scholarly journals Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X

2017 ◽  
Author(s):  
Barbara R Migeon ◽  
Michael A Beer ◽  
Hans T Bjornsson
Keyword(s):  
Copy Number ◽  
Partial Trisomy ◽  
Copy Number Variations ◽  
Sex Bias ◽  
X Chromosomes ◽  
Unique Region ◽  
Human Females ◽  
Specific Transcript ◽  
Embryonic Loss ◽  
Transcript Gene

To compensate for the sex difference in the number of X chromosomes, human females, like human males have only one active X. The other X chromosomes in cells of both sexes are silencedin uterobyXIST, theInactive X Specific Transcript gene, that is present on all X chromosomes. To investigate the means by which the human active X is protected from silencing byXIST, we updated the search for a key dosage sensitiveXISTrepressor using new cytogenetic data with more precise resolution. Here, based on a previously unknown sex bias in copy number variations, we identify a unique region in our genome, and propose candidate genes that lie within, as they could inactivateXIST. Unlike males, the females who duplicate this region of chromosome 19 (partial 19 trisomy) do not survive embryogenesis; this preimplantation loss of females may be one reason that more human males are born than females.

scholarly journals Eight Y chromosome genes show copy number variations in horses

2018 ◽  
Vol 61 (3) ◽  
pp. 263-270
Author(s):  
Haoyuan Han ◽  
Xin Zhang ◽  
Xiaocheng Zhao ◽  
Xiaoting Xia ◽  
Chuzhao Lei ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Distribution Patterns ◽  
Single Copy ◽  
Copy Number Variations ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Specific Transcript ◽  
Copy Numbers ◽  
The Impact

Abstract. Copy number variations (CNVs), which represent a significant source of genetic diversity on the Y chromosome in mammals, have been shown to be associated with the development of many complex phenotypes, such as reproduction and male fertility. The occurrence of CNVs has been confirmed on the Y chromosome in horses. However, the copy numbers (CNs) of Equus caballus Y chromosome (ECAY) genes are largely unknown. To demonstrate the copy number variations of Y chromosome genes in horses, the quantitative real-time polymerase chain reaction (qPCR) method was applied to measure the CNVs of the eukaryotic translation initiation factor 1A Y (EIF1AY), equine testis-specific transcript on Y 1 (ETSTY1), equine testis-specific transcript on Y 4 (ETSTY4), equine testis-specific transcript on Y 5 (ETSTY5), equine transcript Y4 (ETY4), ubiquitin activating enzyme Y (UBE1Y), sex determining region Y (SRY), and inverted repeat 2 Y (YIR2) across 14 Chinese domestic horse breeds in this study. Our results revealed that these eight genes were multi-copy; furthermore, some of the well acknowledged single-copy genes such as SRY and EIF1AY were found to be multi-copy in this research. The median copy numbers (MCNs) varied among different breeds for the same gene. The CNVs of Y chromosome genes showed different distribution patterns among Chinese horse breeds, indicating the impact of natural selection on copy numbers. Our results will provide fundamental information for future functional studies.

scholarly journals Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X

PLoS ONE ◽  
2017 ◽  
Vol 12 (4) ◽  
pp. e0170403 ◽  
Author(s):  
Barbara R. Migeon ◽  
Michael A. Beer ◽  
Hans T. Bjornsson
Keyword(s):  
Partial Trisomy ◽  
Human Females ◽  
Embryonic Loss

scholarly journals A prenatal diagnosis and genetics study of five pedigrees in the Chinese population with Xp22.31 microduplication

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Jianlong Zhuang ◽  
Yuanbai Wang ◽  
Shuhong Zeng ◽  
Chunling Lv ◽  
Yiming Lin ◽  
...  
Keyword(s):  
High Risk ◽  
Copy Number ◽  
Chinese Population ◽  
Phenotypic Diversity ◽  
Copy Number Variants ◽  
Snp Array ◽  
Copy Number Variations ◽  
Serological Screening ◽  
X Chromosomes ◽  
Human Phenotype

Abstract Background Copy number variations (CNVs) can contribute to human phenotype, phenotypic diversity and disease susceptibility, while others may benign. In the current study, an attempt to investigate the pathogenicity of CNVs in chromosome Xp22.31 was explored. Methods G-banding and SNP-array techniques were used to analyze chromosome karyotypes and CNVs in fetuses. Parents associate with five different pedigrees possessing high risk factors in pregnancy were considered with such parameters as advanced age, high risk of serological screening and ultrasound abnormalities. Results The fetuses’ amniotic fluid karyotypes were 46, XX and those of their parents with the five pedigrees revealed no abnormalities. Here, we noticed a series of individuals with Xp22.31 duplications ranging from 534.6 kb to 1.6 Mb. It was detected through SNP array that the fetuses in Pedigree 1 and 2 had ~ 600 kb duplications in the Xp22.31 region of their X chromosomes which contained two OMIM genes, HDHD1 (OMIM: 306480) and part of STS (OMIM: 300747). The fetuses of Pedigrees 3, 4 and 5 had 1.6 Mb duplication in the same chromosome which contained four OMIM genes: HDHD1 (OMIM: 306480), STS (OMIM: 300747), PNPLA4 (OMIM: 300102) and VCX (OMIM: 300229). The duplications in the fetuses of Pedigrees 1 and 5 were inherited from the non-phenotypic parents. Pedigrees 3 and 4 refused to perform parental verification. Finally, four of the five pedigrees continue towards pregnancy with no abnormalities being observed during followed-ups. Conclusion Our study first showed duplications of Xp22.31 in Chinese population. Clinical and genetic investigation on five different pedigrees, we consider the duplication of these fragments as likely benign copy number variants (CNVs). We suggest that the duplications of Xp22.31 with recurrent duplication as a benign CNVs .

scholarly journals Copy number variations of five Y chromosome genes in donkeys

2017 ◽  
Vol 60 (4) ◽  
pp. 391-397 ◽  
Author(s):  
Haoyuan Han ◽  
Xiaocheng Zhao ◽  
Xiaoting Xia ◽  
Hong Chen ◽  
Chuzhao Lei ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Single Copy ◽  
Copy Number Variations ◽  
Sperm Production ◽  
Specific Transcript ◽  
Normal Sperm ◽  
Copy Numbers ◽  
Qpcr Method ◽  
Male Sex

Abstract. In mammals, the Y chromosome plays a pivotal role in male sex determination and is essential for normal sperm production. A number of studies were conducted on Y chromosome genes of various species and identified single-copy and multi-copy genes. However, limited studies about donkey Y chromosome genes have been done. In this study, 263 male samples from 13 Chinese donkey breeds were collected to analyze the copy number variations (CNVs) of five Y chromosome genes using the quantitative PCR (qPCR) method. These five genes (cullin 4 B Y (CUL4BY), equus testis-specific transcript y1 (ETSTY1), equus testis-specific transcript y4 (ETSTY4), equus testis-specific transcript Y 5 (ETSTY5), and sex-determining region Y (SRY) were identified as multi-copy, whose median copy numbers (MCNs) were 5, 45, 2, and 2, and 13 with CNV ranges of 1–57, 1–227, 1–37, 1–86 and 1–152, respectively. The CNVs of these five genes were shared in different breeds. Compared to previous studies, the copy numbers of five genes showed some distinct consequences in this study. In particular, the well-known single-copy SRY gene showed CNVs in donkeys. Our results provided genetic variations of donkey Y chromosome genes.

scholarly journals Global patterns of large copy number variations in the human genome reveal complexity in chromosome organization

2015 ◽  
Vol 97 ◽  
Author(s):  
AVINASH M. VEERAPPA ◽  
RAVIRAJ V. SURESH ◽  
SANGEETHA VISHWESWARAIAH ◽  
KUSUMA LINGAIAH ◽  
MEGHA MURTHY ◽  
...  
Keyword(s):  
Genome Organization ◽  
Copy Number ◽  
Evolutionary Dynamics ◽  
Snp Array ◽  
Variable Region ◽  
Distribution Patterns ◽  
Copy Number Variations ◽  
Sex Bias ◽  
Genome Wide ◽  
Global Patterns

SummaryGlobal patterns of copy number variations (CNVs) in chromosomes are required to understand the dynamics of genome organization and complexity. For this study, analysis was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 chip and CytoScan High-Density arrays. We identified a total of 44 109 CNVs from 1715 genomes with a mean of 25 CNVs in an individual, which established the first drafts of population-specific CNV maps providing a rationale for prioritizing chromosomal regions. About 19 905 ancient CNVs were identified across all chromosomes and populations at varying frequencies. CNV count, and sometimes CNV size, contributed to the bulk CNV size of the chromosome. Population specific lengthening and shortening of chromosomal length was observed. Sex bias for CNV presence was largely dependent on ethnicity. Lower CNV inheritance rate was observed for India, compared to YRI and CEU. A total of 33 candidate CNV hotspots from 5382 copy number (CN) variable region (CNVR) clusters were identified. Population specific CNV distribution patterns in p and q arms disturbed the assumption that CNV counts in the p arm are less common compared to long arms, and the CNV occurrence and distribution in chromosomes is length independent. This study unraveled the force of independent evolutionary dynamics on genome organization and complexity across chromosomes and populations.

Imbalances and loss of heterozygosity (LOH) in endometrial carcinoma detected by array based Copy number variations (aCNV)

2018 ◽  
Author(s):  
A Nusilati ◽  
J Weimer ◽  
K Tiemann ◽  
MB Stope ◽  
A Mustea ◽  
...  
Keyword(s):  
Endometrial Carcinoma ◽  
Loss Of Heterozygosity ◽  
Copy Number ◽  
Copy Number Variations

Assessment of HER-2/neu, с-MYC and CCNE1 gene copy number variations and protein expression in endometrial carcinomas

2019 ◽  
Vol 41 (2) ◽  
Author(s):  
L.G. Buchynska ◽  
◽  
O.V. Brieieva* ◽  
N.P. Iurchenko ◽  
◽  
...  
Keyword(s):  
Protein Expression ◽  
Copy Number ◽  
Gene Copy Number ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Her 2 ◽  
Endometrial Carcinomas

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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