EP170: When cfDNA screening deceives: A rare case of mosaicism for 46,XX/47,XXY with uniparental isodisomy and genital atypia

Abstract

Sex chromosome aneuploidy (SCA) identified on cell free DNA screening (cfDNA) presents a challenge for both prenatal counseling, and care planning for the infant after delivery. It is well understood that post-natal evaluation must include chromosomal analysis to confirm SCAs and evaluate for mosaicism. This is traditionally achieved using karyotype, with or without FISH for Y-component. The findings are important for diagnosis care planning, including for individuals with Intersex/Differences of Sex Development (I/DSD) traits. In the case of I/DSD traits, recommendations of gender of rearing are complex and require consideration of multiple pieces of evidence that include, but are not limited to, chromosomes. Despite being a screening rather than a diagnostic test, the advent of cfDNA analysis has generated added prenatal information that can often color the complex medical and psychosocial thought process of assignment of gender of rearing in cases of ambiguity at birth. I/DSD traits are defined as atypical/non-binary development of chromosomal, gonadal and/or anatomic sex. SCAs are a frequent cause of DSD, most commonly mosaic monosomy X (“Turner cells”) with Y chromosome material. Mosaic SCAs involving 47,XXY (“Klinefelter cells”) is a rare cause of DSDs. Mosaicism involving 47,XXY is typically 46,XY/47,XXY, and is not associated with genital atypia. We present a case of a patient who was initially erroneously reported as 46, XX on cfDNA screening. Post-natal confirmation using genome-wide SNP array showed instead 46,XX/47,XXY mosaicism. Furthermore, both cell lines contained uniparental isodisomy of the entire chromosome X. The infant was evaluated at 6-months-old for non-binary genital (“ambiguity”) first noted at birth. Patient was naturally conceived, born to a G1P0-P1 mother, and with normal prenatal screening and ultrasounds by report. CfDNA screen report was low risk with 46,XX, and the infant was therefore assigned female at birth. Patient was SGA with non-dysmorphic facies, and external genitalia exam notable for: Prader 3 clitorophallus, with one identifiable opening on the ventral aspect, and fused, ruggated scrotolabial folds without palpable gonads. Labs at the time of mini-puberty of infancy (8 weeks of life) provided evidence of gonadal function, despite absence of gonads on imaging: testosterone (188 ng/dL, normal range for 46,XX <10 ng/dL; normal range for 46,XY 60-400 ng/dL); AMH (27.49 ng/mL, normal range for 46,XX 0.53-7.78 ng/mL); estradiol (1.9 pg/mL, normal range for 46,XX 5-50 pg/mL); and pubertal LH and FSH concentrations. This suggested the presence of functional testicular tissue. Karyotype and SNP microarray were completed. SNP initially reported this patient as mosaic for chromosomal complement 45,X/46,XY (arr[hg19] Yp11.32q12(10,814-59,339,753)x0 [75%]). However, karyotype results were then noted to be mosaic for 46, XX [25]/47, XXY [5], with further analysis showing the patient had total uniparental isodisomy of the entire X chromosome in 100% of her cells, with deletion of the entire Y as above in 75% of cells. Uniparental isodisomy of the entire X chromosome is exceedingly rare and is due to monosomy rescue in the case of a 45,X complement, or maternal nondisjunction and lack of paternal sex chromosome complement. It is most commonly reported in the literature in 46,XX female patients with X-linked conditions such as Duchene muscular dystrophy or Fragile X. Our patient showed no true 45,X complement on her microarray, which would be expected in the setting of monosomy rescue. Such a monosomy rescue mechanism is also difficult to reconcile with the presence of Y chromosome. Our hypothesis is that the initial zygote was 47,XXY with the UPD X due to maternal non-disjunction at meiosis II. The Y was later lost in one cell line. However, it is also atypical that her X shows no evidence of crossing over if this was in fact a meiosis II non-disjunction event. Her Y also must have been lost early on in development, as her placenta likely had predominantly 46, XX cells for her cfDNA screen results to show no Y component. Less than ten patients have been previously reported with mosaicism for 46,XX/47,XXY. Of note, the majority of these patients did not have genital differences at birth, and all were assigned male. This is despite well-documented cases in the literature that mosaicism of 45,X/46,XY is commonly associated with genital atypia. Patients with mosaicism for Y containing cells are often picked up as having a Y component on their cfDNA results, where sensitivity to determine presence of a Y chromosome is 99.4%. It is important to understand cfDNA analysis as a screening test, and not a diagnostic test like a karyotype or SNP microarray. Under some circumstances, chromosomal aneuploidies, including SCAs, can be missed. Therefore, regardless of cfDNA screen results, karyotype and SNP microarray are important tests to consider in the setting of a DSD where mosaicism for a Y-containing line is a common diagnosis.