Nasheen Naidoo

Revisiting Mendelian disorders through exome sequencing

Over the past several years, more focus has been placed on dissecting the genetic basis of complex diseases and traits through genome-wide association studies. In contrast, Mendelian disorders have received little attention mainly due to the lack of newer and more powerful methods to study these disorders. Linkage studies have previously been the main tool to elucidate the genetics of Mendelian disorders; however, extremely rare disorders or sporadic cases caused by de novo variants are not amendable to this study design. Exome sequencing has now become technically feasible and more cost-effective due to the recent advances in high-throughput sequence capture methods and next-generation sequencing technologies which have offered new opportunities for Mendelian disorder research. Exome sequencing has been swiftly applied to the discovery of new causal variants and candidate genes for a number of Mendelian disorders such as Kabuki syndrome, Miller syndrome and Fowler syndrome. In addition, de novo variants were also identified for sporadic cases, which would have not been possible without exome sequencing. Although exome sequencing has been proven to be a promising approach to study Mendelian disorders, several shortcomings of this method must be noted, such as the inability to capture regulatory or evolutionary conserved sequences in non-coding regions and the incomplete capturing of all exons.

Exome sequencing: Dual role as a discovery and diagnostic tool

Recent developments in high‐throughput sequence capture methods and next‐generation sequencing technologies have now made exome sequencing a viable approach to elucidate the genetic basis of Mendelian disorders with hitherto unknown etiology. In addition, exome sequencing is increasingly being employed as a diagnostic tool for specific genetic diseases, particularly in the context of those disorders characterized by significant genetic and phenotypic heterogeneity, for example, Charcot‐Marie‐Tooth disease and congenital disorders of glycosylation. Such disorders are challenging to interrogate with conventional polymerase chain reaction–Sanger sequencing methods, because of the inherent difficulty in prioritizing candidate genes for diagnostic testing. Here, we explore the value of exome sequencing as a diagnostic tool and discuss whether exome sequencing can come to serve a dual role in diagnosis and discovery. We summarize the current status of exome sequencing, the technical challenges facing it, and its adaptation to diagnostics, and make recommendations for the use of exome sequencing as a routine diagnostic tool. Finally, we discuss pertinent ethical concerns, such as the use of exome sequencing data, originally generated in a diagnostic context, in research investigations. Ann Neurol 2012;71:5–14

Dietary flavonoids and the development of type 2 diabetes and cardiovascular diseases: review of recent findings.

Purpose of review This review summarizes the results on flavonoid intakes and the development of type 2 diabetes and cardiovascular diseases. Recent findings Recent advances in food composition databases have allowed the evaluation of a more comprehensive range of flavonoids in epidemiological studies. In addition, the number of randomized trials of flavonoid-rich foods has increased rapidly. Results from both cohort studies and randomized trials suggest that anthocyanidins from berries and flavan-3-ols from green tea and cocoa may lower the risk of type 2 diabetes and cardiovascular diseases. Meta-analyses of randomized trials indicate that the strongest evidence exists for a beneficial effect of green tea on LDL-cholesterol and a beneficial effect of flavan-3-ol-rich cocoa on endothelial function and insulin sensitivity. Few randomized trials had a long duration or evaluated pure flavonoid compounds. Summary Evidence from cohort studies and randomized trials suggest beneficial effects of food sources of anthocyanidins (berries) and flavan-3-ols (green tea and cocoa) on cardiovascular health. These findings need to be confirmed in long-term randomized trials, and evaluation of pure compounds will be important to establish what specific flavonoids and doses are effective.

Studying the epigenome using next generation sequencing

The advances in next generation sequencing (NGS) technologies have had a significant impact on epigenomic research. The arrival of NGS technologies has enabled a more powerful sequencing based method—that is, ChIP-Seq—to interrogate whole genome histone modifications, improving on the conventional microarray based method (ChIP-chip). Similarly, the first human DNA methylome was mapped using NGS technologies. More importantly, studies of DNA methylation and histone modification using NGS technologies have yielded new discoveries and improved our knowledge of human biology and diseases. The concept that cytosine methylation was restricted to CpG dinucleotides has only been recently challenged by new data generated from sequencing the DNA methylome. Approximately 25% of all cytosine methylation identified in stem cells was in a non-CG context. The non-CG methylation was more enriched in gene bodies and depleted in protein binding sites and enhancers. The recent developments of third generation sequencing technologies have shown promising results of directly sequencing methylated nucleotides and having the ability to differentiate between 5-methylcytosine and 5-hydroxymethylcytosine. The importance of 5-hydroxymethylcytosine remains largely unknown, but it has been found in various tissues. 5-hydroxymethylcytosine was particularly enriched at promoters and in intragenic regions (gene bodies) but was largely absent from non-gene regions in DNA from human brain frontal lobe tissue. The presence of 5-hydroxymethylcytosine in gene bodies was more positively correlated with gene expression levels. The importance of studying 5-methylcytosine and 5-hydroxymethylcytosine separately for their biological roles will become clearer when more efficient methods to distinguish them are available.

A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease.

The study of de novo point mutations (new germline mutations arising from the gametes of the parents) remained largely static until the arrival of next-generation sequencing technologies, which made both whole-exome sequencing (WES) and whole-genome sequencing (WGS) feasible in practical terms. Single nucleotide polymorphism genotyping arrays have been used to identify de novo copy-number variants in a number of common neurodevelopmental conditions such as schizophrenia and autism. By contrast, as point mutations and microlesions occurring de novo are refractory to analysis by these microarray-based methods, little was known about either their frequency or impact upon neurodevelopmental disease, until the advent of WES. De novo point mutations have recently been implicated in schizophrenia, autism and mental retardation through the WES of case-parent trios. Taken together, these findings strengthen the hypothesis that the occurrence of de novo mutations could account for the high prevalence of such diseases that are associated with a marked reduction in fecundity. De novo point mutations are also known to be responsible for many sporadic cases of rare dominant Mendelian disorders such as Kabuki syndrome, Schinzel–Giedion syndrome and Bohring–Opitz syndrome. These disorders share a common feature in that they are all characterized by intellectual disability. In summary, recent WES studies of neurodevelopmental and neuropsychiatric disease have provided new insights into the role of de novo mutations in these disorders. Our knowledge of de novo mutations is likely to be further accelerated by WGS. However, the collection of case-parent trios will be a prerequisite for such studies. This review aims to discuss recent developments in the study of de novo mutations made possible by technological advances in DNA sequencing.

Coffee and tea consumption in relation to inflammation and basal glucose metabolism in a multi-ethnic Asian population: a cross-sectional study

BackgroundHigher coffee consumption has been associated with a lower risk of type 2 diabetes in cohort studies, but the physiological pathways through which coffee affects glucose metabolism are not fully understood. The aim of this study was to evaluate the associations between habitual coffee and tea consumption and glucose metabolism in a multi-ethnic Asian population and possible mediation by inflammation.MethodsWe cross-sectionally examined the association between coffee, green tea, black tea and Oolong tea consumption and glycemic (fasting plasma glucose, HOMA-IR, HOMA-beta, plasma HbA1c) and inflammatory (plasma adiponectin and C-reactive protein) markers in a multi-ethnic Asian population (N = 4139).ResultsAfter adjusting for multiple confounders, we observed inverse associations between coffee and HOMA-IR (percent difference: - 8.8% for ≥ 3 cups/day versus rarely or never; Ptrend = 0.007), but no significant associations between coffee and inflammatory markers. Tea consumption was not associated with glycemic markers, but green tea was inversely associated with plasma C-reactive protein concentrations (percent difference: - 12.2% for ≥ 1 cup/day versus < 1 cup/week; Ptrend = 0.042).ConclusionsThese data provide additional evidence for a beneficial effect of habitual caffeinated coffee consumption on insulin sensitivity, and suggest that this effect is unlikely to be mediated by anti-inflammatory mechanisms.

DIET AND ENDOTHELIAL FUNCTION: FROM INDIVIDUAL COMPONENTS TO DIETARY PATTERNS

Purpose of review Endothelial dysfunction plays an important role in development and progression of atherosclerosis and may also contribute to the pathogenesis of type 2 diabetes. This review summarizes recent findings on the effects of vitamin D, antioxidant vitamins, polyphenols, polyphenol-rich foods, dietary component combinations and healthy diets on endothelial function. Recent findings Dietary patterns rich in fruit, vegetables, fish and nuts appear to have beneficial effects on endothelial function. With regard to specific foods, cacao and green tea consumption have been associated with improvement in endothelial function and this seems to be due to their flavan-3-ol (catechins and epigallocatechin gallate) content. The evidence for beneficial effects of other foods such as citrus fruit, apples and red wine is less consistent. Recent studies have also suggested beneficial effects of vitamin D and anthocyanins on endothelial function and have provided more insight into potential mechanisms underlying the effect of diet on endothelial function. Summary The currently available evidence supports beneficial effects of various dietary compounds on endothelial function. However, in order to obtain strong evidence for relevant health effects that can be used for specific dietary recommendations, more long-term studies using well characterized diets/supplements in a large number of individuals are needed.

Amount, type, and sources of carbohydrates in relation to ischemic heart disease mortality in a Chinese population: a prospective cohort study

BACKGROUND The relation between carbohydrate intake and risk of ischemic heart disease (IHD) has not been fully explored in Asian populations known to have high-carbohydrate diets. OBJECTIVE We assessed whether intakes of total carbohydrates, different types of carbohydrates, and their food sources were associated with IHD mortality in a Chinese population. DESIGN We prospectively examined the association of carbohydrate intake and IHD mortality in 53,469 participants in the Singapore Chinese Health Study with an average follow-up of 15 y. Diet was assessed by using a semiquantitative food-frequency questionnaire. HRs and 95% CIs were calculated by using a Cox proportional hazards analysis. RESULTS We documented 1660 IHD deaths during 804,433 person-years of follow-up. Total carbohydrate intake was not associated with IHD mortality risk [men: HR per 5% of energy, 0.97 (95% CI: 0.92, 1.03); women: 1.06 (95% CI: 0.99, 1.14)]. When types of carbohydrates were analyzed individually, starch intake was associated with higher risk [men: 1.03 (95% CI: 0.99, 1.08); women: 1.08, (95% CI: 1.02, 1.14)] and fiber intake with lower risk of IHD mortality [men: 0.94 (95% CI: 0.82, 1.08); women: 0.71 (95% CI: 0.60, 0.84)], with stronger associations in women than men (both P-interaction < 0.01). In substitution analyses, the replacement of one daily serving of rice with one daily serving of noodles was associated with higher risk (difference in HR: 26.11%; 95% CI: 10.98%, 43.30%). In contrast, replacing one daily serving of rice with one of vegetables (-23.81%; 95% CI: -33.12%, -13.20%), fruit (-11.94%; 95% CI: -17.49%, -6.00%), or whole-wheat bread (-19.46%; 95% CI: -34.28%, -1.29%) was associated with lower risk of IHD death. CONCLUSIONS In this Asian population with high carbohydrate intake, the total amount of carbohydrates consumed was not substantially associated with IHD mortality. In contrast, the shifting of food sources of carbohydrates toward a higher consumption of fruit, vegetables, and whole grains was associated with lower risk of IHD death.

Technological advances in DNA sequence enrichment and sequencing for germline genetic diagnosis

The potential applications of next-generation sequencing technologies in diagnostic laboratories have become increasingly evident despite the various technical challenges that still need to be overcome to potentiate its widespread adoption in a clinical setting. Whole-genome sequencing is now both technically feasible and ‘cost effective’ using next-generation sequencing techniques. However, this approach is still considered to be ‘expensive’ for a diagnostic test. Although the goal of the US

A Cost-Effectiveness Analysis Evaluating Endoscopic Surveillance for Gastric Cancer for Populations with Low to Intermediate Risk

1000 genome is fast approaching, neither the analytical hurdles nor the ethical issues involved are trivial. In addition, the cost of data analysis and storage has been much higher than initially expected. As a result, it is widely perceived that targeted sequencing and whole-exome sequencing are more likely to be adopted as diagnostic tools in the foreseeable future. However, the information-generating power of whole-exome sequencing has also sparked considerable debate in relation to its deployment in genetic diagnostics, particularly with reference to the revelation of incidental findings. In this review, we focus on the targeted sequencing approach and its potential as a genetic diagnostic tool.