scholarly journals Cytogenetic and molecular analysis of distal 4q duplication with distinctive phenotype using single-nucleotide polymorphism array

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jianlong Zhuang ◽  
Na Zhang ◽  
Wanyu Fu ◽  
Jianfeng Yao ◽  
Yanqing Li ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Clinical Phenotype ◽  
Single Nucleotide Polymorphism Array ◽  
Copy Number Variants ◽  
Snp Array ◽  
Partial Trisomy ◽  
Nucleotide Polymorphism ◽  
Balanced Translocation ◽  
Single Nucleotide ◽  
Mild Clinical Phenotype

Abstract Aims There is little knowledge about partial trisomy 4q and the genotype–phenotype correlation. In this study, we presented the detail of two Chinese families with partial distal 4q duplication in an attempt to clarify the correlation between the genotype and the phenotype. Methods Two pedigrees with distal 4q duplication were enrolled in this study. Karyotype analysis and single-nucleotide polymorphism (SNP) array detection were performed for prenatal diagnosis. Fluorescence in situ hybridization analysis. (FISH) was conducted to verify the copy number variants. Results Two families with partial trisomy 4q were identified. The fetus in pedigree 1 exhibited multiple ultrasound anomalies including intrauterine growth restriction and an atrioventricular septal defect who had a duplication of 4q28.3-qter associate with 6p25.2-p25.3 deletion, which resulted from balanced translocation carried by his father t(4;6)(q28.3;p25.2). The fetus in pedigree 2 had a distal 4q28.3-qter duplication combined with monosomy of Xp21.3-p22.3, and the karyotype was described as 46,X,der(X)t(X;4)(p21.3;q28.3)mat, which originally inherited from the pregnant woman who exhibited a mild clinical phenotype limited to short stature. Conclusions In our study, we for the first time identified the partial trisomy 4q associate with 6p or Xp deletion. In addition, our finding further strengthens that mild clinical phenotype in 4q duplication case may be due to the spreading of X inactivation to the autosomal in derivation of chromosome X.

scholarly journals Development of a 38K Single Nucleotide Polymorphism Array and Application in Henomic Selection for Resistance Against Vibrio harveyi in Chinese Tongue sole, Cynoglossus Semilaevis

2020 ◽  
Author(s):  
Sheng Lu ◽  
Qian Zhou ◽  
Yadong Chen ◽  
Yang Liu ◽  
Yangzhen Li ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Vibrio Harveyi ◽  
Reference Group ◽  
Single Nucleotide Polymorphism Array ◽  
Snp Array ◽  
Cynoglossus Semilaevis ◽  
Breeding Value ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Tongue Sole

Abstract Background: In recent years, the disease outbreak caused by Vibrio harveyi upset the booming development of the Chinese tongue sole (Cynoglossus semilaevis) farming industry. Genomic selection (GS) is a powerful method to improve the traits of interest, which has been proved in livestock and some fishes. Besides, the single nucleotide polymorphism (SNP) array is an efficient genotyping platform that can be used for genetic studies. To improve V. harveyi resistance in C. semilaevis, we firstly constructed a reference group of 1,572 individuals and investigated accuracies of four genomic methods (genomic best linear unbiased prediction (GBLUP), weighted GBLUP, BayesB, and BayesC) at predicting the genomic estimated breeding value (GEBV) using five-fold cross-validation and SNPs varying from 0.5 k to 500 k. Then, an SNP array was developed using the Affymetrix Axiom technology, and its accuracy in genotyping was evaluated by comparing SNPs generated by the array and by the re-sequencing technology. Finally, we selected 44 candidates as the parents of 23 families of C. semilaevis to evaluate the feasibility of the SNP array for GS.Results: all genomic methods outperformed the pedigree-based BLUP (ABLUP) when at least 50 k SNPs used for prediction, of which GBLUP resulted in better estimation than ABLUP when more than 1 k SNPs used. A 38 k SNP array, “Solechip No.1”, was developed with an average of 10.5 kb inter-spacing between two adjacent SNPs. The SNPs generated by the array and by the re-sequencing reached an average consistency of 94.8 %, of which 79.3 % of loci had a more than 90 % of the consistency. The survival rates of these 23 offspring families had a correlation of 0.706 with the family GEBVs (mid-parental GEBVs), and the average survival rate of the top five families in GEBVs (79.1 %) is higher than the bottom five families (58.1 %).Conclusion: GS is an efficient method to improve the V. harveyi resistance in C. semilaevis, and the SNP array “Solechip No.1” is a convenient and reliable tool for the Chinses tongue sole selective breeding practice.

Phylogenetic analysis of wheat cultivars in Kazakhstan based on the wheat 90 K single nucleotide polymorphism array

2015 ◽  
Vol 15 (1) ◽  
pp. 29-35 ◽  
Author(s):  
Yerlan Turuspekov ◽  
Joerg Plieske ◽  
Martin Ganal ◽  
Eduard Akhunov ◽  
Saule Abugalieva
Keyword(s):  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphism ◽  
Single Nucleotide Polymorphism Array ◽  
Genetic Relationships ◽  
Snp Array ◽  
Geographic Origin ◽  
Wheat Cultivars ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The World

The recent introduction of Illumina single nucleotide polymorphism (SNP) arrays is an important step towards comprehensive genome-wide studies of genetic diversity in wheat. In this study, 90 cultivars of hexaploid spring wheat growing in Kazakhstan were genotyped using the high-density wheat 90 K Illumina SNP array. The analysis allowed the identification of 30,288 polymorphic SNPs. A subset of 3541 high-quality SNPs were used for a comparison of 690 wheat accessions representing landraces and varieties, including those from Asia, Australia, Canada, Europe, Kazakhstan, USA and other parts of the world. Phylogenetic analysis showed a clear separation of wheat cultivars according to their geographic origin. In the phylogenetic tree, accessions from Kazakhstan and the USA formed two neighbouring clusters with a common node, and they were distinct from accessions from other regions of the world, including Europe. The results provide important new insights into the genetic relationships between diverse wheat accessions.

scholarly journals Prenatal diagnosis of 22q11.2 copy number abnormalities in fetuses via single nucleotide polymorphism array

2020 ◽  
Vol 47 (10) ◽  
pp. 7529-7535
Author(s):  
Meiying Cai ◽  
Na Lin ◽  
Linjuan Su ◽  
Xiaoqing Wu ◽  
Xiaorui Xie ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Prenatal Diagnosis ◽  
Copy Number ◽  
Single Nucleotide Polymorphism Array ◽  
Snp Array ◽  
Cardiovascular Malformations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Ultrasound Findings ◽  
Kidney Malformations

Abstract The q11.2 region on chromosome 22 contains numerous low-copy repeats that lead to deleted or duplicated regions in the chromosome, thereby resulting in different syndromes characterized by intellectual disabilities or congenital anomalies. The association between patient phenotypes and 22q11.2 copy number abnormalities has been previously described in postnatal cases; however, these features have not been systematically evaluated in prenatal cases because of limitations in phenotypic identification in prenatal testing. In this study, we investigated the detection rate of 22q11.2 copy number abnormalities in 2500 fetuses using single nucleotide polymorphism (SNP) array and determined the common abnormal ultrasound findings in fetuses carrying the 22q11.2 copy number abnormalities. The 22q11.2 copy number abnormalities were identified in 13 fetuses with cardiovascular malformations (6/13), kidney malformations (3/13), isolated ultrasound markers (3/13), or high-risk Down syndrome based on maternal serum screening (1/13). Approximately 0.5% (13/2500) of the fetuses harbored 22q11.2 copy number abnormalities. The most frequent ultrasound findings in fetuses with these abnormalities were cardiovascular malformations, followed by kidney malformations and isolated ultrasound markers. Prenatal diagnosis of these genetic abnormalities allows for the delineation of differential diagnoses, characterization of a wide spectrum of associated malformations, and determination of associations that exist between prenatal diagnosis and obstetrical outcomes.

scholarly journals High concordance between next generation sequencing and single-nucleotide polymorphism array in preimplantation genetic testing for aneuploid

2020 ◽  
Author(s):  
Zhanhui Ou ◽  
Zhiheng Chen ◽  
Yu Deng ◽  
Minna Yin ◽  
Ling Sun
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Next Generation Sequencing ◽  
Single Nucleotide Polymorphism Array ◽  
Snp Array ◽  
Concordance Rate ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
High Concordance ◽  
Generation Sequencing

Abstract Background: Single-nucleotide polymorphism array (SNP array) and next generation sequencing (NGS) in detecting chromosome aneuploidy are widely used in clinical work. Aims: To compare the concordance between NGS and SNP array in 67 embryos (from 23 couples). Methods: In the first part of the study, 28 blastocysts with unknown ploidy were both analyzed with NGS and SNP array. While in the second part, 39 with normal ploidy detected by NGS were re-analyzed with SNP array. Results: In the first part of the study, the concordance rate between NGS and SNP array was 92.9% (26/28). Among the 28 blastocysts, 18 were abnormal and 10 blastocysts were with normal ploidy status when analyzed by NGS. Among the 18 abnormal blastocysts, two blastocysts were with low level of mosaicism as analyzed by NGS, but euploid with SNP array. In the second part, concordance rate between NGS and SNP array was 100% (39/39). At last, one couple had no blastocyst to transfer. The other 22 couples were transferred with single blastocyst. Among them, two couples suffered abortions before 12 weeks, and the karyotype of villus was normal. One couple with only 1 normal blastocyst failed to conceive after the transfer. In total nineteen couples had healthy babies born. Conclusions: There was a high concordance rate between NGS and SNP array. But NGS was also able to detect mosaicism sensitively. Hence, using NGS for PGT-A may increase the chances of having a healthy and live newborn child.

scholarly journals Prenatal diagnosis of 7 cases with uniparental disomy by utilization of single nucleotide polymorphism array

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Lili Zhou ◽  
Zhaoke Zheng ◽  
Yunzhi Xu ◽  
Xiaoxiao Lv ◽  
Chenyang Xu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Prenatal Diagnosis ◽  
Molecular Analysis ◽  
Correct Diagnosis ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Chromosome 1 ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Rescue Mechanism

Abstract Background The phenotypes of uniparental disomy (UPD) are variable, which may either have no clinical impact, lead to clinical signs and symptoms. Molecular analysis is essential for making a correct diagnosis. This study involved a retrospective analysis of 4512 prenatal diagnosis samples and explored the molecular characteristics and prenatal phenotypes of UPD using a single nucleotide polymorphism (SNP) array. Results Out of the 4512 samples, a total of seven cases of UPD were detected with an overall frequency of 0.16%. Among the seven cases of UPD, two cases are associated with chromosomal aberrations (2/7), four cases (4/7) had abnormal ultrasonographic findings. One case presented with iso-UPD (14), and two case presented with mixed hetero/iso-UPD (15), which were confirmed by Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as maternal UPD (15) associated with Prader-Willi syndrome (PWS). Four cases had iso-UPD for chromosome 1, 3, 14, and 16, respectively; this is consistent with the monosomy rescue mechanism. Another three cases presented with mixed hetero/isodisomy were consistent with a trisomy rescue mechanism. Conclusion The prenatal phenotypes of UPD are variable and molecular analysis is essential for making a correct diagnosis and genetic counselling of UPD. The SNP array is a useful genetic test in prenatal diagnosis cases with UPD.

scholarly journals SNP array analysis in hematologic malignancies: avoiding false discoveries

Blood ◽  
2010 ◽  
Vol 115 (21) ◽  
pp. 4157-4161 ◽  
Author(s):  
Stefan Heinrichs ◽  
Cheng Li ◽  
A. Thomas Look
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Resolution ◽  
Snp Array ◽  
Hematologic Malignancies ◽  
Cancer Genome ◽  
Patient Specific ◽  
Nucleotide Polymorphism ◽  
Array Analysis ◽  
Single Nucleotide ◽  
Therapeutic Decisions

Comprehensive analysis of the cancer genome has become a standard approach to identifying new disease loci, and ultimately will guide therapeutic decisions. A key technology in this effort, single nucleotide polymorphism arrays, has been applied in hematologic malignancies to detect deletions, amplifications, and loss of heterozygosity (LOH) at high resolution. An inherent challenge of such studies lies in correctly distinguishing somatically acquired, cancer-specific lesions from patient-specific inherited copy number variations or segments of homozygosity. Failure to include appropriate normal DNA reference samples for each patient in retrospective or prospective studies makes it difficult to identify small somatic deletions not evident by standard cytogenetic analysis. In addition, the lack of proper controls can also lead to vastly overestimated frequencies of LOH without accompanying loss of DNA copies, so-called copy-neutral LOH. Here we use examples from patients with myeloid malignancies to demonstrate the superiority of matched tumor and normal DNA samples (paired studies) over multiple unpaired samples with respect to reducing false discovery rates in high-resolution single nucleotide polymorphism array analysis. Comparisons between matched tumor and normal samples will continue to be critical as the field moves from high resolution array analysis to deep sequencing to detect abnormalities in the cancer genome.

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