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percept ® is different... Australia’s most advanced and comprehensive non-invasive prenatal test perce ® cell-free DNA pt prenatal test Why percept® percept is Australia’s most comprehensive non-invasive prenatal testing (NIPT) service. Advanced bioinformatics means percept is the only NATA/RCPA accredited Australian NIPT service to assess all 24 chromosomes, (chromosomes 1-22 and the X & Y chromosomes). This means we can identify additional genetic conditions like: • rare autosomal trisomies; • large segmental genetic imbalances like deletions and duplications. These are reported as additional findings; • familial balanced translocation analysis; • all our tests are fully supported by clinical interpretation and genetic counselling at no additional cost. 1. percept ® in numbers percept includes our integrated genetic counselling Clinical utility of percept Condition Test Frequency service, so patients and 1 in 74 Conventional NIPT (21,18, 13) (based on VCGS referral data) health professionals are fully percept advanced NIPT Trisomy 21 1 in 113 Trisomy 18 1 in 420 informed and supported Trisomy 13 1 in 436 Additional analysis by percept Rare trisomies (other than 21, 18, 13) 1 in 285 (PPV 50-65%)1,2 Additional findings(dels & dups) 1 in 612 (PPV 53%) Additional high risk cases called by percept 1 in 200 (PPV 50-65%) Additional clinically relevant cases 1 in 300-400 detected by percept Compared to micro-deletion syndrome panels offered by other providers Micro-deletion syndrome panels Approx 1 in 2,100 (PPV 0-18%) 3-8 Therefore... • Our analysis pipeline detects clinically significant genetic changes that occur more frequently and with a higher positive predictive value (PPV) than micro-deletion syndromes offered through other providers. • Using a genome wide approach means genetic changes can be detected across all chromosomes and is not limited to a small number of targeted regions. • The size of the genetic change detectable is dependent on a number of quality measures which includes fetal fraction and genomic location, but on average is approximately 10 mega bases in size. 2. Explained: rare autosomal trisomies & additional findings Rare autosomal trisomies Additional findings • involve all chromosomes other than 21, 18, 13 & the • advanced bioinformatics means the entire length of every sex chromosomes; autosome is analysed, representing an analysis similar to • individually occur less frequently than 21, 18 & 13 but a traditional karyotype; collectively are as frequent as trisomy 13 or 18; • large deletions & duplications can be associated with • up to 76% of rare trisomies detected by percept are serious congenital malformations & intellectual disability; clinically relevant to the pregnancy; • test sensitivity & genomic size of detectable imbalances • rare trisomies may be associated with miscarriages, is dependent on several factors, including fetal fraction; intra-uterine growth retardation, premature labour, • important to note that a low risk NIPT result does not compromised placental function, and as live birth exclude the presence of all deletions & duplications. with serious congenital anomalies. Examples of additional findings from percept® Case report - Pallister-Killian syndrome Chromosome imbalance Condition Chromosome 2 - partial monosomy 2q 2q37 deletion syndrome A. Chromosome 3 - partial monosomy 3p 3p deletion syndrome Chromosome 4 - partial monosomy 4p Wolf-Hirschhorn syndrome Chromosome 5 - partial monosomy 5p Cri-du-chat syndrome Chromosome 9 - tetrasomy 9p Tetrasomy 9p syndrome B. A: WISECONDOR plot showing Chromosome 10 - partial monosomy 10p 16 Mb deletion increased sequence counts for the Chromosome 11 - partial monosomy 11q Jacobsen syndrome p-arm of chromosome 12 (shown Chromosome 12 - tetrasomy 12p Pallister-Killian syndrome by red line & purple block). Chromosome 15 - partial trisomy 15q 27Mb duplication Chromosome 17 - partial monosomy 17p Miller-Dieker lissencephaly syndrome B: Conventional karyotyping on Chromosome 18 - tetrasomy 18p Tetrasomy 18p syndrome amniocytes confirmed this to Chromosome 22 - partial trisomy 22q 11 Mb duplication be mosaicism for tetrasomy of Chromosome 22 - der(22)t(11;22) Emanuel syndrome chromosome 12p. Uniparental disomy post trisomy 15 NIPT Prader-Willi syndrome All confirmed by CVS or amniocentesis ® Test Features for Routine Analysis percept other providers Why percept is different... Analysis of all 24 chromosomes ✘ Screening for rare autosomal trisomies ✘# Additional findings (large segmental deletions/duplications) ✘ VCGS is a not-for-profit Discrimination of mosaicism (maternal & placental) * ✘ Translocation analysis for known carriers ** ✘ specialist genetics service; Co-twin demise ** ✘ Triplet pregnancies ** ✘ all proceeds support VCGS Key Service Features Rapid turn around time 3-5 days 4-10 days medical research Fully integrated laboratory and clinical service variable Lower limit of detection for trisomy 2.5% fetal fraction up to 4% fetal fraction Low test failure rate 0.2% up to 1-3% Full genetic data interrogation & interpretation variable Clinical support provided with all testing variable Conditions detected (n=30,000) Sensitivity PPV Trisomy 21 >99% 99% Trisomy 18 >98% >95% Trisomy 13 >99% >85% Monosomy X >95% >30%*** Other sex chromosome anomalies (XXX, XXY, XYY) LD 75-92% Fetal sex >99% >99% Rare trisomies (n=16,885)1 LD (for each) 50-65%1,2,° Additional findings (dels & dups >10Mb) (n=15,600)^ 78% 53% Known translocations (12 high risk cases/75 tests) 100% 100% # Offered by one other provider * This is not always definitive but can be used to help direct care of the pregnancy ** Prior notification required as additional clinical information is needed and sample collection may vary *** True fetal 45,X (including variants). Most causes of false positive results are confined placental mosaicism & maternal contributions (VCGS data on file) LD = limited data ° This value represents findings confirmed in the fetus & those confined to the placenta but considered clinically relevant1,2 ^ VCGS NATA validation study (2017) (VCGS data on file) 4. References 1. Pertile MD, Halks-Miller M, Flowers N, Barbacioru C, Kinnings SL, Vavrek D, et al. Rare autosomal trisomies, revealed by maternal plasma DNA sequencing, suggest increased risk of feto-placental disease. Sci Transl Med. 2017;9(405). 2. Pertile MD. Chapter 7 - Genome-Wide Cell-Free DNA-Based Prenatal Testing for Rare Autosomal Trisomies and Subchromosomal Abnormalities. In: Page-Christiaens L, Klein H-G, editors. Noninvasive Prenatal Testing (NIPT): Academic Press; 2018. p. 97-123. 3. Hui L. Cell-free DNA testing for 22q11.2 deletion syndrome: appraising the viability, effectiveness and appropriateness of screening. Ultrasound Obstet Gynecol. 2016;47(2):137-41. 4. Yaron Y, Jani J, Schmid M, Oepkes D. Current Status of Testing for Microdeletion Syndromes and Rare Autosomal Trisomies Using Cell-Free DNA Technology. Obstet Gynecol. 2015;126(5):1095-9. ® 5. Valderramos SG, Rao RR, Scibetta EW, Silverman NS, Han CS, Platt LD. Cell-free DNA screening in clinical practice: abnormal perce autosomal aneuploidy and microdeletion results. Am J Obstet Gynecol. 2016;215(5):626 e1- e10. cell-free DNA pt prenatal test 6. Gross SJ, Stosic M, McDonald-McGinn DM, Bassett AS, Norvez A, Dhamankar R, et al. Clinical experience with single- nucleotide polymorphism-based non-invasive prenatal screening for 22q11.2 deletion syndrome. Ultrasound Obstet Gynecol. 2016;47(2):177-83. P) 1300 11 8247 E) [email protected] 7. Martin K, Iyengar S, Kalyan A, Lan C, Simon AL, Stosic M, et al. Clinical experience with a single-nucleotide polymorphism- based non-invasive prenatal test for five clinically significant microdeletions. Clin Genet. 2018;93(2):293-300. 8. National Library of Medicine (US). Genetics Home Reference [Internet]. Bethesda (MD). Available from: https://ghr.nlm.nih.gov/ 5..
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