Isodicentric Yp: prenatal diagnosis and outcome in 12 cases

Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing

The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic villi sampling. However, each technology has its limitations: karyotyping has a low resolution (>5 Mb), FISH is targeted, and CMA does not detect balanced structural variations (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially, to reach a genetic diagnosis. Optical genome mapping (OGM) is an emerging technology that can detect several classes of SVs in a single assay, but it has not been evaluated in the prenatal setting. This validation study analyzed 114 samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity regions, 3 triploid genomes, 4 isochromosomes, and 1 translocation; and the method revealed the identity of 3 marker chromosomes and 1 chromosome with additional material not determined by karyotyping. In addition, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current standard-of-care methods for prenatal diagnostic testing.

Clinical and molecular cytogenetic findings and pregnancy outcomes of fetuses with isochromosome Y

BACKGROUND

The mosaic forms and clinical phenotypes of fetuses with isochromosome Y are difficult to predict. Therefore, we summarized the cases of nine fetuses with isochromosome Y identified in prenatal diagnosis with a combination of molecular cytogenetic techniques, providing clinical evidence for prenatal genetic counseling.

METHODS

The prenatal diagnosis and pregnancy outcomes of nine fetuses with isochromosome Y were obtained by a  retrospective analysis. Isochromosome Y was identified prenatally by different approaches, such as conventional karyotyping, chromosomal microarray analysis (CMA), quantitative fluorescent polymerase chain reaction (QF-PCR) and fluorescence in situ hybridization (FISH).

RESULTS

Seven idic(Y) fetuses and two i(Y) fetuses were identified. One fetus was complete for i(Y)(p10), and the rest with 45,X had mosaic forms. A break and fusion locus was identified in Yp11.3 in one fetus, in Yq11.22 in six fetuses and in Yp10 in two fetuses. The CMA results suggested that different deletions and duplications were found on the Y chromosome. The deletion fragments ranged from 4.7 Mb to the entire Y chromosome, and the duplication fragments ranged from 10.4 to 18.0 Mb. QF-PCR analysis suggested that the AZF region was intact in one fetus, four fetuses had AZFb+c+d deletion, one fetus had AZFa+b+c+d deletion, and one fetus had AZFc+d deletion. Finally, four healthy male neonates were delivered successfully, but the parents of the remaining five fetuses, including three healthy and two unhealthy fetuses, chose to terminate their pregnancies.

CONCLUSION

The fetus and neonate phenotype of prenatally detected isochromosome Y usually is that of a normally developed male, ascertained in the absence of other indicators of a fetal structural anomaly. Our study provides clinical reference materials for risk assessment and permits better prenatally counseling and preparation of parents facing the birth of isochromosome Y fetuses.

High-level mosaicism for 45,X in 45,X/46,X,idic(Y)(q11.2) at amniocentesis in a pregnancy with a favorable outcome and postnatal progressive decrease of the 45,X cell line

OBJECTIVE

We present prenatal diagnosis of high-level mosaicism for 45,X in 45,X/46,X,idic(Y)(q11.2) at amniocentesis in a pregnancy with a favorable outcome and postnatal progressive decrease of the 45,X cell line.

CASE REPORT

A 36-year-old, gravida 4, para 3, woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 45,X[22]/46,X,idic(Y)(q11.2)[4]. Prenatal ultrasound was unremarkable, and the fetus had normal male external genitalia. Repeat amniocentesis was performed at 20 weeks of gestation, and the second amniocentesis revealed a karyotype of 45,X[24]/46,X,idic(Y)(q11.2)[3]. Simultaneous interphase fluorescence in situ hybridization (FISH) analysis on uncultured amniocytes revealed that 60% (62/103 cells) were Y-deleted cells. After genetic counseling, the parents decided to continue the pregnancy, and a 3020-g male baby was delivered with a body length of 52 cm, normal male genital organs and no phenotypic abnormalities. The karyotypes of cord blood, umbilical cord and placenta were 45,X[20]/46,X,idic(Y)(q11.2)[20], 45,X[31]/46,X,idic(Y)(q11.2)[9] and 45,X[40], respectively. At age one month, FISH analysis on urinary cells and buccal mucosal cells revealed 11.5% (7/61 cells) and 13.6% (16/118 cells), respectively for mosaicism for the Y-deleted cells. At age five month, the karyotype of peripheral blood was 45,X[9]/46,X,idic(Y)(q11.2)[31]. FISH analysis on buccal mucosal cells showed no abnormal Y-deleted cell (0/101 cells). At age 11 month, the karyotype of peripheral blood was 45,X[5]/46,X,idic(Y)(q11.2)[35]. FISH analysis on 102 buccal mucosal cells showed no abnormal signals. The infant was doing well with normal physical and psychomotor development.

CONCLUSION

High-level mosaicism for 45,X in 45,X/46,X,idic(Y)(q11.2) at amniocentesis can be associated with a favorable outcome and progressive decrease of the 45,X cell line.

45,X/46,X,psu idic(Y)(q11.2) in a phenotypically normal male with short stature: a case report

We report a case of 15-yr-old phenotypically normal male with short stature associated with the chromosomal abnormalities of 46,X,psu idic(Y)(q11.2)/45,X. At 3 yr of age, he underwent urethroplasty for scrotal hypospadias. At 15 yr of age, he was referred to our hospital due to short stature (–3.71 SD). The results of blood examination were mostly normal. A radiological examination revealed his bone age was 15.7 yr (based on the TW2-RUS method). Chromosome analysis of peripheral lymphocytes revealed 46,X,psu idic(Y)(q11.2)[16]/45,X[14], and array comparative genomic hybridization (aCGH) showed a large deletion of Yq which was located distal to the Y chromosome growth-control gene (GCY) region. It is likely that these structural abnormalities in the Y chromosome were responsible for the short stature. This case might provide new insights regarding GCY and emphasizes the importance of chromosome analysis in not only females but also males with short stature, especially when associated with genital anomalies.

Prenatal genetic analysis and differential pregnancy outcomes of two de novo cases showing mosaic isodicentric Y chromosome

Background

Fetal cells collected from the amniotic fluid of two pregnant women indicated sex chromosome abnormalities. Therefore, we performed G-banded chromosome karyotype analysis, single nucleotide polymorphism array (SNP array), fluorescence in situ hybridization (FISH), and sequence-tagged sites (STS) analysis of the Y chromosome to determine the rare molecular genetics of the two fetuses.

Case presentation

The karyotypes of the fetuses from patients 1 and 2 were mos 45,X[92]/46,X,+idic(Y)(q11.21)[8] and mos 45,X[20]/46,X,+idic(Y)(q11.223)[80], respectively. Fetus 1 had a 7.76 Mb deletion in Yq11.222q11.23 and a 15.68 Mb duplication in Yp11.2q11.21. Fetus 2 had 21 Mb of repetitive segments in Yp11.3q11.223. Azoospermia factor (AZF) detection by STS analysis revealed a missing AZFb+c region in fetus 1 and three functional AZF regions in fetus 2. The isodicentric Y chromosome (idic (Y)) in both fetuses arose de novo. The pregnancy of patient 1 was terminated, whereas the fetus of patient 2 was delivered and is now 10 months old with normal appearance and growth.

Conclusion

A combination of technologies such as chromosome karyotyping, FISH, SNP arrays, and STS analysis of the Y chromosome is important in prenatal diagnosis to reduce birth defect rates and improve the health of the Chinese population.

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.

Discrepancy of QF-PCR, CMA and karyotyping on a de novo case of mosaic isodicentric Y chromosomes

Background

Isodicentric chromosomes are the most frequent structural aberrations of human Y chromosome, and usually present in mosaicism with a 45, X cell line. Several cytogenetic techniques have been used for diagnosing of uncommon abnormal sex chromosome abnormalities in prenatal cases.

Case presentation

A 26-year-old healthy woman was referred to our centre at 24 weeks of gestation age. Ultrasound examination indicated she was pregnant with imbalanced development of twins. Amniocentesis was referred to the patient for further genetic analyses. Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) indicated the existence of an extra Y chromosome or a structurally abnormal Y chromosome in primary amniotic cells. Chromosome microarray (CMA) analysis based on Comparative Genomic Hybridization (aCGH) platform was performed and identified a 10.1 Mb deletion on Y chromosome in 8-days cultured amniotic cells. Combined with the data of QF-PCR and aCGH, karyotyping and fluorescence in situ hybridization (FISH) revealed a mosaic cell line of 45,X[27]/46,X, idic(Y)(q11.22) [14] in fetus.The karyotyping analysis of cord blood sample was consistent with amniotic cells. The parental karyotypes were normal, which indicated this mosaic case of isodicentric Y (idicY) chromosomes of the fetus was a de novo case.

Conclusion

Several approaches have been used for the detection of numerical and structural chromosomal alterations of on prenatal cases. Our report supported the essential role of incorporating multiple genetic techniques in prenatal diagnosing and genetic counseling of potential complex sex chromosomal rearrangements.

Application of molecular cytogenetic techniques to characterize the aberrant Y chromosome arising de novo in a male fetus with mosaic 45,X and solve the discrepancy between karyotyping, chromosome microarray, and multiplex ligation dependent probe amplification

We present a rare male fetus with karyotype of mosaic 45,X that comprises two types of aberrant Y chromosomes arising de novo (Yq12 deletion and isodicentric Yq11.22). Both types of the aberrant Y chromosomes lack the AZFc region which are expected to result in oligospermia but unaffected male external genitalia. Genetic analyses by karyotyping, chromosome microarray (CMA), and multiplex ligation-dependent probe amplification (MLPA) for the fetus revealed conflicting results. Additional molecular cytogenetics tools including fluorescence in situ hybridization (FISH) and multicolor banding (mBAND) were performed, which help resolving the discrepancy and delineated the composition of the aberrant Y chromosomes. This report highlighted the importance of incorporating multiple genetic technologies for accurate characterization of complex chromosomal rearrangements, which aid in the prenatal diagnosis and genetic counseling.

Y chromosome palindromes and gene conversion

The presence of large and near-identical inverted repeat sequences (called palindromes) is a common feature of the constitutively haploid sex chromosomes of different species. Despite the fact palindromes originated in a non-recombining context, they have evolved a strong recombinational activity in the form of abundant arm-to-arm gene conversion. Their independent appearance in different species suggests they can have a profound biological significance that has yet to be fully clarified. It has been theorized that natural selection may have favored palindromic organization of male-specific genes and that the establishment of intra-palindrome gene conversion has strong adaptive significance. Arm-to-arm gene conversion allows the efficient removal of deleterious mutations, increases the fixation rate of beneficial mutations and has played an important role in modulating the equilibrium between gene loss and acquisition during Y chromosome evolution. Additionally, a palindromic organization of duplicates could favor the formation of unusual chromatin structures and could optimize the use of gene conversion as a mechanism to maintain the structural integrity of male-specific genes. In this review, we describe the structural features of palindromes on mammalian sex chromosomes and summarize different hypotheses regarding palindrome evolution and the functional benefits of arm-to-arm gene conversion on the unique haploid portion of the nuclear genome.

A non-mosaic isodicentric Y chromosome resulting from breakage and fusion at the Yq pseudo-autosomal region in a fetus

The dicentric Y chromosomes are the most commonly found in the structural aberration of Y chromosome. If the dicentric chromosome has completely symmetric arms, it is considered an isodicentric chromosome. The sites of breakage and fusion at Yp and Yq are variable, but breakage and fusion at the pseudo-autosomal region has never been reported. Herein we reported identification de novo isodicentric (Yq12) in a fetus. The fusion occurred at Yq pseudo-autosomal region very close the telomere and resulted in duplication of Y chromosome. The baby was grossly normal at birth. In conclusion, isodicentric Y chromosome could result from breakage and fusion at the Yq pseudo-autosomal region.

Is there a correlation between the proportion of cells with isodicentric Yp at amniocentesis and phenotypic sex?

OBJECTIVES

(1) To present a case with prenatally detected idic Yp. (2) To review literature to assess if there is a correlation between the proportion of amniocytes with idic Yp and phenotypic sex.

METHODS

Seventeen cases were reviewed.

RESULTS

Amniocentesis was done due to positive integrated prenatal screening result. Interphase FISH was normal for chromosomes 13, 18, and 21, but mosaic for cell lines with 1 X and 0 to 2 copies of DYZ3, SRY, or DYZ1(Yq12). Amniocytes had 45,X[28]/46,X,idic(Y)(q11.2)[2].ish idic(Y)(DYZ3 + +, SRY + +). An apparently normal female was born at 37 weeks. The umbilical cord had 45,X[50], but cord blood had 45,X[17]/46,X,idic(Y)[31]/47,X,idic(Y)x2[2]. Review of 17 cases showed that 13 cases with 20 to 100% cells with idic Yp all had a male phenotype. Two cases with 3 and 7% of idic Yp cells had a female phenotype. Two cases with 45,X only at prenatal diagnosis but idic Yp detected postnatally were phenotypic male.

CONCLUSION

(1) We present the first report of prenatally detected idic Yp and Yq12 resulting in an apparently normal female at birth. (2) Finding of > 20% of G-banded amniocytes with idic Yp in the absence of other indicators of foetal structural anomalies seems to correlate with phenotypically normal male in most cases.

A case of mosaic Klinefelter syndrome associated with isodicentric Yp

We describe a case of mosaic Klinefelter syndrome demonstrating an isodicentric Y chromosome. A 70-year-old man visited our outpatient clinic complaining of dysuria resulting from atrophy of the penis. His height was 170 cm and his weight was 60 kg. A serum hormonal analysis revealed hypergonadotropic hypogonadism. A chromosomal analysis with fluorescence in situ hybridization revealed four cell lines in which the karyotypes were 47,XXY, 46,XY, 46,XX and 47,XX,idic(Y) (q11.2). To the best of our knowledge this is the first case of mosaic Klinefelter syndrome bearing an isodicentric Y chromosome. The origin of the isodicentric Y is discussed. (Reprod Med Biol 2008; 7: 177-180).