The Impact of Variation in Twin Relatedness on Estimates of Heritability and Environmental Influences

Application of multiple mosaic callers improves post-zygotic mutation detection from exome sequencing data

PURPOSE

The gold standard for identification of post-zygotic variants (PZVs) is droplet digital polymerase chain reaction or high-depth sequencing across multiple tissues types. These approaches are yet to be systematically implemented for monogenic disorders. We developed PZV detection pipelines for correct classification of de novo variants.

METHOD

Our pipelines detect PZV in parents (gonosomal mosaicism [pGoM]) and children (somatic mosaicism, "M3"). We applied them to research exome sequencing (ES) data from the Australian Cerebral Palsy Biobank (n = 145 trios) and Simons Simplex Collection (n = 405 families). Candidate mosaic variants were validated using deep amplicon sequencing or droplet digital polymerase chain reaction.

RESULTS

69.2% (M3trio), 63.9% (M3single), and 92.7% (pGoM) of detected variants were validated, with 48.6%, 56.7%, and 26.2% of variants, respectively, meeting strict criteria for mosaicism. In the Australian Cerebral Palsy Biobank, 16.6% of probands and 20.7% of parents had at least 1 true-positive somatic or pGoM variant, respectively. A large proportion of PZVs detected in Simons Simplex Collection parents (79.8%) and child (94.5%) were not previously reported. We reclassified 3.7% to 8.0% of germline de novo variants as mosaic.

CONCLUSION

Many PZVs were incorrectly classified as germline variants or missed by previous approaches. Systematic application of our pipelines could increase genetic diagnostic rate, improve estimates of recurrence risk in families, and benefit novel disease gene identification.

Heteropaternal Siblings Misclassified as Dizygotic Twins: A Potential Biasing Factor for Heritability Estimates?

Heteropaternal superfecundation (HP) occurs when two or more ova are fertilized by sperm from separate males. The resulting siblings are genetically equivalent to half-siblings and share, on average, 25% of their inherited genetic material. In the absence of genetic testing HP siblings could be treated as dizygotic (DZ) twins in behavioral genetic analyses and bias heritability estimates in phenotypic decomposition models. However, the extent to which such misclassification could affect calculated estimates of heritability is currently unknown. Employing simulation analyses, the current study assessed the potential biasing impact across a variety of conditions varying by proportions of DZ twins, sample sizes, and low, moderate, and high levels of genetic and environmental contribution to phenotypic variance. Overall, the results indicated that misclassified HP siblings had minimal impact on estimates of heritability. Nonetheless, greater attention should be paid to the identification of HP siblings within existing and future twin datasets.

Twin Research in the Post-Genomic Era: Dissecting the Pathophysiological Effects of Adversity and the Social Environment

The role of twins in research is evolving as we move further into the post-genomic era. With the re-definition of what a gene is, it is becoming clear that biological family members who share a specific genetic variant may well not have a similar risk for future disease. This has somewhat invalidated the prior rationale for twin studies. Case co-twin study designs, however, are slowly emerging as the ideal tool to identify both environmentally induced epigenetic marks and epigenetic disease-associated processes. Here, we propose that twin lives are not as identical as commonly assumed and that the case co-twin study design can be used to investigate the effects of the adult social environment. We present the elements in the (social) environment that are likely to affect the epigenome and measures in which twins may diverge. Using data from the German TwinLife registry, we confirm divergence in both the events that occur and the salience for the individual start as early as age 11. Case co-twin studies allow for the exploitation of these divergences, permitting the investigation of the role of not only the adult social environment, but also the salience of an event or environment for the individual, in determining lifelong health trajectories. In cases like social adversity where it is clearly not possible to perform a randomised-controlled trial, we propose that the case co-twin study design is the most rigorous manner with which to investigate epigenetic mechanisms encoding environmental exposure. The role of the case co-twin design will continue to evolve, as we argue that it will permit causal inference from observational data.

Comparison of miRNA Profiles of Cord Blood Stem Cells in Identical and Fraternal Twins

Objective

The role of epigenetic in regulating of the gene expression profile the embryo has been documented. MicroRNAs (miRNAs) are one of these epigenetic mechanisms. Twins are valuable models in determining the relative contributions of genetics and the environment. In this study, we compared differences in the expression levels of 44 miRNAs in hematopoietic stem cells (HSCs) of identical twins to that of fraternal twins as a controls.

Materials and Methods

In this experimental study, CD133⁺ HSCs were isolated from cord blood of identical and fraternal twins via magnetic-activated cell sorting (MACS). Variation in of gene expression levels of 44 miRNAs were evaluated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR).

Results

Significant differences in expression were observed in both fraternal and identical twins to varying degrees, but variations alteration in expression of the miRNAs were higher in fraternal twins.

Conclusion

Identical twins had a positive correlation in miRNA expression, while the correlation was not statistically significant in fraternal twins. Altogether, more differences in miRNA expression level in fraternal twins can be attributed to the both genetics and the intrauterine environment. The contribution of the intrauterine environment and genetics to miRNAs expression in HSCs was estimated 8 and 92%, respectively. By comparing of miRNA expression in identical and fraternal twins and identification of their target genes and biological pathways, it could be possible to estimate the effects of genetics and the environment on a number of biological pathways.

Rigor and reproducibility in genetic research on eating disorders

OBJECTIVE

We explored both within-method and between-method rigor and reproducibility in the field of eating disorders genetics.

METHOD

We present critical evaluation and commentary on component methods of genetic research (family studies, twin studies, molecular genetic studies) and discuss both successful and unsuccessful efforts in the field.

RESULTS

Eating disorders genetics has had a number of robust results that converge across component methodologies. Familial aggregation of eating disorders, twin-based heritability estimates of eating disorders, and genome-wide association studies (GWAS) all point toward a substantial role for genetics in eating disorders etiology and support the premise that genes do not act alone. Candidate gene and linkage studies have been less informative historically.

DISCUSSION

The eating disorders field has entered the GWAS era with studies of anorexia nervosa. Continued growth of sample sizes is essential for rigorous discovery of actionable variation. Molecular genetic studies of bulimia nervosa, binge-eating disorder, and other eating disorders are virtually nonexistent and lag seriously behind other major psychiatric disorders. Expanded efforts are necessary to reveal the fundamental biology of eating disorders, inform clinical practice, and deliver new therapeutic targets.