Seeking Answers, Getting Questions: Genome-wide Prenatal Cell-free DNA Screening in a Case of Multiple Congenital Anomalies
Prenatal Genetics
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Primary Categories:
- Prenatal Genetics
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Secondary Categories:
- Prenatal Genetics
Introduction
Cell-free DNA (cfDNA) screening was first introduced in the United States in 2011 (Palomaki et al., 2013). It is now recommended by the American College of Obstetrics and Gynecology (ACOG) as the most sensitive and specific prenatal screening. Further, ACOG recommends that all pregnant individuals are offered screening and diagnostic options, including cfDNA screening (ACOG, 2020; Dungan, et al., 2023). Diagnostic testing allows for analysis via chromosomal microarray. In cases of structural defect, there is a 6% yield for microarray (Wapner et al., 2012). Most patients who undergo genetic counseling ultimately decline diagnostics (Richards et al., 2012). Core cfDNA screening assesses for Trisomy 21, 18, 13, and sex chromosome aneuploidies. Genome-wide cfDNA screening (Sequenom’s MaterniT Genome) has greater than 94% sensitivity with in-silico models for deletions and duplications ≥7 megabases (Mb) (Soster et al., 2021).
Case Presentation
This fetus was the conceptus of a 27-year-old primigravida couple. Immediate family history was non-contributory. At 20 weeks 2 days (20w2d), ultrasound visualized a closed neural tube defect, thick nuchal fold, and absent cavum septum pellucidum (CSP). Additional ultrasound at 22w2d visualized the CSP, but ultrasound at 23w5d revealed mild bilateral ventriculomegaly and bilaterally enlarged kidneys.
Diagnostic Workup
The couple elected genome-wide cfDNA screening after declining amniocentesis and core cfDNA screening. The cfDNA screened positive for trisomy 14, so they pursued amniocentesis. Karyotype and chromosomal microarray were both abnormal. An unbalanced translocation was identified between the long arm of chromosome 3 and the short arm of chromosome 14 (46,XX,der(14)(3;14)(q27;p11.2).ish der(14)t(3;14)(acro p-,BCL6+)). This resulted in a pathogenic 18.4 Mb duplication from 3q26.33 to 3q29. Uniparental disomy studies (UPD) for chromosome 14 were normal and parental fluorescence in situ hybridization for the translocation event were also normal.
Treatment and Management
The pregnancy was terminated at 27w6d.
Outcome and Follow-Up
Placental biopsies were performed and detected the 3;14 unbalanced translocation event, without evidence of trisomy 14.
Discussion
In this case, the most likely mechanism is early 3;1 nondisjunction resulting in cells with structurally normal chromosome 3 and 14, a der(14), and subsequent trisomy rescue leading to loss of the structurally normal chromosome 14. Gondal mosaicism is also possible. Although trisomy 14 was not confirmed by chromosome or microarray analyses for our patient, we cannot rule out a low level mosaic cell population, nor occult trisomy in other cell lines.
This case highlights the utility and limitations of genome-wide cfDNA screening. A study of 86,902 clinical genome-wide cfDNA screening specimens (with 4,121 screen positive results) screening had a positive predictive value of 71.8% (Rafalko et al., 2021). They identified 63 discordant results, and 40 (63%) had a probable explanation for the abnormal result (e.g. mosaicism, UPD/rescue, maternal event, etc.). For multiple cases where only one of the two findings from cfDNA screening were confirmed, the discordant abnormality demonstrated sequencing data suggestive of mosaicism; however, in at least one of these cases, the mosaic copy number variant was identified in the placenta, which was not the case for our patient. For our patient, it is unknown why cfDNA screening identified trisomy 14, instead of gain of chromosome 3 material, but may reflect the fact that cfDNA is a snapshot in time of the placental trophoblast.
Conclusion
This case highlights a need for further elucidating the performance of genome-wide cfDNA screening with respect to unbalanced translocations. The patient elected to receive genome-wide cfDNA screening in her subsequent pregnancy, which demonstrates a perceived benefit: the abnormal screening result was a catalyst for pursuing concrete information via diagnostic testing.
References
American College of Obstetricians and Gynecologists’ Committee on Practice
Bulletins—Obstetrics, Committee on Genetics, & Society for Maternal-Fetal Medicine (2020). Screening for Fetal Chromosomal Abnormalities: ACOG Practice Bulletin, Number 226. Obstetrics and gynecology, 136(4), e48–e69. https://doi.org/10.1097/AOG.0000000000004084
Dungan, J. S., Klugman, S., Darilek, S., Malinowski, J., Akkari, Y. M. N., Monaghan, K. G., Erwin,
A., Best, R. G., & ACMG Board of Directors. (2023). Noninvasive prenatal screening (NIPS) for fetal chromosome abnormalities in a general-risk population: An evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genetics in medicine : official journal of the American College of Medical Genetics, 25(2), 100336. https://doi.org/10.1016/j.gim.2022.11.004
Palomaki, G. E., Knight, G. J., Ashwood, E. R., Best, R. G., & Haddow, J. E. (2013). Screening
for down syndrome in the United States: results of surveys in 2011 and 2012. Archives of pathology & laboratory medicine, 137(7), 921–926. https://doi.org/10.5858/arpa.2012-0319-CP
Rafalko, J., Soster, E., Caldwell, S., Almasri, E., Westover, T., Weinblatt, V., & Cacheris, P.
(2021). Genome-wide cell-free DNA screening: a focus on copy-number variants. Genetics in medicine : official journal of the American College of Medical Genetics, 23(10), 1847–1853. https://doi.org/10.1038/s41436-021-01227-5
Richards, D., Rodriguez, L., Adamsky, M., & Davidson, K. (2012). 718: Why do women
decline genetic amniocentesis? American Journal of Obstetrics and Gynecology, 206(1). https://doi.org/10.1016/j.ajog.2011.10.736
Soster, E., Boomer, T., Hicks, S., Caldwell, S., Dyr, B., Chibuk, J., & Almasri, E. (2021). Three
years of clinical experience with a genome-wide cfDNA screening test for aneuploidies and copy-number variants. Genetics in medicine : official journal of the American College of Medical Genetics, 23(7), 1349–1355. https://doi.org/10.1038/s41436-021-01135-8
Wapner, R. J., Martin, C. L., Levy, B., Ballif, B. C., Eng, C. M., Zachary, J. M., Savage, M., Platt, L.
D., Saltzman, D., Grobman, W. A., Klugman, S., Scholl, T., Simpson, J. L., McCall, K., Aggarwal, V. S., Bunke, B., Nahum, O., Patel, A., Lamb, A. N., Thom, E. A., … Jackson, L. (2012). Chromosomal microarray versus karyotyping for prenatal diagnosis. The New England journal of medicine, 367(23), 2175–2184. https://doi.org/10.1056/NEJMoa1203382
Acknowlegements
Amanda Sussman, PhD, FACMG, FCCMG, Laura Kline MS, CGC, Samantha Caldwell MS, LCGC
Cell-free DNA (cfDNA) screening was first introduced in the United States in 2011 (Palomaki et al., 2013). It is now recommended by the American College of Obstetrics and Gynecology (ACOG) as the most sensitive and specific prenatal screening. Further, ACOG recommends that all pregnant individuals are offered screening and diagnostic options, including cfDNA screening (ACOG, 2020; Dungan, et al., 2023). Diagnostic testing allows for analysis via chromosomal microarray. In cases of structural defect, there is a 6% yield for microarray (Wapner et al., 2012). Most patients who undergo genetic counseling ultimately decline diagnostics (Richards et al., 2012). Core cfDNA screening assesses for Trisomy 21, 18, 13, and sex chromosome aneuploidies. Genome-wide cfDNA screening (Sequenom’s MaterniT Genome) has greater than 94% sensitivity with in-silico models for deletions and duplications ≥7 megabases (Mb) (Soster et al., 2021).
Case Presentation
This fetus was the conceptus of a 27-year-old primigravida couple. Immediate family history was non-contributory. At 20 weeks 2 days (20w2d), ultrasound visualized a closed neural tube defect, thick nuchal fold, and absent cavum septum pellucidum (CSP). Additional ultrasound at 22w2d visualized the CSP, but ultrasound at 23w5d revealed mild bilateral ventriculomegaly and bilaterally enlarged kidneys.
Diagnostic Workup
The couple elected genome-wide cfDNA screening after declining amniocentesis and core cfDNA screening. The cfDNA screened positive for trisomy 14, so they pursued amniocentesis. Karyotype and chromosomal microarray were both abnormal. An unbalanced translocation was identified between the long arm of chromosome 3 and the short arm of chromosome 14 (46,XX,der(14)(3;14)(q27;p11.2).ish der(14)t(3;14)(acro p-,BCL6+)). This resulted in a pathogenic 18.4 Mb duplication from 3q26.33 to 3q29. Uniparental disomy studies (UPD) for chromosome 14 were normal and parental fluorescence in situ hybridization for the translocation event were also normal.
Treatment and Management
The pregnancy was terminated at 27w6d.
Outcome and Follow-Up
Placental biopsies were performed and detected the 3;14 unbalanced translocation event, without evidence of trisomy 14.
Discussion
In this case, the most likely mechanism is early 3;1 nondisjunction resulting in cells with structurally normal chromosome 3 and 14, a der(14), and subsequent trisomy rescue leading to loss of the structurally normal chromosome 14. Gondal mosaicism is also possible. Although trisomy 14 was not confirmed by chromosome or microarray analyses for our patient, we cannot rule out a low level mosaic cell population, nor occult trisomy in other cell lines.
This case highlights the utility and limitations of genome-wide cfDNA screening. A study of 86,902 clinical genome-wide cfDNA screening specimens (with 4,121 screen positive results) screening had a positive predictive value of 71.8% (Rafalko et al., 2021). They identified 63 discordant results, and 40 (63%) had a probable explanation for the abnormal result (e.g. mosaicism, UPD/rescue, maternal event, etc.). For multiple cases where only one of the two findings from cfDNA screening were confirmed, the discordant abnormality demonstrated sequencing data suggestive of mosaicism; however, in at least one of these cases, the mosaic copy number variant was identified in the placenta, which was not the case for our patient. For our patient, it is unknown why cfDNA screening identified trisomy 14, instead of gain of chromosome 3 material, but may reflect the fact that cfDNA is a snapshot in time of the placental trophoblast.
Conclusion
This case highlights a need for further elucidating the performance of genome-wide cfDNA screening with respect to unbalanced translocations. The patient elected to receive genome-wide cfDNA screening in her subsequent pregnancy, which demonstrates a perceived benefit: the abnormal screening result was a catalyst for pursuing concrete information via diagnostic testing.
References
American College of Obstetricians and Gynecologists’ Committee on Practice
Bulletins—Obstetrics, Committee on Genetics, & Society for Maternal-Fetal Medicine (2020). Screening for Fetal Chromosomal Abnormalities: ACOG Practice Bulletin, Number 226. Obstetrics and gynecology, 136(4), e48–e69. https://doi.org/10.1097/AOG.0000000000004084
Dungan, J. S., Klugman, S., Darilek, S., Malinowski, J., Akkari, Y. M. N., Monaghan, K. G., Erwin,
A., Best, R. G., & ACMG Board of Directors. (2023). Noninvasive prenatal screening (NIPS) for fetal chromosome abnormalities in a general-risk population: An evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genetics in medicine : official journal of the American College of Medical Genetics, 25(2), 100336. https://doi.org/10.1016/j.gim.2022.11.004
Palomaki, G. E., Knight, G. J., Ashwood, E. R., Best, R. G., & Haddow, J. E. (2013). Screening
for down syndrome in the United States: results of surveys in 2011 and 2012. Archives of pathology & laboratory medicine, 137(7), 921–926. https://doi.org/10.5858/arpa.2012-0319-CP
Rafalko, J., Soster, E., Caldwell, S., Almasri, E., Westover, T., Weinblatt, V., & Cacheris, P.
(2021). Genome-wide cell-free DNA screening: a focus on copy-number variants. Genetics in medicine : official journal of the American College of Medical Genetics, 23(10), 1847–1853. https://doi.org/10.1038/s41436-021-01227-5
Richards, D., Rodriguez, L., Adamsky, M., & Davidson, K. (2012). 718: Why do women
decline genetic amniocentesis? American Journal of Obstetrics and Gynecology, 206(1). https://doi.org/10.1016/j.ajog.2011.10.736
Soster, E., Boomer, T., Hicks, S., Caldwell, S., Dyr, B., Chibuk, J., & Almasri, E. (2021). Three
years of clinical experience with a genome-wide cfDNA screening test for aneuploidies and copy-number variants. Genetics in medicine : official journal of the American College of Medical Genetics, 23(7), 1349–1355. https://doi.org/10.1038/s41436-021-01135-8
Wapner, R. J., Martin, C. L., Levy, B., Ballif, B. C., Eng, C. M., Zachary, J. M., Savage, M., Platt, L.
D., Saltzman, D., Grobman, W. A., Klugman, S., Scholl, T., Simpson, J. L., McCall, K., Aggarwal, V. S., Bunke, B., Nahum, O., Patel, A., Lamb, A. N., Thom, E. A., … Jackson, L. (2012). Chromosomal microarray versus karyotyping for prenatal diagnosis. The New England journal of medicine, 367(23), 2175–2184. https://doi.org/10.1056/NEJMoa1203382
Acknowlegements
Amanda Sussman, PhD, FACMG, FCCMG, Laura Kline MS, CGC, Samantha Caldwell MS, LCGC
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