Creating basis for introducing NIPT in the Estonian public health setting

Objective The study aimed to validate a whole-genome sequencing-based NIPT method and our newly developed NIPTmer analysis software with the potential to integrate the pipeline into prenatal clinical care in Estonia. Method In total, 447 maternal blood samples were included to the study. Analysis pipeline involved whole-genome library preparation and massively parallel sequencing on Illumina NextSeq 500. Aneuploidy status was determined with NIPTmer software, which is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data. To estimate fetal fraction (FF) from total cell-free DNA SeqFF was implemented. Results NIPTmer software allowed to identify correctly all samples of non-mosaic T21 (15/15), T18 (9/9) and T13 (4/4) cases. However, one mosaic T18 remained undetected. Six false positive results were observed, including three for T18 (specificity 99.3%) and three for T13 (specificity 99.3%). FF < 4% (2.8-3.99%) was estimated in eight samples, including two samples with T13 and T18. Despite low FF, these two samples were determined as aneuploid with NIPTmer software. Conclusion Our NIPT analysis pipeline proved to perform efficiently in detecting common fetal aneuploidies T21, T18 and T13 and is feasible for implementation into clinical service in Estonia.

[1]  Tianya Liu,et al.  Non-invasive prenatal testing in detecting sex chromosome aneuploidy: A large-scale study in Xuzhou area of China. , 2018, Clinica chimica acta; international journal of clinical chemistry.

[2]  Anne Mari Roost,et al.  NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies , 2018, Scientific Reports.

[3]  L. Hudgins,et al.  Current controversies in prenatal diagnosis 2: Cell‐free DNA prenatal screening should be used to identify all chromosome abnormalities , 2018, Prenatal diagnosis.

[4]  K. Hens.  Chromosome Screening Using Noninvasive Prenatal Testing Beyond Trisomy-21: What to Screen for and Why It Matters. , 2018, The Journal of medicine and philosophy.

[5]  W. Holzgreve,et al.  Non-invasive prenatal testing (NIPT): Europe’s first multicenter post-market clinical follow-up study validating the quality in clinical routine , 2017, Archives of Gynecology and Obstetrics.

[6]  S. Patton,et al.  Recommended practice for laboratory reporting of non‐invasive prenatal testing of trisomies 13, 18 and 21: a consensus opinion , 2017, Prenatal diagnosis.

[7]  L. Wilkins-Haug,et al.  Sex chromosome aneuploidy detection by noninvasive prenatal testing: helpful or hazardous? , 2017, Prenatal diagnosis.

[8]  Line Kristensen,et al.  The rate of invasive testing for trisomy 21 is reduced after implementation of NIPT. , 2017, Danish medical journal.

[9]  Bin Zhang,et al.  Noninvasive prenatal screening for fetal common sex chromosome aneuploidies from maternal blood , 2017, The Journal of international medical research.

[10]  L. Hui,et al.  Noninvasive prenatal testing for fetal aneuploidy and single gene disorders. , 2017, Best practice & research. Clinical obstetrics & gynaecology.

[11]  E. Bernabé,et al.  Analysis of cell‐free fetal DNA in maternal blood for detection of trisomy 21, 18 and 13 in a general pregnant population and in a high risk population – a systematic review and meta‐analysis , 2017, Acta obstetricia et gynecologica Scandinavica.

[12]  A. Sekizawa,et al.  Factors affecting parental decisions to terminate pregnancy in the presence of chromosome abnormalities: a Japanese multicenter study , 2016, Prenatal diagnosis.

[13]  D. Oepkes,et al.  Trial by Dutch laboratories for evaluation of non‐invasive prenatal testing. Part II—women's perspectives† , 2016, Prenatal diagnosis.

[14]  D. Oepkes,et al.  Trial by Dutch laboratories for evaluation of non‐invasive prenatal testing. Part I—clinical impact , 2016, Prenatal diagnosis.

[15]  M. Watson,et al.  Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics , 2016, Genetics in Medicine.

[16]  K. Nicolaides,et al.  Clinical implementation of routine screening for fetal trisomies in the UK NHS: cell‐free DNA test contingent on results from first‐trimester combined test , 2016, Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology.

[17]  Aileen Clarke,et al.  Accuracy of non-invasive prenatal testing using cell-free DNA for detection of Down, Edwards and Patau syndromes: a systematic review and meta-analysis , 2016, BMJ Open.

[18]  S. Warsof,et al.  Overview of the impact of noninvasive prenatal testing on diagnostic procedures , 2015, Prenatal diagnosis.

[19]  John Tynan,et al.  Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts , 2015, Prenatal diagnosis.

[20]  R. Hochstenbach,et al.  Cell-free fetal DNA in the maternal circulation originates from the cytotrophoblast: proof from an unique case , 2015, Clinical case reports.

[21]  H. Peeters,et al.  Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management , 2015, European Journal of Human Genetics.

[22]  F. D’Antonio,et al.  Procedure‐related risk of miscarriage following amniocentesis and chorionic villus sampling: a systematic review and meta‐analysis , 2015, Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology.

[23]  A. Clarke,et al.  For Your Interest? The Ethical Acceptability of Using Non‐Invasive Prenatal Testing to Test ‘Purely for Information’ , 2015, Bioethics.

[24]  Y. Liu,et al.  Detection of fetal sex chromosome aneuploidy by massively parallel sequencing of maternal plasma DNA: initial experience in a Chinese hospital , 2014, Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology.

[25]  L. Hui,et al.  Noninvasive prenatal testing for trisomy 21: Challenges for implementation in Australia , 2013, The Australian & New Zealand journal of obstetrics & gynaecology.

[26]  K. Nicolaides,et al.  Noninvasive prenatal testing for fetal trisomies in a routinely screened first-trimester population. , 2012, American journal of obstetrics and gynecology.

[27]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[28]  S. Nelson,et al.  DNA sequencing of maternal plasma to detect Down syndrome: An international clinical validation study , 2011, Genetics in Medicine.

[29]  Stephen R Quake,et al.  Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing. , 2010, Clinical chemistry.

[30]  H. C. Fan,et al.  Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood , 2008, Proceedings of the National Academy of Sciences.

[31]  Tze Kin Lau,et al.  Microfluidics digital PCR reveals a higher than expected fraction of fetal DNA in maternal plasma. , 2008, Clinical chemistry.

[32]  R. Chiu,et al.  Noninvasive prenatal diagnosis of fetal chromosomal aneuploidies by maternal plasma nucleic acid analysis. , 2008, Clinical chemistry.

[33]  P. Jacobs,et al.  X chromosome loss and ageing , 2007, Cytogenetic and Genome Research.

[34]  R. B. van der Luijt,et al.  Earliest gestational age for fetal sexing in cell‐free maternal plasma , 2003, Prenatal diagnosis.

[35]  A. Benachi,et al.  Kinetics of SRY gene appearance in maternal serum: detection by real time PCR in early pregnancy after assisted reproductive technique. , 2003, Human reproduction.

[36]  L. Dugoff.  Cell-Free DNA Screening for Fetal Aneuploidy , 2017 .

[37]  Committee Opinion Summary No. 640: Cell-Free DNA Screening For Fetal Aneuploidy. , 2015, Obstetrics and gynecology.

[38]  B. Levy,et al.  Noninvasive prenatal testing: the future is now. , 2013, Reviews in obstetrics & gynecology.