Whole-exome characterization of pancreatic neuroendocrine tumor cell lines BON-1 and QGP-1.

The human BON-1 and QGP-1 cell lines are two frequently used models in pancreatic neuroendocrine tumor (PNET) research. Data on the whole-exome genetic constitution of these cell lines is largely lacking. This study presents, to our knowledge, the first whole-exome profile of the BON-1 and QGP-1 cell lines. Cell line identity was confirmed by short tandem repeat profiling. Using GTG-banding and a CytoSNP-12v2 Beadchip array, cell line ploidy and chromosomal alterations were determined in BON-1 and QGP-1. The exomes of both cell lines were sequenced on Ilumina's HiSeq next-generation sequencing (NGS) platform. Single-nucleotide variants (SNVs) and insertions and deletions (indels) were detected using the Genome Analysis ToolKit. SNVs were validated by Sanger sequencing. Ploidy of BON-1 and QGP-1 was 3 and 4 respectively, with long stretches of loss of heterozygosity across multiple chromosomes, which is associated with aggressive tumor behavior. In BON-1, 57 frameshift indels and 1725 possible protein-altering SNVs were identified in the NGS data. In the QGP-1 cell line, 56 frameshift indels and 1095 SNVs were identified. ATRX, a PNET-associated gene, was mutated in both cell lines, while mutation of TSC2 was detected in BON-1. A mutation in NRAS was detected in BON-1, while KRAS was mutated in QGP-1, implicating aberrations in the RAS pathway in both cell lines. Homozygous mutations in TP53 with possible loss of function were identified in both cell lines. Various MUC genes, implicated in cell signaling, lubrication and chemical barriers, which are frequently expressed in PNET tissue samples, showed homozygous protein-altering SNVs in the BON-1 and QGP-1 cell lines.

The analysis of one or two blastomeres for PGD using fluorescence in-situ hybridization.

BACKGROUND: The analysis of one or two blastomeres for PGD using fluorescence in-situ hybridization (FISH) is debated. The proportion of analysable embryos, false negatives, false positives, sensitivity, specificity, negative predictive value (NPV), positive predictive value (PPV) and efficiency were evaluated when one or two blastomeres were analysed. METHODS: Embryos of patients having PGD for aneuploidy screening were assigned non-randomly to two groups: group I (n = 413), more slow cleaving embryos with one nucleus for analysis, and group II (n = 1366), regularly cleaving embryos with two nuclei for analysis. A two-round FISH procedure was performed investigating seven chromosomes; 486 embryos were reanalysed. RESULTS: The proportion of analysable embryos was significantly higher in group II (98.2 versus 95.9%) (P = 0.04). Despite the apparently increased false-positive rate (group I: 25.6% and group II: 13.6%) and the decreased PPV (group I: 91.9% and group II: 96.7%), specificity (group I: 74.4% and group II: 86.4%) and efficiency (group I: 93.5% and group II: 97.3%) in group I, no significance was reached (P = 0.11, P = 0.053, P = 0.11 and P = 0.06, respectively). CONCLUSIONS: Although the analysis of one blastomere generates statistically significantly fewer embryos with a diagnosis than does the analysis of two blastomeres, the 2% difference may not be clinically relevant. The diagnostic accuracy is not significantly different between the two groups, hence not favouring the analysis of one or two blastomeres.

The importance of aneuploidy screening in reciprocal translocation carriers.

The purpose of this study is to investigate the aneuploidy rate and the mosaicism of chromosomes not involved in reciprocal translocations. Aneuploidy screening (AS) (13, 16, 18, 21 and 22) was performed as a re-analysis on fixed blastomeres from 126 embryos already analysed in preimplantation genetic diagnosis (PGD) cycles of eight female and five male reciprocal translocation carriers who had not achieved a pregnancy. A successful diagnosis for AS was achieved in 91.3% of embryos; 30.9% were euploid and 60.3% were aneuploid for the five chromosomes analysed. Of the embryos, 8.7% were euploid for AS and normal-balanced for the translocation and 22.2% were euploid for AS but unbalanced for the translocation; 8% of the embryos were aneuploid for AS but normal-balanced for the translocation and 52.4% were aneuploid for AS and also unbalanced for the translocation. At least 58.7% of the embryos were mosaic regarding mosaicism for the chromosomes involved and not involved in the translocations. Six of the 16 embryos transferred in the PGD cycles were aneuploid for the AS study; four of them were also mosaics. AS should be performed in reciprocal translocation carriers after segregation analysis in PGD.

Chromosomal segregation in spermatozoa of 14 Robertsonian translocation carriers.

Male carriers of Robertsonian (Rob) translocations can have fertility problems associated with low sperm counts and abnormal sperm morphology. In this study, spermatozoa from 14 Rob translocation carriers, seven der(13;14), two der(13;15), two der(14;15), two der(14;21) and one der(21;22), were tested by fluorescence in-situ hybridization (FISH) for the chromosomes involved, to study meiotic segregation behaviour. It was shown that in each type of Rob translocation, meiotic segregation behaviour is similar, comparable and occurs non-randomly. Most of the spermatozoa results from alternate segregation (range: 76-89.47%). There is, however, still much unbalanced spermatozoa resulting from adjacent segregation mode (range: 10.24-23.41%). These data provide useful information for genetic counselling purposes. Moreover, aneuploidy for chromosomes 13,18, 21, X and Y was studied in five patients and suggested an inter-chromosomal effect.

Prenatal testing in ICSI pregnancies: incidence of chromosomal anomalies in 1586 karyotypes and relation to sperm parameters.

BACKGROUND: Prenatal testing was offered in all pregnancies obtained after ICSI with ejaculated or non-ejaculated sperm as part of the evaluation of the safety of ICSI. METHODS: Between 1990 and 2001, a chorionic villus sampling (CVS) or amniocentesis was offered for multiple or singleton pregnancies respectively during a genetic counselling session for all couples applying for ICSI. ICSI was carried out using ejaculated, epididymal or testicular sperm. RESULTS: In total, 1586 ICSI fetuses obtained after fresh embryo transfer were tested by CVS (n = 698) or by amniocentesis (n = 888). Abnormal fetal karyotypes were found in 47 samples [3.0%; 95% confidence interval (CI) 2.2-3.9%]; 25 anomalies (1.6%; 95% CI 1.0-2.3%) were de novo. These were 10 sex chromosomal anomalies and 15 autosomal anomalies [either numerical (n = 8) or structural (n = 7)], and 22 inherited abnormalities (1.4%; 95% CI 0.9-2.1%) (21 balanced, one unbalanced). In 17/22 inherited cases the chromosomal structural defect was inherited from the father. A significantly higher percentage of 2.1% de-novo prenatal chromosomal anomalies was observed for sperm concentrations of <20x10(6) sperm per ml, as compared with 0.24% if the sperm concentration was vertical line 20x10(6) sperm per ml (Fisher's exact test, P = 0.006). No statistical difference in frequency of chromosomal anomalies was observed for lower threshold values of sperm concentration (<1x10(6), <5x10(6), <10x10(6) and <15x10(6)). A statistical difference was observed for motility criteria, but not morphology. Three chromosomal anomalies were found prenatally after use of epididymal or testicular sperm in a total of 94 samples; two (of 83 tested) were from patients with obstructive and one (of nine tested) was from a patient with non-obstructive azoospermia. CONCLUSIONS: A significantly higher rate of de-novo chromosomal anomalies (1.6 versus 0.5% in amniocentesis for a mean maternal age of 33.5 years; P < 0.007) was observed in ICSI offspring, relating mainly to a higher number of sex chromosomal anomalies and partly to a higher number of autosomal structural anomalies. This finding was related to sperm concentration and motility. The significantly higher rate of observed inherited anomalies (1.4 versus 0.3-0.4% in prenatal tests in the general population; P < 0.001) was related to a higher rate of constitutional chromosomal anomalies, mainly in the fathers. The hypothesis of a higher risk of post-zygotic events as a consequence of the ICSI procedure leading to a higher proportion of chromosomal mosaicism was not confirmed in this study. Couples should be informed of the risks of an abnormal result related to sperm quality, and of the risk linked to a prenatal procedure as well as about the relatively benign character of some chromosomal anomalies such as de-novo structural anomalies or sex chromosomal anomalies in order to be able to make a choice for prenatal testing, or not.

Post-zygotic origin of isochromosome 12p.

OBJECTIVE: Advance knowledge about the mechanism of isochromosome formation. METHODS: Echographic examination of the foetus. G- and/or T-banded chromosome and FISH analysis using chromosome 12p subtelomeric probes on short- and long-term CVS cultures, amniocytes and foetal fibroblasts. Polymorphic CA repeat analysis on DNA from the foetus and both parents. RESULTS: Short-term CVS cultures showed a 46,XX karyotype, whilst long-term CVS cultures showed a 47,XX,+12 karyotype. FISH on amniocytes indicated 2, 3 and 4 signals. Foetal fibroblasts showed both 47,XX,+12 and 47,XX,+i(12)(p10) karyotypes. DNA analysis revealed the isochromosome to be paternal in origin, whilst the other two foetal chromosomes 12 were maternal, part iso- and part heterodisomy. CONCLUSION: The cytogenetic and DNA constitution of the foetus indicated the isochromosome 12p to be of paternal origin, and implied post-zygotic formation of the isochromosome 12p in the Pallister-Killian syndrome.

Comparison of blastocyst transfer with or without preimplantation genetic diagnosis for aneuploidy screening in couples with advanced maternal age: a prospective randomized controlled trial.

BACKGROUND: It is generally accepted that the age-related increased aneuploidy rate is correlated with reduced implantation and a higher abortion rate. Therefore, advanced maternal age (AMA) couples are a good target group to assess the possible benefit of preimplantation genetic diagnosis for aneuploidy screening (PGD-AS) on the outcome after assisted reproductive technology (ART). METHODS: A prospective randomized controlled clinical trial (RCT) was carried out comparing the outcome after blastocyst transfer combined with PGD-AS using fluorescence in situ hybridization (FISH) for the chromosomes X, Y, 13, 16, 18, 21 and 22 in AMA couples (aged > or =37 years) with a control group without PGD-AS. From the 400 (200 for PGD-AS and 200 controls) couples that were allocated to the trial, an oocyte pick-up was performed effectively in 289 cycles (148 PGD-AS cycles and 141 control cycles). RESULTS: Positive serum HCG rates per transfer and per cycle were the same for PGD-AS and controls: 35.8% (19.6%) [%/per embryo transfer (per cycle)] and 32.2% (27.7%), respectively (NS). Significantly fewer embryos were transferred in the PGD-AS group than in the control group (P<0.001). The implantation rate (with fetal heart beat) was 17.1% in the PGD-AS group versus 11.5% in the control group (not significant; P=0.09). We observed a normal diploid status in 36.8% of the embryos. CONCLUSIONS: This RCT provides no arguments in favour of PGD-AS for improving clinical outcome per initiated cycle in patients with AMA when there are no restrictions in the number of embryos to be transferred.