
Copy Number Variations ◽  
The Other ◽  
Molecular Karyotyping ◽  
Powerful Method ◽  
Oligo Microarray

Abstract The high frequency (3.0-5.0%) of congenital anomalies (CA) and intellectual disabilities (IDs), make them a serious problem, responsible for a high percentage (33.0%) of neonatal mortality. The genetic cause remains unclear in 40.0% of cases. Recently, molecular karyotyping has become the most powerful method for detection of pathogenic imbalances in patients with multiple CAs and IDs. This method is with high resolution and gives us the opportunity to investigate and identify candidate genes that could explain the genotype-phenotype correlations. This article describes the results from analysis of 81 patients with congenital malformations (CMs), developmental delay (DD) and ID, in which we utilized the CytoChip ISCA oligo microarray, 4 × 44 k, covering the whole genome with a resolution of 70 kb. In the selected group of patients with CAs, 280 copy number variations (CNVs) have been proven, 41 were pathogenic, 118 benign and 121 of unknown clinical significance (average number of variations 3.5). In six patients with established pathogenic variations, our data revealed eight pathogenic aberrations associated with the corresponding phenotype. The interpretation of the other CNVs was made on the basis of their frequency in the investigated group, the size of the variation, content of genes in the region and the type of the CNVs (deletion or duplication).

X-linked CNV and skewed X-chromosome inactivation

2020 ◽  
pp. 19-21
Author(s):  
Е.А. Фонова ◽  
Е.Н. Толмачева ◽  
А.А. Кашеварова ◽  
М.Е. Лопаткина ◽  
К.А. Павлова ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Intellectual Disability ◽  
X Chromosome ◽  
Copy Number ◽  
Copy Number Variations ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Chromosome X ◽  
Skewed X Chromosome Inactivation

Смещение инактивации Х-хромосомы может быть следствием и маркером нарушения клеточной пролиферации при вариациях числа копий ДНК на Х-хромосоме. Х-сцепленные CNV выявляются как у женщин с невынашиванием беременности и смещением инактивации Х-хромосомы (с частотой 33,3%), так и у пациентов с умственной отсталостью и смещением инактивацией у их матерей (с частотой 40%). A skewed X-chromosome inactivation can be a consequence and a marker of impaired cell proliferation in the presence of copy number variations (CNV) on the X chromosome. X-linked CNVs are detected in women with miscarriages and a skewed X-chromosome inactivation (with a frequency of 33.3%), as well as in patients with intellectual disability and skewed X-chromosome inactivation in their mothers (with a frequency of 40%).

scholarly journals Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans

2021 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Nayoung Han ◽  
Jung Mi Oh ◽  
In-Wha Kim
Keyword(s):  
Copy Number ◽  
Genome Wide Association Study ◽  
Copy Number Gain ◽  
Copy Number Variations ◽  
Gene Gain ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Control And Prevention

For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.

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