Molecular Study of Preterm Birth: Genomic Ancestry, Race, and Ethnicity

BACKGROUND: Inova Translational Medicine Institute (ITMI) initiated a study to identify genomic markers predictive of preterm birth (PTB). Molecular Study of Preterm Birth evaluated ancestral reference genomes, self-reported country of birth, race and ethnicity, as well as data from the electronic medical records (EMR). Family and racial predispositions to PTB suggest genomic characterizations may confer increased risk. OBJECTIVE: To investigate genomic ancestry utilizing the electronic medical record, self-reported race/ethnicity, and principle component analysis to determine the molecular characterization of genomics and preterm birth

Computerised interpretation of fetal heart rate during labour (INFANT): a randomised controlled trial

Background. Continuous electronic fetal heart-rate monitoring is widely used during labour, and computerised interpretation could increase its usefulness. We aimed to establish whether the addition of decision-support software to assist in the interpretation of cardiotocographs affected the number of poor neonatal outcomes. Methods. In this unmasked randomised controlled trial, we recruited women in labour aged 16 years or older having continuous electronic fetal monitoring, with a singleton or twin pregnancy, and at 35 weeks’ gestation or more at 24 maternity units in the UK and Ireland. They were randomly assigned (1:1) to decision support with the INFANT system or no decision support via a computer-generated stratified block randomisation schedule. The primary outcomes were poor neonatal outcome (intrapartum stillbirth or early neonatal death excluding lethal congenital anomalies, or neonatal encephalopathy, admission to the neonatal unit within 24 h for ≥48 h with evidence of feeding difficulties, respiratory illness, or encephalopathy with evidence of compromise at birth), and developmental assessment at age 2 years in a subset of surviving children. Analyses were done by intention to treat. This trial is completed and is registered with the ISRCTN Registry, number 98680152. Findings. Between Jan 6, 2010, and Aug 31, 2013, 47062 women were randomly assigned (23515 in the decision-support group and 23547 in the no-decision-support group) and 46042 were analysed (22987 in the decision-support group and 23055 in the no-decision-support group). We noted no difference in the incidence of poor neonatal outcome between the groups—172 (0·7%) babies in the decision-support group compared with 171 (0·7%) babies in the no-decision-support group (adjusted risk ratio 1·01, 95% CI 0·82–1·25). At 2 years, no significant differences were noted in terms of developmental assessment. Interpretation. Use of computerised interpretation of cardiotocographs in women who have continuous electronic fetal monitoring in labour does not improve clinical outcomes for mothers or babies

Linkage Disequilibrium and Inference of Ancestral Recombination in 538 Single-Nucleotide Polymorphism Clusters across the Human Genome

The prospect of using linkage disequilibrium (LD) for fine-scale mapping in humans has attracted considerable attention, and, during the validation of a set of single-nucleotide polymorphisms (SNPs) for linkage analysis, a set of data for 4,833 SNPs in 538 clusters was produced that provides a rich picture of local attributes of LD across the genome. LD estimates may be biased depending on the means by which SNPs are first identified, and a particular problem of ascertainment bias arises when SNPs identified in small heterogeneous panels are subsequently typed in larger population samples. Understanding and correcting ascertainment bias is essential for a useful quantitative assessment of the landscape of LD across the human genome. Heterogeneity in the population recombination rate, ρ=4Nr, along the genome reflects how variable the density of markers will have to be for optimal coverage. We find that ascertainment-corrected ρ varies along the genome by more than two orders of magnitude, implying great differences in the recombinational history of different portions of our genome. The distribution of [Formula: see text] is unimodal, and we show that this is compatible with a wide range of mixtures of hotspots in a background of variable recombination rate. Although [Formula: see text] is significantly correlated across the three population samples, some regions of the genome exhibit population-specific spikes or troughs in ρ that are too large to be explained by sampling. This result is consistent with differences in the genealogical depth of local genomic regions, a finding that has direct bearing on the design and utility of LD mapping and on the National Institutes of Health HapMap project

A 3.9-Centimorgan-Resolution Human Single-Nucleotide Polymorphism Linkage Map and Screening Set

Recent advances in technologies for high-throughout single-nucleotide polymorphism (SNP)–based genotyping have improved efficiency and cost so that it is now becoming reasonable to consider the use of SNPs for genomewide linkage analysis. However, a suitable screening set of SNPs and a corresponding linkage map have yet to be described. The SNP maps described here fill this void and provide a resource for fast genome scanning for disease genes. We have evaluated 6,297 SNPs in a diversity panel composed of European Americans, African Americans, and Asians. The markers were assessed for assay robustness, suitable allele frequencies, and informativeness of multi-SNP clusters. Individuals from 56 Centre d'Etude du Polymorphisme Humain pedigrees, with >770 potentially informative meioses altogether, were genotyped with a subset of 2,988 SNPs, for map construction. Extensive genotyping-error analysis was performed, and the resulting SNP linkage map has an average map resolution of 3.9 cM, with map positions containing either a single SNP or several tightly linked SNPs. The order of markers on this map compares favorably with several other linkage and physical maps. We compared map distances between the SNP linkage map and the interpolated SNP linkage map constructed by the deCode Genetics group. We also evaluated cM/Mb distance ratios in females and males, along each chromosome, showing broadly defined regions of increased and decreased rates of recombination. Evaluations indicate that this SNP screening set is more informative than the Marshfield Clinic’s commonly used microsatellite-based screening set