Clinical and cytogenomic studies in a case of infertility associated with a nonmosaic dicentric Y chromosome

Whole-genome sequencing identifies new candidate genes for nonobstructive azoospermia

BACKGROUND

Genetic causes that lead to spermatogenetic failure in patients with nonobstructive azoospermia (NOA) have not been yet completely established.

OBJECTIVE

To identify low-frequency NOA-associated single nucleotide variants (SNVs) using whole-genome sequencing (WGS).

MATERIALS AND METHODS

Men with various types of NOA (n = 39), including samples that had been previously tested with whole-exome sequencing (WES; n = 6) and did not result in diagnostic conclusions. Variants were annotated using the Ensembl Variant Effect Predictor, utilizing frequencies from GnomAD and other databases to provide clinically relevant information (ClinVar), conservation scores (phyloP), and effect predictions (i.e., MutationTaster). Structural protein modeling was also performed.

RESULTS

Using WGS, we revealed potential NOA-associated SNVs, such as: TKTL1, IGSF1, ZFPM2, VCX3A (novel disease causing variants), ESX1, TEX13A, TEX14, DNAH1, FANCM, QRICH2, FSIP2, USP9Y, PMFBP1, MEI1, PIWIL1, WDR66, ZFX, KCND1, KIAA1210, DHRSX, ZMYM3, FAM47C, FANCB, FAM50B (genes previously known to be associated with infertility) and ALG13, BEND2, BRWD3, DDX53, TAF4, FAM47B, FAM9B, FAM9C, MAGEB6, MAP3K15, RBMXL3, SSX3 and FMR1NB genes, which may be involved in spermatogenesis.

DISCUSSION AND CONCLUSION

In this study, we identified novel potential candidate NOA-associated genes in 29 individuals out of 39 azoospermic males. Note that in 5 out of 6 patients subjected previously to WES analysis, which did not disclose potentially causative variants, the WGS analysis was successful with NOA-associated gene findings.

A rare karyotype of nonmosaic isodicentric (Y) (p11.31) with azoospermia and short stature

Chromosome aberration is one of the common causes of male infertility. Isodicentric chromosome is a chromosomal aberration in which two arms of a chromosome are identical in morphology and genetics and connected by two centromeres. We firstly reported a case of infertile male with nonmosaic 46, X, idic (Y) (qter-p11.31::p11.31-qter) but with the sex-determining region Y (SRY). The broken site is the chromosome Y (p11.31). The patients' clinical phenotype was azoospermia and short stature. Fluorescence in situ hybridisation (FISH), chromosomal microarray comparative genomic hybridisation (array CGH) and related molecular analysis were performed. Azoospermia of this case may be caused by the abnormal chromosome structure, which leads to abnormal chromosome synapsis in spermatogenesis. Loss of genes in PAR1 and gain of genes copies in azoospermia factor (AZF) region on the Y chromosome may also contribute to the pathogenesis of azoospermia.

Clinical, cytogenetic, and molecular findings of isodicentric Y chromosomes

Background

Isodicentric Y chromosomes [idic(Y)] are one of the most common structural abnormalities of the Y chromosome. The prenatal diagnosis of isodicentric Y chromosomes is of vital importance, and the postnatal phenotypes vary widely. Therefore, we present six patients prenatally diagnosed with isodicentric Y chromosomes and review the literature concerning the genotype-phenotype correlations.

Method

The clinical materials of six patients were obtained. Cytogenetic and molecular approaches were carried out for these six patients.

Results

Isodicentric Y chromosomes were found in all sixpatients. Among them, four patients presented with a mosaic 45,X karyotype, one patient had a 46,XY cell line, and one patient was nonmosaic. Five of these six isodicentric Y chromosomes had a breakpoint in Yq11.2, and the other had a breakpoint in Yp11.3. The molecular analysis demonstrated different duplications and deletions of the Y chromosome. Finally, three patients chose to terminate the pregnancy, two patients gave birth to normal-appearing males, and one patient was lost to follow-up.

Conclusion

The incorporation of multiple cytogenetic and molecular techniques would offer a more comprehensive understanding of this structural chromosomal abnormality for genetic counselling.

Molecular cytogenetic characterization of an isodicentric Yq and a neocentric isochromosome Yp in an azoospermic male

Isodicentric Y chromosomes are considered one of the most common structural abnormalities of the Y chromosome. Neocentric marker chromosomes, with neocentromeres, have drawn increasing attention in recent years. The present study reported an azoospermic male with a neocentric isochromosome Yp, neo(Yp), and an isodicentric Yq, idic(Yq). The karyotype was analyzed using G‑banding, chromosome microarray analysis (CMA), and fluorescence in situ hybridization (FISH) with various detection probes, including sex‑determining region on the Y chromosome (SRY) and Y centromeric, applied at the same time. G‑banding initially revealed the karyotype 47,X,i(Y)(q10),+mar. CMA indicated the presence of an extra Y chromosome, seemingly equivalent to 47,XYY males. FISH delineated the existence of two centromeres on the idic(Yq). For the marker chromosome, two SRY signals were detected instead of the Y‑specific centromere signal, and a visual centromere was observed. This indicated the possible existence of a neocentromere in the marker chromosome, located in the connected region in Yp11.2 band. Finally, the patient's karyotype was established as 47,X,idic(Y)(p11.2), neo(Y)(pter→Yp11.2::Yp11.2→pter). The findings suggested that both idic(Yq) and neo(Yp) could be the main causes of the patient's azoospermia, despite the fact that the partial disomy of Ypter to Yp11.2 did not lead to any major malformations. The present study not only improves the understanding of karyotype/phenotype relationships between neocentric marker Y chromosomes and male infertility, but also supports the hypothesis that the combined application of molecular cytogenetic analysis could aid in reliably confirming breakpoints, origins, and the constitution of the marker chromosomes.

A Rare Mosaic Karyotype of 45,X/46,X,psu idic(Y)(p11.32)/46,XY with SHOX Haploinsufficiency, External Male Genitalia, and Short Stature

In this case study, we describe a 3-year-old boy who was referred to the Inonu University Hospital with short stature complaint. His height was 86 cm (-2.96 SDS), weight was 12 kg (-2.43 SDS), and head circumference was 46.5 cm (-2.34 SDS). Chromosomal analyses were performed on cultured peripheral blood lymphocytes of the patient and his parents and showed the patient's karyotype mos 45,X[20]/46,X,idic(Y)(p11.32)[29]/46,XY[1]. The karyotypes of the parents were normal. Subsequently, specific FISH probes were hybridized to the related regions of the sex-determining region Y (SRY), centromere X/Y (CEP X/Y), and short stature homeobox (SHOX) genes. Simultaneous SNP array-CGH was conducted. As to our knowledge, we present the first patient with mosaic isodicentric Y chromosome with 3 different cell lines and normal male external genitalia. Our results suggest that it would be beneficial to study cytogenetic and molecular cytogenetic methods together for better diagnostic accuracy and treatment.

A de novo derivative Y chromosome (partial Yq deletion and partial duplication of Yp and Yq) in a female with disorders of sex development

We report an atypical disorders of sex development (DSD) case with no mutation of SYR gene but partial Yq deletion and partial duplication of Yp and Yq. This case emphasizes duplicated region Yp11.2→Yq11.223 with partial deletion of Yq11.223→Yqter most probably perturbed the sex differentiation and led to female phenotype.

Hypospadias in a male infant with an unusual mosaic 45,X/46,X,psu idic(Y)(p11.32)/46,XY and haploinsufficiency of SHOX: A case report

A male newborn presented with hypospadias and differential testicular volumes. Short femur length was detected four times during pregnancy, at 23, 31, 32 and 33 weeks, by ultrasonographic examination. Chromosome analysis was performed on peripheral lymphocytes obtained from the infant and his parents. Fluorescent in situ hybridization (FISH), using sex determining region Y (SRY)/DXZ1 and DYZ3 probes, was performed to verify the deletion of the SRY gene (located on Yp11.3 region) and the activation of Y chromosomal centromeres. Single nucleotide polymorphism (SNP)-array comparative genomic hybridization (CGH) was used to detect copy number variations in the infant. The results revealed a ~2.2 Mb mircodeletion on Yp11.32 containing the short stature homeobox (SHOX) gene. According to the above examinations, the abnormal Y chromosome of the patient was identified as a dicentric derivate of the Y chromosome with pseudoinactivation of one of the two centromeres. The karyotype is therefore: 45,X[20]/46,X,idic(Y)(p11.3).ish psu idic(Y)(p11.3) (SRY++, DYZ3++). array Yp11.32 (118,551–2,393,500)x0[26]/46,X,ishY(SRY+, DYZ3+)[4]. The combination of cytogenetic, FISH and SNP-array CGH technologies was beneficial for diagnosing the karyotype accurately, predicting the prognosis, and preparing an effective treatment plan for the patient.

FISH and array CGH characterization of de novo derivative Y chromosome (Yq duplication and partial Yp deletion) in an azoospermic male

This study presents a 28-year-old infertile male who was referred to the cytogenetic laboratory for chromosomal analysis after 4 years of regular unprotected intercourse in whom non-obstructive azoospermia was revealed. Standard cytogenetic G-banding was performed on metaphase spreads and a de-novo karyotype 46,X,der(Y)(q11.22;p11.3) was identified. This analysis was followed by flourescence in-situ hybridization(FISH) and array comparative genomic hybridization (aCGH). Finally, the patient's karyotype was identified as 46,X,der(Y)(qter→q11.221::p11.31→qter).ish der(Y) (qter+,pter-,SHOX+,SRY+,Ycen+,DYZ3+;DYZ1+,qter+).arrYq11.221q12(14,448,863-59,288,511) x2, Yp11.32p11.31(104,062-266,388) x0. It is proposed that de-novo derivative monocentric Y chromosome with duplicated region Y qter→q11.221::p11.31→qter with partial deletion of Yp PAR1 region most probably can perturb the conjugation of sex chromosomes during first meiotic division of spermatogenic arrested differentiation (development).