Genetic variation, classification and race. Nat Genet. 2004;36:S28–S33. [PMID: 15508000 DOI: 10.1038/ng1435]

The reporting of social determinants of health in pediatric dermatology clinical trials: a systematic review

Background

Despite the acknowledgment of the importance of social determinants of health (SDOH) on clinical outcomes, few clinical trials provide information about SDOH. Including these markers in pediatric dermatologic clinical trials may lead to improved care and novel observations about the disease.

Objective

Using a systematic review, assess the use of SDOH in pediatric dermatology clinical trials.

Methods

CINAHL Plus, Cochrane: CENTRAL, Embase, PubMed, and Scopus were searched. English language randomized controlled trials about pediatric dermatology diseases published from January 2011 to May 2022 were included. Two authors independently screened all records using Covidence at 2 levels. Two authors independently collected data using Covidence and Microsoft Excel and assessed study quality. A protocol was registered at Open Science Framework: https://doi.org/10.17605/OSF.IO/B93VY.

Results

A total of 6463 records were retrieved and 4298 were screened at title/abstract. Next, 1738 records were screened at full text and 1085 were included. Of these, 119 reported an SDOH factor for a pediatric dermatology disease. Income or socioeconomic status was the factor most reported followed by social support, location, and health insurance. Most of the studies were conducted outside of the United States.

Limitations

There are a limited number of dermatology clinical trials that include a pediatric population.

Conclusion

Despite including over 1000 pediatric dermatology clinical trials, only 119 used SDOH. Pediatric dermatology researchers must prioritize including and reporting additional SDOH in clinical trials if the goal is to impact and improve clinical care and innovate for diverse populations of patients.

Duration of Residence and Hypertension in Black Foreign-Born Residents: NHIS, 2004-2017

BACKGROUND

Black Americans have the highest prevalence of hypertension in the USA. Black immigrants, who, by definition, have time-limited exposure to the USA, may provide insight into the relationship between exposure to the US environment, Black race, and hypertension.

METHODS

This is a cross-sectional analysis of pooled National Health Interview Survey (2004-2017) data of foreign-born White European and Black adults (N = 11,516). Multivariable robust Poisson regressions assessed the relationship between self-reported hypertension and duration of the residency (< 5, 5-9, 10-14, ≥ 15 years) among Black, Black African, Black Caribbean, and White European foreign-born residents.

RESULTS

In multivariable analyses-controlling for age, sex, education, poverty-to-income ratio, insurance status, recent encounter with a clinician, and BMI-Black foreign-born residents (PR = 1.40, 95% CI = 1.03, 1.90) and Black Africans (10-14 years.: PR = 1.70, 95% CI = 1.13, 2.56; ≥ 15 years.: PR = 1.56, 95% CI = 1.04, 2.34) with a duration of residency of at least 15 and 10 years, respectively, had a greater prevalence of hypertension than those with duration less than 5 years. A nonsignificant positive association between a duration of residency of at least 15 years (compared to less than 5 years) and self-reported hypertension was observed for White Europeans (PR 1.49, 95% CI = 0.88, 2.51) and Black Caribbeans (PR = 1.09, 95% CI = 0.69, 1.72).

CONCLUSION

Duration of residency is particularly associated with hypertension among Black Africans after migration to the USA. This discrepancy may be explained by differences in primary care utilization and awareness of hypertension diagnoses among recent African immigrants, along with greater stress associated with living in the USA.

Ancestry, race and ethnicity: the role and relevance of language in clinical genetics practice

BACKGROUND

The terms ancestry, race and ethnicity are used variably within the medical literature and within society and clinical care. Biological lineage can provide an important context for the interpretation of genomic data, but the language used, and practices around when to ascertain this, vary.

METHODS

Using a fictional case scenario we explore the relevance of questions around ancestry, race and ethnicity in clinical genetic practice.

RESULTS

In the UK, data on 'ethnicity' are routinely collected by those using genomic medicine, as well as within the wider UK National Health Service, although the reasons for this are not always clear to practitioners and patients. Sometimes it is requested as a proxy for biological lineage to aid variant interpretation, refine estimations of carrier frequency and guide decisions around the need for pharmacogenetic testing.

CONCLUSION

There are many challenges around the use and utility of these terms. Currently, genomic databases are populated primarily with data from people of European descent, and this can lead to health disparities and poorer service for minoritised or underserved populations. Sensitivity and consideration are needed when communicating with patients around these areas. We explore the role and relevance of language around biological lineage in clinical genetics practice.

A Systems Biology Approach to Understand the Racial Disparities in Colorectal Cancer

Racial disparities between Black/African Americans (AA) and White patients in colorectal cancer are an ever-growing area of concern. Black/AA show the highest incidence and have the highest mortality among major U.S. racial groups. There is no definite cause other than possible sociodemographic, socioeconomic, education, nutrition, delivery of healthcare, screening, and cultural factors. A primary limitation in this field is the lack of and small sample size of Black/AA studies. Thus, this study aimed to investigate whether differences in gene expression contribute to this ongoing unanswered racial disparity issue. In this study, we examined transcriptomic data of Black/AA and White patient cohorts using a bioinformatic and systems biology approach. We performed a Kaplan-Meier overall survival analysis between both patient cohorts across critical colorectal cancer signal transduction networks (STN), to determine the differences in significant genes across each cohort. Other bioinformatic analyses performed included PROGENy (pathway responsive genes for activity inference), RNA sequencing differential expression using DESeq2, multivariable-adjusted regression, and other associated Kaplan-Meier analyses. These analyses identified novel prognostic genes independent from each cohort, 176 differentially expressed genes, and specific patient cohort STN survival associations. Despite the overarching limitation, the results revealed several novel differences in gene expression between the colorectal cancer Black/AA and White patient cohorts, which allows one to dive deeper into and understand the behavior on a systems level of what could be driving this racial difference across colorectal cancer. Concretely, this information can guide precision medicine approaches tailored specifically for colorectal cancer racial disparities.

SIGNIFICANCE

The purpose of this work is to investigate the racial disparities in colorectal cancer between Black/AA and White patient cohorts using a systems biology and bioinformatic approach. Our study investigates the underlying biology of each patient cohort. Concretely, the findings of this study include disparity-associated genes and pathways, which provide a tangible starting point to guide precision medicine approaches tailored specifically for colorectal cancer racial disparities.

Constructing a South Asian cardiovascular disease: a qualitative analysis on how researchers study cardiovascular disease in South Asians

BACKGROUND

Debates on the use of race in biomedical research have typically overlooked immigrant groups outside of the black-white racial dichotomy. Recent biomedical research on South Asians and cardiovascular disease provides an opportunity to understand how scientists define race and interpret racial health disparities from an underexamined perspective.

PURPOSE

To examine how researchers in the Mediators of Atherosclerosis in South Asians Living in America (MASALA) study defined a South Asian population, and then compared health differences between South Asians and other populations.

METHODS

Qualitative content analysis was performed on eleven articles from August 2013 to January 2021 that directly compared the South Asian cohort in MASALA to four other groups. The MASALA study design article was also included in this analysis. Articles were analysed for how South Asians were defined, and for how health differences between South Asians and other populations were studied and discussed.

RESULTS

Researchers in MASALA were neither clear nor precise in defining South Asians as either an ancestral group or ethnic group. Their studies also prioritised investigating genetic and molecular causes of the cardiovascular health disparity between South Asians and other populations and failed to examine possible social factors.

CONCLUSIONS

These findings reflect a broader trend in biomedical research in which race and racial health disparities are poorly defined and studied, limiting scientists' understanding of the relationship between race and health. I propose methodologies to help researchers define populations and design studies without relying on biologically reductive assumptions.

Reconsidering the use of race adjustments in maternal serum screening

The use of race in maternal serum screening is problematic because race is a social construct rather than a distinct biological classifier. Nevertheless, laboratories offering this testing are encouraged to use race-specific cutoff values for maternal serum screening biomarkers to determine the risk of fetal abnormalities. Large cohort studies examining racial differences in maternal serum screening biomarker concentrations have yielded conflicting results, which we postulate may be explained by genetic and socioeconomic differences between racial cohorts in different studies. We recommend that the use of race in maternal serum screening should be abandoned. Further research is needed to identify socioeconomic and environmental factors that contribute to differences in maternal serum screening biomarker concentrations observed between races. A better understanding of these factors may facilitate accurate race-agnostic risk estimates for aneuploidy and neural tube defects.

Coarse Race and Ethnicity Labels Mask Granular Underdiagnosis Disparities in Deep Learning Models for Chest Radiograph Diagnosis

See also the editorial by Nikolic in this issue.

Scientific supremacy: How do genetic narratives relate to racism?

Recent research suggests that contemporary American society is marked by heightened hostile racial rhetoric, alongside increasing salience of White nationalists who justify an ideology of racial hierarchy with claims of biological superiority. Media coverage of such genetics research has often emphasized a deterministic (or causal) narrative by suggesting that specific genes directly increase negative outcomes and highlighting reported genetic differences between racial groups. Across two experimental studies, we examine the effect of the media's portrayal of scientific findings linking genes with negative health and behavioral outcomes on measures of racism. We find that deterministic genetic attributions for health and behavioral outcomes can lead to more negative racial out-group attitudes. Importantly, we also investigate potential interventions in the presentation of genetic science research. Our research has implications for understanding racial attitudes and racialized ideology in contemporary American politics, as well as for framing scientific communication in intergroup contexts.

Racism, Power, And Health Equity: The Case Of Tenant Organizing

Racial disparities in health are among the most disconcerting forms of inequity in the United States. Divergent health outcomes between Americans racialized as White and those racialized as Black, Latinx, and Indigenous do not stem from biological or genetic differences. To the contrary, "race" comes to have concrete consequences through social, economic, and political systems. Yet the political contours of health equity remain especially understudied. This article places the politics of health equity in the foreground through the lens of housing, a critical determinant of health. Drawing on in-depth qualitative evidence rooted in the experiences of tenants who confront health-threatening housing conditions, I examine how people within racially and economically marginalized communities organize to build political power in response to those conditions. By charting how tenants navigate state and local political processes, I demonstrate the possibilities for organized tenants to wield power in ways that help advance health equity in the face of structural racism.

Promoting Equity In Clinical Decision Making: Dismantling Race-Based Medicine

As the use of artificial intelligence has spread rapidly throughout the US health care system, concerns have been raised about racial and ethnic biases built into the algorithms that often guide clinical decision making. Race-based medicine, which relies on algorithms that use race as a proxy for biological differences, has led to treatment patterns that are inappropriate, unjust, and harmful to minoritized racial and ethnic groups. These patterns have contributed to persistent disparities in health and health care. To reduce these disparities, we recommend a race-aware approach to clinical decision support that considers social and environmental factors such as structural racism and social determinants of health. Recent policy changes in medical specialty societies and innovations in algorithm development represent progress on the path to dismantling race-based medicine. Success will require continued commitment and sustained efforts among stakeholders in the health care, research, and technology sectors. Increasing the diversity of clinical trial populations, broadening the focus of precision medicine, improving education about the complex factors shaping health outcomes, and developing new guidelines and policies to enable culturally responsive care are important next steps.

Is everyone a mix of straight and gay? A social pressure theory of sexual orientation, with supporting data from a large global sample

Sigmund Freud, Alfred Kinsey, E.O. Wilson, and others have suggested that social pressure suppresses natural tendencies for humans to express bisexuality, the apparent norm for one of our two closest genetic relatives, the bonobo. An analysis of data obtained from a new online sample of 1,150,938 people in 215 countries and territories (63.9% from the United States, United Kingdom, and Canada) who completed the English version of a validated questionnaire of sexual orientation lends support to this idea. A histogram of scores from 0 (exclusive opposite-sex inclinations) to 18 (exclusive same-sex inclinations) forms a near-normal distribution. Although this distribution was likely caused to some extent by sampling bias, it may also reflect the unusual honesty people show when taking online tests anonymously, as an increasing body of evidence demonstrates. We present a formal mathematical expression of a social pressure theory of sexual orientation, along with empirical evidence and computational explorations that support the theory. We also present an analysis of the new data set. Among other findings: sexual orientation labels corresponded to broad, skewed, overlapping distributions of scores. Self-labeled gays/lesbians and, to a greater extent, self-labeled straights, reported that the larger the mismatch between their sexual orientation label and their actual sexual inclinations, the more distress they felt regarding their sexual orientation, a finding that is predictable from cognitive dissonance theory. Educating the public about the true nature of sexual orientation might quell the often rancorous public debates on this topic, as well as give comfort to a large number of mislabeled people.

AACC/NKF Guidance Document on Improving Equity in Chronic Kidney Disease Care

BACKGROUND

Kidney disease (KD) is an important health equity issue with Black, Hispanic, and socioeconomically disadvantaged individuals experiencing a disproportionate disease burden. Prior to 2021, the commonly used estimated glomerular filtration rate (eGFR) equations incorporated coefficients for Black race that conferred higher GFR estimates for Black individuals compared to non-Black individuals of the same sex, age, and blood creatinine concentration. With a recognition that race does not delineate distinct biological categories, a joint task force of the National Kidney Foundation and the American Society of Nephrology recommended the adoption of the CKD-EPI 2021 race-agnostic equations.

CONTENT

This document provides guidance on implementation of the CKD-EPI 2021 equations. It describes recommendations for KD biomarker testing, and opportunities for collaboration between clinical laboratories and providers to improve KD detection in high-risk populations. Further, the document provides guidance on the use of cystatin C, and eGFR reporting and interpretation in gender-diverse populations.

SUMMARY

Implementation of the CKD-EPI 2021 eGFR equations represents progress toward health equity in the management of KD. Ongoing efforts by multidisciplinary teams, including clinical laboratorians, should focus on improved disease detection in clinically and socially high-risk populations. Routine use of cystatin C is recommended to improve the accuracy of eGFR, particularly in patients whose blood creatinine concentrations are confounded by processes other than glomerular filtration. When managing gender-diverse individuals, eGFR should be calculated and reported with both male and female coefficients. Gender-diverse individuals can benefit from a more holistic management approach, particularly at important clinical decision points.

Refractive development I: Biometric changes during emmetropisation

PURPOSE

Although there are many reports on ocular growth, these data are often fragmented into separate parameters or for limited age ranges. This work intends to create an overview of normal eye growth (i.e., in absence of myopisation) for the period before birth until 18 years of age.

METHODS

The data for this analysis were taken from a search of six literature databases using keywords such as "[Parameter] & [age group]", with [Parameter] the ocular parameter under study and [age group] an indication of age. This yielded 34,409 references that, after screening of title, abstract and text, left 294 references with usable data. Where possible, additional parameters were calculated, such as the Bennett crystalline lens power, whole eye power and axial power.

RESULTS

There were 3422 average values for 17 parameters, calculated over a combined total of 679,398 individually measured or calculated values. The age-related change in refractive error was best fitted by a sum of four exponentials (r²  = 0.58), while all other biometric parameters could be fitted well by a sum of two exponentials and a linear term ('bi-exponential function'; r² range: 0.64-0.99). The first exponential of the bi-exponential fits typically reached 95% of its end value before 18 months, suggesting that these reached genetically pre-programmed passive growth. The second exponentials reached this point between 4 years of age for the anterior curvature and well past adulthood for most lenticular dimensions, suggesting that this part represents the active control underlying emmetropisation. The ocular components each have different growth rates, but growth rate changes occur simultaneously at first and then act independently after birth.

CONCLUSIONS

Most biometric parameters grow according to a bi-exponential pattern associated with passive and actively modulated eye growth. This may form an interesting reference to understand myopisation.

Anti-Melanogenic Potential of Natural and Synthetic Substances: Application in Zebrafish Model

Melanogenesis is a biosynthetic pathway for the formation of the pigment melanin in human skin. A key enzyme in the process of pigmentation through melanin is tyrosinase, which catalyzes the first and only limiting step in melanogenesis. Since the discovery of its methanogenic properties, tyrosinase has been the focus of research related to the anti-melanogenesis. In addition to developing more effective and commercially safe inhibitors, more studies are required to better understand the mechanisms involved in the skin depigmentation process. However, in vivo assays are necessary to develop and validate new drugs or molecules for this purpose, and to accomplish this, zebrafish has been identified as a model organism for in vivo application. In addition, such model would allow tracking and studying the depigmenting activity of many bioactive compounds, important to genetics, medicinal chemistry and even the cosmetic industry. Studies have shown the similarity between human and zebrafish genomes, encouraging their use as a model to understand the mechanism of action of a tested compound. Interestingly, zebrafish skin shares many similarities with human skin, suggesting that this model organism is suitable for studying melanogenesis inhibitors. Accordingly, several bioactive compounds reported herein for this model are compared in terms of their molecular structure and possible mode of action in zebrafish embryos. In particular, this article described the main metabolites of Trichoderma fungi, in addition to substances from natural and synthetic sources.

Investigation of racial differences in survival from non-small cell lung cancer with immunotherapy use: A Texas study

Background

The use of immunotherapy is associated with improved survival among patients with Non-Small Cell Lung Cancer (NSCLC) and has gained widespread use in its management. However, there is limited information on whether the survival benefits associated with immunotherapy differ among races and ethnicities.

Objective

This study aimed to investigate racial differences in survival amongst patients with NSCLC who received immunotherapy as the first-line treatment in Texas.

Methods

Patients with NSCLC who received immunotherapy between October 2015 to December 2018 were identified from the Texas Cancer Registry (TCR). Disease-specific survival was evaluated and compared among patients across racial/ethnic categories using the Kaplan-Meier survival analysis, log-rank test, and a multivariable Cox proportional hazard regression model following an inverse probability treatment weighting (IPTW) propensity score analysis.

Results

A total of 1453 patients were included in the analysis. Median survival (in months) was longest among Asians (34, 95% CI: 15-Not Estimable), followed by African Americans (AAs) (23, 95% CI: 15-34), Hispanics (22, 95% CI: 16-26), and Whites (19, 95% CI: 17-22). The adjusted regression estimates had no statistically significant differences in survival among AAs (aHR = 0.97; 95% CI = 0.78-1.20; P =0.77) and Hispanics (aHR = 0.96; 95% CI = 0.77-1.19, P =0.73) when compared to White patients. Asians on the other hand, had 40% reduction in mortality risk compared to Whites (aHR = 0.60; 95% CI = 0.39-0.94, P = 0.03).

Conclusions

Our study indicated that African Americans and Hispanics do not have poorer survival compared to White patients when receiving immunotherapy as first-line treatment. Asians however had longer survival compared to Whites. Our findings suggest that existing racial disparity in NSCLC survival might be mitigated with the use of immunotherapy and should be considered in providing care to these minority groups.

Evaluation of alveolar antral anastomosis in south Indian population using cone beam computed tomography: a prospective study

OBJECTIVES

The posterior superior alveolar artery (PSAA) and the infraorbital artery (IOA), both of which are ultimate branches of the maxillary artery, are connected by a horizontal anastomosis. PSAA anastomoses intraosseously and extraosseously with IOA. Profuse bleeding from the lateral wall while performing the direct sinus augmentation is a significant intraoperative complication.Thus the present study focused to assess the location of an alveolar antral anastomosis (AAA) in relation to the crest of the alveolar bone using cone beam computed tomography (CBCT).

METHODS

A total of 200 CBCT scans of patients who were indicated for implant surgery were chosen and assessed. Group 1 includes 100 dentate patients and Group 2 includes 100 partially edentulous patients. The location of anastomosis along the lateral wall of the maxillary sinus was evaluated in association with alveolar bone height with respect to three posterior maxillary teeth: first premolar, second premolar, and first molar.

RESULTS

The mean distance for P1, P2, and M1 was 21.94 ± 1.02 mm, 19.41 ± 0.40 mm, and 17.36 ± 0.51 mm, respectively, in the dentate group, whereas in the edentulous group, it was 20.07 ± 0.46 mm, 18.95 ± 0.32 mm, and 16.08 ± 0.16 mm. In 80% of participants, the distance of an AAA from the alveolar crest was between 16 and 23 mm, whereas in 12% of the participants the distance of an AAA from the alveolar crest was less than 16 mm.

CONCLUSION

The present study concludes that the first premolar region is safe for preparing the lateral window but for the second premolar and first molar additional care should be taken prior to surgery.

Laboratory Result Reference Ranges Stratified for Patient-Reported Sex and Ethnicity Are More Closely Associated With Postoperative Outcomes Than Currently Used Reference Ranges: A Retrospective Data Analysis

BACKGROUND

A single laboratory range for all individuals may fail to take into account underlying physiologic differences based on sex and genetic factors. We hypothesized that laboratory distributions differ based on self-reported sex and ethnicity and that ranges stratified by these factors better correlate with postoperative mortality and acute kidney injury (AKI).

METHODS

Results from metabolic panels, complete blood counts, and coagulation panels for patients in outpatient encounters were identified from our electronic health record. Patients were grouped based on self-reported sex (2 groups) and ethnicity (6 groups). Stratified ranges were set to be the 2.5th/97.5th percentile for each sex/ethnic group. For patients undergoing procedures, each patient/laboratory result was classified as normal/abnormal using the stratified and nonstratified (traditional) ranges; overlap in the definitions was assessed between the 2 classifications by looking for the percentage of agreement in result classifications of normal/abnormal using the 2 methods. To assess which definitions of normal are most associated with adverse postoperative outcomes, the odds ratio (OR) for each outcome/laboratory result pair was assessed, and the frequency that the confidence intervals of ORs for the stratified versus nonstratified range did not overlap was examined.

RESULTS

Among the 300 unique combinations (race × sex × laboratory type), median proportion overlap (meaning patient was either "normal" or "abnormal" for both methodologies) was 0.86 [q1, 0.80; q3, 0.89]. All laboratory results except 6 overlapped at least 80% of the time. The frequency of overlap did not differ among the racial/ethnic groups. In cases where the ORs were different, the stratified range was better associated with both AKI and mortality (P < .001). There was no trend of bias toward any specific sex/ethnic group.

CONCLUSIONS

Baseline "normal" laboratory values differ across sex and ethnic groups, and ranges stratified by these groups are better associated with postoperative AKI and mortality as compared to the standard reference ranges.

Physicians' Perceptions of Race and Engagement in Race-Based Clinical Practice: a Mixed-Methods Systematic Review and Narrative Synthesis

BACKGROUND

Using race-a socially assigned identity that does not adequately capture human genetic variation-to guide clinical care can result in poor outcomes for racially minoritized patients. This study assessed (1) how physicians conceptualize and use race in their clinical care (race-based care) and (2) physician characteristics associated with race-based care.

METHODS

PubMed, CINAHL, EMBASE, and Scopus databases were searched. Qualitative, quantitative, and mixed-methods studies written in peer-reviewed, English-language journal articles evaluating US physicians' perceptions of race and physician factors associated with race-based care were included. Risk of bias was assessed using the Mixed Methods Appraisal Tool. Qualitative studies were evaluated using thematic analysis, and quantitative findings were summarized and combined with qualitative findings in a narrative synthesis.

RESULTS

A total of 1149 articles were identified; 9 (4 qualitative, 5 quantitative) studies met inclusion criteria. Five themes emerged: (1) the belief in race as biological; (2) the use of race to contextualize patients' health; (3) the use of race to counsel patients and determine care; (4) justifications for race-based practice (evidence-based, personal experience, addresses disparities, provides personalized care, increases compliance); and (5) concerns with race-based practice (poorly characterizes patients, normalizes disparities, patient distrust, clinician discomfort, legitimized biological race). In quantitative studies, older age was positively associated with race-based care.

DISCUSSION

Physicians had varied perceptions of race, but many believed race was biological. Concern and support for race-based practice were related to beliefs regarding the evidence for using race in care and the appropriateness of race as a variable in medical research. Older physicians were more likely to use race, which could be due to increased exposure to race-based medical literature, in addition to generational differences in conceptualizations of race. Additional research on the evolution of physicians' perceptions of race, and the role of medical literature in shaping these perceptions, is needed.

Metabolic diversity in human populations and correlation with genetic and ancestral geographic distances

DNA polymorphic markers and self-defined ethnicity groupings are used to group individuals with shared ancient geographic ancestry. Here we studied whether ancestral relationships between individuals could be identified from metabolic screening data reported by the California newborn screening (NBS) program. NBS data includes 41 blood metabolites measured by tandem mass spectrometry from singleton babies in 17 parent-reported ethnicity groupings. Ethnicity-associated differences identified for 71% of NBS metabolites (29 of 41, Cohen's d &gt; 0.5) showed larger differences in blood levels of acylcarnitines than of amino acids (P &lt; 1e-4). A metabolic distance measure, developed to compare ethnic groupings based on metabolic differences, showed low positive correlation with genetic and ancient geographic distances between the groups' ancestral world populations. Several outlier group pairs were identified with larger genetic and smaller metabolic distances (Black versus White) or with smaller genetic and larger metabolic distances (Chinese versus Japanese) indicating the influence of genetic and of environmental factors on metabolism. Using machine learning, comparison of metabolic profiles between all pairs of ethnic groupings distinguished individuals with larger genetic distance (Black versus Chinese, AUC = 0.96), while genetically more similar individuals could not be separated metabolically (Hispanic versus Native American, AUC = 0.51). Additionally, we identified metabolites informative for inferring metabolic ancestry in individuals from genetically similar populations, which included biomarkers for inborn metabolic disorders (C10:1, C12:1, C3, C5OH, Leucine-Isoleucine). This work sheds new light on metabolic differences in healthy newborns in diverse populations, which could have implications for improving genetic disease screening.

Society for Maternal-Fetal Medicine Special Statement: Race in maternal-fetal medicine research- Dispelling myths and taking an accurate, antiracist approach

Profound inequities in maternal and infant outcomes based on race exist, and the maternal-fetal medicine community has an important role in eliminating these disparities. Accurately employing race and ethnicity as social constructs within research that guides clinical practice is essential to achieving health equity. We must abandon commonly propagated myths that race is a surrogate for genetics or economic status and that data are exempt from potential bias. These myths can lead to harmful misconceptions that exacerbate racial disparities in maternal and infant health outcomes. Furthermore, these myths obscure racism as the true underlying etiology of racial disparities. Understanding that race is a social construct and using an antiracist approach to research are essential in combating racism and eliminating unacceptable disparities in maternal and infant health. This document provides specific suggestions to approach the research process with an antiracist framework.

Racial Disparities in Ion Channelopathies and Inherited Cardiovascular Diseases Associated With Sudden Cardiac Death

Cardiovascular disease (CVD) continues to be the most common cause of death worldwide, and cardiac arrhythmias account for approximately one half of these deaths. The morbidity and mortality from CVD have been reduced significantly over the past few decades; however, disparities in racial or ethnic populations still exist. This review is based on available literature to date and focuses on known cardiac channelopathies and other inherited disorders associated with sudden cardiac death in African American/Black subjects and the role of epigenetics in phenotypic manifestations of CVD, and illustrates existing disparities in treatment and outcomes. The review also highlights the knowledge gaps that limit understanding of the manifestation of phenotypic abnormalities across racial or ethnic groups and discusses disparities associated with device underuse in the management of patients at risk for sudden cardiac death. We discuss factors related to reports in the United States, that the overall mortality attributed to CVD and the number of out‐of‐hospital cardiac arrests are higher among African American/Black subjects when compared with other racial or ethnic groups. African American/Black subjects are disproportionally affected by CVD, including cardiac arrhythmias and sudden cardiac death, thus highlighting a major concern in this population that remains underrepresented in clinical trials with limited genetic testing and device underuse. The proposed solutions include (1) early identification of genetic variants, which is crucial in tailoring a preventive management strategy; (2) inclusion of diverse racial or ethnic groups in clinical trials; (3) compliance with guideline‐directed medical treatment and referral to cardiovascular subspecialists; and (4) training and mentoring of underrepresented junior faculty in cardiovascular health disparities research.

Multimodal Imaging Comparison of Polypoidal Choroidal Vasculopathy Between Asian and Caucasian Populations

PURPOSE

Differences in multimodal imaging features between Asian and Caucasian eyes may contribute to our understanding of the etiology of the polypoidal choroidal vasculopathy (PCV). The purpose of this study was to compare the multimodal imaging features of Asian and Caucasian eyes with PCV.

DESIGN

Cross-sectional, retrospective, multicenter, observational case series.

METHODS

Consecutive treatment-naïve patients diagnosed with PCV based on indocyanine green angiography in accordance with published guidelines. Demographic and multimodal imaging findings based on color fundus photography, spectral domain optical coherence tomography, fluorescein angiography, and indocyanine green angiography were graded.

RESULTS

A total of 250 participants with PCV (128 Asian vs 122 Caucasian participants) were included. Asian participants presented with lower best-corrected visual acuity (mean ± SD: 0.7 ± 0.6 logMAR vs 0.4 ± 0.3 logMAR; P < .001) compared with Caucasian participants. More Asian eyes had subretinal hemorrhage (mean ± SD: 53.9% vs 24.6%; P < .001) and larger areas of hemorrhage (mean ± SD: 7.5 ± 15.2 mm² vs 1.3 ± 3.3 mm²; P < .001). More Asian eyes had pachyvessels (84.4% vs 28.7%; P < .001), choroidal vascular hyperpermeability (70.3% vs 17.2%; P < .001), and widespread polypoidal lesions (19.5% vs 8.2%; P = .005), and Caucasian eyes had more drusen (79.5% vs 49.2%; P = .02).

CONCLUSIONS

Multimodal imaging analysis revealed ethnic differences in disease characteristics of PCV, suggesting pathophysiologic mechanism of the disease vary based on ethnicity.

Convolutional Embedded Networks for Population Scale Clustering and Bio-Ancestry Inferencing

The study of genetic variants (GVs) can help find correlating population groups and to identify cohorts that are predisposed to common diseases and explain differences in disease susceptibility and how patients react to drugs. Machine learning techniques are increasingly being applied to identify interacting GVs to understand their complex phenotypic traits. Since the performance of a learning algorithm not only depends on the size and nature of the data but also on the quality of underlying representation, deep neural networks (DNNs) can learn non-linear mappings that allow transforming GVs data into more clustering and classification friendly representations than manual feature selection. In this paper, we propose convolutional embedded networks (CEN) in which we combine two DNN architectures called convolutional embedded clustering (CEC) and convolutional autoencoder (CAE) classifier for clustering individuals and predicting geographic ethnicity based on GVs, respectively. We employed CAE-based representation learning to 95 million GVs from the '1000 genomes' (covering 2,504 individuals from 26 ethnic origins) and 'Simons genome diversity' (covering 279 individuals from 130 ethnic origins) projects. Quantitative and qualitative analyses with a focus on accuracy and scalability show that our approach outperforms state-of-the-art approaches such as VariantSpark and ADMIXTURE. In particular, CEC can cluster targeted population groups in 22 hours with an adjusted rand index (ARI) of 0.915, the normalized mutual information (NMI) of 0.92, and the clustering accuracy (ACC) of 89 percent. Contrarily, the CAE classifier can predict the geographic ethnicity of unknown samples with an F1 and Mathews correlation coefficient (MCC) score of 0.9004 and 0.8245, respectively. Further, to provide interpretations of the predictions, we identify significant biomarkers using gradient boosted trees (GBT) and SHapley Additive exPlanations (SHAP). Overall, our approach is transparent and faster than the baseline methods, and scalable for 5 to 100 percent of the full human genome.

Estimating prevalence of human traits among populations from polygenic risk scores

The genetic basis of phenotypic variation across populations has not been well explained for most traits. Several factors may cause disparities, from variation in environments to divergent population genetic structure. We hypothesized that a population-level polygenic risk score (PRS) can explain phenotypic variation among geographic populations based solely on risk allele frequencies. We applied a population-specific PRS (psPRS) to 26 populations from the 1000 Genomes to four phenotypes: lactase persistence (LP), melanoma, multiple sclerosis (MS) and height. Our models assumed additive genetic architecture among the polymorphisms in the psPRSs, as is convention. Linear psPRSs explained a significant proportion of trait variance ranging from 0.32 for height in men to 0.88 for melanoma. The best models for LP and height were linear, while those for melanoma and MS were nonlinear. As not all variants in a PRS may confer similar, or even any, risk among diverse populations, we also filtered out SNPs to assess whether variance explained was improved using psPRSs with fewer SNPs. Variance explained usually improved with fewer SNPs in the psPRS and was as high as 0.99 for height in men using only 548 of the initial 4208 SNPs. That reducing SNPs improves psPRSs performance may indicate that missing heritability is partially due to complex architecture that does not mandate additivity, undiscovered variants or spurious associations in the databases. We demonstrated that PRS-based analyses can be used across diverse populations and phenotypes for population prediction and that these comparisons can identify the universal risk variants.

Chasing Ghosts: Race, Racism, and the Future of Microbiome Research

In this article, we argue that a careful examination of human microbiome science's relationship with race and racism is necessary to foster equitable social and ecological relations in the field. We point to the origins and evolution of the problematic use of race in microbiome literature by demonstrating the increased usage of race both explicitly and implicitly in and beyond the human microbiome sciences. We demonstrate how these uses limit the future of rigorous and just microbiome research. We conclude with an outline of alternative actionable ways to build a more effective, antiracist microbiome science.

Racial disparities in bariatric surgery postoperative weight loss and patient satisfaction

BACKGROUND

A growing body of evidence has demonstrated racial disparities in bariatric surgery (BS) outcomes. We aimed to investigate the impact of race on postoperative percent excess weight loss (%EWL) and patient satisfaction.

METHODS

Single center retrospective study of patients who underwent BS January 2012 to November 2017. Statistical analysis utilized Chi-squared, ANOVA and multivariable regression.

RESULTS

A total of 378 patients were included. African American patients lost significantly less weight compared to Caucasian and Hispanic patients (39.0 %EWL, 53.4 %EWL and 52.3 %EWL, respectively). A significant difference remained after adjustment for possible confounders. No difference in postoperative satisfaction was found.

CONCLUSIONS

Our study adds to the existing literature demonstrating racial disparities in BS postoperative EWL, despite adjusting for possible confounders, while contributing to the limited literature examining Hispanic patients. Furthermore, we examined an understudied outcome in postoperative patient satisfaction and found no racial disparity despite disparity in EWL.

How White nationalists mobilize genetics: From genetic ancestry and human biodiversity to counterscience and metapolitics

OBJECTIVES

Our aim in this study was to understand how genetics ideas are appropriated and mobilized online toward the political projects of White nationalism and the alt right. Studying three different online venues, we investigated how genetics is used to support racial realism, hereditarianism, and racial hierarchy. We analyzed how these ideas are connected to political and metapolitical projects. In addition, we examined the strategies used to build authority for these interpretations.

METHODS

We analyze three online venues in which genetics has been mobilized to advance racial realism and hereditarian explanations of racial differences. These were (a) the use of genetic ancestry tests in online nationalist discussions, (b) blogs and other venues in which the human biodiversity ideas are articulated, (c) activities surrounding the OpenPsych collection of online journals. Ethnographic and interpretive methods were applied to investigate scientific and political meanings of efforts to mobilize genetic ideas.

RESULTS

We found that White nationalists use genetic ancestry tests to align White identity with ideas of racial purity and diversity, educating each other about genetics, and debating the boundaries of Whiteness. "Human biodiversity" has been mobilized as a movement to catalog and create hereditarian ideas about racial differences and to distribute them as "red pills" to transform online discourse. The OpenPsych journals have allowed amateur hereditarian psychologists to publish papers, coordinate activity, and legitimate their project at the academic margins.

CONCLUSIONS

These various appropriations of genetics aim to further racial realism and hereditarian explanations of racial social and behavioral differences. Beyond these substantive aims, on a "metapolitical" level, they serve to reframe concepts and standards for political and scientific discussion of race, challenge structures of academic legitimacy and expertise, and build a cadre of ideological foot soldiers armed with an argumentative toolkit. As professional anthropologists and geneticists aim to accurately communicate their science and its implications for understanding human differences to the public, they must contend with these substantive claims and metapolitical contexts.

Molecules from the Microbiome

The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses.

Global, regional and national epidemiology and prevalence of child stunting, wasting and underweight in low- and middle-income countries, 2006-2018

In 2016, undernutrition, as manifested in childhood stunting, wasting, and underweight were estimated to cause over 1.0 million deaths, 3.9% of years of life lost, and 3.8% of disability-adjusted life years globally. The objective of this study is to estimate the prevalence of undernutrition in low- and middle-income countries (LMICs) using the 2006-2018 cross-sectional nationally representative demographic and health surveys (DHS) data and to explore the sources of regional variations. Anthropometric measurements of children 0-59 months of age from DHS in 62 LMICs worldwide were used. Complete information was available for height-for-age (n = 624,734), weight-for-height (n = 625,230) and weight-for-age (n = 626,130). Random-effects models were fit to estimate the pooled prevalence of stunting, wasting, and underweight. Sources of heterogeneity in the prevalence estimates were explored through subgroup meta-analyses and meta-regression using generalized linear mixed-effects models. Human development index (a country-specific composite index based on life expectancy, literacy, access to education and per capita gross domestic product) and the United Nations region were explored as potential sources of variation in undernutrition. The overall prevalence was 29.1% (95% CI 26.7%, 31.6%) for stunting, 6.3% (95% CI 4.6%, 8.2%) for wasting, and 13.7% (95% CI 10.9%, 16.9%) for underweight. Subgroup analyses suggested that Western Africa, Southern Asia, and Southeastern Asia had a substantially higher estimated prevalence of undernutrition than global average estimates. In multivariable meta-regression, a combination of human development index and United Nations region (a proxy for geographical variation) explained 54%, 56%, and 66% of the variation in stunting, wasting, and underweight prevalence, respectively. Our findings demonstrate that regional, subregional, and country disparities in undernutrition remain, and the residual gaps to close towards achieving the second sustainable development goal-ending undernutrition by 2030.

Extrapyramidal side effects in first-episode schizophrenia treated with flupenthixol decanoate

Background

Concern for the development of extrapyramidal side effects (EPSEs) represents a barrier to the routine use of long-acting injectable (LAI) antipsychotic medication in patients with first-episode schizophrenia (FES). Flupenthixol decanoate is a first-generation antipsychotic, which is readily available in the public healthcare system in South Africa.

Aim

The aim of this study was to describe the nature, occurrence and severity of EPSEs and their impact on patients with FES over 12 months of treatment with flupenthixol decanoate (fluanxol depot).

Setting

The study was based in Cape Town, South Africa, and patients with FES were recruited from inpatient services at Stikland and Tygerberg Hospitals and surrounding psychiatric clinics. This was a sub-study of a larger study, which examined several outcomes in patients with FES treated with the lowest effective dose of flupenthixol decanoate.

Methods

The Extrapyramidal Symptom Rating Scale (ESRS) was used to assess both subjective experience and objective measures of EPSEs in a cohort of patients with FES (N = 130). The relationship between demographic and clinical risk factors for individual subsets of EPSEs was also determined.

Results

In the context of an overall good 12-month tolerability, EPSEs peaked at month 3. Patients with akathisia were more likely to have greater symptoms of depression, and Parkinsonism was predicted by higher Positive and Negative Syndrome Scale scores (independent of medication dosage). Black and white patients showed higher total ESRS and higher subjective ESRS scores, compared with patients of mixed ancestry, and white patients scored higher on Parkinsonism ratings.

Conclusion

Flupenthixol decanoate is well tolerated in patients with FES. Certain clinical features of schizophrenia may be related to EPSEs. Ethnicity is a socio-cultural construct, and hence the differential risk of EPSEs should be interpreted according to ethnicity. Variations in the environment, diet, substance use and genetics may all affect the pharmacokinetics and pharmacodynamics of psychotropic drugs and warrant further investigation.

An uncertainty estimate of the prevalence of stunting in national surveys: the need for better precision

Background

Stunting is determined by using the World Health Organization (WHO) child growth standard which was developed using precise measurements. However, it is unlikely that large scale surveys maintain the same level of rigour and precision when measuring the height of children. The population measure of stunting in children is sensitive to over-dispersion, and the high prevalence of stunting observed in surveys in low and middle-income countries (LMIC) could partly be due to lower measurement precison.

Objectives

To quantify the incongruence in the dispersion of height-for-age in national surveys of < 5 y children, in relation to the standard WHO Multicenter Growth Reference Study (MGRS), and propose a measure of uncertainty in population measures of stunting.

Methods

An uncertainty factor was proposed and measured from the observed incongruence in dispersion of the height-for-age of < 5 y children in the MGRS against carefully matched populations from the Demographic Health Survey of 17 countries (‘test datasets’, based on the availability of data). This also allowed for the determination of uncertainty-corrected prevalence of stunting (height-for-age Z score < − 2) in < 5 y children.

Results

The uncertainty factor was estimated for 17 LMICs. This ranged from 0.9 to 2.1 for Peru and Egypt respectively (reference value 1). As an explicit country example, the dispersion of height-for-age in the Indian National Family Health Survey-4 test dataset was 39% higher than the MGRS study, with an uncertainty factor of 1.39. From this, the uncertainty-adjusted Indian national stunting prevalence estimate reduced to 18.7% from the unadjusted estimate of 36.2%.

Conclusions

This study proposes a robust statistical method to estimate uncertainty in stunting prevalence estimates due to incongruent dispersions of height measured in national surveys for children < 5 years in relation to the WHO height-for-age standard. The uncertainty is partly due to population heterogeneity, but also due to measurement precision, and calls for better quality in these measurements.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-020-09753-8.

NCMHap: a novel method for haplotype reconstruction based on Neutrosophic c-means clustering

BACKGROUND

Single individual haplotype problem refers to reconstructing haplotypes of an individual based on several input fragments sequenced from a specified chromosome. Solving this problem is an important task in computational biology and has many applications in the pharmaceutical industry, clinical decision-making, and genetic diseases. It is known that solving the problem is NP-hard. Although several methods have been proposed to solve the problem, it is found that most of them have low performances in dealing with noisy input fragments. Therefore, proposing a method which is accurate and scalable, is a challenging task.

RESULTS

In this paper, we introduced a method, named NCMHap, which utilizes the Neutrosophic c-means (NCM) clustering algorithm. The NCM algorithm can effectively detect the noise and outliers in the input data. In addition, it can reduce their effects in the clustering process. The proposed method has been evaluated by several benchmark datasets. Comparing with existing methods indicates when NCM is tuned by suitable parameters, the results are encouraging. In particular, when the amount of noise increases, it outperforms the comparing methods.

CONCLUSION

The proposed method is validated using simulated and real datasets. The achieved results recommend the application of NCMHap on the datasets which involve the fragments with a huge amount of gaps and noise.

A case-control study of perfluoroalkyl substances and the risk of breast cancer in Taiwanese women

Breast cancer (BC) is a common cancer in women worldwide; however, the incidence of BC is increasing in younger women, possibly associated with the environment. Perfluoroalkyl substances (PFAS) are one of endocrine disruptors that accumulate in environment and impact human health. This study aimed to investigate whether the PFAS and BC are associated. We enrolled 120 BCE patients and 119 controls at National Taiwan University Hospital (NTUH) and also collected bio-specimen and questionnaire from 2013 to 2015. All subjects' plasma PFAS levels were analyzed by ultra-performance liquid chromatography tandem mass spectrometry method with electrospray ionization (UHPLC-ESI-MS/MS). A logistic regression model was used to estimate the association between PFAS and BC. In the ≤50 years age group, the adjusted odds ratio (OR) was 2.34 (95% CI = 1.02, 5.38) for perfluorooctane sulfonate (PFOS) exposure per natural log unit increase. After stratifying the estrogen receptor (ER) status and age group, we obtained a positive association for PFHxS and PFOS concentrations with respect to the risk of ER positive tumors for ≤50 years age group. In conclusion, we found that PFAS were associated with the BC risk of ER positive tumors in young Taiwanese women. Further studies are needed to follow and explore whether these associations are causal.

Genetic Analysis of Pharmacogenomic VIP Variants of ABCB1, VDR and TPMT Genes in an Ethnically Isolated Population from the North Caucasus Living in Jordan

Background:

Differences in individual responses to the same medications remarkably differ among populations. A number of genes that play integral roles in drug responses have been designated as very important pharmacogenes (VIP), as they are responsible for differences in drug safety, efficacy, and adverse drug reactions among certain ethnic groups. Identifying the polymorphic distribution of VIP in a range of ethnic groups will be conducive to population-based personalized medicine.

Objective:

The aim of the current study is to identify the polymorphic distribution of VIP regarding the Chechen minority group from Jordan and compare their allele frequencies with other populations.

Methods:

A total of 131 unrelated Chechen individuals from Jordan were randomly recruited for blood collection. Identification of allelic and genotypic frequencies of eleven VIP variants within the genes of interest (ABCB1, VDR and TPMT) was carried out by means of the MassARRAY®System (iPLEX GOLD).

Results:

Within ABCB1, we found that the minor allele frequencies of the rs1128503 (A: 0.43), rs2032582 (A: 0.43), rs1045642 (A: 0.43). For VDR, the minor allele frequencies of rs11568820 (T: 0.18), rs1540339 (T: 0.30), rs1544410 (T: 0.41), rs2228570 (T: 0.24), rs3782905 (C: 0.28) and rs7975232 (C: 0.45). Finally, the minor allele frequencies for the TPMT rs1142345 and rs1800460 polymorphisms were found to be (C: 0.02) and (T: 0.01), respectively.

Conclusion:

Significant differences in allelic frequencies of eleven ABCB1, VDR and TPMT VIP variants were found between Jordanian Chechens and other populations. In our study, most populations that are similar to Chechens are those from South Asian, European (Finnish) and European, including: Utah residents with Northern and Western European ancestry, Toscani in Italia, Mexican ancestry in Los Angeles and Circassian from Jordan. The level of similarity between Chechens and those populations means that they might have shared high levels of gene flow in the past. The results obtained in this study will contribute to the worldwide pharmacogenomic databases and provide valuable information for future studies and better individualized treatments.

A meta-analysis and meta-regression of association between MTHFR A1298C polymorphism and nonsyndromic cleft lip/palate risk: An evaluation based on five genetic models

OBJECTIVE

The present meta-analysis is intended to assess the association between NSCL/P risk and methylenetetrahydrofolate reductase (MTHFR) A1298C polymorphism in case-control studies.

MATERIALS AND METHODS

The Web of Science, PubMed/Medline, Scopus, and Cochrane Library databases were searched for related articles published by April 2019. Review Manager 5.3 was applied to measure the odds ratios (ORs) with 95% confidence interval (CI) in the analyses assessing the strength of the association between A1298C polymorphism and NSCL/P risk. Results Sixteen studies were involved and analysed in this meta-analysis. Altogether, the reviewed articles included 2677 NSCL/P patients and 3669 controls. The pooled ORs of the allele, homozygote, heterozygote, dominant, and recessive models were 1.11 (95% CI: 0.94, 1.30; P=0.21), 1.14 (95% CI: 0.94, 1.37; P=0.18), 0.98 (95% CI: 0.80, 1.20; P=0.87), 1.03 (95% CI: 0.86, 1.22; P=0.79), and 1.18 (95% CI: 0.99, 1.41; P=0.07), respectively. The analysis did not identify any significant association between the polymorphism and the risk of NSCL/P in any ethnicity or source of controls.

CONCLUSIONS

This meta-analysis revealed that A1298C polymorphism is not associated with NSCL/P susceptibility, and the subgroup analyses based on ethnicity and the source of cases further confirmed this result.

Human gene and disease associations for clinical-genomics and precision medicine research

We are entering the era of personalized medicine in which an individual's genetic makeup will eventually determine how a doctor can tailor his or her therapy. Therefore, it is becoming critical to understand the genetic basis of common diseases, for example, which genes predispose and rare genetic variants contribute to diseases, and so on. Our study focuses on helping researchers, medical practitioners, and pharmacists in having a broad view of genetic variants that may be implicated in the likelihood of developing certain diseases. Our focus here is to create a comprehensive database with mobile access to all available, authentic and actionable genes, SNPs, and classified diseases and drugs collected from different clinical and genomics databases worldwide, including Ensembl, GenCode, ClinVar, GeneCards, DISEASES, HGMD, OMIM, GTR, CNVD, Novoseek, Swiss-Prot, LncRNADisease, Orphanet, GWAS Catalog, SwissVar, COSMIC, WHO, and FDA. We present a new cutting-edge gene-SNP-disease-drug mobile database with a smart phone application, integrating information about classified diseases and related genes, germline and somatic mutations, and drugs. Its database includes over 59 000 protein-coding and noncoding genes; over 67 000 germline SNPs and over a million somatic mutations reported for over 19 000 protein-coding genes located in over 1000 regions, published with over 3000 articles in over 415 journals available at the PUBMED; over 80 000 ICDs; over 123 000 NDCs; and over 100 000 classified gene-SNP-disease associations. We present an application that can provide new insights into the information about genetic basis of human complex diseases and contribute to assimilating genomic with phenotypic data for the availability of gene-based designer drugs, precise targeting of molecular fingerprints for tumor, appropriate drug therapy, predicting individual susceptibility to disease, diagnosis, and treatment of rare illnesses are all a few of the many transformations expected in the decade to come.

Detecting sequence variants in clinically important protozoan parasites

Second and third generation sequencing methods are crucial for population genetic studies, and variant detection is a popular approach for exploiting this sequence data. While mini- and microsatellites are historically useful markers for studying important Protozoa such as Toxoplasma and Plasmodium spp., detecting non-repetitive variants such as those found in genes can be fundamental to investigating a pathogen's biology. These variants, namely single nucleotide polymorphisms and insertions and deletions, can help elucidate the genetic basis of an organism's pathogenicity, identify selective pressures, and resolve phylogenetic relationships. They also have the added benefit of possessing a comparatively low mutation rate, which contributes to their stability. However, there is a plethora of variant analysis tools with nuanced pipelines and conflicting recommendations for best practise, which can be confounding. This lack of standardisation means that variant analysis requires careful parameter optimisation, an understanding of its limitations, and the availability of high quality data. This review explores the value of variant detection when applied to non-model organisms such as clinically important protozoan pathogens. The limitations of current methods are discussed, including special considerations that require the end-users' attention to ensure that the results generated are reproducible, and the biological conclusions drawn are valid.

Population Demography, Ancestry, and the Biological Concept of Race

For more than 50 years, biological anthropology has argued against the use of the biological race concept. Despite such efforts, aspects of the concept remain in circulation within society and within the discipline itself. As commonly articulated, anthropology's rejection of the biological race concept lacks an evolutionarily based explanatory grounding. Biological patterns of variation in living humans do not map onto commonly utilized categorizations of race, but this knowledge does not explain why human evolution has not produced such structures. This article attempts to offer one such explanation by constructing a biocultural framing of race around ancestry. By examining ancestry through two related lenses, genealogical and genetic, it is shown that the coherence of race as a biological concept has been disrupted by demographic changes in our recent evolutionary past. The biological construction of race is invalid not because it is impossible but because evolutionary forces have actively worked against such patterns in our evolutionary past.

"We Don't Need a Swab in Our Mouth to Prove Who We Are": Identity, Resistance, and Adaptation of Genetic Ancestry Testing among Native American Communities

Genetic ancestry testing (GAT) provides a specific type of knowledge about ancestry not previously available to the general public, prompting questions about the conditions whereby genetic articulations of ancestry present opportunities to forge new identities and social ties but also new challenges to the maintenance of existing social structures and cultural identities. The opportunities and challenges posed by GAT are particularly significant for many indigenous communities-whose histories are shaped by traumatic interactions with colonial powers and Western science-and for whom new applications of GAT may undermine or usurp long-standing community values, systems of governance, and forms of relationality. We conducted 13 focus groups with 128 participants and six in-depth, semistructured interviews with a variety of community leaders examining the perceptions of GAT within indigenous communities across Oklahoma. Our interviews and focus groups suggest that participants-through the articulation of indigeneity as experiential and relational in nature and inherently distinct from genetic notions of ancestry-resist much of the challenge presented by GAT in usurping traditional forms of identity while at the same time recognizing the utility of the technology for tracing unknown ancestry and identifying health risks in the community.

Application of ACMG criteria to classify variants in the human gene mutation database

This study aimed to obtain a quantitative assessment of the occurrence of contradictory evidence in functional classification of genetic variation, according to the American College of Medical Genetics and Genomics (ACMG) guidelines. We analyzed 140,883 genetic variation in the Human Gene Mutation Database (HGMD). The 2014 release of the HGMD dataset before the publication of the ACMG guidelines was used for its independence from the ACMG guidelines. Evidence for benign classification, BS2 (0.37%), was identified among variants classified as pathogenic. For likely pathogenic variation, BP1 (2.99%) and BS2 (0.37%) were identified. PM1 is commonly observed among variants classified as benign (28.45%), while PM2 and PM1 are commonly identified among variants classified as likely benign (48.91% and 42.95%, respectively). Taken together, these observations will inform better approaches to apply the ACMG guidelines.

Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins

Calling variants from next-generation sequencing (NGS) data or discovering discordant sequences between two NGS data sets is challenging. We developed a computer algorithm, ADIScan1, to call variants by comparing the fractions of allelic reads in a tester to the universal reference genome. We then created ADIScan2 by modifying the algorithm to directly compare two sets of NGS data and predict discordant sequences between two testers. ADIScan1 detected >99.7% of variants called by GATK with an additional 724 393 SNVs. ADIScan2 identified ∼500 candidates of discordant sequences in each of two pairs of the monozygotic twins. About 200 of these candidates were included in the ∼2800 predicted by VarScan2. We verified 66 true discordant sequences among the candidates that ADIScan2 and VarScan2 exclusively predicted. ADIScan2 detected many discordant sequences overlooked by VarScan2 and Mutect, which specialize in detecting low frequency mutations in genetically heterogeneous cancerous tissues. Numbers of verified sequences alone were >5 times more than expected based on recently estimated mutation rates from whole genome sequences. Estimated post-zygotic mutation rates were 1.68 × 10⁻⁷ in this study. ADIScan1 and 2 would complement existing tools in screening causative mutations of diverse genetic diseases and comparing two sets of genome sequences, respectively.

Selective mortality and the anthropometric status of children in low- and middle-income countries

Despite a close relationship between the childrens' anthropometric status and mortality rates, the highest mortality rates are concentrated in sub-Saharan Africa, while the lowest anthropometric indicators, in particular the height-for-age z-scores, are concentrated in South Asia. This discrepancy should, however, be expected to decrease when one accounts for the survivorship bias, i.e. selective mortality. We analyse whether the survivorship bias can explain these observed differences in three standard anthropometric indicators (stunting, underweight and wasting) by using individual data of children from six waves of Demographic and Health Surveys for a large cross-section of 37 low- and middle-income countries between 1991 and 2016. We use both a matching approach and semi-parametric regression to estimate the values for the anthropometric status of deceased children. The results are twofold: first, both methods reveal that the imputed values for the anthropometric indicators are, on average, between 0.10 and 0.25 standard deviations lower than the observed anthropometric indicators. Second, since the share of deceased children in our sample is below ten per cent, the contribution of the anthropometric status of deceased children to overall anthropometric indicators is small and therefore only influences it marginally.