Whole-exome sequencing in patients with maturation arrest: a potential additional diagnostic tool for prevention of recurrent negative testicular sperm extraction outcomes.

STUDY QUESTION: Could whole-exome sequencing (WES) be useful in clinical practice for men with maturation arrest (MA) after a first testicular sperm extraction (TESE)? SUMMARY ANSWER: WES in combination with TESE yields substantial additional information and may potentially be added as a test to predict a negative outcome of a recurrent TESE in patients with MA. WHAT IS KNOWN ALREADY: At present, the only definitive contraindications for TESE in men with non-obstructive azoospermia (NOA) are a 46,XX karyotype and microdeletions in the azoospermia factor a (AZFa) and/or AZFb regions. After a first negative TESE with MA, no test currently exists to predict a negative outcome of a recurrent TESE. STUDY DESIGN, SIZE, DURATION: In a cohort study, we retrospectively included 26 patients with idiopathic NOA caused by complete MA diagnosed after a first TESE. PARTICIPANTS/MATERIALS, SETTING, METHODS: Twenty-six men with MA at the spermatocyte stage in all seminiferous tubules, according to a histopathological analysis performed independently by two expert histologists, and a normal karyotype (i.e. no AZF gene microdeletions on the Y chromosome) were included. Single-nucleotide polymorphism comparative genomic hybridization array and WES were carried out. The results were validated with Sanger sequencing. For all the variants thought to influence spermatogenesis, we used immunohistochemical techniques to analyse the level of the altered protein. MAIN RESULTS AND THE ROLE OF CHANCE: Deleterious homozygous variants were identified in all seven consanguineous patients and in three of the 19 non-consanguineous patients. Compound heterozygous variants were identified in another 5 of the 19 non-consanguineous patients. No recurrent variants were identified. We found new variants in genes known to be involved in azoospermia or MA [including testis expressed 11 (TEX11), meiotic double-stranded break formation protein 1 (MEI1), proteasome 26s subunit, ATPase 3 interacting protein (PSMC3IP), synaptonemal complex central element protein 1 (SYCE1) and Fanconi anaemia complementation group M (FANCM) and variants in genes not previously linked to human MA (including CCCTC-binding factor like (CTCFL), Mov10 like RISC complex RNA helicase 1 (MOV10L1), chromosome 11 open reading frame 80 (C11ORF80) and exonuclease 1 (EXO1)]. LARGE SCALE DATA: Data available on request. LIMITATIONS, REASONS FOR CAUTION: More data are required before WES screening can be used to avoid recurrent TESE, although screening should be recommended for men with a consanguineous family background. WES is still a complex technology and can generate incidental findings. WIDER IMPLICATIONS OF THE FINDINGS: Our results confirmed the genetic aetiology of MA in most patients: the proportion of individuals with at least one pathologic variant was 50% in the overall study population and 100% in the consanguineous patients. With the exception of MEI1 (compound heterozygous variants of which were identified in two cases), each variant corresponded to a specific gene-confirming the high degree of genetic heterogeneity in men with MA. Our results suggest that WES screening could help to avoid recurrent, futile TESE in men with MA in general and in consanguineous individuals in particular, but these results need to be confirmed in future studies before clinical implementation. STUDY FUNDING/COMPETING INTEREST(S): The study was funded by the Fondation Maladies Rares (Paris, France), Merck (Kenilworth, NJ, USA), IRSF (Montigny le Bretonneux, France) and Agence de la Biomédecine (Saint Denis, France). There are no competing interests. TRIAL REGISTRATION NUMBER: N/A.

The emerging microduplication 3q13.31: Expanding the genotype-phenotype correlations of the reciprocal microdeletion 3q13.31 syndrome.

Microdeletion and microduplication syndromes are well-known causes of developmental delay and/or malformations of differing severity. It was recently reported that a microdeletion at the 3q13.31 locus is associated with a new syndrome combining developmental delay, postnatal overgrowth and dysmorphic features. However, the reciprocal microduplication has only been described in a few case reports displaying some clinical features of the microdeletion syndrome. Here, we report on a female infant with a 3.34 Mb microduplication of the 3q13.2q13.31 region inherited from her mother. The infant presented with severe intellectual disability, learning difficulties, intrauterine and postnatal growth retardation and skeletal particularities but no dysmorphic traits. This microduplication encompassed the previously described shortest region of overlap, which contains five genes (DRD3, ZNF80, TIGIT, MIR568 and ZBTB20). We reviewed the phenotypes described in the literature on microduplications and in the well-characterized 3q13.31 microdeletion syndrome. In agreement with the literature data, DRD3 and ZBTB20 appear to be strong candidate genes for neurodevelopmental defects and growth retardation. Lastly, we consider the putative mechanism of this rearrangement, which may involve a particular kind of nonallelic homologous recombination of human endogenous retrovirus elements.

Low-level mosaicism of a de novo derivative chromosome 9 from a t(5;9)(q35.1;q34.3) has a major phenotypic impact.

Microdeletion and microduplication syndromes are well-known causes of developmental delay and/or malformations of differing severity. Although homogeneous abnormalities can now be detected relatively easily using microarray technologies, they are more difficult to detect and interpret in cases of mosaicism. Here, we report on a male infant with a mosaic de novo derivative chromosome 9, featuring a 10.2 Mb 5q35 duplication (including the NSD1 gene) and a 687 kb 9q34 deletion (including EHMT1). The infant presented developmental delay, short stature, brachy/plagiocephaly and hyperactivity. The proportion of abnormal cells was 50% in saliva (in a microarray analysis) and 25% in lymphocytes (in a FISH analysis). Despite the low-level mosaicism in lymphocytes, this imbalance appears to be responsible for a distinctive phenotype (suggesting the presence of variable clinical expression and/or major somatic mosaicism).

Birth of a boy with isolated short stature after prenatal diagnosis of a Xp22.3 nullosomy due to an inherited t(X;15) (p22.3;p10) translocation.

KEY CLINICAL MESSAGE: Translocations between X and acrocentric chromosomes are rare. We report on the inheritance of a familial t(X;15)(p22.3;p10) translocation in a fetus referred for short long bones. Cytogenetic analysis revealed an unbalanced translocation combined with a three-gene nullosomy. After genetic counseling, a prognosis was established and a healthy boy was delivered.

A French collaborative survey of 272 fetuses with 22q11.2 deletion: ultrasound findings, fetal autopsies and pregnancy outcomes.

OBJECTIVE: The 22q11.2 deletion (del22q11.2) is one of the most common microdeletions. We performed a collaborative, retrospective analysis in France of prenatal diagnoses and outcomes of fetuses carrying the del22q11.2. METHODS: A total of 272 fetuses were included. Data on prenatal diagnosis, ultrasound findings, pathological features, outcomes and inheritance were analyzed. RESULTS: The mean time of prenatal diagnosis was 25.6 ± 6 weeks of gestation. Most of the diagnoses (86.8%) were prompted by abnormal ultrasound findings [heart defects (HDs), in 83.8% of cases]. On fetal autopsy, HDs were again the most common disease feature, but thymus, kidney abnormalities and facial dysmorphism were also described. The deletion was inherited in 27% of cases. Termination of pregnancy (TOP) occurred in 68.9% of cases and did not appear to depend on the inheritance status. However, early diagnosis was associated with a higher TOP rate. CONCLUSION: This is the largest cohort of prenatal del22q11.2 diagnoses. As in postnatally diagnosed cases, HDs were the most frequently observed abnormalities. However, thymus and kidney abnormalities and polyhydramnios should also be screened for in the prenatal diagnosis of del22q11.2. Only the time of diagnosis appeared to be strongly associated with the pregnancy outcome: the earlier the diagnosis, the higher the TOP rate.

Sperm FISH analysis of a 44,X,der(Y),t(Y;15)(q12;q10)pat,rob(13;14)(q10;q10)mat complex chromosome rearrangement.

Complex chromosome rearrangements (CCR) with two independent chromosome rearrangements are rare. Although CCRs lead to high unbalanced gamete rates, data on meiotic segregation in this context are scarce. A male patient was referred to our clinic as part of a family screening programme prompted by the observation of a 44,X,der(Y),t(Y;15)(q12;q10)pat,rob(13;14)(q10;q10)mat karyotype in his brother. Karyotyping identified the same CCR. Sperm FISH (with locus-specific probes for the segments involved in the translocations and nine chromosomes not involved in both rearrangements) was used to investigate the rearrangements meiotic segregation products and establish whether or not an inter-chromosomal effect was present. Sperm nuclear DNA fragmentation was also evaluated. For rob(13;14) and der(Y), the proportions of unbalanced products were, respectively, 26.4% and 60.6%. Overall, 70.3% of the meiotic segregation products were unbalanced. No evidence of an inter-chromosomal effect was found, and the sperm nuclear DNA fragmentation rate was similar to our laboratory's normal cut-off value. In view of previously published sperm FISH analyses of Robertsonian translocations (and even though the mechanism is still unknown), we hypothesise that cosegregation of der(Y) and rob(13;14) could modify rob(13;14) meiotic segregation.

Molecular characterization of 39 de novo sSMC: contribution to prognosis and genetic counselling, a prospective study.

Small supernumerary marker chromosomes (sSMCs) are structurally abnormal chromosomes that cannot be characterized by karyotype. In many prenatal cases of de novo sSMC, the outcome of pregnancy is difficult to predict because the euchromatin content is unclear. This study aimed to determine the presence or absence of euchromatin material of 39 de novo prenatally ascertained sSMC by array-comparative genomic hybridization (array-CGH) or single nucleotide polymorphism (SNP) array. Cases were prospectively ascertained from the study of 65,000 prenatal samples [0.060%; 95% confidence interval (CI), 0.042-0.082]. Array-CGH showed that 22 markers were derived from non-acrocentric markers (56.4%) and 7 from acrocentic markers (18%). The 10 additional cases remained unidentified (25.6%), but 7 of 10 could be further identified using fluorescence in situ hybridization; 69% of de novo sSMC contained euchromatin material, 95.4% of which for non-acrocentric markers. Some sSMC containing euchromatin had a normal phenotype (31% for non-acrocentric and 75% for acrocentric markers). Statistical differences between normal and abnormal phenotypes were shown for the size of the euchromatin material (more or less than 1 Mb, p = 0.0006) and number of genes (more or less than 10, p = 0.0009). This study is the largest to date and shows the utility of array-CGH or SNP array in the detection and characterization of de novo sSMC in a prenatal context.

A genome-wide DNA methylation study in azoospermia.

The objective of this study was to assess genome-wide DNA methylation in testicular tissue from azoospermic patients. A total of 94 azoospermic patients were recruited and classified into three groups: 29 patients presented obstructive azoospermia (OA), 26 displayed non-obstructive azoospermia (NOA) and successful retrieval of spermatozoa by testicular sperm extraction (TESE+) and 39 displayed NOA and failure to retrieve spermatozoa by TESE (TESE-). An Illumina Infinium Human Methylation27 BeadChip DNA methylation array was used to establish a testicular DNA methylation pattern for each type of azoospermic patient. The OA and NOA groups were compared in terms of the relative M-value (the log2 ratio between methylated and non-methylated probe intensities) for each CpG site. We observed significantly different DNA methylation profiles for the NOA and OA groups, with differences at over 9000 of the 27 578 CpG sites; 212 CpG sites had a relative M-value >3. The results highlighted 14 testis-specific genes. Patient clustering with respect to these 212 CpG sites corresponded closely to the clinical classification. The DNA methylation patterns showed that in the NOA group, 78 of the 212 CpG sites were hypomethylated and 134 were hypermethylated (relative to the OA group). On the basis of these DNA methylation profiles, azoospermic patients could be classified as OA or NOA by considering the 212 CpG sites with the greatest methylation differences. Furthermore, we identified genes that may provide insight into the mechanism of idiopathic NOA.

Tumor necrosis factor-308 polymorphism increases the embryo implantation rate in women undergoing in vitro fertilization.

STUDY QUESTION: Do TNF-308 and -238 polymorphisms impact the embryo implantation rate after in vitro fertilization (IVF) in women without female infertility factor? SUMMARY ANSWER: The presence of the TNF-308A allele is associated with high implantation and multiple pregnancy rates in women without known infertility factors after ovarian hyperstimulation with exogenous FSH. WHAT IS ALREADY KNOWN: Multiple pregnancies are frequent after the use of Assisted Reproductive Technologies. Single embryo transfer (SET) has been proposed as a simple way to prevent these risks. However, the extension of SET indications to patients not selected based on specific criteria is controversial because of reduced pregnancy rates. To date, the predictive value of the parameters used for SET (age, gynecological history of the patient and uterine characteristics) allows a pregnancy rate of ~30%. STUDY DESIGN, SIZE, DURATION: The potential predictive value of TNF polymorphisms (-308, rs1800629 and -238, rs361525) on implantation rate was evaluated in 424 women requiring IVF due to male fertility factors. This cohort retrospective study was conducted over 4 years in University-affiliated hospitals. PARTICIPANTS, SETTING, METHODS: The entire patient group included 424 women undergoing intracytoplasmic sperm injection (ICSI) due to male fertility factors without the contribution of any female factor. From among this group, a selected patient group included 120 women with a normal karyotype, age under 38 years, serum follicle-stimulating hormone (Day-3 FSH) levels below 10 IU/l, a long agonist desensitization protocol associated with recombinant FSH treatment and a Caucasian background. MAIN RESULTS AND THE ROLE OF CHANCE: The TNF-238 polymorphism was not associated with implantation rate. In contrast, the presence of the TNF-308A allele was associated with increased Day 3-E2 levels as well as higher implantation and multiple pregnancy rates after fresh embryo transfer in women from the entire and selected patient groups. Moreover, in the selected patient group, the presence of the TNF-308A allele was also associated with a decrease in the miscarriage rate. The benefit of the TNF-308A allele in predicting implantation rates was not observed after the use of frozen embryos. LIMITATIONS, REASONS FOR CAUTION: Future studies are needed to evaluate whether the TNF-308A allele might also be a biomarker in women with infertility factors. WIDER IMPLICATIONS OF THE FINDING: The TNF-308A allele may represent a good candidate for a potential predictive, non-invasive biomarker in the SET strategy. However, its impact should be evaluated in prospective studies. STUDY FUNDING/COMPETING INTEREST: This study was conducted with financial support from the French Institute for Health and Medical Research (INSERM), Organon France for a FARO (Fond d'Aide à la Recherche Organon) fellowship (to V.T.) and CHU Nice PHRC (PHRC 09-279).There are no competing interests.

[What does a thorough personality questionnaire, the MMPI-2, tell us about psychological aspects of recurrent miscarriage?]. / Étude des aspects psychologiques des fausses couches à répétition à l'aide d'un questionnaire de personnalité approfondi : le MMPI-2.

OBJECTIVES: Try to analyse the experience of couples undergoing repeated miscarriages by answering the following questions: what can we learn from these men and women who suffered from repeated miscarriages? PATIENTS AND METHODS: A thorough personality questionnaire, the MMPI-2, presented to 50 couples who have had repeated miscarriages. RESULTS: Through a hierarchical classification, different profiles appear in the men's group as well as in the women's group, revealing a somatization of psychological suffering. It is also revealing acute defensive personality profiles showing restricted affects in a lot of these men whose partners have suffered from multiple procreation failures. Such a narrower range of emotions can be a cause of additional pain for their partner and for themselves. DISCUSSION AND CONCLUSION: We can therefore establish that, in these circumstances, the medical and/or psychological treatment should include both couple members to improve the marital adjustment and ease the couple towards another pregnancy which is always apprehended with the fear of another failure. A few etiological hypothesis may be evoked.

Prenatal diagnosis of the duplication 17p11.2 associated with Potocki-Lupski syndrome in a foetus presenting with mildly dysmorphic features.

Duplication 17p11.2 (Potocki-Lupski syndrome (PTLS) MIM# 610883) is a genomic disorder with an estimated incidence of 1 in 25,000 births. As for other genomic disorders this duplication is typically de novo and is not associated with advanced maternal age or advanced paternal age. Herein we describe a prenatal diagnosis of duplication 17p11.2. This diagnosis was not suspected as the prenatal ultrasound findings were non-specific; however, BACs-on-Beads™ technology and array comparative genomic hybridization (aCGH) confirmed the common ∼3.7 Mb duplication. Evaluation of the foetus following termination of pregnancy revealed mildly dysmorphic features as well as congenital anomalies not previously reported in PTLS, specifically left pulmonary isomerism, an abnormally positioned left coronary orifice and nodular cerebellar heterotopia. This report exemplifies the utility of prenatal testing using new genomic technologies even when there are no multiple anomalies on foetal ultrasound. This report also exemplifies the utility of foetal autopsy in the identification of "occult" congenital anomalies.

Prenatal BACs-on-Beads™ : a new technology for rapid detection of aneuploidies and microdeletions in prenatal diagnosis.

OBJECTIVE: Molecular cytogenetic techniques on uncultured prenatal samples are the sole tests applied in some countries in cases with advanced maternal age (AMA) or increased risk after prenatal screening. Moreover, there is a trend to perform invasive prenatal diagnosis (PD) during the first trimester before ultrasound manifestations, so new rapid and reliable assays are necessary to investigate microdeletions not detectable with the conventional karyotype. We report the validation study of the prenatal bacterial artificial chromosomes-on-Beads™ (BoBs™ ; CE-IVD), a bead-based multiplex assay detecting chromosomes 13, 18, 21, X/Y aneuploidies and nine microdeletion regions having an overall detection rate of 1/1700. METHOD: We retrospectively studied 408 selected samples and prospectively tested 212 consecutive samples ascertained for conventional karyotyping. RESULTS: We did not find false-positive results. Triploidies were not detected. Maternal cell contamination of male samples up to 90% was unmasked inspecting gonosome profiles. Mosaic conditions at 20 to 30% were revealed. Failures were due to low amount of DNA. CONCLUSION: Prenatal BoBs™ is a robust technology for the investigation of fetuses with normal karyotype with or without sonographic abnormalities. Running in parallel with the karyotype analysis, it can be proposed instead of rapid FISH or QF-PCR providing rapid results on common aneuploidies and additional information regarding the microdeletion syndromes.

Predisposition to aneuploidy in the oocyte.

While the incidence of predisposition to aneuploidy in the oocyte increases with age, there is also evidence of increased incidence in young women with recurrent miscarriage, recurrent aneuploidy, or recurrent implantation failure after in vitro fertilization. There is evidence from mouse models and from observations in humans that follicle-stimulating hormone (FSH) probably has a direct or indirect effect on the occurrence of oocyte aneuploidy. It seems that increased endogenous or exogenous FSH could induce meiotic disruption. Although the effect of FSH may explain the age-related increase in aneuploidy rate, many questions remain regarding young women, even if their FSH level is sometimes increased. Disruption of meiotic gene expression caused by exposure to environmental contaminants or by gene defects could also predispose to oocyte aneuploidy. Such abnormalities could impact on the oocyte pool, recombination and synapsis during fetal life, or oocyte growth.

[New technologies for genome analysis: Which use in prenatal diagnosis]. / Les nouvelles technologies d'analyse du génome : quelles utilisations en diagnostic prénatal.

Array-CGH emergence allowed important diagnosis progress, and a better care of patients in postnatal. So, there is a great temptation to use it also in prenatal diagnosis. The point of view objective is to make a rapid overview of cytogenetic diagnosis evolution during the last 50 years, and to show all questions raised by the use of array-CGH, and problems that could arise in prenatal diagnosis. While array-CGH just comes in genetic laboratories, new diagnosis approaches emerged like whole genome sequencing or non-invasive prenatal diagnosis. The 2nd objective will be to review all these techniques for a probably close future.

[Psychological assistance for men with failures of procreation: look out for the secret wound!]. / Prise en charge psychologique des échecs de procréation, au masculin : une blessure peut en cacher une autre.

When one thinks of the failures of ART one naturally thinks of the suffering that they generate; but behind this pain, there is the suffering of infertility and, behind this latter, other distress we showed at the time of a recent research that they could play a part in infertility itself. The psychotherapy will help assume the failures, so that the traumatisms do not come to solidify in an impossible mourning, covering non elaborate former grieves. A sublimation of the desire of reproduction can make it possible for the unfertile man to peacefully consider other forms of paternity. For it to be possible, it is necessary that the subject should not be in the refusal of the psychic effraction, which the announcement of its infertility produces. When it is the case, to put on the couple on psychological assistance may help to restore a share of the narcissistic wounds; more particularly the one related to the suffering of the couple that often comes to be added to the wound of infertility.

Array comparative genomic hybridization in prenatal diagnosis: another experience.

OBJECTIVES: Etiologic diagnosis of multiple congenital abnormalities (MCAs) is often lacking. Large chromosome abnormalities can be detected by conventional cytogenetic methods, but more subtle chromosome micro-rearrangements and/or de novo abnormalities require multi-FISH analysis, which is hampered by the amount of material available in prenatal testing. METHODS: We used the comparative genomic hybridization (CGH) array, Genosensor Array 300, to screen for classic microdeletion syndromes and subtelomeric rearrangements in 39 consecutive fetuses with MCAs, after termination of pregnancy, in a prospective study. Thirty-seven of them had a normal karyotype, and two had a de novo unbalanced karyotype that could not be characterized with conventional cytogenetic methods. RESULTS: Two de novo unbalanced karyotypes were characterized by array CGH, and four additional abnormalities were diagnosed: an unbalanced inherited cryptic translocation, a deletion in band 22q11.2, a 1p36 deletion, and a 6p12.1-21.2 duplication. CONCLUSION: Chromosomal imbalances were therefore detected and/or characterized in 6 of 39 (15.4%) fetuses, indicating the value of routine array CGH in cases of MCAs and in uncharacterized chromosome rearrangements. Extension to all prenatal diagnoses may be warranted when copy number variation is identified and all FISH probes are commercially available.

Case report: Meiotic segregation in spermatozoa of a 46,X,t(Y;10)(q11.2;p15.2) fertile translocation carrier.

Translocations involving gonosomes are frequent in azoospermic patients and sometimes in oligozoospermic ones, conditions that lead to request for assisted reproduction treatment. This study reports an unexpectedly fertile 49-year-old man bearing a de-novo translocation 46,X,t(Y;10)(q11.2;q15.2) associated with a high chromosomal risk for offspring, and referred for familial investigations after the diagnosis of an unbalanced translocation 46,XX,der(10)t(Y;10)(q11.2;p15.2) in his naturally conceived and mentally retarded daughter. Chromosome molecular investigation confirmed Y long-arm inheritance in the daughter and absence of the Yq deletion in the father. Semen analysis showed a normal sperm count associated with moderate asthenospermia and severe teratospermia. A total of 984 spermatozoa were analysed using fluorescence in-situ hybridization (FISH). Alternate segregation pattern was found in 50.31% of the spermatozoa studied. The frequencies of adjacent I, adjacent II, 3:1 segregation, and diploidy (or 4:0 segregation) were respectively 39.62, 1.63, 7.83, and 0.61%. No interchromosomal effect was observed. This patient is the first fertile man in whom the meiotic segregation pattern of a Y-autosome translocation has been analysed. The imbalance risk was close to those observed for reciprocal translocations, and emphasizes the value of FISH studies in males with a chromosomal translocation in order to provide them a personalized risk evaluation.

Preconceptional diagnosis for Robertsonian translocation as an alternative to preimplantation genetic diagnosis in two situations: a pilot study.

INTRODUCTION: Preimplantation genetic diagnosis (PGD) is widely used for women heterozygous for a Robertsonian translocation. Preconceptional diagnosis (PCD), performed before fertilization, may be an alternative to PGD, especially in countries where PGD is restricted or prohibited, as in France. It could also give different information and clarify the influence of reproductive and obstetric history. METHODS: In our study, translocation was diagnosed before ICSI in five cases (group A), and after newborn or fetal aneuploidy or miscarriage in two cases, (group B). RESULTS: First polar body (PB1) analysis using acrocentric centromeric probes was done for 85 PB1s, and aneuploidy rate was at 42.4%. Oocyte aneuploidy rate differed (p<0.0001) between groups A and B (30% vs 84%). Despite the small group sizes, we demonstrate a correlation (p=0.0358) of aneuploidy rate in polar bodies after 2 or more attempts. Three live births were recorded, all in group A. DISCUSSION: PCD could thus be an alternative to PGD. This pilot study also provides new prognostic information taking into account the women's natural history, but further confirmation is required.