46,XY/46,XY Chimerism: Prenatal Presentation and Postnatal Outcome

ABSTRACT

Background

Human chimerism is rare, and most prevalent with discordant chromosomal sex. We report a male 46,XY/46,XY chimera, born through a spontaneously conceived pregnancy to a healthy 32‐year‐old G1P0 Indian, African, and Scottish female and her 34‐year‐old healthy Chinese partner. The prenatal presentation and postnatal outcomes are described.

Methods

A prenatal cell‐free DNA screening test, amniocentesis with QF‐PCR and SNP microarray, and postnatal microarray and FISH study on peripheral blood, placenta, and umbilical cord were used to evaluate chimerism.

Results

The prenatal cell‐free screening test revealed high risk for triploidy/vanishing twin, but there was no confirmation from early ultrasound. Subsequent QF‐PCR on amniocytes showed a profile suggestive of a tetragametic chimera. G‐banding showed a 46,XY karyotype. A SNP microarray detected two copy number gains of uncertain significance on chromosome 6q, derived from the father who was a balanced carrier of ins(6;11). A postnatal microarray and FISH study confirmed the presence of two cell lines, each with a 46,XY complement but with different submicroscopic structural changes including recombinant and insertion changes. Clinical evaluations of the child at birth and 8 weeks of age were coordinated to detect the presence of chimeric symptoms.

Conclusion

With a confirmed incidental finding of 46,XY/46,XY chimerism, we present that underlying same‐sex chimerism may be under‐recognized.

This study reports a rare case of same‐sex chimerism identified incidentally during prenatal screening, highlighting the importance of comprehensive genetic testing. The findings underscore the complexity of chimerism diagnosis and emphasize the need for increased awareness and research in this field.

1. Introduction

Human chimerism is a rare phenomenon, with limited reports of its occurrence in current medical literature. The first case of chimerism was described in 1962 (Gartler et al. 1962), and there have been subsequently around 100 reported cases following that first presentation (Madan 2020).

Various forms of chimerism are possible (Madan 2020). In artificial chimerism, a person receiving tissue transfusions or transplants from another individual may permanently assimilate the donated cells into their body later in life. This is far less common now with radiation treatment of donated products. Contrarily, constitutional chimerism is present from birth, which can be further classified into partial or whole‐body chimerism. Partial chimerism can be microchimerism, from absorption of fetal cells by the pregnant mother and vice versa, or twin chimerism, produced by feto‐fetal transfusions during the prenatal period. Fusion chimerism is caused by the fusion of two or more genetically distinct zygotes in one person.

The presentation of chimerism varies largely between individuals, ranging from no signs or symptoms to a constellation of traits. Classically, the most commonly expressed signs include hyper‐ or hypopigmentation, heterochromia, or ambiguous genitalia. The presence of ambiguous genitalia is a substantial influence for the focus of current literature on cases with discordant chromosomal sex of coexisting XX and XY chromosomal complements. However, most chimeras are undetected, as is the case with concordant sex chimeras who are often phenotypically normal and discovered by chance. Thus, the incidence of chimerism remains unknown.

In our case, we present the prenatal and postnatal outcomes of a same‐sex male chimera, incidentally discovered through genetic testing, further signifying that same‐sex chimerism is likely underreported.

2. Case Report

2.1. Prenatal

This was a spontaneously conceived pregnancy, from a 32‐year‐old G1P0 woman of Indian, African, and Scottish descent and a 34‐year‐old healthy partner of Chinese descent. The family history was significant for one case of autism and one case of learning disability on the paternal side. There was no exposure to alcohol, smoking, or recreational drugs. The woman had no other medications besides prenatal vitamins and DHA supplementation. Their past medical history was unremarkable and healthy, and there was no family history of spontaneous miscarriages or genetic conditions.

2.2. Postnatal

The patient is a male, born at 41 + 2 weeks through C‐section due to fetal tachycardia and chorioamnionitis. His birth weight was 3654 g (55–60th percentile), length was 50 cm (25th percentile), and head circumference was 35 cm (50th percentile). APGAR scores were 2 and 9, at 1 and 5 min, respectively. Presenting flat and non‐vigorous at birth, he required positive pressure ventilation and CPAP for 20 min. He had delayed passage of meconium at 36 h following a glycerin suppository, with dry skin on his cheeks bilaterally and cradle cap. He has been otherwise well with no other concerns, and his development has been on track. A blood group antibody screen was also conducted, and there were no abnormalities with ABO and Rh factor. He has three hair whorls spaced equally on the top and midline of his scalp in a horizontal line orientation (Figure 1E) and a slate gray nevus on his buttock. At his 3‐year pediatrician appointment, he was developmentally on track, with mild eczema, hazelnut and sesame allergies, and an innocent heart murmur after an unremarkable echocardiogram.

FIGURE 1.

(A) Representative short tandem repeat profiles from amniocytes for regions (right to left) of the sex chromosomes (AMEL), ratio of chromosome 3 to X (TAF9L), chromosomes X, Y, 13, 18 and 21 (DXS6803, SRY, D13S252, D18S386, D21S11, respectively) showing the presence of an equal ratio of chromosome X to Y (AMEL), a 2:1 ratio for chromosome 3 to X (TAF9L), two distinct X chromosomes (DXS6803), the SRY locus (SRY), and two distinct maternal alleles with one or two distinct paternal alleles for chromosomes 13 (D13S252), 18 (D18S386) and 21 (D21S11). (B) Representative microarray profiles from amniocytes (left to right): (left panel) Representative example of chromosome 1 microarray result showing no copy number change, with a B‐allele frequency plot showing five distinct tracks which equates to four genotypes. A similar pattern was observed across all of the autosomes; (center panel) the B‐allele plots of the X chromosomes show a pattern consistent with two unique X chromosome genotypes (3 tracks), while the pseudoautosomal regions are plotted at termini of Xp and Xq and show a pattern consistent with four genotypes (5 tracks); (right panel) the Y chromosome pattern is consistent with a single genotype (2 tracks). (C) Microarray profile of chromosome 6 obtained from postnatal peripheral blood showing interstitial gains of 6q14.1 (3.0 Mb) and 6q16.2 (1.3 Mb). Complex B‐allele frequency plots were observed across all autosomes and the X chromosome. The presence of 9 B‐allele tracks across the majority of most chromosomes was suggestive of chimeric zygote fusion with ~25% mosaicism for cell line 1 (2 copies of 6q14.1 and 6q16.2) relative to ~75% of cell line 2 (3 copies of 6q14.1 and 6q16.2) as determined with the help of fluorescence in situ hybridization (FISH). (D) Inverted DAPI images with FISH utilizing probes specific to 6q14.1 (RP11‐17086 in Spectrum green) and 6q16.2 (RP11‐464P14 in Spectrum orange); (left panel) Cell line 1 shows balanced insertional translocation of 6q14.1 and 6q16.2 into derivative chromosome 11 and loss of the 6q14.1 and 6q16.2 segments from the derivative chromosome 6 in 50 of 200 nuclei; (right panel) Cell line 2 shows an unbalanced gain of 6q14.1 and 6q16.2 on the derivative 11 together with normal hybridization patterns on the normal chromosomes 6 in 150 of 200 nuclei. (E) Photograph of proband's triple hair whorl.

3. Methods

Consent was obtained as per Trillium Health Partners research ethics board.

The couple had self‐paid for prenatal cell‐free screening using single nucleotide polymorphism (SNP) technology (Panorama, Natera). An anatomy scan ultrasound and fetal echocardiogram were carried out at 19 + 4 weeks. DNA from direct amniotic fluid (27 weeks gestation) and parental blood samples was extracted using Qiamp DNA Mini Kit, or Puregene DNA Isolation Kit (Qiagen), respectively. Amniotic fluid was cultured in Complete AmnioMax media (ThermoFisher). Rapid aneuploidy testing was performed by quantitative fluorescence PCR (QF‐PCR) on DNA from direct amniotic fluid using the Q*STR kit (Elucigene) and resolved by capillary electrophoresis on the 3100 Genetic Analyzer (Applied Biosystems). Ratios of short tandem repeats (STR) alleles were compared relative to the parental specimens. Maternal cell contamination of the amniotic fluid sample was excluded by comparison of the fetal and maternal QF‐PCR profiles. Zygosity testing was performed similarly. Chromosomal SNP microarray analysis was performed using the Infinium CytoSNP 850K platform (Illumina) and analyzed using BlueFuse (Illumina) and Alissa (Agilent) software. Complex B‐allele frequency patterns were assessed using guidance from Conlin et al. (2010). G‐banded chromosome analysis and fluorescence in situ hybridization (FISH) were performed using traditional methods. FISH on cultured amniotic fluid cells and parental blood samples used probes RP11‐170B6 for chromosome region 6q14.1 labeled with Spectrum Green dye (Vysis), and RP11‐484P14 for chromosome region 6q16.2 labeled with Spectrum Orange dye (Vysis) at The Centre for Applied Genomics (Toronto, Canada). Clinical evaluations of the child at birth and 8 weeks of age were coordinated to detect the presence of chimeric symptoms.

4. Results

The prenatal cell‐free screening revealed a high risk for triploidy/vanishing twin. Further analysis with the anatomy scan ultrasound showed no evidence of a vanishing twin and an unremarkable fetal echocardiogram. The couple then underwent an amniocentesis, which revealed a dispermic chimera with zygote/embryo fusion, resulting in a tetragametic chimera with four unique alleles in the amniotic fluid through qfPCR, suggesting an XY/XY chimerism based on fetal epidermal cells from amniocentesis (Figure 1A). The pattern showed two different maternal alleles and two different paternal alleles, in comparison to the parental blood samples. A G‐banded chromosome analysis also detected a small population of tetraploid cells. Within the two flasks of cultured amniocyte cells, the majority of the individual cells showed 46,XY complement. Flask A showed 15% of cells with a 92,XXYY karyotype and flask B showed 4% of the 92,XXYY karyotype. The tetraploidy was believed to be an artifact of the amniocyte tissue culture process. The SNP microarray showed B‐allele frequencies across the autosomes and pseudoautosomal regions of the X and Y chromosomes with 5 SNP tracks, consistent with 50:50 chimerism due to zygote/embryo fusion (Conlin et al. 2010) (Figure 1B). Furthermore, the SNP microarray revealed two copy number gains on chromosome 6 at 6q14.1 and 6q16.2q16.3 (arr[GRCh37] 6q14.1(78718367_81745936)x2~3,6q16.2q16.3(99672014_100936628)x2~3). The 3.0 Mb gain of 6q13.1 and 1.3 Mb gain of 6q16.2q16.3 encompassed 8 and 9 protein coding genes, respectively. None of these genes were intersected by the breakpoints, nor were they known to be triplosensitive. The clinical significance of these gains was uncertain. Ultrasounds and echocardiogram done during the pregnancy showed the growth was on track, except for a slight growth lag at 33 + 6 weeks.

A QF‐PCR postnatally showed four alleles in multiple tissues, including the placenta, umbilical cord, and peripheral blood, similar to the prenatal results with two distinct maternal and paternal chromosome sets. A microarray showed a tetragametic chimerism with a mixture of two cell lines (estimated to be present at a 25:75 ratio). Gains of 6q14.1 and 6q16.2q16.3 were observed but could not be clearly attributed to cell line 1 versus cell line 2 by the microarray analysis (Figure 1C). The FISH analysis showed the presence of two cell lines (Figure 1D). In one cell line, there was 25% of the blood demonstrating a balanced insertion of 6q14.1 and 6q16.2q16.3 into chromosome 11p, identical to the father who was also a balanced carrier of ins(11;6). In the other cell line, 75% of the blood showed an unbalanced insertion of 6q14.1 and 6q16.2q16.3 into chromosome 11p, resulting in gain of these regions, which are of uncertain clinical significance. Consistent with our findings, the child demonstrated chimerism with a karyotype designation of chi 46,XY/46,XY.ish der(11)ins(11;6)(p11.2;q14.1q14.1)ins(11;6)(p11.2;q16.2q16.3)(RP11‐170B6+,RP11‐484P14+)dpat[150/200]/ins(11;6)(p11.2;q14.1q14.1)ins(11;6)(p11.2;q16.2q16.3)(RP11‐170B6+,RP11‐484P14+;RP11‐170B6‐,RP11‐484P14‐)pat[50/200].

5. Discussion

We report a case of concordant sex chimera in a child discovered incidentally through follow‐up of an inconclusive result on self‐paid prenatal cell‐free screening. To the best of our knowledge, only a few cases of same‐sex chromosomal chimerism have been reported in the medical literature. One notable case involved Karen Keegan (Wolinsky 2007). In 1998, during a pretransplant tissue typing for a kidney transplant, it was discovered that her three sons were not biologically related to her (Wolinsky 2007). Further investigation revealed that Karen was a chimera, with two different complements of DNA (Wolinsky 2007). Her blood cells contained one complement of DNA, while her reproductive organs contained another (Wolinsky 2007). This case was the first to demonstrate the complexity and challenges of determining genetic relationships among family members, and even within the same individual. Similarly, another high‐profile case involved Lydia Fairchild, a woman from Washington state, who made headlines in 2002 when a DNA test revealed that she was not the biological mother of her children (Darby 2021). Despite having given birth to the children, the DNA testing indicated that she was not a match (Darby 2021). Further investigation revealed that Lydia was a same‐sex chimera, with two distinct cell populations in her body (Darby 2021). One population had her DNA, while the other had DNA from an absorbed twin, specifically in her cervix, and presumably in the germ cells that gave rise to her offspring, challenging the understanding of maternal identity and genetic testing (Darby 2021). Both of these cases highlight the clinical variability and challenges in diagnosing same‐sex chromosomal chimerism.

Prenatal cell‐free screening, specifically on single nucleotide polymorphism (SNP) platforms, has emerged as a method for inadvertently identifying cases of chimerism during pregnancy. This screening method involves the extraction and analysis of cell‐free placental DNA circulating in the mother's blood and leveraging SNP‐based analysis by examining the individual variations in single nucleotides within the placental DNA, typically performed during the first trimester of pregnancy. Through this high‐resolution genotyping technique, subtle genetic differences associated with chimerism, which involve the presence of cells from distinct origins within an individual, can be detected. The use of SNP platforms in prenatal cell‐free screening allows for the precise identification of specific genetic markers, enabling healthcare professionals to uncover unexpected instances of chimerism. This incidental discovery not only underscores the importance of comprehensive prenatal genetic testing but also highlights the intricate complexities of early fetal development. By identifying chimerism, healthcare providers can ensure the timely management and appropriate counseling for expectant mothers, facilitating optimal care for both the mother and the developing fetus.

Recognizing and diagnosing same‐sex chimerism can be a challenging process. In itself, chimerism is a rare phenomenon, and with sex‐concordant chimeras, it becomes more difficult to identify them based on external physical characteristics alone or even with advanced molecular cytogenetic techniques. Additionally, chimerism can occur at varying levels, from whole‐body chimerism to limited regions or organs, adding to the complexity of detection. The lack of awareness and limited research and medical literature on chimerism, particularly in the context of same‐sex chimerism, contributes to the difficulty in recognizing and diagnosing these cases. The development of more advanced genetic testing techniques and increased understanding of chimerism will likely improve the ability to identify and diagnose same‐sex chimerism more effectively in the future.

When chimerism is suspected, comprehensive evaluation and clinical management are crucial. In our case, the concordance of the chromosomal patterns in the peripheral blood, placental, and umbilical cord samples suggests that the chimeric cells are relatively widespread throughout the body. Further investigation may include imaging studies such as magnetic resonance imaging (MRI) to assess the internal organs and the extent of chimerism if there are clinical symptoms to indicate concerns. A skin biopsy may also be considered to provide additional insight into the tissue distribution of the chimeric lines—a limitation in our study. In terms of clinical management, an interdisciplinary approach involving specialists in endocrinology, genetics, and pediatric urology is essential. The primary goal is to assess the overall health of the child and address any immediate medical concerns, particularly any autoimmune conditions. Genetic counseling should be offered to the family to provide a comprehensive understanding of the condition and its potential long‐term implications, especially concerning reproduction and genetic screening. Long‐term follow‐up is essential to monitor the child's physical, psychological, and social development, to ensure the child's well‐being and to make informed decisions regarding their future.

In conclusion, the discovery of a concordant sex chimera is an extremely rare occurrence with important clinical implications. Our case adds to the limited body of literature on this topic and highlights the challenges in diagnosing and managing such cases. Further research is warranted to explore the underlying mechanisms and potential long‐term consequences of concordant sex chimerism. Follow‐up studies, potentially involving multiple testing modalities, are required to determine appropriate pregnancy management. Thus, this case of an incidentally found male on prenatal genetic screening with same‐sex chimerism, who has been otherwise well, suggests that same‐sex chimerism may be under‐recognized.

Author Contributions

E.S.G., A.B., J.S., and M.S. were involved in the clinical encounters and investigations. A.K.V. and M.K. carried out the genetic analysis methods. W.B. wrote the manuscript and obtained ethics approval. E.S.G. supervised the project. All authors contributed to manuscript revision.

Conflicts of Interest

The authors declare no conflicts of interest.

Baqri, W. , Goh E. S., Berndl A., et al. 2025. “46,XY/46,XY Chimerism: Prenatal Presentation and Postnatal Outcome.” Molecular Genetics & Genomic Medicine 13, no. 9: e70138. 10.1002/mgg3.70138.

Data Availability Statement

The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.