Supplementary Material for: Noninvasive Prenatal Detection of Trisomy 21 by Targeted Semiconductor Sequencing: A Technical Feasibility Study Xi Y. Arbabi A. McNaughton A.J.M. Hamilton A. Hull D. Perras H. Chiu T. Morrison S. Goldsmith C. Creede E. Anger G.J. Honeywell C. Cloutier M. Macchio N. Kiss C. Liu X. Crocker S. Davies G.A. Brudno M. Armour C.M. 10.6084/m9.figshare.5008808.v1 https://karger.figshare.com/articles/dataset/Supplementary_Material_for_Noninvasive_Prenatal_Detection_of_Trisomy_21_by_Targeted_Semiconductor_Sequencing_A_Technical_Feasibility_Study/5008808 <p><b><i>Objective:</i></b> To develop an alternate noninvasive prenatal testing method for the assessment of trisomy 21 (T21) using a targeted semiconductor sequencing approach. <b><i>Methods:</i></b> A customized AmpliSeq panel was designed with 1,067 primer pairs targeting specific regions on chromosomes 21, 18, 13, and others. A total of 235 samples, including 30 affected with T21, were sequenced with an Ion Torrent Proton sequencer, and a method was developed for assessing the probability of fetal aneuploidy via derivation of a risk score. <b><i>Results:</i></b> Application of the derived risk score yields a bimodal distribution, with the affected samples clustering near 1.0 and the unaffected near 0. For a risk score cutoff of 0.345, above which all would be considered at “high risk,” all 30 T21-positive pregnancies were correctly predicted to be affected, and 199 of the 205 non-T21 samples were correctly predicted. The average hands-on time spent on library preparation and sequencing was 19 h in total, and the average number of reads of sequence obtained was 3.75 million per sample. <b><i>Conclusion:</i></b> With the described targeted sequencing approach on the semiconductor platform using a custom-designed library and a probabilistic statistical approach, we have demonstrated the feasibility of an alternate method of assessment for fetal T21.</p> 2017-05-16 13:23:04 Noninvasive prenatal testing Cell-free fetal DNA Semiconductor sequencing Targeted sequencing Trisomy 21