BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis.

We describe a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts or genomic regions from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, which are all pre-selected and optimized in silico. By applying the matrices in a novel workflow named Barcode Assembly foR Targeted Sequencing (BART-Seq), we analyze developmental states of thousands of single human pluripotent stem cells, either in different maintenance media or upon Wnt/beta-catenin pathway activation, which identifies the mechanisms of differentiation induction. Moreover, we apply BART-Seq to the genetic screening of breast cancer patients and identify BRCA mutations with very high precision. The processing of thousands of samples and dynamic range measurements that outperform global transcriptomics techniques makes BART-Seq first targeted sequencing technique suitable for numerous research applications

Dehydroepiandrosterone supplementation improves ovarian response and cycle outcome in poor responders

Ozmen, Batuhan/0000-0002-4504-669X; Atabekoglu, Cem Somer/0000-0003-0264-0709; Ozkavukcu, Sinan/0000-0003-4525-9027WOS: 000271046800009PubMed: 19909591The effect of dehydroepiandrosterone (DHEA) supplementation on cycle outcome was assessed in patients with poor ovarian response. In total, 19 poor responder patients who were scheduled to undergo a second intracytoplasmic sperm injection (ICSI)/embryo transfer cycle were enrolled and first ICSI/embryo transfer cycles were taken as the control group. All subjects were given DHEA supplementation (25 me, t.i.d.) for at least 3 months prior to their second ICSI/embryo transfer cycle. In both cycles a fixed dose of rFSH (300 IU/day) and human menopausal gonadotrophin (HMG) (75 or 150 IU/day) along with a flexible gonadotrophin-releasing hormone (GnRH) antagonist protocol were administered. A favourable decrease was noted in mean day 3 serum oestradiol concentrations after DHEA Supplementation (75.14 +/- 28.93 versus 43.07 +/- 11.77; P 17 mm follicles (3 +/- 0.7 versus 1.9 +/- 1.3; P < 0.05), MII oocytes (4 +/- 1.8 versus 2.1 +/- 1.8; P < 0.05), top quality day 2 (2.2 +/- 0.8 versus 1.3 +/- 1.1: P < 0.05) and day 3 embryos (1.9 +/- 0.8 versus 0.7 +/- 0.6; P < 0.05) were achieved in DHEA-supplemented cycles. Cycle cancellation rates were reduced (5.3% versus 42.1%; P < 0.01), and the pregnancy rate per patient and clinical pregnancy rate per embryo transfer (47.4% versus 10.5%; P<0.01 and 44.4% versus 0%; P < 0.01) were improved after DHEA supplementation. DHEA supplementation might enhance ovarian response, reduce cycle cancellation rates and increase embryo quality in poor responders

Serum anti-Mullerian hormone levels correlate with ovarian response in idiopathic hypogonadotropic hypogonadism

PURPOSE: The role of serum AMH levels in prediction of ovarian response in idiopathic hypogonadotropic hypogonadism (IHH) was evaluated. MATERIAL METHOD(S): Twelve patients with IHH underwent controlled ovarian hyperstimulation (COH) for IVF were enrolled in this prospective study. Serum AMH levels were studied on the 2nd or 3rd day of an induced menstrual cycle by a preceding low-dose oral contraceptive pill treatment. A fixed dose (150–300 IU/day) of hMG was given in all COH cycles. Correlations between serum AMH levels, COH outcomes and embryological data were investigated. RESULTS: Mean serum AMH levels was 3.47 ± 2.15 ng/mL and mean serum peak estradiol was 2196 ± 1705 pg/mL. Mean number of follicles >14 mm, >17 mm on hCG day and MII oocytes were 4.14 ± 3.2, 4 ± 2.5 and 7.28 ± 3.5, respectively. Mean number of grade A embryos and transferred embryos were 3.28 ± 2.4 and 2.5 ± 0.7, respectively. The clinical pregnancy rate per patient was 41.6 % (5/12). Positive correlations were observed between serum AMH levels and MII oocytes (r = 0.84), grade A embryos (r = 0.85), serum peak estradiol levels (r = 0.87), and number of follicles >14 mm (r = 0.83) and >17 mm (r = 0.81) on hCG day, respectively. CONCLUSION: AMH appears as a promising marker of ovarian response in patients with IHH undergoing IVF

First pregnancy and live birth in Turkey following frozen-thawed ovarian tissue transplantation in a patient with acute lymphoblastic leukemia who underwent cord blood transplantation

PURPOSE: To report the first live birth after frozen-thawed ovarian transplantation in Turkey and the second case for an acute lymphoblastic leukemia (ALL) survivor in the world. METHODS: A 19-year-old patient underwent ovarian tissue cryopreservation (OTC) before cord blood transplantation in 2010. She was diagnosed as ALL with a bone marrow biopsy revealing 90% blast ALL-L2 type, and karyotype analyses indicated reciprocal translocation at t(9;22)(q34;q11). The patient received the Berlin-Frankfurt-Munster (BFM) protocol, and complete remission was achieved before fertility preservation. Serum AMH level was measured as 1.5 ng/ml, and 12 antral follicles were counted on ultrasound. She was informed about fertility preservation options and decided to proceed with OTC, with her signed consent before cord blood transplantation in April 2011. Ovarian tissue transplantation (OTT) was performed in 2017 when the patient was menopausal with serum FSH levels > 100 IU/ml and estradiol < 20 pg/ml and hematologically in molecular remission. Detailed molecular analysis, standard histology, and immunohistochemistry demonstrated that the thawed tissue is free of malignant cells. RESULTS: Six months following OTT, she had spontaneous menstruation with serum FSH 11 IU/ml and estradiol 53 pg/ml. Two consecutive IVF cycles yielded three top-quality embryos. Following three embryo transfer cycles, one fresh and two frozen, a healthy term live birth was achieved. Frozen-thawed-transplanted tissues were extracted during caesarean delivery upon the patient’s request after a total period of 25 months in vivo, and histopathological evaluation revealed that the tissue was free of leukemic infiltration. CONCLUSION: The authors report the first pregnancy and live birth in Turkey and the second live birth in the world following transplantation of frozen-thawed ovarian tissue in a leukemia survivor. As the transplanted tissues were removed during caesarean delivery, histological findings prove the functionality and the malignant-free status of the transplanted tissue during the grafted period