Technologies in Reproductive Screening and Diagnosis Research Update

 Natalie Chandler and Francesca Romana Grati
Technologies in Reproductive Screening and Diagnosis SIG Co-Chairs

 

Uncertainty with fetal exome sequencing

Natalie Chandler1 (FRCPath, PhD); Francesca Romana Grati2, MSCs, Ph.D.
1. North Thames Genomic Laboratory, Great Ormond Street Hospital, London, UK
2. TOMA Advanced Biomedical Assays S.p.A., Impact Lab, Busto Arsizio (Varese), Italy

As fetal exome sequencing is being implemented internationally, there has been a number of articles published focusing on the uncertainties associated with the technique, which guidelines are available, and differences in practice around the world. We would like to highlight two interesting articles on this topic; the first (“How to deal with uncertainty in prenatal genomics: A systematic review of guidelines and policies” by Klapwijk et al. 2021, Clinical Genetics. 2021;1–12. DOI: 10.1111/cge.14010) provides a description of the different types of uncertainties and a review of the current guidelines available and identifies a number of gaps that need to be addressed. The second article (“Dealing with uncertain results from chromosomal microarray and exome sequencing in the prenatal setting” Prenatal Diagnosis. 2021;41:720–732 DOI: 10.1002/pd.5932) is a cross-sectional study carried out on health professionals dealing with the uncertainties and highlights a number of the challenges faced. Interestingly, both studies also include microarray where there has already been a wealth of studies and guidelines are available. Many of the uncertainties identified are shared between the two methods, however exome sequencing has greater sensitivity resulting in larger numbers or variants of uncertain clinical significance and incidental findings , which are major challenges for health professionals. Another major difference is the need to filter variants to be able to provide results in a timely manner. An area that both studies highlight is that internationally there is a large variety in the methods used to deal with these uncertainties which are dependent on local cultural and legislation policies and therefore universal guidelines may be challenging. 

Placental mosaicism: a never-ending story

Francesca Romana Grati1, MSCs, Ph.D.; Jose Ferreira2, MD, Ph.D.; Susan Gross3, MD, FRCSC, FACOG, FACMG
1. TOMA Advanced Biomedical Assays S.p.A., Impact Lab, Busto Arsizio (Varese), Italy
2. Hospital de Santa Maria, Lisbon, Portugal
3. Cradle Genomics, San Diego, CA

Dr. Costello and Dr. Fisher1 wrote a commentary on the clinical implications of Coorens et al., study2 where they confirmed, at sequencing level, that clonal genetic mosaicism is a typical feature of the placenta. However, they do not mention that this phenomenon has been known at the chromosomal level for decades, since the time that cytotrophoblasts cytogenetic analysis was established.3 That discovery resulted in profound changes in first-trimester prenatal diagnosis as placental mesenchyme analysis would be required and, in cases of placental chromosomal mosaicism, amniocentesis would be offered to discriminate between a confined placental mosaicism (CPM) and a true fetal mosaicism (TFM). After ~40 years of chorionic villi cytogenetic analysis, it is well known that placental chromosomal mosaicism has a 2% frequency but true fetal mosaicism occurs in only ~13% of those.4

The understanding of placental mosaicism includes research documenting false positive and negative rates based on the chromosome in question in CVS karyotyping, that was found to be specific for each chromosome and this knowledge is already incorporated into prenatal aneuploidy testing by analyzing circulating cfDNA.5-7 Positive cell-free DNA aneuploidy screening tests require diagnostic confirmation to avoid a false positive due to placental mosaicism.8-10

We agree with the authors that Coorens’ study, provides clinicians and investigators with new molecular insights that builds upon current knowledge. 

References

  1. Costello JF, Fisher SJ. The Placenta - Fast, Loose, and in Control. N Engl J Med. 2021 Jul 1;385(1):87-89.
  2. Coorens THH, Oliver TRW, Sanghvi R, Sovio U, Cook E, Vento-Tormo R, Haniffa M, Young MD, Rahbari R, Sebire N, Campbell PJ, Charnock-Jones DS, Smith GCS, Behjati S. Inherent mosaicism and extensive mutation of human placentas. Nature. 2021 Apr;592(7852):80-85.
  3. Simoni G, Brambati B, Danesino C, Rossella F, Terzoli GL, Ferrari M, Fraccaro M. Efficient direct chromosome analyses and enzyme determinations from chorionic villi samples in the first trimester of pregnancy. Hum Genet. 1983;63(4):349-57.
  4. Malvestiti F, Agrati C, Grimi B, Pompilii E, Izzi C, Martinoni L, Gaetani E, Liuti MR, Trotta A, Maggi F, Simoni G, Grati FR. Interpreting mosaicism in chorionic villi: results of a monocentric series of 1001 mosaics in chorionic villi with follow-up amniocentesis. Prenat Diagn. 2015 Nov;35(11):1117-27.
  5. Grati FR, Bajaj K, Malvestiti F, Agrati C, Grimi B, Malvestiti B, Pompilii E, Maggi F, Gross S, Simoni G, Ferreira JC. The type of feto-placental aneuploidy detected by cfDNA testing may influence the choice of confirmatory diagnostic procedure. Prenat Diagn. 2015 Oct;35(10):994-8.
  6. Hartwig TS, Ambye L, Sørensen S, Jørgensen FS. Discordant non-invasive prenatal testing (NIPT) - a systematic review. Prenat Diagn. 2017 Jun;37(6):527-539
  7. Srebniak MI, Diderich KE, Noomen P, Dijkman A, de Vries FA, van Opstal D. Abnormal non-invasive prenatal test results concordant with karyotype of cytotrophoblast but not reflecting abnormal fetal karyotype. Ultrasound Obstet Gynecol. 2014 Jul;44(1):109-11.
  8. American College of Obstetricians and Gynecologists’ Committee on Practice Bulletins—Obstetrics; Committee on Genetics; Society for Maternal-Fetal Medicine. Screening for Fetal Chromosomal Abnormalities: ACOG Practice Bulletin, Number 226. Obstet Gynecol. 2020 Oct;136(4):e48-e69. doi: 10.1097/AOG.0000000000004084. PMID: 32804883.
  9. Benn P, Borrell A, Chiu RW, Cuckle H, Dugoff L, Faas B, Gross S, Huang T, Johnson J, Maymon R, Norton M, Odibo A, Schielen P, Spencer K, Wright D, Yaron Y. Position statement from the Chromosome Abnormality Screening Committee on behalf of the Board of the International Society for Prenatal Diagnosis. Prenat Diagn. 2015 Aug;35(8):725-34.
  10. Gregg AR, Skotko BG, Benkendorf JL, Monaghan KG, Bajaj K, Best RG, Klugman S, Watson MS. Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics. Genet Med. 2016 Oct;18(10):1056-65.