Alberti 2015.

Study characteristics
Patient sampling	Study design: case‐control study (1:2) from a prospective cohort. Participants: pregnant women selected from a high‐risk population of fetal aneuploidy. Inclusion criteria: pregnant women who had a risk of fetal trisomy 21 (> 1 in 250), based on the combination of maternal age with ultrasound and maternal serum markers during the first or second trimester and prior invasive testing. Exclusion criteria: multifetal pregnancies, absence of medical coverage by the National Health System and women declining an invasive procedure.
Patient characteristics and setting	Number enrolled: 976 pregnant women. Number available for 2 x 2 table: 183 pregnant women (subgroup of 19%). 23 euploid samples were used as reference set and 8 samples randomly chosen for pretesting phase. Setting: 3 centres in France. Recruitment period: March 2010 to April 2013. Ethnicity: not reported. Mean gestational age (± SD): 14 (± 2) weeks. Mean maternal age (± SD): 35.2 (± 6.7) years. Relevant tests carried out prior to index test: ultrasonography (nuchal translucency measurement) and biochemical screening. Language of the study: English.
Index tests	gNIPT by MPSS on Illumina HiSeq 2000 without multiplexing. Each library was sequenced using 50 bases‐length reads chemistry in a single end‐flow cell. Mean fetal fraction DNA: (male only) euploid: 20.11% and T21: 16.86%. Blood samples for gNIPT were collected before reference standard. Cutpoint: positive if Z score > 3. In‐house gNIPT.
Target condition and reference standard(s)	Target condition: T21. Reference standard: fetal karyotype of chorionic villi or amniotic fluid.
Flow and timing	Blood samples were obtained prior to the invasive procedure (reference standard). gNIPT was a second‐tier test. 701/976 samples were not selected for the case‐control study. 50/275 samples were excluded during DNA extraction (47 for low amount of DNA and 3 for haemolysis) (no gNIPT results). 31/225 samples were excluded from analysis (8 for pretesting phase and 23 for reference set). 11/194 samples were excluded from analysis for insufficient fetal fraction DNA (no gNIPT results). No repeated test reported.
Comparative
Aim to study	To evaluate the implementation of gNIPT for trisomy 21 into a cytogenetics laboratory in a university teaching hospital as well as validate gNIPT’s clinical use on samples collected prospectively.
Funding source or sponsor of the study	Study not funded by industry.
Informations about the authors contacted	Authors were contacted on: 23 March and 4 May 2016. Last reply received on: 16 May 2016.
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?	No
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