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Unsupervised clustering based on all Infinium probes (excluding those on the sex chromosomes) clearly separated all samples by gestational age, with first trimester samples clustering away from second and third trimester samples.
In second trimester samples gestational age was determined initially by ultrasound examination, followed by direct measurement of foot length.
The principal limiting criterion was the availability of first trimester samples as the median entry time into the study for the whole CPP population was 20 weeks gestation.
The sex of first trimester samples was determined by PCR for the SRY gene as previously described (Gaskell et al., 2004).
More specifically, second trimester samples did not cluster with either the first trimester or term samples, suggesting a progressive change in methylation across gestation.
Regional or rural areas were identified on the basis of the number of first trimester samples sent to the centralised laboratory at GHSV in 2004.
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The first trimester sampling was performed before the first ultrasound examination.
A significant increase in IgG antibody levels (against CBV4 or EV peptide antigen or both) occurred between the first trimester sample and the cord blood sample in 10.5% of the mothers of type 1 diabetic children and in 8.5% of the mothers of the control children, respectively (not significant).
Digestion-resistant VAPA-APCDD1 DNA was readily detected in 26 maternal plasma samples (5/6 (83%) first-trimester, 8/10 (80%) second-trimester and 10/10 (100%) third-trimester samples).
We used third-trimester samples for 27 cases of schizophrenia spectrum disorder and 54 matched controls.
Second-trimester samples were available for 44 cases and 75 matched controls (one to two controls per case).
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