Highly parallelizable electronic transport calculations in periodic rhodium and copper nanostructures.

We extend the highly-parallelizable open-source electronic transport code TRANSEC (Feldmanet al2014Phys. Rev.B90035445;https://gitlab.com/computational-physics2/transec/) to perform real-space atomic-scale electronic transport calculations with periodic boundary conditions in the lateral dimensions. We demonstrate the use of TRANSEC in periodic Cu and Rh bulk structures and in large periodic Rh point contacts, in preparation to perform calculations of reflection probability across Rh grain boundaries.

Outcomes of BRCA pre-implantation genetic testing according to the parental mutation origin: a cohort study.

BACKGROUND: The process of gamete formation and early embryonic development involves rapid DNA replication, chromosome segregation and cell division. These processes may be affected by mutations in the BRCA1/2 genes. The aim of this study was to evaluate BRCA mutation inheritance and its effect on early embryonic development according to the parental origin of the mutation. The study question was approached by analyzing in vitro fertilization cycles (IVF) that included pre-implantation testing (PGT-M) for a BRCA gene mutation. METHODS: This retrospective cohort study compared cycles of pre-implantation genetic testing for mutations (PGT-M) between male and female patients diagnosed with BRCA 1/2 mutations (cases), to a control group of two other mutations with dominant inheritance (myotonic dystrophy (MD) and polycystic kidney disease (PKD)). Results were compared according to mutation type and through a generalized linear model analysis. RESULTS: The cohort included 88 PGT-M cycles (47 BRCA and 41 non-BRCA) among 50 patients. Maternal and paternal ages at oocyte retrieval were comparable between groups. When tested per cycle, FSH dose, maximum estradiol level, oocytes retrieved, number of zygotes, and number of embryos available for biopsy and affected embryos, were not significantly different among mutation types. All together 444 embryos were biopsied: the rate of affected embryos was comparable between groups. Among BRCA patients, the proportion of affected embryos was similar between maternal and paternal mutation origin (p = 0.24). In a generalized linear model analysis, the relative oocyte yield in maternal BRCA patients was significantly lower (0.7, as related to the non BRCA group)(p < 0.001). Zygote formation and blastulation were not affected by the BRCA gene among paternal cases (P = 0.176 and P = 0.293 respectively), nor by paternal versus maternal BRCA carriage (P = 0.904 and P = 0.149, respectively). CONCLUSIONS: BRCA PGT-M cycles performed similarly compared to non-BRCA cycles. Inheritance rate and cycle parameters were not affected by the parental origin of the mutation.

The new face of cystic fibrosis in the era of population genetic carrier screening.

BACKGROUND: Population genetic carrier screening (PGCS) for cystic fibrosis (CF) has been offered to couples in Israel since 1999 and was included in a fully subsidized national program in 2008. We evaluated the impact of PGCS on CF incidence, genetic and clinical features. METHODS: This was a retrospective national study. Demographic and clinical characteristics of children with CF born in Israel between 2008 and 2018 were obtained from the national CF registry and from patients' medical records. Data on CF births, preimplantation genetic testing (PGT), pregnancy termination and de-identified data from the PGCS program were collected. RESULTS: CF births per 100,000 live births decreased from 8.29 in 2008 to 0.54 in 2018 (IRR = 0.84, p < 0.001). The CF pregnancy termination rate did not change (IRR = 1, p=  0.9) while the CF-related PGT rate increased markedly (IRR = 1.33, p < 0.001). One hundred and two children were born with CF between 2008 and 2018 with a median age at diagnosis of 4.8 months, range 0-111 months. Unlike the generally high uptake nationally, 65/102 had not performed PGCS. Even if all had utilized PGCS, only 51 would have been detected by the existing genetic screening panel. Clinically, 34 % of children were pancreatic sufficient compared to 23 % before 2008 (p = 0.04). CONCLUSIONS: Since institution of a nationwide PGCS program, the birth of children with CF decreased markedly. Residual function variants and pancreatic sufficiency were more common. A broader genetic screening panel and increased PGCS utilization may further decrease the birth of children with CF.

Is Day-4 morula biopsy a feasible alternative for preimplantation genetic testing?

OBJECTIVE: To assess the efficacy and clinical outcome of PGT-M undertaken on Day-3, Day-4 and Day-4 "delayed" embryos that were unsuitable for biopsy on Day-3. DESIGN AND SETTING: Cohort-historical study of all consecutive patients admitted to the IVF-PGT-M program in a large tertiary center. MAIN OUTCOME MEASURE(S): The pregnancy rates and the percentages of complete, incomplete diagnosis, PCR failure, abnormal embryos in PGT of Day-3 cleavage-stage, Day-4 and Day-4 "delayed" embryos. PATIENTS AND METHODS: We reviewed the medical files of all consecutive patients admitted to our IVF for a fresh IVF-PGT-M cycle. Patients were divided into 3 groups according to the day of blastomere biopsy: Day 3 cleavage-stage, Day-4 morula and Day-4 "delayed" embryos. The laboratory data, genetic diagnostic and clinical results were collected and compared between the different study groups. RESULTS: Nine hundred and six patients underwent PGT-M cycles in our PGT program: 747, 127 and 32 in the Day-3, Day- 4 and Day-4 "delayed" groups, respectively. Ongoing pregnancy rates per transfer and per patient (15.8% and 9.4%, respectively) were non-significantly lower in the Day-4 "delayed", compared to Day-3 (21.4% and 17.5%, respectively) and Day-4 (24.3% and 19.7%, respectively). When comparing ALL morulas (Day-4 and Day-4 "delayed") to ALL cleavage-stage embryos (Day-3, Day-4 and Day-4 "delayed"), a significantly higher ongoing pregnancy rate was demonstrated following the transfer of embryos derived from morula biopsy, as compared to biopsy at the cleavage-stage (33.3% vs 20.5%, p<0.03, respectively). CONCLUSION: Day-4 embryo biopsy is feasible and yields comparable and even higher ongoing pregnancy rate if undertaken at the morula stage. Further studies evaluating the cumulative live-birth rate per started cycles in Day-3 vs Day-4 embryo biopsy for PGT-M are warranted.

Obstetric and Perinatal Outcomes in Pregnancies Conceived After Preimplantation Genetic Testing for Monogenetic Diseases.

OBJECTIVE: To investigate whether the addition of embryo biopsy performed during preimplantation genetic testing for monogenic diseases is associated with a higher risk of obstetric and neonatal complications compared with in vitro fertilization (IVF) without preimplantation genetic testing or spontaneously conceived pregnancies. METHODS: This is a cohort study of all pregnancies conceived after preimplantation genetic testing for monogenic diseases (PGT-M group) from 2006 to 2018 at Sheba Medical Center, Israel. The control groups included patients who had conceived spontaneously (spontaneous conception group) or by IVF without preimplantation genetic testing (IVF group) and delivered at Sheba Medical Center. The obstetrics outcomes were compared among the groups. Multivariable regression modeling was performed, focusing on the relationship between preimplantation genetic testing and adverse outcomes. RESULTS: Final analysis included 345 singleton and 76 twin deliveries in the PGT-M group. The spontaneous conception group included 5,290 singleton and 92 twin deliveries. The IVF group included 422 singleton and 101 twin deliveries. Among singleton pregnancies, patients in the PGT-M group had a higher rate of hypertensive disorders (6.9%) compared with those in the spontaneous conception group (2.3%; odds ratio [OR] 3.3; 95% CI 1.9-4.8; adjusted odds ratio [aOR] 14.8; 95% CI 7.4-29.8) and the IVF group (4.7%; OR 1.5; 95% CI 0.8-2.7; aOR 5.9; 95% CI 1.9-18.2). Likewise, patients in the PGT-M group had a higher rate of small-for-gestational age neonates (12.4%) compared with those in the spontaneous conception group (3.9%; OR 3.4; 95% CI 2.4-4.9; aOR 2.3; 95% CI 1.5-3.4) and the IVF group (4.5%; OR 3; 95% CI 1.7-5.2; aOR 2.5; 95% CI 1.7-5.2). Among twin pregnancies, patients in the PGT-M group also had an increased rate of hypertensive disorders compared with those in the spontaneous conception group (4.3%; OR 4.1; 95% CI 1.2-13.3; aOR 10.9; 95% CI 2.3-50) and the IVF group (4%; OR 4.5; 95% CI 1.4-14.7; aOR 3.7; 95% CI 1.1-12.8). CONCLUSION: Pregnancies conceived after preimplantation genetic testing for monogenic disorders were associated with an increased risk of obstetric complications compared with pregnancies conceived spontaneously or by IVF without preimplantation genetic testing.

Preimplantation embryos sex ratios in couples with four or more children of same sex, what should be expected from a preimplantation genetic diagnosis cycle?

Our aim was to assess the preimplantation embryos' sex ratios in couples with four or more children of same sex, undergoing sex selection for nonmedical reasons. We conducted a cohort-historical study of all consecutive patients admitted to the IVF-PGD program in a large tertiary center. We reviewed the computerized files of all consecutive women admitted to our IVF for sex selection for nonmedical reasons. Patients and their PGD cycle characteristics were compared according to the desired sex of their embryo and the mode of fertilization. Nine patients underwent a total of 19 PGD cycle attempts during the study period. Of the 77 embryos with complete molecular diagnosis, 41 revealed a male embryo and 36 a female embryo. Thirty-five percent of all the diagnosed embryos were of the desired sex. For couples desiring a boy, IVF cycles achieved a higher ratio of the desired embryonal sex compared to ICSI (52% vs 18.7%, p = .03). For couples desiring a girl, ICSI cycles had a higher percentage of the desired embryonal sex compared to IVF cycles (38% vs 23%). Moreover, 29.7% of ICSI and 40% of IVF embryos achieved the desired sex. In conclusion, PGD for sex selection results in a relatively low percentage (35%) of embryos demonstrating the desired sex. Nonetheless, selecting the mode of fertilization (ICSI/IVF) might improve the success rate. Further studies are required to explore the appropriate and cost-effective method for sex selection for nonmedical reasons.

Pre-implantation genetic diagnosis-should we use ICSI for all?

OBJECTIVE: Intracytoplasmic sperm injection (ICSI) is commonly used during pre-implantation genetic diagnosis (PGD) in vitro fertilization (IVF), aiming to eliminate the risk of contamination from extraneous sperm DNA. Recently, ICSI "overuse" in non-male infertility has been doubted, since it does not offer an advantage over IVF. Prompted by the aforementioned observations, we sought to assess the accuracy of IVF vs ICSI in PGD cases, as might be reflected by a difference in the prevalence of discarded embryos as a consequent of parental contamination. METHODS: Cohort-historical study of all consecutive patients admitted to the IVF-PGD program in a large tertiary center. The percentages of complete, incomplete diagnosis, PCR failure, abnormal embryos, and the contamination rate with paternal DNA in the IVF-only and the ICSI-only groups. We reviewed the computerized files of all consecutive women admitted to our IVF for a PGD-PCR cycle. Patients were divided accordingly into three groups: an IVF group-where all the oocytes underwent IVF only, an ICSI group-where all oocytes underwent ICSI, and a mixed group-where sibling oocytes underwent both IVF and ICSI. The laboratory data and the genetic diagnostic results were collected and compared between the different insemination groups. RESULTS: Nine-hundred and twenty-seven patients underwent IVF-PGD cycles in our program, 315 in the IVF group, 565 in the ICSI group, and 47 in the mixed group. No differences were observed in fertilization rates, the percentage of embryos available for biopsy, and the percentages of complete, incomplete diagnosis, PCR failure, or abnormal embryos, between the IVF-only and the ICSI-only groups and between the IVF and the ICSI of sibling oocytes in the mixed group. Moreover, contamination with paternal DNA, through contamination with sperm cells, was negligible. Not one single case of misdiagnosis was encountered during the study period. CONCLUSION: It might be therefore concluded that IVF should be the preferred insemination methods in PGD cycles, and ICSI should be indicated only in cases of male-factor infertility.

Performing and Declining PGD: Accounts of Jewish Israeli Women Who Carry a BRCA1/2 Mutation or Partners of Male Mutation Carriers.

To describe factors associated with preimplantation genetic diagnosis (PGD) decisions among Jewish Israeli BRCA1/2 carriers or spouses of a male carrier, we contacted all women who initiated PGD consultation for embryonic BRCA1/2 mutation detection at Sheba Medical Center, prior to March 2014. Applying a qualitative approach, we asked women to elaborate on the factors they considered in either opting for PGD or discontinuing the screening procedure. Participants were 18 Jewish Israeli women; 14 were carriers of one of the Ashkenazi founder mutations in BRCA1/2, and four were spouses of male mutation carriers, who underwent at least one cycle of PGD. Prior to seeking PGD, ten of the women had no children. At the time of the interview, all but three had at least one child. Three factors emerged as key motivators for PGD: having witnessed the disease in a close relative (n = 12); prior IVF treatment for infertility (n = 12); and having pre-existing frozen embryos (n = 6). Ten women withdrew from the PGD process due to clinical, logistical, and financial reasons. In conclusion, most women decided to withdraw from PGD instead of continuing until a successful conception was achieved. Those who opted for PGD attributed their discontinuation of further screening to the emotional burden that is greatly intensified by practical difficulties.

Should pre-implantation genetic screening be implemented to routine clinical practice?

The utilization of trophectoderm biopsy combined with comprehensive chromosome screening (CCS) tests for embryonic aneuploidy was recently suggested to improve IVF outcome, however, not without criticisms. Since mosaicism has been reported in as high as 90% of blastocyst-stage embryos, we aimed to evaluate the accuracy of trophectoderm multiple biopsies using next-generation sequencing (NGS). Eight top quality blastocysts underwent three trophectoderm biopsies each, followed by NGS. In four blastocysts, the rest of the embryo, which included the inner cell mass, was also analyzed. Five of the 24 (20.8%) trophectoderm biopsies revealed inconclusive results, while 4 (16.6%) demonstrated embryonic mosaicism. Overall, 10 (35.7%) of the 28 (24 trophectoderms and 4 inner cell masses) biopsies revealed mosaicism or inconclusive results. Our preliminary observations contribute to the ongoing discussion on the unrestricted clinical adoption of PGS, suggesting, that until proper evaluation of its effectiveness and cost-effectiveness will be provided, PGS should be offered only under study conditions, and with appropriate informed consents.

BRCA mutation carriers show normal ovarian response in in vitro fertilization cycles.

OBJECTIVE: To evaluate the association between carriage of BRCA1/2 mutations and ovarian performance, as demonstrated by in vitro fertilization (IVF) outcomes. DESIGN: Retrospective cohort study. SETTING: Two tertiary IVF centers. PATIENT(S): BRCA mutation carriers undergoing IVF for preimplantation genetic diagnosis (PGD) or fertility preservation were compared with non-BRCA PGD or fertility preservation patients, matched by age, IVF protocol, IVF center, and cancer disease status. INTERVENTION(S): In vitro fertilization cycles for PGD and fertility preservation. MAIN OUTCOME MEASURE(S): Outcome of IVF: oocyte yield, poor response rate, number of zygotes, pregnancy rates. RESULT(S): A total of 62 BRCA mutation carriers and 62 matched noncarriers were included; 42 were fertility preservation breast cancer patients, and 82 were PGD non-cancer patients. Mean (± SD) age of patients was 32 ± 3.58 years. Number of stimulation days and total stimulation dose were comparable between carriers and noncarriers. Their cycles resulted in comparable oocyte yield (13.75 vs. 14.75) and low response rates (8.06% vs. 6.45%). Number of zygotes, fertilization rates, and conception rates were also comparable. CONCLUSION(S): Both healthy and cancer-affected BRCA mutation carriers demonstrated normal ovarian response in IVF cycles.

A novel approach to normal responder patient with repeated implantation failures--a case report.

We describe a case of normal responder patients with repeated implantation failure who was offered the combination of the ultrashort GnRH-ag/ GnRH-ant COH protocol, followed by endometrial injury and a subsequent natural cycle frozen-thawed embryos transfer. The patient conceived following the natural FET cycle that was supported by luteal daily progesterone, with the additional single injection of HCG and GnRH-agonist, on day of ET and 4 days later, respectively. This combined approach seems to be a valuable tool in the armamentarium for treating normal responder patients with repeated implantation failures and should be further examined in large randomized controlled trials.

Elevated levels of FMR1 mRNA in granulosa cells are associated with low ovarian reserve in FMR1 premutation carriers.

AIM: To assess the role of mRNA accumulation in granulosa cells as the cause of low ovarian response among FMR1 premutation carriers undergoing pre-implantation genetic diagnosis (PGD). DESIGN: Case control study in an academic IVF unit. Twenty-one consecutive FMR1 premutation carriers and 15 control women were included. After oocyte retrieval the granulosa cells mRNA levels of FMR1 was measured using RT-PCR. RESULTS: In FMR1 premutation carriers, there was a significant non-linear association between the number of CGG repeats and the number of retrieved oocytes (p<0.0001) and a trend to granulosa cells FMR1 mRNA levels (p = 0.07). The lowest number of retrieved oocytes and the highest level of mRNA were seen in women with mid-size CGG repeats (80-120). A significant negative linear correlation was observed between the granulosa cells FMR1 mRNA levels and the number of retrieved oocytes (R2 linear = 0.231, P = 0.02). CONCLUSION: We suggest that there is a no-linear association between the number of CGG repeats and ovarian function, resulting from an increased granulosa cells FMR1 mRNA accumulation in FMR1 carriers in the mid-range (80-120 repeats).

Pregestational, periconceptional, and gestational primary maternal cytomegalovirus infection: prenatal diagnosis in 508 pregnancies.

OBJECTIVE: The objective of the study was to evaluate the vertical transmission rate and fetal risk following primary maternal cytomegalovirus infection before and around conception. STUDY DESIGN: Data of patients referred to fetal medicine clinic in 1 tertiary center in Israel were evaluated. Each included subject had primary maternal cytomegalovirus infection determined by serology, precise gestational dating, and testing of fetal infection. Subjects were assigned to five subgroups: pregestational, periconception, and first, second, or third trimester of pregnancy. RESULTS: Five hundred eight pregnancies were included. None of the 97 pregnancies in the preconception group and 6 of the 130 periconception subjects (4.6%) were congenitally infected. Transmission rates were 34.8%, 42.0%, and 58.6% for the first, second, and third trimesters, respectively (P = .049). Prenatal and postnatal follow-up indicated that third-trimester infection has no clinical effect on the fetus. CONCLUSION: Pre- and periconception maternal infection carries small risk for fetal infection, whereas it is positively correlated to time of maternal infection during pregnancy.

The single cell as a tool for genetic testing: credibility, precision, implication.

PURPOSE: To investigate the influence of amplicons size and cell type on allele dropout and amplification failures in single-cell based molecular diagnosis. METHODS: 730 single lymphocytes and amniotic cells were collected from known heterozygotes individuals to one of the common Ashkenazi Jewish mutations: 1278+TATC and IVS12+1G>C which cause Tay Sachs Disease, IVS20+6T and 854A>C which underlie Familial Dysautonomia and Canavan Disease. DNA was extracted and analyzed by our routine methods. RESULTS: Reduced rates of allele dropout and amplification failure were found when smaller amplification product were designed and in amniotic cultured cells compared to peripheral lymphocytes. Cultured lymphocytes, induced to divide, demonstrated significantly less allele dropout than non induced lymphocytes suggesting the role of division potential on amplification efficiency. CONCLUSION: Single cell based diagnosis should be designed for each mutation. Minimal sized amplicons and cell having division potential should be preferred, as well as sensitive techniques to detect preferential amplification.

Parental karyotype and subsequent live births in recurrent miscarriage.

OBJECTIVE: To compare the subsequent live birth rate in recurrently miscarrying women with and without parental balanced chromosomal aberrations. DESIGN: Retrospective comparative cohort study. SETTING: Tertiary referral unit in a university hospital. PATIENT(S): Nine hundred sixteen patients with 3-16 miscarriages before 20 weeks: 99 patients with and 817 patients without chromosomal aberrations. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Outcome of the subsequent pregnancy in terms of live births or repeat miscarriage. RESULT(S): Of the 916 patients, 661 subsequently conceived, 73 (73.7%) with parental chromosomal aberrations and 588 (71.9%) without aberrations. In patients with and without chromosomal aberrations, 33 of 73 pregnancies (45.2%) and 325 of 588 pregnancies (55.3%), respectively, resulted in live births. The difference is not statistically significant. There was a similar prevalence of aberrations in primary, secondary, and tertiary aborters. The prevalence of aberrations was not related to the number of previous miscarriages. Translocations, inversions, and mosaicism were followed by a similar live birth rate. CONCLUSION(S): Patients with parental chromosomal rearrangements do not have a significantly lower live birth rate than patients without aberrations. Parental karyotyping might not be a good predictor of the outcome of subsequent pregnancies.

Demographic factors for utilization of invasive genetic testing after multifetal pregnancy reduction.

OBJECTIVE: Pregnant infertility patients are commonly old enough to be offered prenatal diagnosis. However, they may be reluctant to undergo an additional invasive procedure. We, therefore, sought to determine what demographic factors, including race and ethnic group, influenced patients' decisions to undergo genetic testing in addition to multifetal pregnancy reduction (MFPR). METHODS: We retrospectively reviewed MFPR patients from July 1997 to June 1999 at our institution. Invasive genetic testing was routinely discussed. Maternal age, race, ethnicity, religion, egg source for in vitro fertilization (IVF) patients, and the remaining fetuses following MFPR were analyzed for invasive genetic testing determinants and were compared to our experiences with genetic referents to us for singleton pregnancies. 132 consecutive patients, of whom 49 were >/=35 years, including 15 having IVF with donor eggs, were included. RESULTS: Maternal age was the single most significant determinant of testing. In donor egg cases, donor age was significant. Ethnic background, previous children, and the remaining number of fetuses after MFPR were also significant determinants. CONCLUSION: MFPR patients share similar demographics to the advanced maternal age population. Despite the very stressful situations, our data suggest that maternal age, and therefore genetic risk, is the most important determinant of choosing whether or not to have testing. However, patients' decisions are, to varying degrees, modified by religious and ethnic considerations.

Spontaneous abortions in couples declining multifetal pregnancy reduction.

Multifetal pregnancy reduction (MFPR) has clearly improved the outcomes of multifetal gestations. Several recent reports have also suggested improved outcomes in nonreduced cases, but there have been methodologic concerns about the denominators, i.e. have all cases been included and is there a 'hidden mortality' of unknown lost cases. Here we assessed the outcome of patients telephoning to discuss MFPR, but who chose not to have the procedure. Over a 3-year period, 446 patients had MFPR by one operator. Nineteen patients chose not to have the procedure. There were 11 preterm births, 1 term delivery, and 5 spontaneous losses (7 of 17) prior to 24 weeks, a loss rate of 35%. Two patients delivering triplets had a loss of 1 fetus/neonate. These data suggest that the loss rates of nonreduced pregnancies may be higher than generally thought, making the improvements with MFPR even bigger than generally realized.