scholarly journals Whole Genome Amplification of Day 3 or Day 5 Human Embryos Biopsies Provides a Suitable DNA Template for PCR-Based Techniques for Genotyping, a Complement of Preimplantation Genetic Testing

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Elizabeth Schaeffer ◽  
Bruno López-Bayghen ◽  
Adina Neumann ◽  
Leonardo M. Porchia ◽  
Rafael Camacho ◽  
...  

Our objective was to determine if whole genome amplification (WGA) provides suitable DNA for qPCR-based genotyping for human embryos. Single blastomeres (Day 3) or trophoblastic cells (Day 5) were isolated from 342 embryos for WGA. Comparative Genomic Hybridization determined embryo sex as well as Trisomy 18 or Trisomy 21. To determine the embryo’s sex, qPCR melting curve analysis for SRY and DYS14 was used. Logistic regression indicated a 4.4%, 57.1%, or 98.8% probability of a male embryo when neither gene, SRY only, or both genes were detected, respectively (accuracy = 94.1%, kappa = 0.882, andp<0.001). Fluorescent Capillary Electrophoresis for the amelogenin genes (AMEL) was also used to determine sex. AMELY peak’s height was higher and this peak’s presence was highly predictive of male embryos (AUC = 0.93, accuracy = 81.7%, kappa = 0.974, andp<0.001). Trisomy 18 and Trisomy 21 were determined using the threshold cycle difference for RPL17 and TTC3, respectively, which were significantly lower in the corresponding embryos. The Ct difference for TTC3 specifically determined Trisomy 21 (AUC = 0.89) and RPL17 for Trisomy 18 (AUC = 0.94). Here, WGA provides adequate DNA for PCR-based techniques for preimplantation genotyping.

2006 ◽  
Vol 87 (1) ◽  
pp. 75-83 ◽  
Author(s):  
Edurne Arriola ◽  
Maryou B K Lambros ◽  
Chris Jones ◽  
Tim Dexter ◽  
Alan Mackay ◽  
...  

ISRN Oncology ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Nona Arneson ◽  
Juan Moreno ◽  
Vladimir Iakovlev ◽  
Arezou Ghazani ◽  
Keisha Warren ◽  
...  

To understand cancer progression, it is desirable to study the earliest stages of its development, which are often microscopic lesions. Array comparative genomic hybridization (aCGH) is a valuable high-throughput molecular approach for discovering DNA copy number changes; however, it requires a relatively large amount of DNA, which is difficult to obtain from microdissected lesions. Whole genome amplification (WGA) methods were developed to increase DNA quantity; however their reproducibility, fidelity, and suitability for formalin-fixed paraffin-embedded (FFPE) samples are questioned. Using aCGH analysis, we compared two widely used approaches for WGA: single cell comparative genomic hybridization protocol (SCOMP) and degenerate oligonucleotide primed PCR (DOP-PCR). Cancer cell line and microdissected FFPE breast cancer DNA samples were amplified by the two WGA methods and subjected to aCGH. The genomic profiles of amplified DNA were compared with those of non-amplified controls by four analytic methods and validated by quantitative PCR (Q-PCR). We found that SCOMP-amplified samples had close similarity to non-amplified controls with concordance rates close to those of reference tests, while DOP-amplified samples had a statistically significant amount of changes. SCOMP is able to amplify small amounts of DNA extracted from FFPE samples and provides quality of aCGH data similar to non-amplified samples.


Author(s):  
Д.И. Жигалина ◽  
Н.А. Скрябин ◽  
О.Р. Канбекова ◽  
А.Н. Марошкина ◽  
Е.О. Чуркин ◽  
...  

Актуальность: Ограниченный репродуктивный потенциал у человека и прогрессирующее ухудшение репродуктивного здоровья населения стали причиной развития вспомогательных репродуктивных технологий в последние десятилетия. С целью повышения вероятности имплантации бластоцисты, снижения частоты спонтанных абортов у семейных пар, которые имеют проблемы репродукции, в клиническую практику был введен преимплантационный генетический скрининг (ПГС). Культивирование эмбрионов человека in vitro в циклах экстракорпорального оплодотворении (ЭКО), а также возможность получения генетического материала при проведении ПГС позволяют оценить частоту и спектр хромосомных нарушений в бластоцистах человека. Цель: Анализ частоты и спектра числовых хромосомных аномалий в бластоцистах, полученных в рамках циклов ЭКО-ПГС. Материалы и методы. Проведен ретроспективный анализ молекулярных кариотипов 113 бластоцист, полученных в рамках циклов ЭКО-ПГС от 47 женщин. Полногеномная амплификация (ПГА) ДНК из клеток трофэктодермы проводилась с использованием набора реактивов PicoPlex (Rubicon Genomics, США). Анализ образцов ДНК, полученных после ПГА, был проведен методом микроматричной сравнительной геномной гибридизации (aCGH) с использованием микрочипа GenetiSure Pre-Screen, 8×60K (Agilent Technologies, США). Результаты: Эффективность ПГА составила 97,3% (110/113). Сбалансированный кариотип был установлен в 31% (34/110) бластоцист. Частота бластоцист с хромосомным дисбалансом в группе женщин моложе 35 лет оказалась значимо ниже (46,9 %) по сравнению с частотой бластоцист с хромосомным дисбалансом в группе женщин старше 35 лет (81,0 %) (р < 0,001). Хромосомные аномалии были представлены анеуплоидиями (74 %), в 26 % - структурными нарушениями хромосом. Распределение анеуплоидий имело следующую структуру: трисомии аутосом составили 41 %, моносомии аутосом - 48 %, анеуплоидии половых хромосом - 7%, тетрасомии аутосом - 3 %, нуллисомии аутосом - 1 %. Наиболее часто отмечались анеуплоидии хромосом 5, 15, 16, 17, 19, 21 и 22. Выводы: Анализ хромосомных аберраций в бластоцистах продемонстрировал высокую частоту хромосомного дисбаланса (69%) и широкий спектр как числовых, так и структурных нарушений хромосом. ПГС методом aCGH позволяет отобрать бластоцисты со сбалансированным набором хромосом. По результатам переносов бластоцист в циклах ЭКО-ПГС клиническая беременность наступила в 32% случаев. Introduction: Limited reproductive potential in humans and the progressive decline of the reproductive health of the population have led to the development of assisted reproductive technologies in recent decades. In order to improve pregnancy rates in couples with reproduction problems, preimplantation genetic screening was introduced into clinical practice. Cultivation of human embryos in vitro in in vitro fertilization cycles (IVF), as well as the possibility of obtaining genetic material during preimplantation genetic screening and diagnosis (PGS / PGD), allow us to estimate the frequency and spectrum of chromosomal abnormalities in human blastocysts. Aim: Analysis of the rate and spectrum of aneuploidies in human blastocysts obtained in the IVF-PGD cycles. Material and methods: A retrospective analysis of the molecular karyotypes of 113 blastocysts obtained in the cycles of assisted reproductive technology IVF-PGD from 47 women was carried out. The whole genomic amplification of DNA from trophectoderm cells was performed using the PicoPlex reagent kit (Rubicon Genomics, USA). Analysis of DNA samples obtained after whole genome amplification was carried out by array comparative genomic hybridization (aCGH) using a GenetiSure Pre-Screen microchip, 8×60K (Agilent Technologies, USA). Results: The efficiency of whole genome amplification was 97.3% (110/113). A balanced karyotype was established in 31% (34/110) blastocysts. The rate of a blastocyst with chromosomal imbalance in the group of women under 35 years old was lower (46.9%) compared to the rate of blastocyst with chromosomal imbalance in the group of women over 35 years old (81.0%) (p < 0.001). 74% of the identified chromosomal abnormalities were aneuploidy, 26% - structural chromosomal abberations. The distribution of aneuploidies had the following structure: autosomal trisomies (41%), autosomal monosomies (48%), aneuploidies of sex chromosomes (7%), autosomal tetrasomies (3%), autosomal nullisomies (1%). Aneuploidies of chromosomes 5, 15, 16, 17, 19, 21 and 22 were noted with the greatest frequency. Conclusions: Analysis of chromosomal aberrations in human embryos at the blastocyst stage showed a high frequency of chromosomal imbalance (69%) and a wide range of both numerical and structural abnormalities of chromosomes. PGS with aCGH allows the selection of blastocysts with a balanced karyotype. According to the results of blastocyst transfers in IVF-PGD cycles, clinical pregnancy occurred in 32 % of cases.


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