What is the impact of undiagnosed microdeletion and microduplication syndromes (MMS) for men with idiopathic low sperm count? Among idiopathic male infertility, ∼2% of cases harbour known disease-causing microdeletions and duplications linked to clinically well-established syndromes, representing ∼2.5-fold higher prevalence than in the general population. While infertility affects up to 10% of men, a substantial proportion of cases remain with no identifiable underlying cause. Recurrent submicroscopic losses or gains cause MMS, some of which also impact reproductive phenotypes, including cryptorchidism and reduced fertility. This retrospective study investigated the proportion of undiagnosed MMS among idiopathic male infertility cases. Patients with unexplained low total sperm counts (TSC; defined as ≤39 million sperm per ejaculate) were recruited to the ESTonian ANDrology (ESTAND) cohort at the Andrology Clinic of Tartu University Hospital (AC-TUH) in Estonia. A total of 504 men were included in the analysis, and the study capitalized on available whole-exome sequencing (WES) data to explore large (>500 kb) chromosomal deletions and duplications. Copy number variant (CNV) calling was executed on the WES dataset, followed by a stringent, custom-developed filtering pipeline that retained only high-confidence CNVs larger than 500 kb. Candidate CNVs were validated by chromosomal microarray analysis (CMA) or whole-genome sequencing (WGS). Prevalence of identified MMS-linked deletions and duplications in the ESTAND cohort was compared to general population literature data. A total of nine patients (1.8%) carried losses and gains linked to clinically well-characterized MMS-recurrent microdeletions at 16p11.2 (two cases), 2q13-14.1, and 15q13.2-13.3, and microduplications at 22q11.21 (three cases), 16p11.2, and 8p23.1. The total burden of MMS among infertile men was ∼2.5-fold higher compared to the general population (P = 0.01, χ2 test). Cryptorchidism was a novel shared feature among all individuals with 16p11.2 rearrangements, suggesting a potential role in disrupting testicular development. Three subjects with MMS-linked microduplications, but none with a microdeletion, had achieved biological fatherhood. An oligozoospermia case (TSC 1.92 × 106/ej.) with 16p11.2 duplication had a naturally conceived child in youthhood. For two men carrying 22q11.21 duplication (TSC 0 and 4.2 × 106/ej., respectively), implementation of ARTs-ICSI with or without preceding testicular sperm aspiration-resulted in successful conception and childbirth. Evidence for a plausible link to male gonadal development and function has been reported for MAZ and KCTD13 at 16p11.2, and LZTR1 at 22q11.21. As an additional finding, a novel ∼3.8 Mb microduplication at 3p25.1 was identified in an oligozoospermia patient and his azoospermic son, conceived naturally at the age of 28 years. This region encompasses a triplosensitive gene, NR2C2, linked to affected meiosis and oligozoospermia in mouse models. WES may not detect all structural variations, such as inversions or balanced translocations. As some MMS CNVs were only identified in singleton cases (8p23.1 duplication, 2q13-14.1 and 15q13.2-13.3 deletions), the link to male infertility could not be clarified. Further data are needed about the novel large 3p25.1 microduplication to understand its effect on spermatogenesis. The yield of identified MMS in idiopathic cases with low sperm counts (∼2%) was close to the carriership of Y-chromosome microdeletions, tested in routine infertility workup. Early identification of MMS can inform genetic counselling regarding congenital health risks to the patient and future offspring and options for decision-making in ART. This study was supported by the Estonian Research Council (Grant number PRG1021 to M.L.). The authors declare that they have no conflict of interest in relation to the data in this paper. N/A.

Advances in fetal fraction amplification in prenatal cell-free DNA screening now allow for high-resolution detection of copy-number variants (CNVs). However, approaches to interpreting CNVs as part of a primary screen are still evolving and require consensus. Here, we present a conservative, patient-centered framework for reporting fetal CNVs. Syndromes described in the literature were evaluated for inclusion based on a definable minimal critical region, disease severity, penetrance, and age of onset. The reporting framework required that a CNV overlap a defined minimal critical region and/or that it be ≥5 Mb and contain at least 1 OMIM disease-associated gene. This framework was then applied to CNVs identified from a cohort of 313,544 prenatal cfDNA screening patient samples. Patient-friendly terminology describing syndrome phenotypes was developed by scientists with training in genetic counseling. 65 syndromes met criteria for inclusion and represented the second most common class of CNVs in a retrospective cohort, more so than an established panel of microdeletions (1p36, 4p, 5p, 15q11.2-q13, and 22q11.2). Frequencies were concordant with reported syndrome incidence rates. The most common CNVs were those ≥5 Mb encompassing an OMIM disease gene(s). This framework for genome-wide fetal-CNV reporting carefully prioritizes findings with the potential to affect reproductive decision making.

Otofaciocervical syndrome (OTFCS) is a rare disorder characterized by facial, auditory, and shoulder girdle anomalies. Its significant phenotypic overlap with branchiootorenal spectrum disorders (BORSD)-both linked to EYA1 (EYA transcriptional coactivator and phosphatase 1) gene defects-has raised questions about whether they are distinct entities or part of a single clinical spectrum. We report a novel OTFCS patient with a de novo microdeletion spanning EYA1 and review all published cases of EYA1-related disorders. Our analysis reveals that all EYA1 variant types (truncating, missense, CNV, etc.) can cause BORSD, OTFCS, or hybrid phenotypes, firmly supporting their status as allelic disorders. Crucially, all reported OTFCS patients with EYA1 variants had renal anomalies, a feature previously considered a hallmark of BORSD. We conclude that BORSD and OTFCS constitute a single EYA1-related diagnostic continuum. This reclassification mandates the development of follow-up protocols that integrate renal, otologic, and skeletal surveillance in EYA1-related disorders, including OTFCS, and refines prognostic and genetic counseling.

To genetically analyze a prenatal specimen exhibiting mosaic 20q11.2 microdeletion syndrome with uniparental disomy of chromosome 20 (UPD20). The aim is to summarize the symptoms and prognosis of fetuses with this condition and provide guidance for genetic counseling and prenatal diagnosis in similar cases. Chromosomal karyotyping and Chromosomal Microarray Analysis (CMA) were performed on prenatal amniotic fluid specimens and peripheral blood samples from the parents. The karyotype analysis of the fetal amniotic fluid cells revealed a mosaic pattern of 46,XN,+20[80]/46,XN[20], indicating an 80 % mosaicism ratio. The CMA results showed arr20p13q13.33(61,662-62,913,645)x2-3 mos with an 11 % mosaicism ratio and arr20p12.2q13.2(9,484,368-50,586,616)x2 hmz, inherited from the mother. Through interdisciplinary team discussion and analysis of a 42-year-old pregnant woman's fetus exhibiting mosaic 20q11.2 microdeletion syndrome with mixed-type maternal UPD20, relevant genetic counseling was provided to the pregnant woman, assisting in informed decision-making. The reporting of this case is significant for summarizing the symptoms and prognosis of fetuses with this condition and guiding prenatal diagnosis and genetic counseling in similar cases.

A case of prenatal diagnosis of familial 15q13.2q13.3 microdeletion is presented. A 35-year-old, gravida 2, para 1, woman was referred for genetic counseling because of 15q13.2q13.3 microdeletion in the fetus and the mother. The carrier mother was asymptomatic and normal in phenotype. The woman underwent amniocentesis at 17 weeks of gestation because of short nasal bone on fetal ultrasound. Amniocentesis revealed a karyotype of 46,XX. Simultaneous array comparative genomic hybridization (aCGH) analysis on the DNA extracted from uncultured amniocytes revealed the result of arr [GRCh37] 15q13.2q13.3 (30,954,726-32,509,926) × 1 with a 1.56-Mb 15q13.2q13.3 microdeletion encompassing six OMIM genes of FAN1, TRPM1, MIR211, KLF13, OTUD7A and CHRNA7. Prenatal ultrasound was normal. The woman had a 4-year-old healthy daughter. Four years ago, during her first pregnancy, she underwent expanded non-invasive prenatal testing (NIPT) in the first trimester, and the result was 15q13.2q13.3 deletion. Subsequent amniocentesis revealed a karyotype of 46,XX, and aCGH analysis on uncultured amniocytes revealed no genomic imbalance. However, no further genetic test in the woman and her husband had been made. Therefore, the woman was not aware of her carrier status when she was pregnant again. During this pregnancy, subsequent aCGH analysis on the parental bloods revealed a 1.56-Mb 15q13.2q13.3 microdeletion in the mother and no genomic imbalance in the father. The woman was hesitant to keep the baby. However, following the genetic counseling, the woman's parents were advised to receive genetic testing for 15q13.2q13.3 microdeletion. The 68-year-old asymptomatic healthy grandfather carried the same 15q13.2q13.3 microdeletion, and the grandmother did not have such a microdeletion. The woman finally decided to continue the pregnancy, and a healthy 2750-g baby was delivered at term with no phenotypic abnormalities. Familial 15q13.2q13.3 microdeletion may present no phenotypic abnormalities in three generations.