Johansen 2016.

Study characteristics
Patient sampling	Study design: prospective cohort study. Participants: pregnant women selected at high risk of fetal aneuploidy presenting for invasive testing. Inclusion criteria: singleton pregnancies. Exclusion criteria: multifetal pregnancies.
Patient characteristics and setting	Number enrolled: 375 pregnant women (184 for the validation set). Number available for 2 x 2 table: 173 pregnant women (subgroup of 94%). Setting: Danish public health setting. Recruitment period: not reported. Ethnicity: not reported. Median gestational age (range): 13.4 (10.6 to 31) weeks. Maternal age: not reported. Relevant tests carried out prior to index test: ultrasonography (nuchal translucency measurement) or biochemical screening or both. Language of the study: English.
Index tests	gNIPT by MPSS on Ion Proton™ sequencer in 5‐plex. Fetal fraction DNA: amount measured but not reported. Blood samples for gNIPT were collected just before reference standard. Cutpoint: positive if Z score ≥ 4 and WISECONDOR ≥ 1% (unclassified if Z score between 3 and 4). In‐house test.
Target condition and reference standard(s)	Target conditions: T21, T18 and T13. Reference standard: fetal karyotype of chorionic villi or amniotic fluid.
Flow and timing	Blood samples for gNIPT were obtained just prior the invasive procedure (reference standard). gNIPT was a second‐tier test. 191/375 not selected, samples for the validation set were excluded. 11/184 samples failed during sequencing process for low fetal fraction DNA (no gNIPT result). 2/173 samples were resequenced because gNIPT results were in the inconclusive zone and 2 results were obtained.
Comparative
Aim to study	To introduce gNIPT for fetal autosomal trisomies and gender in a Danish public health setting, using semi‐conductor sequencing and published open source scripts for analysis.
Funding source or sponsor of the study	No funding source was reported.
Informations about the authors contacted	No need for further contact.
Notes
Methodological quality
Item	Authors' judgement	Risk of bias	Applicability concerns
DOMAIN 1: Patient Selection
Was a consecutive or random sample of patients enrolled?	No
Was a case‐control design avoided?	Yes
Did the study avoid inappropriate exclusions?	No
		High	Low
DOMAIN 2: Index Test MPSS
Were the index test results interpreted without knowledge of the results of the reference standard?	Yes
If a threshold was used, was it pre‐specified?	Yes
		Low	Low
DOMAIN 3: Reference Standard
Is the reference standards likely to correctly classify the target condition?	Yes
Were the reference standard results interpreted without knowledge of the results of the index tests?	Yes
		Low	Low
DOMAIN 4: Flow and Timing
Was there an appropriate interval between index test and reference standard?	Yes
Did all analysed patients receive the reference standard?	Yes
Were all patients included in the analysis?	No
		High