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

2022 ◽  
Vol 49 (1) ◽  
pp. 1
Author(s):  
Zhanhui Ou ◽  
Zhiheng Chen ◽  
Yu Deng ◽  
Ling Sun
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Single Nucleotide Polymorphism Array ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Preimplantation Genetic Testing ◽  
Single Nucleotide ◽  
High Concordance ◽  
Generation Sequencing

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 Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Abinaya Manivannan ◽  
Jin-Hee Kim ◽  
Eun-Young Yang ◽  
Yul-Kyun Ahn ◽  
Eun-Su Lee ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Disease Resistance ◽  
Next Generation Sequencing ◽  
Molecular Mechanisms ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
The Impact ◽  
Generation Sequencing

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

scholarly journals Các biến thể gene OsTZF1 liên quan đến khả năng chịu mặn ở giống lúa Đốc Phụng bằng phương pháp giải trình tự bộ gene

2021 ◽  
Vol 57 (4) ◽  
pp. 159-168
Author(s):  
Huỳnh Kỳ ◽  
Đặng Thành Phát Trần ◽  
Thị Kim Phụng Nguyễn ◽  
Văn Quốc Giang ◽  
Văn Mạnh Nguyễn ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Next Generation Sequencing ◽  
Amino Acid ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Generation Sequencing

Trong nghiên cứu này, kỹ thuật giải trình tự thế hệ mới (next generation sequencing) được ứng dụng để giải trình tự của bộ gene 2 giống lúa Đốc Phụng (giống chống chịu mặn) và giống Nếp Mỡ (giống mẫn cảm với mặn), nhằm tìm các chỉ thị phân tử là gene chức năng mà các gene này liên quan đến cơ chế chống chịu mặn có trong giống lúa Đốc Phụng. Kết quả so sánh với bộ gene tham chiếu, bộ gene của giống lúa Đốc Phụng có khoảng 1.918.726 biến thể dạng thay đổi một nucleotide (Single Nucleotide Polymorphism) và và chèn vào khoảng 81.435, mất đi khoảng 81.974. Trong khi đó ở giống Nếp Mỡ, có khoảng 1.931.380 SNP và chèn vào khoảng 88.473, mất đi khoảng 83.190 vùng DNA. Đa số các biến thể xuất hiện ở các vùng không mang chức năng như trước sau và giữa các gene chiếm tỉ lệ trên 75%. Kết quả khảo sát biến thể xuất hiện trong vùng gene OsTZF1 (LOC_Os05g10670.1), có chức năng điều hòa các nhóm gene liên quan đến các yếu tố stress sinh học và phi sinh học, cho thấy ở giống Đốc Phụng có 7 biến thể SNP và có chèn thêm 9 nucleotide mã hóa 3 amino acid arginine khi so với giống Nếp Mỡ dựa trên bộ gene tham chiếu. Thông tin này giúp cho các nhà chọn giống sử dụng nó như chi thị phân tử, chọn tạo giống chống chịu...

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