Longitudinal studies of bipolar patients and their families: translating findings to advance individualized risk prediction, treatment and research

BACKGROUND

Bipolar disorder is a broad diagnostic construct associated with significant phenotypic and genetic heterogeneity challenging progress in clinical practice and discovery research. Prospective studies of well-characterized patients and their family members have identified lithium responsive (LiR) and lithium non-responsive (LiNR) subtypes that hold promise for advancement.

METHOD

In this narrative review, relevant observations from published longitudinal studies of well-characterized bipolar patients and their families spanning six decades are highlighted. DSM diagnoses based on SADS-L interviews were decided in blind consensus reviews by expert clinicians. Genetic, neurobiological, and psychosocial factors were investigated in subsets of well-characterized probands and adult relatives. Systematic maintenance trials of lithium, antipsychotics, and lamotrigine were carried out. Clinical profiles that included detailed histories of the clinical course, symptom sets and disorders segregating in families were documented. Offspring of LiR and LiNR families were repeatedly assessed up to 20 years using KSADS-PL format interviews and DSM diagnoses and sub-threshold symptoms were decided by expert clinicians in blind consensus reviews using all available clinical and research data.

RESULTS

A characteristic clinical profile differentiated bipolar patients who responded to lithium stabilization from those who did not. The LiR subtype was characterized by a recurrent fully remitting course predominated by depressive episodes and a positive family history of episodic remitting mood disorders, and not schizophrenia. Response to lithium clustered in families and the characteristic clinical profile predicted lithium response, with the episodic remitting course being a strong correlate. There is accumulating evidence that genetic and neurobiological markers differ between LiR and LiNR subtypes. Further, offspring of bipolar parents subdivided by lithium response differed in developmental history, clinical antecedents and early course of mood disorders. Moreover, the nature of the emergent course bred true from parent to offspring, independent of the nature of emergent psychopathology.

CONCLUSIONS

Bipolar disorders are heterogeneous and response to long-term lithium is associated with a familial subtype with characteristic course, treatment response, family history and likely pathogenesis. Incorporating distinctive clinical profiles that index valid bipolar subtypes into routine practice and research will improve patient outcomes and advance the development and translation of novel treatment targets to improve prevention and early intervention.

What are Jews: interrogating genetic studies and the reification of race

Scientific studies on the genetic proximity of Jews undertake to shed light on "who or what Jews really are". However, various scientists and scholars have warned that such studies reify racial thinking. This essay delineates and contextualizes the debate held between various geneticists and social scientists on the danger of reification within the Jewish context. This is mainly a debate about the impact of (traditional, religious, and Zionist) narratives on scientific research as well as on the ethical responsibility of scientists. The paper claims that such genetic studies test Jewish religious narratives against genetic research results and do not necessarily enforce old notions of distinctiveness.

Genetic Studies Investigating Susceptibility to Psoriatic Arthritis: A Narrative Review

PURPOSE

Approximately 30% of patients with psoriasis will develop psoriatic arthritis (PsA), leading to a decreased quality of life for the patient caused by increasing disability and additional health complications. The identification of risk factors for the development of PsA would facilitate the development of risk prediction models in which patients with psoriasis at high risk of developing PsA could be targeted in a stratified medicine approach, enabling early intervention and treatment. PsA is known to have a genetic contribution to susceptibility, and the identification of genetic risk factors that differentiate PsA from cutaneous-only psoriasis is a key area of research. This narrative review summarizes the discovery of genetic risk factors and, with the aid of a primer on risk prediction models, discusses their potential role for the classification of PsA risk and diagnosis.

METHODS

All relevant research articles were identified through searches of the PubMed database for literature published up until December 2022. Search terms included psoriatic arthritis, genetic susceptibility, genetic association, genome-wide association study, GWAS, prediction, and polygenic risk score.

FINDINGS

The current literature reveals considerable overlap between the genetic susceptibility loci for PsA and psoriasis. Several PsA-specific genetic risk factors have been reported, and most notably these implicate the HLA-B and IL23R genes. Efforts to include genetic risk factors in prediction models for the development of PsA have reported good discrimination.

IMPLICATIONS

Key messages emerging from this narrative are as follows: the limited number of PsA-specific susceptibility loci reported to date suggest larger studies are required, facilitated by international collaboration, to achieve the power to detect further genetic factors; the early promising results for genetic-based risk prediction require further validation in independent datasets; and risk prediction models combining clinical and genetic risk factors have yet to be explored.

Mitochondrial neurogastrointestinal encephalomyopathy in a Pakistani female: a case report

Background

Mitochondrial neurogastrointestinal encephalopathy is a rare multisystem autosomal recessive disease caused by mutations in the TYMP gene, that encodes for thymidine phosphorylase. Mitochondrial neurogastrointestinal encephalopathy is a progressive degenerative disease characterized by a distinctive tetrad of gastrointestinal dysmotility, peripheral neuropathy, ophthalmoplegia with ptosis, and asymptomatic leukoencephalopathy. It provides a diagnostic dilemma to physicians in regions like Pakistan because of a lack of genetic study availability and associated financial constraints of the population. However, with careful examination and a few basic investigations, mitochondrial neurogastrointestinal encephalopathy can be diagnosed by ruling out most of the close differentials.

Case presentation

We report the case of a 23-year-old Asian female whose chief complaints were epigastric pain, bilious emesis, weight loss for 3 months, and bilateral lower limb weakness for 20 days. All clinical signs and symptoms along with relevant investigations including nerve conduction studies, electromyography, and magnetic resonance imaging of the brain were highly suggestive of mitochondrial neurogastrointestinal encephalopathy syndrome. Because of financial constraints, genetic studies could not be performed. The patient was managed with a multidisciplinary approach involving gastroenterology, physiotherapy, and nutrition departments. Currently, therapeutic options for the disease include allogeneic hematopoietic stem cell transplant and carrier erythrocyte entrapped thymidine phosphorylase; however, these could not be provided to the patient owing to certain limitations.

Conclusions

As misdiagnosis and delayed diagnosis are quite common in this disease, the prime objective of this case report is to increase the basic understanding of this disease, especially its signs and symptoms, and address the limitations regarding the diagnostic investigations and management of patients with mitochondrial neurogastrointestinal encephalopathy.

Genetic variants associated with the occurrence and progression of adolescent idiopathic scoliosis: a systematic review protocol

BACKGROUND

Adolescent idiopathic scoliosis (AIS) is a structural lateral spinal curvature of ≥ 10° with rotation. Approximately 2-3% of children in most populations are affected with AIS, and this condition is responsible for approximately $1.1 billion in surgical costs to the US healthcare system. Although a genetic factor for AIS has been demonstrated for decades, with multiple potentially contributory loci identified across populations, treatment options have remained limited to bracing and surgery.

METHODS

The databases MEDLINE (via PubMed), Embase, Google Scholar, and Ovid MEDLINE will be searched and limited to articles in English. We will conduct title and abstract, full-text, and data extraction screening through Covidence, followed by data transfer to a custom REDCap database. Quality assessment will be confirmed by multiple reviewers. Studies containing variant-level data (i.e., GWAS, exome sequencing) for AIS subjects and controls will be considered. Outcomes of interest will include presence/absence of AIS, scoliosis curve severity, scoliosis curve progression, and presence/absence of nucleotide-level variants. Analyses will include odds ratios and relative risk assessments, and subgroup analysis (i.e., males vs. females, age groups) may be applied. Quality assessment tools will include GRADE and Q-Genie for genetic studies.

DISCUSSION

In this systematic review, we seek to evaluate the quality of genetic evidence for AIS to better inform research efforts, to ultimately improve the quality of patient care and diagnosis.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration #CRD42021243253.

Recruiting for diversity: a pilot test of recruitment strategies for a national alcohol survey with mail-in genetic data collection

We assessed the feasibility and acceptability of collecting a saliva sample for DNA through the mail from a national sample of drinkers and examined whether targeted messaging would increase the response rates of Black/African American and Hispanic/Latino participants. We invited respondents from two prior national population surveys to participate in a brief telephone survey regarding recent alcohol use and to mail in a self-administered saliva sample. Blacks/African Americans, Hispanics/Latinos, and Whites had similar rates of consenting to participate. A higher proportion of respondents with a college education and a family history of alcohol problems consented. The differences in participation between respondents receiving targeted and general messaging were not statistically significant. This study provides preliminary evidence for the feasibility of recruiting diverse participants into a genetic study of alcohol use disorder.

In vitro Differentiation of Human iPSC-derived Cardiovascular Progenitor Cells (iPSC-CVPCs)

Induced pluripotent stem cell derived cardiovascular progenitor cells (iPSC-CVPCs) provide an unprecedented platform for examining the molecular underpinnings of cardiac development and disease etiology, but also have great potential to play pivotal roles in the future of regenerative medicine and pharmacogenomic studies. Biobanks like iPSCORE ( Stacey et al., 2013 ; Panopoulos et al., 2017 ), which contain iPSCs generated from hundreds of genetically and ethnically diverse individuals, are an invaluable resource for conducting these studies. Here, we present an optimized, cost-effective and highly standardized protocol for large-scale derivation of human iPSC-CVPCs using small molecules and purification using metabolic selection. We have successfully applied this protocol to derive iPSC-CVPCs from 154 different iPSCORE iPSC lines obtaining large quantities of highly pure cardiac cells. An important component of our protocol is Cell confluency estimates (ccEstimate), an automated methodology for estimating the time when an iPSC monolayer will reach 80% confluency, which is optimal for initiating iPSC-CVPC derivation, and enables the protocol to be readily used across iPSC lines with different growth rates. Moreover, we showed that cellular heterogeneity across iPSC-CVPCs is due to varying proportions of two distinct cardiac cell types: cardiomyocytes (CMs) and epicardium-derived cells (EPDCs), both of which have been shown to have a critical function in heart regeneration. This protocol eliminates the need of iPSC line-to-line optimization and can be easily adapted and scaled to high-throughput studies or to generate large quantities of cells suitable for regenerative medicine applications.

What do we know about the role of lipoprotein(a) in atherogenesis 57 years after its discovery?

Elevated circulating concentrations of lipoprotein(a) [Lp(a)] is strongly associated with increased risk of atherosclerotic cardiovascular disease (CVD) and degenerative aortic stenosis. This relationship was first observed in prospective observational studies, and the causal relationship was confirmed in genetic studies. Everybody should have their Lp(a) concentration measured once in their lifetime. CVD risk is elevated when Lp(a) concentrations are high i.e. > 50 mg/dL (≥100 mmol/L). Extremely high Lp(a) levels >180 mg/dL (≥430 mmol/L) are associated with CVD risk similar to that conferred by familial hypercholesterolemia. Elevated Lp(a) level was previously treated with niacin, which exerts a potent Lp(a)-lowering effect. However, niacin is currently not recommended because, despite the improvement in lipid profile, no improvements on clinical outcomes have been observed. Furthermore, niacin use has been associated with severe adverse effects. Post hoc analyses of clinical trials with proprotein convertase subtilisin/kexin type-9 (PCSK9) inhibitors have shown that these drugs exert clinical benefits by lowering Lp(a), independent of their potent reduction of low-density lipoprotein cholesterol (LDL-C). It is not yet known whether PCSK9 inhibitors will be of clinical use in patients with elevated Lp(a). Apheresis is a very effective approach to Lp(a) reduction, which reduces CVD risk but is invasive and time-consuming and is thus reserved for patients with very high Lp(a) levels and progressive CVD. Studies are ongoing on the practical application of genetic approaches to therapy, including antisense oligonucleotides against apolipoprotein(a) and small interfering RNA (siRNA) technology, to reduce the synthesis of Lp(a).

Pharmacogenetic investigation of efficacy response to mepolizumab in eosinophilic granulomatosis with polyangiitis

Treatment of patients with the rare disease eosinophilic granulomatosis with polyangiitis (EGPA) with mepolizumab, a monoclonal antibody to interleukin-5 (IL-5) that reduces blood eosinophil counts, as an add-on therapy to glucocorticoid treatment, results in more accrued weeks in remission, reductions in glucocorticoid use and reductions in relapse rate. However, treatment response varies across a continuum. Therefore, to investigate if large genetic effects could identify responders, the impact of genetic variants on efficacy in EGPA subjects taking mepolizumab and glucocorticoids was assessed in this post hoc study. Using linear regression and a negative binomial model, genetic variant association with three endpoints (accrued duration of remission, average oral glucocorticoid dose, and frequency of relapse) was tested in 61 EGPA subjects dosed with mepolizumab from MIRRA, a phase 3 trial. Candidate gene and genome-wide approaches were used. The candidate gene analysis was designed to investigate drug target effects with eight gene regions selected that were focused on the intersection of the glucocorticoid response (steroidal response) and IL-5 response mechanisms and recognizing potential overlap between EGPA and severe eosinophilic asthma diseases for which mepolizumab is used. The sample size was insufficient to enable testing of rare variants for effects. No genetic variant from either the candidate gene analysis or the GWAS associated with any endpoint. Thresholds to declare significance were p < 0.0008 (candidate variant) and p < 2.5 × 10^–8 (genome-wide) analyses. Large genetic effects on mepolizumab-treatment response were not identified which could help differentiate responders from non-responders.

Imaging diagnosis of Crouzon syndrome in two cases confirmed on genetic studies - with a brief review

Crouzon syndrome is the most common form of craniofacial dysostosis, characterised by a classical triad of abnormal skull shape, abnormal facies, and exophthalmos. The clinically overt dental abnormalities in these patients, distracts clinicians from the developmental neurological defects and therefore this entity remains relatively under - highlighted in radiology literature. We report and highlight the role of imaging in diagnosis of Crouzon syndrome in two patients, and discuss the relevant differential diagnosis. Moreover, our report is among the few Indian studies in which Crouzon syndrome was confirmed by genetic studies. The classical clinical triad of Crouzon syndrome was observed in both patients. The skull radiographs and cranial CT with 3D reconstruction VRT (Volume rendered technique), revealed characteristic radiological features. Genetic studies reconfirmed the clinical and radiological diagnosis of Crouzon syndrome, in both patients.

In vitro Differentiation of Human iPSC-derived Retinal Pigment Epithelium Cells (iPSC-RPE)

Induced Pluripotent Stem Cells (iPSCs) serve as an excellent model system for studying the molecular underpinnings of tissue development. Human iPSC-derived retinal pigment epithelium (iPSC-RPE) cells have fetal-like molecular profiles. Hence, biobanks like iPSCORE, which contain iPSCs generated from hundreds of individuals, are an invaluable resource for examining how common genetic variants exert their effects during RPE development resulting in individuals having different propensities to develop Age-related Macular Degeneration (AMD) as adults. Here, we present an optimized, cost-effective and highly reproducible protocol for derivation of human iPSC-RPE cells using small molecules under serum-free condition and for their quality control using flow cytometry and immunofluorescence. While most previous protocols have required laborious manual selection to enrich for iPSC-RPE cells, our protocol uses whole culture passaging and yields a large number of iPSC-RPE cells with high purity (88-98.1% ZO-1 and MiTF double positive cells). The simplicity and robustness of this protocol would enable its adaption for high-throughput applications involving the generation of iPSC-RPE samples from hundreds of individuals.

Determining the Polymorphism Information Content of a molecular marker

This review was carried out with the purpose of contributing to the discussion on the equations used in calculating the Polymorphism Information Content (PIC) of molecular markers. PIC measures the ability of a marker to detect polymorphisms, and therefore has enormous importance in selecting markers for genetic studies. We perform a summary analysis of PIC and its difference in relation to heterozygosity, another parameter used to evaluate the quality of a marker, presenting and discussing the several equations registered in the literature for both dominant and codominant markers. Finally, we present a brief direction on estimating PIC for dominant markers.

Commonly used estimates of the genetic contribution to disease are subject to the same fallacies as bad luck estimates

The scientific debate following the initial formulation of the "bad luck" hypothesis in cancer development highlighted how measures based on analysis of variance are inappropriately used for risk communication. The notion of "explained" variance is not only used to quantify randomness, but also to quantify genetic and environmental contribution to disease in heritability coefficients. In this paper, we demonstrate why such quantifications are generally as problematic as bad luck estimates. We stress the differences in calculation and interpretation between the heritability coefficient and the population attributable fraction, the estimated fraction of all disease events that would not occur if an intervention could successfully prevent the excess genetic risk. We recommend using the population attributable fraction when communicating results regarding the genetic contribution to disease, as this measure is both more relevant from a public health perspective and easier to understand.

Pharmacogenetics of Glucagon-like Peptide-1 Agonists for the Treatment of Type 2 Diabetes Mellitus

BACKGROUND

Pharmacogenetics is a promising area of medical research, providing methods to identify the appropriate pharmaceutical agent and dosing for each unique patient. Glucagon- like peptide-1 (GLP-1) agonists are a novel therapeutic choice used in the treatment of type 2 diabetes mellitus (T2DM), demonstrating efficacy regarding glycemic control and weight loss. Therapeutic response to GLP-1 agonist treatment is a complex biophenomenon, dependent on a plethora of modifiable (diet, exercise, adherence) and non-modifiable (genetic individual variants, ethnic characteristics) parameters. Ιn this context, it has been hypothesized that genetic polymorphisms of GLP-1 related genes may be associated with the therapeutic response to GLP-1 agonist treatment. This review focuses on the most important polymorphisms of the GLP-1 biological network that could affect clinical response to GLP-1 agonist treatment.

METHODS

Biomedical databases were searched to identify key articles in the field and their results are critically presented in this review.

RESULT

Recent pharmacological and clinical studies demonstrated a significant variation in GLP-1 agonist treatment, in cohorts with homogeneous adherence to diet, exercise and antidiabetic treatment. These studies identified several cases of non-responders to GLP-1 agonist therapy, in association with specific allelic patterns of GLP-1 receptor or other biomolecules implicated in glucose homeostasis.

CONCLUSION

Although the exact DNA sequences that cause the molecular changes leading to a variable response to GLP-1 agonists have not been yet fully identified, these findings underline the importance of an individualized approach in anti-diabetic treatment.

Genome-wide researches and applications on Dendrobium

This review summarizes current knowledge of chromosome characterization, genetic mapping, genomic sequencing, quality formation, floral transition, propagation, and identification in Dendrobium. The widely distributed Dendrobium has been studied for a long history, due to its important economic values in both medicine and ornamental. In recent years, some species of Dendrobium and other orchids had been reported on genomic sequences, using the next-generation sequencing technology. And the chloroplast genomes of many Dendrobium species were also revealed. The chromosomes of most Dendrobium species belong to mini-chromosomes, and showed 2n = 38. Only a few of genetic studies were reported in Dendrobium. After revealing of genomic sequences, the techniques of transcriptomics, proteomics and metabolomics could be employed on Dendrobium easily. Some other molecular biological techniques, such as gene cloning, gene editing, genetic transformation and molecular marker developing, had also been applied on the basic research of Dendrobium, successively. As medicinal plants, insights into the biosynthesis of some medicinal components were the most important. As ornamental plants, regulation of flower related characteristics was the most important. More, knowledge of growth and development, environmental interaction, evolutionary analysis, breeding of new cultivars, propagation, and identification of species and herbs were also required for commercial usage. All of these studies were improved using genomic sequences and related technologies. To answer some key scientific issues in Dendrobium, quality formation, flowering, self-incompatibility and seed germination would be the focus of future research. And genome related technologies and studies would be helpful.

The Susceptibility Genes in Diabetic Nephropathy

Background

Diabetes mellitus (DM) poses a severe threat to global public health. Diabetic nephropathy (DN) is one of the most common complications of diabetes and the leading cause of end-stage renal disease (ESRD). Approximately 30-40% of DM patients in the world progress to ESRD, which emphasizes the effect of genetic factors on DN. Family clustering also supports the important role of hereditary factors in DN and ESRD. Therefore, a large number of genetic studies have been carried out to identify susceptibility genes in different diabetic cohorts. Extensive susceptibility genes of DN and ESRD have not been identified until recently.

Summary and Key Messages

Some of these associated genes function as pivotal regulators in the pathogenesis of DN, such as those related to glycometabolism and lipid metabolism. However, the functions of most of these genes remain unclear. In this article, we review several susceptibility genes according to their genetic functions to make it easier to determine their exact effect on DN and to provide a better understanding of the advancements from genetic studies. However, several challenges associated with investigating the genetic factors of DN still exist. For instance, it is difficult to determine whether these variants affect the expression of the protein they encode or other cytokines. More efforts should be made to determine how these genes influence the progression of DN. In addition, many results could not be replicated among races, suggesting that the association between genetic polymorphisms and DN is race-specific. Therefore, large, well-designed studies involving more relevant variables and ethnic groups and more relevant functional studies are urgently needed. These studies may be beneficial and retard the progression of DN by early intervention, especially for patients who carry certain risk alleles or genotypes.

Genome-wide QTL analysis for anxiety trait in bipolar disorder type I

BACKGROUND

Genetic studies have been consistent that bipolar disorder type I (BPI) runs in families and that this familial aggregation is strongly influenced by genes. In a preliminary study, we proved that anxiety trait meets endophenotype criteria for BPI.

METHODS

We assessed 619 individuals from the Central Valley of Costa Rica (CVCR) who have received evaluation for anxiety following the same methodological procedure used for the initial pilot study. Our goal was to conduct a multipoint quantitative trait linkage analysis to identify quantitative trait loci (QTLs) related to anxiety trait in subjects with BPI. We conducted the statistical analyses using Quantitative Trait Loci method (Variance-components models), implemented in Sequential Oligogenic Linkage Analysis Routines (SOLAR), using 5606 single nucleotide polymorphism (SNPs).

RESULTS

We identified a suggestive linkage signal with a LOD score of 2.01 at chromosome 2 (2q13-q14).

LIMITATIONS

Since confounding factors such as substance abuse, medical illness and medication history were not assessed in our study, these conclusions should be taken as preliminary.

CONCLUSIONS

We conclude that region 2q13-q14 may harbor a candidate gene(s) with an important role in the pathophysiology of BPI and anxiety.

The Genetic and Environmental Factors of Primary Membranous Nephropathy: An Overview from China

Background

Primary membranous nephropathy (pMN) is the most common cause of nephrotic syndrome in adults. The discovery of the 2 autoantigens, M-type phospholipase A2 receptor (PLA2R) and thrombospondin type-1 domain-containing 7A (THSD7A), has defined pMN as an autoimmune disease. A remarkable increase in the frequency of pMN in primary glomerular disease was witnessed in China. The genetic and environmental contributors to disease susceptibility have been investigated in these patients.

Summary

We reviewed recent publications in genetic and environmental studies of pMN, focusing mainly on those undertaken in China. Following a genome-wide association study, the gene-gene interaction between the 2 most significant risk factors, PLA2R1 and DQA1, was validated in Chinese patients with MN. Fine mapping on human leukocyte antigen (HLA) locus found that DRB1*1501 and DRB1*0301 were risk alleles. Three amino acid residues on positions 13 and 71 of HLA-DRβ1 chain may confer the susceptibility to pMN by presenting T-cell epitopes on PLA2R. Another study found that DRB3*0202 was the most likely culprit allele for the signal at DRB1*0301. One environmental risk factor for pMN has been identified as the long-term exposure to high levels of PM_2.5 in Chinese patients with MN. Each 10 μg/m³ increase in PM_2.5 concentration was associated with 14% higher odds for pMN in the regions with PM_2.5 above 70 μg/m³.

Key Message

A gene-environment interaction is suspected as an underlying mechanism for the increasing trend of pMN in China.

Cost and yield considerations when expanding recruitment for genetic studies: the primary open-angle African American glaucoma genetics study

Background

African Americans have been historically under-represented in genetic studies. More research is needed on effective recruitment strategies for this population, especially on approaches that supplement traditional clinic enrollment. This study evaluates the cost and efficacy of four supplemental recruitment methods employed by the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study.

Methods

After enrolling 2304 patients from University of Pennsylvania ophthalmology clinics, the POAAGG study implemented four new recruitment methods to supplement clinic enrollment. These methods included: 1) outreach in the local community, 2) in-house screening of community members (“in-reach”), 3) expansion to two external sites, and 4) sampling of the Penn Medicine Biobank. The cost per subject was calculated for each method and enrollment among cases, controls, and suspects was reported.

Results

The biobank offered the lowest cost ($5/subject) and highest enrollment yield (n = 2073) of the four methods, but provided very few glaucoma cases (n = 31). External sites provided 88% of cases recruited from the four methods (n = 388; $85/subject), but case enrollment at these sites declined over the next 9 months as the pool of eligible subjects was depleted. Outreach and in-reach screenings of community members were very high cost for low return on enrollment ($569/subject for 102 subjects and $606/subject for 45 subjects, respectively).

Conclusions

The biobank offered the most cost-effective method for control enrollment, while expansion to external sites was necessary to recruit richly phenotyped cases. These recruitment methods helped the POAAGG study to exceed enrollment of the discovery cohort (n = 5500) 6 months in advance of the predicated deadline and could be adopted by other large genetic studies seeking to supplement clinic enrollment.

"I passed the test!" Evidence of diagnostic misconception in the recruitment of population controls for an H3Africa genomic study in Cape Town, South Africa

Background

Advances in genetic and genomic research have introduced challenges in obtaining informed consent for research in low and middle-income settings. However, there are only few studies that have explored challenges in obtaining informed consent in genetic and genomic research in Africa and none in South Africa. To start filling this gap, we conducted an empirical study to investigate the efficacy of informed consent procedures for an H3Africa genomic study on Rheumatic Heart Disease (RHDGen) at the University of Cape Town in South Africa. The main aim of the study was to understand ethical challenges in obtaining informed consent in the RHDGen study.

Methods

We used a qualitative study methodology involving in-depth interviews and participant observations. Our study participants were RHDGen cases (patients), healthy controls and research staff involved in the recruitment of RHDGen cases and controls. In total, we conducted 32 in-depth interviews with RHDGen cases and controls, 2 in-depth interviews with research staff and 57 direct observations of the consent procedures of RHDGen cases and controls. The interviews were conducted in English, audio-recorded and transcribed verbatim. Data were analyzed using thematic content analysis. The study was conducted in 3 sites within Cape Town, South Africa.

Results

Most healthy controls joined the RHDGen study in order to be screened for rheumatic heart disease (diagnostic misconception). A majority of RHDGen cases decided to join the RHDGen study because of therapeutic misconception.

Conclusion

The ethical challenges that impacted on obtaining informed consent in the RHDGen study were complex. In this study, the main challenges were diagnostic misconception among RHDGen controls and therapeutic misconception among RHDGen cases.

Gastric cancer related genes

Gastric cancer is one of the most common malignant tumors. In addition to environmental, socioeconomic, and dietary factors, hereditary factors also play an important role in the development of gastric cancer. Although some driver genes have been identified in gastric cancer, the molecular compositions of gastric cancer have not been fully understood. Genome-wide association studies, copy number variations and next-generation sequencing provide systematic methods to identify all genetic alterations in the cancer genome, especially in the field of mutation detection. Here we make a brief review of the current status of research on gastric cancer genetics.

Candidate gene studies of diabetic retinopathy in human

Diabetic retinopathy (DR) is a multifactorial disease with complex pathophysiology. It is the main cause of blindness among the people in productive age. The purpose of this literature review is to highlight recent achievements in the genetics of diabetic retinopathy with particular focus on candidate gene studies. We summarized most of the available published data about candidate genes for diabetic retinopathy with the goal to identify main genetic aspects. We conclude that genetic studies reported contradictory findings and no genetic variants meet criteria of a diagnostic marker, or significantly elucidate the root of DR development. Based on these findings it is important to continue with the research in the field of DR genetics, mainly due to the fact that currently new possibilities and approaches associated with utilization of next-generation sequencing are available.

SHEsisPCA: a GPU-based software to correct for population stratification that efficiently accelerates the process for handling genome-wide datasets

Population stratification is a problem in genetic association studies because it is likely to highlight loci that underlie the population structure rather than disease-related loci. At present, principal component analysis (PCA) has been proven to be an effective way to correct for population stratification. However, the conventional PCA algorithm is time-consuming when dealing with large datasets. We developed a Graphic processing unit (GPU)-based PCA software named SHEsisPCA (http://analysis.bio-x.cn/SHEsisMain.htm) that is highly parallel with a highest speedup greater than 100 compared with its CPU version. A cluster algorithm based on X-means was also implemented as a way to detect population subgroups and to obtain matched cases and controls in order to reduce the genomic inflation and increase the power. A study of both simulated and real datasets showed that SHEsisPCA ran at an extremely high speed while the accuracy was hardly reduced. Therefore, SHEsisPCA can help correct for population stratification much more efficiently than the conventional CPU-based algorithms.

The prevalence and genetics of Parkinson's disease in sub-Saharan Africans

Parkinson's disease (PD) is under-studied in Black Sub-Saharan African (SSA) populations. To date, there have been only six prevalence and no incidence studies. The crude prevalence of PD in SSA varies from 7 to 20 per 100,000, which is appreciably lower than in Caucasian populations. There are a limited number of published studies (nine) on the genetic factors associated with PD in SSA populations. Mutations have been reported in the parkin gene, and are restricted to only three patients (two Black South Africans and one Zambian). No mutations have been identified in the LRRK2, SNCA, PINK, or DJ-1 genes. Given the unique ancestry of SSA populations, their inclusion in genetic studies may provide a substantial contribution to the identification of novel genetic factors and genetic-environmental interactions underlying this disorder. More initiatives are needed to drive further research on PD in these populations and to facilitate collaborative projects across Africa.

Genetic Polymorphisms of Human Parotid Saliva and Their Application to Forensic Science

Human saliva is one of the valuable resources for the identification of genetic markers. A number of polymorphisms are found in salivary proteins and enzymes. They could provide the important information for genetic studies and forensic science. Polymorphic proteins in saliva show very unique composition of amino acids, which are named proline-rich proteins (PRPs). Proline-rich proteins have some biochemical and immunological similarities and linkage has been shown to occur among them. Recent deoxyribonucleic acid (DNA) analysis suggests that PRP genes have to be reconsidered on the gene structure. This review includes the polymorphisms of salivary proteins and enzymes and their application for human genetics and forensic science. Recent DNA studies that suggest the reorganization of the loci controlling the production of PRPs are also discussed.