Genetic Consequences of the Transatlantic Slave Trade in the Americas

According to historical records of transatlantic slavery, traders forcibly deported an estimated 12.5 million people from ports along the Atlantic coastline of Africa between the 16th and 19th centuries, with global impacts reaching to the present day, more than a century and a half after slavery's abolition. Such records have fueled a broad understanding of the forced migration from Africa to the Americas yet remain underexplored in concert with genetic data. Here, we analyzed genotype array data from 50,281 research participants, which-combined with historical shipping documents-illustrate that the current genetic landscape of the Americas is largely concordant with expectations derived from documentation of slave voyages. For instance, genetic connections between people in slave trading regions of Africa and disembarkation regions of the Americas generally mirror the proportion of individuals forcibly moved between those regions. While some discordances can be explained by additional records of deportations within the Americas, other discordances yield insights into variable survival rates and timing of arrival of enslaved people from specific regions of Africa. Furthermore, the greater contribution of African women to the gene pool compared to African men varies across the Americas, consistent with literature documenting regional differences in slavery practices. This investigation of the transatlantic slave trade, which is broad in scope in terms of both datasets and analyses, establishes genetic links between individuals in the Americas and populations across Atlantic Africa, yielding a more comprehensive understanding of the African roots of peoples of the Americas.

Phenome-wide investigation of health outcomes associated with genetic predisposition to loneliness

Humans are social animals that experience intense suffering when they perceive a lack of social connection. Modern societies are experiencing an epidemic of loneliness. Although the experience of loneliness is universally human, some people report experiencing greater loneliness than others. Loneliness is more strongly associated with mortality than obesity, emphasizing the need to understand the nature of the relationship between loneliness and health. Although it is intuitive that circumstantial factors such as marital status and age influence loneliness, there is also compelling evidence of a genetic predisposition toward loneliness. To better understand the genetic architecture of loneliness and its relationship with associated outcomes, we extended the genome-wide association study meta-analysis of loneliness to 511 280 subjects, and detect 19 significant genetic variants from 16 loci, including four novel loci, as well as 58 significantly associated genes. We investigated the genetic overlap with a wide range of physical and mental health traits by computing genetic correlations and by building loneliness polygenic scores in an independent sample of 18 498 individuals with EHR data to conduct a PheWAS with. A genetic predisposition toward loneliness was associated with cardiovascular, psychiatric, and metabolic disorders and triglycerides and high-density lipoproteins. Mendelian randomization analyses showed evidence of a causal, increasing, the effect of both BMI and body fat on loneliness. Our results provide a framework for future studies of the genetic basis of loneliness and its relationship to mental and physical health.

"Score the Core" Web-based pathologist training tool improves the accuracy of breast cancer IHC4 scoring

Hormone receptor status is an integral component of decision-making in breast cancer management. IHC4 score is an algorithm that combines hormone receptor, HER2, and Ki-67 status to provide a semiquantitative prognostic score for breast cancer. High accuracy and low interobserver variance are important to ensure the score is accurately calculated; however, few previous efforts have been made to measure or decrease interobserver variance. We developed a Web-based training tool, called "Score the Core" (STC) using tissue microarrays to train pathologists to visually score estrogen receptor (using the 300-point H score), progesterone receptor (percent positive), and Ki-67 (percent positive). STC used a reference score calculated from a reproducible manual counting method. Pathologists in the Athena Breast Health Network and pathology residents at associated institutions completed the exercise. By using STC, pathologists improved their estrogen receptor H score and progesterone receptor and Ki-67 proportion assessment and demonstrated a good correlation between pathologist and reference scores. In addition, we collected information about pathologist performance that allowed us to compare individual pathologists and measures of agreement. Pathologists' assessment of the proportion of positive cells was closer to the reference than their assessment of the relative intensity of positive cells. Careful training and assessment should be used to ensure the accuracy of breast biomarkers. This is particularly important as breast cancer diagnostics become increasingly quantitative and reproducible. Our training tool is a novel approach for pathologist training that can serve as an important component of ongoing quality assessment and can improve the accuracy of breast cancer prognostic biomarkers.

Abstract P2-01-06: How much agreement can we expect on BI-RADS mammographic findings? Observer agreement among 10 expert mammographers

Purpose: To determine the agreement between expert readers on mammographic findings and calcification patterns.

Materials and Methods: Ten academic radiologists from 5 centers reviewed 250 de-identified mammographic cases without prior exams which were previously assessed as BI-RADS 4 or 5 with subsequent pathologic diagnosis by percutaneous or surgical biopsy. For benign cases diagnosed by percutaneous biopsy, 1 year of benign or negative imaging follow-up was required. Using standardized forms, each radiologist assessed the presence of any suspicious mammographic findings (microcalcifications, asymmetry (1-vew), focal asymmetry (2-view), architectural distortion), and the morphology (none, round/punctate, amorphous, coarse heterogeneous, fine pleomorphic, fine linear branching) and distribution (none, diffuse, regional, grouped, linear, segmental) of any identified microcalcifications. Agreement between radiologists for presence/absence of findings, morphology, and distribution of calcifications was determined by calculating the Kappa (k) coefficient with 95% confidence interval (95% CI). The kappa coefficient proposed strength of agreement is ≤0 = poor, .01-.20 = slight, .21-.40 = fair, .41-.60 = moderate, .61-.80 = substantial, and .81-1 = almost perfect, as established by Landis and Koch.1

Results: Of the 250 lesions, 156 (62%) were benign and 94 (38%) malignant. Agreement among the 10 expert readers was strongest for recognizing the presence/absence of calcifications (k = 0.82, 95% CI: 0.80-84), “almost perfect”). There was substantial agreement among the readers for the identification of a mass (k = 0.67, 95% CI: 0.66-69), whereas agreement was fair for the presence of a focal (2-view) asymmetry (k = 0.21, 95% CI: 0.1900.23) or architectural distortion (k = 0.28, 95%CI: 0.26-0.30). Agreement for asymmetries (1-view) was slight (k = 0.09, 95%CI: 0.08-0.11). Among the 6 categories of microcalcification distribution and morphology, reader agreement was moderate (distribution k = 0.60, 95%CI:0.59-0.61; morphology k = 0.51, 95%CI: 0.50-0.52).

Conclusion: When asked to characterize suspicious mammographic findings, this sampling of 10 expert academic breast imagers across 5 centers revealed varying strength of agreement for different findings, ranging from slight to almost perfect. Strongest agreement (“almost perfect”) was found for identifying the presence or absence of microcalcifications, although agreement drops to moderate when readers are asked to specify microcalcification morphology and distribution.

1 Landis JR, Koch GG. The measurement of observer agreement for categorical data. Biometrics.1977;33:159-174.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-01-06.

Raising the bar: Breast cancer biomarkers IHC4 harmonization from University of California-Athena pathology collaboration

80

Background: Breast cancer treatment depends on the accurate analysis of immunohistochemical biomarkers (IHC4): estrogen and progesterone receptors, Ki-67, HER2. The Athena Harmonization project was undertaken to reduce technical and scoring variances between different laboratories and different pathologists. Methods: Initial assessment: Five breast cancer samples were sectioned and distributed to 5 UC campuses, where IHC4 and HER2 FISH tests were done per usual methods. Samples were selected to cover the range of negative, positive, and moderate for each antigen. Stained slides were circulated to 10 pathologists for scoring. Digital whole slide images (WSI) were made and scored. Technical variance reduction: A Delphi voting process identified an ideal histology slide for each IHC4 antigen. Laboratories adjusted techniques to match the appearance of the ideal slides, followed by pathologist and quantitative image analysis (QIA) validation. Scoring variance reduction: A digital pathology training tool was created where pathologists scored breast cancer tissue microarrays with known scores for the IHC4 antigens. Results: Scoring variance did not exceed clinical thresholds, although there were significant technical and scoring variances between laboratories that could affect research outcomes. The mean values and variance were similar for WSI and glass slides, except for HER2 (higher scores on WSI but without benefit of workstation calibration). Each laboratory adjusted technical parameters to more closely match the ideal IHC4. Early QIA data indicate reduced variance between adjusted and ideal histology slides. Conclusions: Considerable and significant technical and interpretational variances between five University of California laboratories can be overcome by harmonizing protocols, setting new inter-institutional standards for pathology and histology best practices. Quantitative image analysis and whole slide imaging were instrumental. Subsequent harmonization will include cases near thresholds for clinical treatment guidelines.

Regional access to acute ischemic stroke intervention

BACKGROUND AND PURPOSE

Benefit-risk ratios from recombinant tissue plasminogen activator (rtPA) therapy for acute ischemic stroke demonstrate lack of efficacy if intravenous administration is commenced beyond 3 hours of symptom onset. We undertook to enhance therapeutic effectiveness by ensuring equitable access to rtPA for patients affected by acute ischemic stroke within a 20 000 km(2) population referral base served by a tertiary facility.

METHODS

Representatives of all provider groups involved in emergency medical services developed a Regional Acute Stroke Protocol (RASP), a coordinated regional system response by dispatch personnel, paramedics, physicians, community service providers, emergency and inpatient staff in community hospitals, and the tertiary facility acute stroke team.

RESULTS

As of July 26, 1999, all ambulance services in Southeastern Ontario began bypassing the closest hospital to deliver patients meeting the criteria for the RASP to the Kingston General Hospital. At 12 months, approximately 403 ischemic strokes have occurred in the region, the RASP has been activated 191 times, and 42 patients have received rtPA.

CONCLUSIONS

We conclude that (1) acute stroke patients in Southeastern Ontario have improved access to interventions for stroke care; (2) geography of the region is not a barrier to access to interventions for patients with acute stroke; and (3) acute ischemic stroke patients treated with rtPA account for 5% of all acute strokes and 10% of all ischemic strokes in this region.

SB-253514 and analogues; novel inhibitors of lipoprotein-associated phospholipase A2 produced by Pseudomonas fluorescens DSM 11579. I. Fermentation of producing strain, isolation and biological activity

Two new classes of inhibitors of LpPLA2 have been identified in fermentations of Pseudomonas fluorescens. The two structurally isomeric series differ in the geometry of closure of the bicyclic carbamate and comprise a range of compounds varying only in length of their lipophilic sidechain. The most abundant species were extracted from the cells and purified by silica and C18 chromatography. Members of the more stable class were shown to be potent and selective competitive inhibitors of LpPLA2.

Drawing a stripe in Drosophila imaginal disks: negative regulation of decapentaplegic and patched expression by engrailed

During development of the Drosophila adult appendage precursors, the larval imaginal disks, the decapentaplegic (dpp) gene is expressed in a stripe just anterior to the anterior/posterior (A/P) compartment boundary. Here, we investigate the genetic controls that lead to production of this stripe. We extend previous observations on leaky engrailed (en) mutations by showing that mutant clones completely lacking both en and invected (inv) activity ectopically express dpp-lacZ reporter genes in the posterior compartment, where dpp activity ordinarily is repressed. Similarly, patched (ptc) is also ectopically expressed in such posterior compartment en-inv- null clones. In contrast, these en-inv- clones exhibit loss of hedgehog (hh) expression. We suggest that the absence of dpp expression in the posterior compartment is due to direct repression by en. Ubiquitious expression of en in imaginal disks, produced by a hs-en construct, eliminates the expression of dpp-lacZ in its normal A/P boundary stripe. We identify three in vitro Engrailed binding sites in one of our dpp-lacZ reporter gene. Mutagenesis of these Engrailed binding sites results in ectopic expression of this reporter gene, but does not alter the normal stripe of expression at the A/P boundary. We propose that the en-hh-ptc regulatory loop that is responsible for segmental expression of wingless in the embryo is reutilized in imaginal disks to create a stripe of dpp expression along the A/P compartment boundary.

Non-epileptic attack disorder: a clinical audit

The results of an audit of all patients with non-epileptic attack disorder admitted over a 1-year period to a neuropsychiatry tertiary referral centre are presented. The high incidence of: sexual abuse, previous psychiatric history and previous brain injury is noted. Reference is made to the reaction of patients and relatives to disclosure of the diagnosis and the management difficulties which this group of patients pose. The different underlying psychopathological processes are discussed and it is suggested that the diagnosis of NEAD, purely by the exclusion of epilepsy, might carry the risk of treating these patients as a homogenous group. An eclectic approach by an experienced, multi-disciplinary team is probably the most appropriate way of successfully managing the condition.

Setting community health goals: one District Health Councils experience

The Niagara District Health Council has embarked on a strategic planning exercise to develop health goals, objectives and preliminary targets for action. This process was approached in three phases: establishment of a Health Goals Task Force and adoption of the five goals developed by the Premier's Council on Health Strategy; planning and implementation of a Health Goals Consultation Day to involve community members in the identification and priority ranking of objectives; and development of measurable and realistic preliminary targets through consultations with expert groups and individuals. This process is a practical planning tool applicable across sectors and communities.

Inhibition of the -lactamases of Escherichia coli and Klebsiella aerogenes by semi-synthetic penicillins

1. A new automated micro-iodometric method is described for screening compounds for inhibitory action against beta-lactamase enzymes. 2. Over 1000 semi-synthetic penicillins were tested for inhibitory activity against the beta-lactamase of Escherichia coli B11 and 18 showed a fractional inhibition similar to or higher than that of methicillin. 3. The best inhibitors were alkoxy- and halogen-substituted phenyl-, naphthyl- or quinolyl-penicillins. 2-Isopropoxy-1-naphthylpenicillin (BRL 1437) was clearly the best and had a K(i) value about 1% of that of methicillin. 4. The inhibition of the beta-lactamase of E. coli B11 by BRL 1437 was shown to be reversible and competitive. The K(i) was 0.004mum and K(i)/K(m) with ampicillin and p-hydroxyampicillin (BRL 2333) was about 0.0001. The K(m) and V(max.) values were determined for the beta-lactamases of E. coli B11 and Klebsiella aerogenes A against a variety of penicillins. Cell-bound and solubilized enzymes gave similar K(i) and K(m) values. 5. BRL 1437 was superior to cloxacillin and methicillin for inhibition of the beta-lactamase of live, fully grown cultures of several strains of E. coli and K. aerogenes. Of a group of inhibitors BRL 1437 was the most stable to the beta-lactamase of E. coli B11.