Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The role of clinic-based breastfeeding peer counseling on breastfeeding rates among low-income patients

Background: Despite the benefits of breastfeeding (BF), rates remain lower than public health targets, particularly among low-income Black populations. Community-based breastfeeding peer counselor (BPC) programs have been shown to increase BF. We sought to examine whether implementation of a BPC program in an obstetric clinical setting serving low-income patients was associated with improved BF initiation and exclusivity. Methods: This is a quasi-experimental time series study of pregnant and postpartum patients receiving care before and after implementation of a BPC program in a teaching hospital affiliated prenatal clinic. The role of the BPC staff included BF classes, prenatal counseling and postnatal support, including in-hospital assistance and phone triage after discharge. Records were reviewed at each of 3 time points: immediately before the hire of the BPC staff (2008), 1-year post-implementation (2009), and 5 years post-implementation (2014). The primary outcomes were rates of breastfeeding initiation and exclusivity prior to hospital discharge, secondary outcomes included whether infants received all or mostly breastmilk during inpatient admission and by 6 weeks post-delivery. Bivariable and multivariable analyses were utilized as appropriate. Results: Of 302 patients included, 52.3% identified as non-Hispanic Black and 99% had Medicaid-funded prenatal care. While there was no improvement in rates of BF initiation, exclusive BF during the postpartum hospitalization improved during the 3 distinct time points examined, increasing from 13.7% in 2008 to 32% in 2014 (2009 aOR 2.48, 95%CI 1.13-5.43; 2014 aOR 1.82, 95%CI 1.24-2.65). This finding was driven by improved exclusive BF for patients who identified as Black (9.4% in 2008, 22.9% in 2009, and 37.9% in 2014, p = 0.01). Conclusion: Inpatient BF exclusivity significantly increased with the tenure of a BPC program in a low-income clinical setting. These findings demonstrate that a BPC program can be a particularly effective method to address BF disparities among low-income Black populations.</p

Maternal plasma and salivary anelloviruses in pregnancy and preterm birth

Introduction: Human anelloviruses, including torque teno virus (TTV) and torque teno mini virus (TTMV), are ubiquitous in the general population and have no known pathogenicity. We investigated the prevalence and viral load of TTV and TTMV in plasma and saliva over pregnancy, and assessed their association with spontaneous or medically indicated preterm birth. Methods: This is a secondary analysis of the Measurement of Maternal Stress (MOMS) study, which recruited 744 individuals with singleton pregnancies from 4 US sites (Chicago, Pittsburgh, San Antonio, and rural Pennsylvania). Baseline outpatient visits took place in the second trimester (between 12′0 and 20′6/7  weeks’ gestation), and follow-up visits in the third trimester (between 32′0 and 35′6/7  weeks’ gestation). In a case-control study design, participants who delivered preterm ( Results: TTV was detected in plasma from 81% (second trimester) and 77% (third trimester) of participants, and in saliva from 64 and 60%. Corresponding detection rates for TTMV were 59 and 41% in plasma, and 35 and 24% in saliva. TTV and TTMV concentrations were similar between matched plasma and saliva samples. TTV prevalence and concentrations were not significantly different between groups (sPTB, iPTB, and controls). However, plasma TTMV in the third trimester was associated with sPTB and earlier gestational age at delivery. The iPTB group was not different from either the sPTB or the control group. In saliva, concentrations of TTV and TTMV were similar among the three groups. Both TTV and TTMV were more prevalent with increasing parity and were more common in Black and Hispanic participants compared to non-Hispanic White participants. Conclusion: Anellovirus presence (specifically, TTMV) in the third trimester may be associated with preterm birth. Whether this association is causative remains to be determined.</p

Using graph learning to understand adverse pregnancy outcomes and stress pathways.

To identify pathways between stress indicators and adverse pregnancy outcomes, we applied a nonparametric graph-learning algorithm, PC-KCI, to data from an observational prospective cohort study. The Measurement of Maternal Stress study (MOMS) followed 744 women with a singleton intrauterine pregnancy recruited between June 2013 and May 2015. Infant adverse pregnancy outcomes were prematurity (<37 weeks' gestation), infant days spent in hospital after birth, and being small for gestational age (percentile gestational weight at birth). Maternal adverse pregnancy outcomes were pre-eclampsia, gestational diabetes, and gestational hypertension. PC-KCI replicated well-established pathways, such as the relationship between gestational weeks and preterm premature rupture of membranes. PC-KCI also identified previously unobserved pathways to adverse pregnancy outcomes, including 1) a link between hair cortisol levels (at 12-21 weeks of pregnancy) and pre-eclampsia; 2) two pathways to preterm birth depending on race, with one linking Hispanic race, pre-gestational diabetes and gestational weeks, and a second pathway linking black race, hair cortisol, preeclampsia, and gestational weeks; and 3) a relationship between maternal childhood trauma, perceived social stress in adulthood, and low weight for gestational age. Our approach confirmed previous findings and identified previously unobserved pathways to adverse pregnancy outcomes. It presents a method for a global assessment of a clinical problem for further study of possible causal pathways