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